In the developed world, most people eat the root vegetable cassava only in tapioca pudding or bubble tea. But in sub-Saharan Africa, its the primary staple for half a billion people and is the continents most popular crop.It has gained prominence due to its tolerance to extreme weather conditions, making it a reliable food security crop.

But its future is in danger. It is threatened by twoviruses: brown streak (CBSD) and mosaic (CMD). Its estimated that $1.25 billion worth of cassava plants succumb to theviruses every year. It is the

African cassava mosaic virus

dream of farmers, scientists, and affected African governments to developa variety that is resistant to both of these killer diseases.

Previous efforts through conventional breeding have resulted in several tolerant varieties. These conventionally bred varieties, however, succumb to the virus after a short time and do not stay long enough in the ground to take subsistence farmers through dry spells. Farmers tend to prefer varieties with tubers that remain in the ground for long periods of time without rotting.

Geneticsolution?

In has stepped the Bill & Melinda Gates Foundation. The Foundation has releaseda $10.46 million grant through the Donald Danforth Plant Science Center for developing virus resistant cassava varieties. The project addressed varieties that would be grown inEast Africa (virus resistance) and West Africa (virus resistance & nutrients enhancement).

According to the Danforth Center, VIRCA Plusa collaborative project involving American and African institutions will use the grant to further joint efforