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Building a ‘doomsday vault’ to save the kangaroo and koala from extinction – CNET

The road into Batlow is littered with the dead.

In the smoky, gray haze of the morning, it's hard to make out exactly what Matt Roberts' camera is capturing. Roberts, a photojournalist with the Australian Broadcasting Corporation, keeps his lens focused on the road as he rolls into the fire-ravaged town 55 miles west of Canberra, Australia's capital. At the asphalt's edge, blackened livestock carcasses lie motionless.

The grim scene, widely shared on social media, is emblematic of the impact the 2019-20 bushfire season has had on Australia's animal life. Some estimates suggest "many, many billions" of animals have been killed, populations of endemic insects could be crippled and, as ash washes into riverways, marine life will be severely impacted. The scale of the bushfires is so massive, scientists are unlikely to know the impact on wildlife for many years.

But even before bushfires roared across the country, Australia's unique native animals were in a dire fight for survival. Habitat destruction, invasive species, hunting and climate change have conspired against them. Populations of native fauna are plummeting or disappearing altogether, leaving Australia with an unenviable record: It has the highest rate of mammal extinctions in the world.

A large share of Australia's extinctions have involved marsupials -- the class of mammals that includes the nation's iconic kangaroos, wallabies, koalas and wombats. A century ago, the Tasmanian tiger still padded quietly through Australia's forests. The desert rat-kangaroo hopped across the clay pans of the outback, sheltering from the sun in dug-out nests.

Now they're gone.

Australia's 2019-20 bushfire season has been devastating for wildlife.

In a search for answers to the extinction crisis, researchers are turning to one lesser-known species, small enough to fit in the palm of your hand: the fat-tailed dunnart. The carnivorous mouse-like marsupial, no bigger than a golf ball and about as heavy as a toothbrush, has a tiny snout, dark, bulbous eyes and, unsurprisingly, a fat tail. It's Baby Yoda levels of adorable -- and it may be just as influential.

Mapping the dunnart's genome could help this little animal become the marsupial equivalent of the lab mouse -- a model organism scientists use to better understand biological processes, manipulate genes and test new approaches to treating disease. The ambitious project, driven by marsupial geneticist Andrew Pask and his team at the University of Melbourne over the last two years, will see scientists take advantage of incredible feats of genetic engineering, reprogramming cells at will.

It could even aid the creation of a frozen Noah's Ark of samples: a doomsday vault of marsupial cells, suspended in time, to preserve genetic diversity and help prevent further decline, bringing species back from the brink of extinction.

If that sounds far-fetched, it isn't. In fact, it's already happening.

Creating a reliable marsupial model organism is a long-held dream for Australian geneticists, stretching back to research pioneered by famed statistician Ronald Fisher in the mid-20th century. To understand why the model is so important, we need to look at the lab mouse, a staple of science laboratories for centuries.

"A lot of what we know about how genes work, and how genes work with each other, comes from the mouse," says Jenny Graves, a geneticist at La Trobe University in Victoria, Australia, who has worked with marsupials for five decades.

The mouse is an indispensable model organism that shares many genetic similarities with humans. It has been key in understanding basic human biology, testing new medicines and unraveling the mysteries of how our brains work. Mice form such a critical part of the scientific endeavor because they breed quickly, have large litters, and are cheap to house, feed and maintain.

The lab mouse has been indispensable in understanding physiology, biology and genetics.

In the 1970s, scientists developed a method to insert new genes into mice. After a decade of refinement, these genetically modified mice (known as "transgenic mice") provided novel ways to study how genes function. You could add a gene, turning its expression up to 11, or delete a gene entirely, shutting it off. Scientists had a powerful tool to discover which genes performed the critical work in reproduction, development and maturation.

The same capability does not exist for marsupials. "At the moment, we don't have any way of manipulating genes in a devil or a kangaroo or a possum," says Graves. Without this capability, it's difficult to answer more pointed questions about marsupial genes and how they compare with mammal genes, like those of mice and humans.

So far, two marsupial species -- the Tammar wallaby and the American opossum -- have been front and center of research efforts to create a reliable model organism, but they both pose problems. The wallaby breeds slowly, with only one baby every 18 months, and it requires vast swaths of land to maintain.

The short-tailed opossum might prove an even more complicated case. Pask, the marsupial geneticist, says the small South American marsupial is prone to eating its young, and breeding requires researchers to sift through hours of video footage, looking for who impregnated whom. Pask also makes a patriotic jab ("they're American so we don't like them") and says their differences from Australian marsupials make them less useful for the problems Australian species face.

But the dunnart boasts all the features that make the mouse such an attractive organism for study: It is small and easy to house, breeds well in captivity and has large litters.

"Our little guys are just like having a mouse basically, except they have a pouch," Pask says.

Pask (front) and Frankenberg inspect some of their dunnarts at the University of Melbourne.

A stern warning precedes my first meeting with Pask's colony of fat-tailed dunnarts.

"It smells like shit," he says. "They shit everywhere."

I quickly discover he's right. Upon entering the colony's dwellings on the third floor of the University of Melbourne's utilitarian BioSciences building, you're punched in the face by a musty, fecal smell.

Pask, a laid-back researcher whose face is almost permanently fixed with a smile, and one of his colleagues, researcher Stephen Frankenberg, appear unfazed by the odor. They've adapted to it. Inside the small room that houses the colony, storage-box-cages are stacked three shelves high. They're filled with upturned egg cartons and empty buckets, which work as makeshift nests for the critters to hide in.

Andrew Pask

Frankenberg reaches in without hesitation and plucks one from a cage -- nameless but numbered "29" -- and it hides in his enclosed fist before peeking out of the gap between his thumb and forefinger, snout pulsing. As I watch Frankenberg cradle it, the dunnart seems curious, and Pask warns me it's more than agile enough to manufacture a great escape.

In the wild, fat-tailed dunnarts are just as inquisitive and fleet-footed. Their range extends across most of southern and central Australia, and the most recent assessment of their population numbers shows they aren't suffering population declines in the same way many of Australia's bigger marsupial species are.

Move over, Baby Yoda.

As I watch 29 scamper up Frankenberg's arm, the physical similarities between it and a mouse are obvious. Pask explains that the dunnart's DNA is much more closely related to the Tasmanian devil, an endangered cat-sized carnivore native to Australia, than the mouse. But from a research perspective, Pask notes the similarities between mouse and dunnart run deep -- and that's why it's such an important critter.

"The dunnart is going to be our marsupial workhorse like the mouse is for placental mammals," Pask says.

For that to happen, Pask's team has to perfect an incredible feat of genetic engineering: They have to learn how to reprogram its cells.

To do so, they collect skin cells from the dunnart's ear or footpad and drop them in a flask where scientists can introduce new genes into the skin cell. The introduced genes are able to trick the adult cell, convincing it to become a "younger," specialized cell with almost unlimited potential.

The reprogrammed cells are known as "induced pluripotent stem cells," or iPS cells, and since Japanese scientists unraveled how to perform this incredible feat in 2006, they have proven to be indispensable for researchers because they can become any cell in the body.

"You can grow them in culture and put different sorts of differentiation factors on them and see if they can turn into nerve cells, muscle cells, brain cells, blood vessels," Pask explains. That means these special cells could even be programmed to become a sperm or an egg, in turn allowing embryos to be made.

Implanting the embryo in a surrogate mother could create a whole animal.

It took about 15 minutes to get this dunnart to sit still.

Although such a technological leap has been made in mice, it's still a long way from fruition for marsupials. At present, only the Tasmanian devil has had iPS cells created from skin, and no sperm or egg cells were produced.

Pask's team has been able to dupe the dunnart's cells into reverting to stem cells -- and they've even made some slight genetic tweaks in the lab. But that's just the first step.

He believes there are likely to be small differences between species, but if the methodology remains consistent and reproducible in other marsupials, scientists could begin to create iPS cells from Australia's array of unique fauna. They could even sample skin cells from wild marsupials and reprogram those.

Doing so would be indispensable in the creation of a biobank, where the cells would be frozen down to -196 degrees Celsius (-273F) and stored until they're needed. It would act as a safeguard -- a backup copy of genetic material that could, in some distant future, be used to bring species back from the edge of oblivion, helping repopulate them and restoring their genetic diversity.

Underneath San Diego Zoo's Beckman Center for Conservation Research lies the Frozen Zoo, a repository of test tubes containing the genetic material of over 10,000 species. Stacked in towers and chilled inside giant metal vats, the tubes contain the DNA of threatened species from around the world, suspended in time.

It's the largest wildlife biobank in the world.

"Our goal is to opportunistically collect cells ... on multiple individuals of as many species as we can, to provide a vast genetic resource for research and conservation efforts," explains Marlys Houck, curator at the Frozen Zoo.

The Zoo's efforts to save the northern white rhino from extinction have been well publicized. Other research groups have been able to create a northern white rhino embryo in the lab, combining eggs of the last two remaining females with frozen sperm from departed males. Scientists propose implanting those embryos in a surrogate mother of a closely related species, the southern white rhino, to help drag the species back from the edge of oblivion.

For the better part of a decade, conservationists have been focused on this goal, and now their work is paying off: In the "coming months," the lab-created northern white rhino embryo will be implanted in a surrogate.

Sudan, the last male northern white rhinoceros, was euthanized in 2018.

Marisa Korody, a conservation geneticist at the Frozen Zoo, stresses that this type of intervention was really the last hope for the rhino, a species whose population had already diminished to just eight individuals a decade ago.

"We only turn to these methods when more traditional conservation methods have failed," she says.

In Australia, researchers are telling whoever will listen that traditional conservation methods are failing.

"We've been saying for decades and decades, many of our species are on a slippery slope," says John Rodger, a marsupial conservationist at the University of Newcastle, Australia, and CEO of the Fauna Research Alliance, which has long advocated for the banking of genetic material of species in Australia and New Zealand.

In October, 240 of Australia's top scientists delivered a letter to the government detailing the country's woeful record on protecting species, citing the 1,800 plants and animals in danger of extinction, and the "weak" environmental laws which have been ineffective at keeping Australian fauna alive.

Institutions around Australia, such as Taronga Zoo and Monash University, have been biobanking samples since the '90s, reliant on philanthropic donations to stay online, but researchers say this is not enough. For at least a decade, they've been calling for the establishment of a national biobank to support Australia's threatened species.

John Rodger

"Our real problem in Australia ... is underinvestment," Rodger says. "You've got to accept this is not a short-term investment."

The current government installed a threatened-species commissioner in 2017 and committed $255 million ($171 million in US dollars) in funding to improve the prospects of 20 mammal species by 2020. In the most recent progress report, released in 2019, only eight of those 20 were identified as having an "improved trajectory," meaning populations were either increasing faster or declining slower compared to 2015.

A spokesperson for the commissioner outlined the $50 million investment to support immediate work to protect wildlife following the bushfires, speaking to monitoring programs, establishment of "insurance populations" and feral cat traps. No future strategies regarding biobanking were referenced.

Researchers believe we need to act now to preserve iconic Australian species like the koala.

In the wake of the catastrophic bushfire season and the challenges posed by climate change, Australia's extinction crisis is again in the spotlight. Koalas are plastered over social media with charred noses and bandaged skin. On the front page of newspapers, kangaroos bound in front of towering walls of flame.

Houck notes that San Diego's Frozen Zoo currently stores cell lines "from nearly 30 marsupial species, including koala, Tasmanian devil and kangaroo," but that's only one-tenth of the known marsupial species living in Australia today.

"Nobody in the world is seriously working on marsupials but us," Rodger says. "We've got a huge interest in maintaining these guys for tourism, national icons... you name it."

There's a creeping sense of dread in the researchers I talk to that perhaps we've passed a tipping point, not just in Australia, but across the world. "We are losing species at an alarming rate," says Korody from the Frozen Zoo. "Some species are going extinct before we even know they are there."

With such high stakes, Pask and his dunnarts are in a race against time. Perfecting the techniques to genetically engineer the tiny marsupial's cells will help enable the preservation of all marsupial species for generations to come, future-proofing them against natural disasters, disease, land-clearing and threats we may not even be able to predict right now.

Pask reasons "we owe it" to marsupials to develop these tools and, at the very least, biobank their cells if we can't prevent extinction. "We really should be investing in this stuff now," he says. He's optimistic.

In some distant future, years from now, a bundle of frozen stem cells might just bring the koala or the kangaroo back from the brink of extinction.

And for that, we'll have the dunnart to thank.

Originally published Feb. 18, 5 a.m. PT.

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Human behavior at the intersection of many sciences – Dailyuw

People frequently ask themselves, Why did I do that? Attempting to understand how we react to and interact with changing environments has resulted in years of research on human behavior.

Neurobiologists and psychologists study the biological basis of how the brain responds under certain situations. Social scientists like anthropologists explain what factors guide our behavior and engineers are taking all these studies to design tools that enforce human interaction, intelligence, and growth.

Human nature is complex, and interdisciplinary considerations may help us answer some interesting questions about how people think, remember, and behave.

Things that are good for one's health and longevity such as finding mates, food, and children; the dopamine reward or evaluation system is important to recall that success, Sheri Mizumori, a professor in the department of psychology who studies behavioral neuroscience, said.

Dopamine is known as the feel-good neurotransmitter, a chemical messenger that relays information between neurons. It is released by the brain when we eat food, exercise, and crave sex, helping reinforce desirable behaviors by encoding values of rewards. Psychologists and neurologists have studied this through animal models that help explain how humans access their own memory to guide their actions.

From a young age, babies learn that if an outcome is not what they want, they will change, Mizumori said. Much of the brain has evolved to be a predictor of outcomes.

Memory can be thought of as a repository of past experiences that did and did not work. When we are placed in a new situation, we use strategies we learned from previous experiences to guide our actions.

You are driving behavior based on memory and [guiding] behavior correctly the next time, Mizumori said.

The brain uses decision circuits that integrate information about past values from memory and evaluates it against our motivational, or internal, state. Understanding how the brain can switch behaviors or learn new ones is known as flexible decision making.

Theoretical psychologists study human behavior from a philosophical and social standpoint. A commonly known study argues if nature or nurture genetic or acquired influences behavior.

Maslows hierarchy of needs outlines a five-tier pyramid of deficiency and being needs. Once deficiency needs the first tier are met, people strive for self-fulfillment and personal growth, behaviors that encompass the fifth tier of the pyramid.

Depression is an interesting example of behavior at the intersection of social sciences and biology. Behavioral theory argues depression results from peoples interactions with the environment and psychodynamic theory states it stems from inwardly-directed anger or loss of self-esteem.

Conversely, Mizumori explained depression from a behavioral switch, or flexible decision-making standpoint.

Researchers in human centered design and engineering (HCDE) are attempting to design technologies that can support or prompt changes in peoples behaviors.

A lot of the research projects we explore are real-world-problem driven, Gary Hsieh, an associate professor in HCDE, said. How do we encourage users to eat healthier or exercise more? These are health-related problems aligned to behavior-related problems.

By studying the needs and values of certain groups, researchers like Hsieh are able to design technologies that encourage people to communicate and interact in welfare-improving ways. In a growing age of data, engineers and scientists are able to learn about people from social networks.

Data allows us to study people in ways that we could not before, Hsieh said. It ties in with the types of interventions and applications that we can build.

Human behavior presents unknown complexities that arise from cultural, social, internal, environmental, and biological factors. Being able to integrate all those is a challenge that many will be addressing for generations to follow.

Reach reporter Vidhi Singh at Twitter: @vidhisvida

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Have Humans Evolved Beyond Natureand Do We Even Need It? – Singularity Hub

Such is the extent of our dominion on Earth, that the answer to questions around whether we are still part of nature, and whether we even need some of it, rely on an understanding of what we want as Homo sapiens. And to know what we want, we need to grasp what we are.

It is a huge question, but they are the best. And as a biologist, here is my humble suggestion to address it, and a personal conclusion. You may have a different one, but what matters is that we reflect on it.

Perhaps the best place to start is to consider what makes us human in the first place, which is not as obvious as it may seem.

Many years ago, a novel written by Vercors called Les Animaux Dnaturs (Denatured Animals) told the story of a group of primitive hominids, the Tropis, found in an unexplored jungle in New Guinea, who seem to constitute a missing link.

However, the prospect that this fictional group may be used as slave labor by an entrepreneurial businessman named Vancruysen forces society to decide whether the Tropis are simply sophisticated animals or whether they should be given human rights. And herein lies the difficulty.

Human status had hitherto seemed so obvious that the book describes how it is soon discovered that there is no definition of what a human actually is. Certainly, the string of experts consultedanthropologists, primatologists, psychologists, lawyers and clergymencould not agree. Perhaps prophetically, it is a layperson who suggested a possible way forward.

She asked whether some of the hominids habits could be described as the early signs of a spiritual or religious mind. In short, were there signs that, like us, the Tropis were no longer at one with nature, but had separated from it, and were now looking at it from the outsidewith some fear.

It is a telling perspective. Our status as altered or denatured animalscreatures who have arguably separated from the natural worldis perhaps both the source of our humanity and the cause of many of our troubles. In the words of the books author: All mans troubles arise from the fact that we do not know what we are and do not agree on what we want to be.

We will probably never know the timing of our gradual separation from naturealthough cave paintings perhaps contain some clues. But a key recent event in our relationship with the world around us is as well documented as it was abrupt. It happened on a sunny Monday morning, at 8:15am precisely.

The atomic bomb that rocked Hiroshima on August 6 1945, was a wake-up call so loud that it still resonates in our consciousness many decades later.

The day the sun rose twice was not only a forceful demonstration of the new era that we had entered, it was a reminder of how paradoxically primitive we remained: differential calculus, advanced electronics, and almost godlike insights into the laws of the universe helped build, well a very big stick. Modern Homo sapiens seemingly had developed the powers of gods, while keeping the psyche of a stereotypical Stone Age killer.

We were no longer fearful of nature, but of what we would do to it, and ourselves. In short, we still did not know where we came from, but began panicking about where we were going.

We now know a lot more about our origins but we remain unsure about what we want to be in the futureor, increasingly, as the climate crisis accelerates, whether we even have one.

Arguably, the greater choices granted by our technological advances make it even more difficult to decide which of the many paths to take. This is the cost of freedom.

I am not arguing against our dominion over nature nor, even as a biologist, do I feel a need to preserve the status quo. Big changes are part of our evolution. After all, oxygen was first a poison which threatened the very existence of early life, yet it is now the fuel vital to our existence.

Similarly, we may have to accept that what we do, even our unprecedented dominion, is a natural consequence of what we have evolved into, and by a process nothing less natural than natural selection itself. If artificial birth control is unnatural, so is reduced infant mortality.

I am also not convinced by the argument against genetic engineering on the basis that it is unnatural. By artificially selecting specific strains of wheat or dogs, we had been tinkering more or less blindly with genomes for centuries before the genetic revolution. Even our choice of romantic partner is a form of genetic engineering. Sex is natures way of producing new genetic combinations quickly.

Even nature, it seems, can be impatient with itself.

Advances in genomics, however, have opened the door to another key turning point. Perhaps we can avoid blowing up the world, and instead change itand ourselvesslowly, perhaps beyond recognition.

The development of genetically modified crops in the 1980s quickly moved from early aspirations to improve the taste of food to a more efficient way of destroying undesirable weeds or pests.

In what some saw as the genetic equivalent of the atomic bomb, our early forays into a new technology became once again largely about killing, coupled with worries about contamination. Not that everything was rosy before that. Artificial selection, intensive farming, and our exploding population growth were long destroying species quicker than we could record them.

The increasing silent springs of the 1950s and 60s caused by the destruction of farmland birdsand, consequently, their songwas only the tip of a deeper and more sinister iceberg. There is, in principle, nothing unnatural about extinction, which has been a recurring pattern (of sometimes massive proportions) in the evolution of our planet long before we came on the scene. But is it really what we want?

The arguments for maintaining biodiversity are usually based on survival, economics, or ethics. In addition to preserving obvious key environments essential to our ecosystem and global survival, the economic argument highlights the possibility that a hitherto insignificant lichen, bacteria, or reptile might hold the key to the cure of a future disease. We simply cannot afford to destroy what we do not know.

But attaching an economic value to life makes it subject to the fluctuation of markets. It is reasonable to expect that, in time, most biological solutions will be able to be synthesized, and as the market worth of many lifeforms falls, we need to scrutinize the significance of the ethical argument. Do we need nature because of its inherent value?

Perhaps the answer may come from peering over the horizon. It is somewhat of an irony that as the third millennium coincided with decrypting the human genome, perhaps the start of the fourth may be about whether it has become redundant.

Just as genetic modification may one day lead to the end of Homo sapiens naturalis (that is, humans untouched by genetic engineering), we may one day wave goodbye to the last specimen of Homo sapiens genetica. That is the last fully genetically based human living in a world increasingly less burdened by our biological formminds in a machine.

If the essence of a human, including our memories, desires, and values, is somehow reflected in the pattern of the delicate neuronal connections of our brain (and why should it not?) our minds may also one day be changeable like never before.

And this brings us to the essential question that surely we must ask ourselves now: if, or rather when, we have the power to change anything, what would we not change?

After all, we may be able to transform ourselves into more rational, more efficient, and stronger individuals. We may venture out further, have greater dominion over greater areas of space, and inject enough insight to bridge the gap between the issues brought about by our cultural evolution and the abilities of a brain evolved to deal with much simpler problems. We might even decide to move into a bodiless intelligence: in the end, even the pleasures of the body are located in the brain.

And then what? When the secrets of the universe are no longer hidden, what makes it worth being part of it? Where is the fun?

Gossip and sex, of course! some might say. And in effect, I would agree (although I might put it differently), as it conveys to me the fundamental need that we have to reach out and connect with others. I believe that the attributes that define our worth in this vast and changing universe are simple: empathy and love. Not power or technology, which occupy so many of our thoughts but which are merely (almost boringly) related to the age of a civilization.

Like many a traveller, Homo sapiens may need a goal. But from the strengths that come with attaining it, one realizes that ones worth (whether as an individual or a species) ultimately lies elsewhere. So I believe that the extent of our ability for empathy and love will be the yardstick by which our civilization is judged. It may well be an important benchmark by which we will judge other civilizations that we may encounter, or indeed be judged by them.

There is something of true wonder at the basis of it all. The fact that chemicals can arise from the austere confines of an ancient molecular soup, and through the cold laws of evolution, combine into organisms that care for other lifeforms (that is, other bags of chemicals) is the true miracle.

Some ancients believed that God made us in his image. Perhaps they were right in a sense, as empathy and love are truly godlike features, at least among the benevolent gods.

Cherish those traits and use them now, as they hold the solution to our ethical dilemma. It is those very attributes that should compel us to improve the well-being of our fellow humans without lowering the condition of what surrounds us.

Anything less will pervert (our) nature.

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Image Credit: David Mark from Pixabay

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The Possibilities and Pitfalls of Genetic Engineering in …

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With the advancements in the field of genetic engineering, science in the future may give us the power to genetically modify and create near perfect life. Read this write-up to know more about genetic engineering in humans.

The term genetic engineering was first used in Dragons Island, a science fiction novel by Jack Williamson in 1951. With the discovery of deoxyribonucleic acid or mitochondrial DNA by James Watson and Francis Crick, this fictional plot started to turn into a reality. Watson and Crick, with their experiments, could prove that DNA was the genetic material that was transferred generation to generation, with genetic information. This genetic information determined all the characteristics of a living being.

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The tiny, microscopic DNA contained all the genetic information related to the person, like color of the eyes, hair, skin tone, height, weight, IQ, EQ, diseases, disorders, etc., and was even able to determine a smile or the shape of ones nose. This blueprint of life is the most important ingredient of genetic engineering.

This biotechnology was first applied to produce synthetic human insulin. This technology was gradually used to apply to a number of vaccines and drugs that would prove to be beneficial to the human race. It was applied to plants in order to produce genetically modified foods, with higher resistance to infections and high nutritional values.

With the advancement in technologies and major breakthroughs in genetic engineering, more and more scientists are experimenting with human genes. The completion of the Human Genome Project in 2006 has given a major opening to medical companies, to carry out experiments and tests using genetic engineering.

There are many possible benefits of genetic engineering in humans, like end of hunger, cure for all ailments, long life, ageless beauty, super intelligent humans, etc. But one should always give a thought to all the disadvantages listed. It is often said that man should not attempt to play God. Thats correct. But if God has bestowed us the power to make some beneficial changes to his creations, then we should surely do so wisely.

Genetic engineers have turned into modern-day alchemists, who are searching for the ultimate elixir of life, to produce the genetically modified, perfect human. This precious knowledge is being exploited by greedy men, who are using it just to earn more money. Nothing is bad if exploited within limits. When we harness our present, we should keep in mind all the possible effects it will have on our future. We may not be alive to view the beauty and the ugliness of the future, but our beloved children may have to face the consequences.

Learn some genetic engineering ethics when it comes to practices like cloning, that are in the eyes of many, immoral and a perverse attack on creation.

Genetic engineering process manipulates the DNA sequence to create a new one. The write-up focuses on the various benefits of genetic engineering.

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Researchers Discover Mechanism Proteins Use To Find And Control Genes | Newsroom – UC Merced University News

Bioengineering Professor Victor Muoz has answered a long-standing genetic mystery, and his research suggests that someday, bioengineers could devise ways to control gene activity manually switching off the genes that contribute to cancer, for instance.

If this mechanism turns out to be as powerful as we anticipate, engineering it will be relatively straightforward, Muoz said. Controlling the output of genes could be done in a targeted way by new genome editing technologies such as CRISPR.

In a new paper published in Nature Communications, Muoz and some of his colleagues detail how certain proteins use a smart trick to find the specific genes they need to control out of the genomic soup comprising tens of thousands of genes inside each cell of even the most complex organisms.

Turns out, they use tiny DNA antennas to track the genes.

Every process in every living system from a simple bacterium to a complex human is based on turning specific genes on or off at just the right time, in the right place and at just the right levels.

That process is called transcription, and the proteins that complete that process are called transcription factors (TF). The TF must recognize and bind themselves to specific, tiny, six-letter sequences in DNA next to their target genes. To do that, the TF must sort through the DNA sequence of the entire organism's genome thats 2.5 trillion letters in humans and find their targets quickly enough to allow cells to grow, respond to stimuli, move and multiply in real time, Muoz explained.

But how do TF track their target genes within the ocean of genomic DNA in any organism? Muoz and his lab found the answer is a surprisingly simple mechanism that acts as an antenna.

The mechanism allows the TF to recognize partial sequences of the six-letter words they need to find and to detect where in the genome those partial sequences have accumulated in numbers large enough to signify that they are near the target gene.

The accumulations themselves act as beacons for the TF.

Rather than moving around the whole cell nucleus randomly reading the genome sequence, the TF hovers around the target gene so it can quickly find it and turn it on or off on demand, Muoz said. This mechanism offers a straightforward strategy for reengineering.

Muoz, chair of the Bioengineering graduate group, director of the NSF-CREST Center for Cellular and Biomolecular Machines, an affiliate of the Health Sciences Research Institute and a faculty member in the School of Engineering, collaborated on this work with postdoctoral researcher Milagros Castellanos from his previous lab in Spainand UC Merced graduate student Nivin Mothi, both of whom are listed as authors on the paper.

We are still in the stages of understanding the mechanism as well as possible and exploring how we can change it to induce changes in phenotypes, Muoz explained. Phenotypes are the biological effects of gene change. For instance, one gene change alters the color of a pea from green to yellow that difference in color is the phenotype.

The researchers had originally thought the mechanism might be based on a structural change in the TF, but it turned out to be a combination of specific sequence patterns built into the DNA and the TFs ability to bind to the partial sequences known as binding promiscuity.

In proteins, promiscuity is typically associated with poorly evolved or primitive proteins or functions, yet here we find a perfect counterexample in which the most complex organisms exploit it to solve a problem associated with their increasing genomic size and complexity, Muoz said.

Muoz and his lab are working to get a grant to conduct the next stage of research.

We are interested in further characterizing how this mechanism works at the molecular level, and also its implications for the operation of real, living systems, he said.

He and his lab are forming a collaboration with Professor Aaron Herndays group, which looks at yeast cells, one of the worlds simplest eukaryotic organisms. The researchers are interested in manipulating the antenna mechanism in the yeast cells using genome-editing techniques. Theyll make the antennas weaker or stronger, eliminate them or add them to areas where they arent usually found, and see how the yeasts react.

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Using plants as bioreactors to produce proteins for therapeutics – European Pharmaceutical Review

European Pharmaceutical Review explores how plants can be used for large-scale, glycosylated protein bioproduction for the pharma industry.

Plants can be used to produce large quantities of complex proteins, particularly glycosylated proteins, which are becoming more widely used in a range of therapies. Monoclonal antibodies (mAbs) are among the types of glycosylated proteins that plants can produce, but while there are multiple benefits to their use as bioreactors, there are also some key considerations.

This article explores why and how plants can be used to produce proteins for use in therapies, but also the factors that show this method may not be applicable to all protein products.

For plants to produce synthetic proteins, they must first be expressed somewhere within their genome. This requires some form of recombinant protein expression or genetic engineering, and to achieve optimum yield just implanting the gene is insufficient. To achieve a high level of transcription, which allows for downstream translation and protein modification for stability, the regulatory gene elements including the promoter and polyadenylation site must also be expressed.1

Techniques for gene expression:

There are three commonly used types of expression mechanisms for plant bioproduction: nuclear, chloroplast and transient expression.

Nuclear expression involves genetically modifying the genome in the nuclei of plants cells to express a protein. This is the simplest and most widely used approach in the pharmaceutical industry, as it can be achieved with viral vectors, but a more modern technique is CRISPR-Cas9 technologies.1 A 2018 study showed that in cotton, CRISPR showed no offtarget editing and an editing efficiency of 66.7 to 100 percent at each of multiple sites.2 The nuclear expression techniques, although reliable, are becoming less popular as they typically require more time to develop.

The second method involves expression of a recombinant protein in the chloroplasts requires a particle gun to insert the transgene. There are several benefits to this technique, including the ease of manipulating the chloroplast genome compared with the nucleus and the number of chloroplasts per cell, which increases yield. Using a transgene cassette to precisely target and insert the foreign gene avoids placing it into a poorly transcribed part of the genome, ensuring a high level of expression and little chance of silencing. Transgenes are commonly integrated between the trnltrnA genes in the rrn operon, as this is a transcriptionally active region offering high levels of gene expression.1

The third mechanism, transient expression, is becoming more common as it allows the rapid insertion of proteins, with little time required for the production, modification and optimisation of the expression system. Some companies have begun marketing this kind of expression for the rapid, large-scale production of proteins for therapeutics. The Agrobacteriummediated transient expression technique is purported to have better efficiency than the integrated gene systems and the ability to reach a high percentage of cells in a treated tissue, resulting in higher yields.1

In prokaryotic cells, like Escherichia coli (E. coli), protein size is limited to less than 30 kilodaltons, mainly due to reliability of production and yield. However, in eukaryotic cells, eg, Chinese hamster ovary (CHO) andplant cells, it is easier to produce larger proteins with high yields.1

According to experts, when using cell line or bacterial production methods such as CHO cells and E. coli to produce proteins, once the initial cell line is created it is often difficult to scale up, as glycosylation profiles become variable.3 The inconsistencies in protein product both cost money and result in waste.

On the other hand, dependent on expression mechanisms, plants can reliably maintain the glycosylation profile required even as bioreactor volume increases.

As a result of consistent production capabilities, plants do not require scale-up protocols. This saves both time and money when setting up a bioreactor.

A further advantage is that, if the plant is made to generate the protein through a transient expression system, there is very little time required to set up a production system. One company claims their tobacco plant-based system can be tailored for large-scale fabrication of a protein product in under 12 months, compared to 20-22 months with CHO or E. coli, 3 and one study suggests this could be done in a matter of weeks.1

There are multiple options for plant expression systems, particularly with regards to species, and each is best suited to produce different proteins. Genetic engineering can also be employed to allow customised N-glycosylation to generate different target products.

The plant industry is well established, with conditions for growth often being less complex than that of cell lines or bacteria and, dependent on choice of plant species, cultivation costs can be further reduced.

A techno-economic analysis of the theoretical set-up of a new large-scale biomanufacturing facility, producing mAbs using tobacco plants, found that compared to CHO production platforms, the plant system resulted in significantly reduced capital investment. Moreover, the model calculated that there would be more than a 50 percent reduction in the cost of goods, compared with published values for similar products at this production scale.4

One company has paved the way for the creation of biobetters, using their FastGlycaneering Development Service. iBio has shown that certain methods of plant bioproduction can improve the potency and homogeneity of biological medicines and ensure fully humanised glycosylation patterns.

iBio have also stated that their system, due to its consistencies in upstream processing, is compatible with artificial intelligence (AI). The company aim to implement a new end-to-end manufacturing process using AI and blockchain to reduce costs through optimising both the process and workflows.3

Some of the major challenges include regulatory approval, environmental contamination, protein stability and the immunogenicity of non-human post-translational modifications.1

Environmental concerns are predominantly from the possibility of spreading genetic modifications to food crops through pollination. This is more of a concern with the nuclear expression systems than transient or chloroplast expression. However, this can be overcome with geographical or physical containment, using a less transferable genetic modification method or through using a self-pollenating species.1

A review suggested that companies are unlikely to go through the cost of a shift from an already approved production system to seek regulatory approval for a new one.1 While altering an approved process is often unfeasible, setting up systems for the production of new products in the pipeline could prove to be more cost effective in the long run. Another consideration is the rising need for quick, large-scale vaccine production in response to pandemics and epidemics such as the Covid-19 coronavirus and Ebola which, due to the speed at which a transient expression production system can be constructed, could encourage companies to branch into this type of production.

Protein stability is a concern, as plants have endogenous enzymes that can break down the protein products. Some methods to overcome this include changing plant species and co-expressing peptides to fuse and stabilise the produced proteins together.

Post-translational modifications such as Asparagine-linked glycosylation (N-glycosylation) are one of the key worries, as they can be immunogenic. Particularly likely to cause unfavourable side effects are N-glycan modifications, because they differ in plants and humans.

N-glycosylation is a post-translational modification conducted on many secreted or membrane proteins in plants and mammals. Endogenously, it enables protein folding, stabilisation and protein-protein interactions. It is similarly used in pharmaceutical bioproduction to stabilise products and provide antibodies and other proteins the correct pharmacokinetic properties and immunogenicity.5,6

The plant industry is well established, with conditions for growth often being less complex than that of cell lines or bacteria

While early N-glycosylation and N-glycan modifications are highly conserved between yeast, mammals and plants, later N-glycan modifications differ; they are more simplified in plants than mammals.5,6 So, to use plants as producers of fully humanised proteins, the plant glycosylation machinery is often removed and replaced with human machinery when the plant is modified to express the protein. Of note, chloroplasts have no glycosylation machinery, so cannot perform these modifications without the insertion of foreign DNA; although this can reduce immunogenicity of the products, it can limit which proteins can be produced by chloroplast expression.

Tobacco is the most widely used plant for production of recombinant proteins in the lab. High yield and rapid scale-up, due to large numbers of seeds produced, are the primary benefits. However, proteins stored in the leaves are vulnerable to degradation and must be stored or extracted appropriately, in a timely manner. Tobacco tissues can also contain phenols and toxic alkaloids that must be removed in downstream processing to make products safe.1

Cereals are primarily used due to their seed protein storage capabilities; cereal seeds have protein storage vesicles and a dry intracellular environment. Once dried, the seeds can be stored at room temperature with limited degradation to protein products or loss of activity. Use of food crops is particularly attractive as they offer the opportunity to administer oral vaccines produced in the crop by feeding them to patients with minimal processing. Some edible vaccines have reached Phase I trials.1

Peas are a particularly attractive option, as they have high protein content in their seeds similar to cereals and have lower nitrogen requirements, reducing cultivation costs. However, legumes usually have less leaf biomass than tobacco, meaning they require a larger area to produce the same quantity.1

Plants can be modified through several methods to express proteins and the requisite promoters and transcription controllers, for the production of therapeutic proteins. There are several important considerations, including protein expression methods and plant species; however, the many benefits, including reduced costs, adaptability and speed associated with plant bioproduction systems make them an attractive option.

A particular driver of this bioproduction process is the possibility of using transient expression to produce vast quantities of highly potent, fully humanised vaccines in response to pandemics and epidemics.


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Using plants as bioreactors to produce proteins for therapeutics - European Pharmaceutical Review

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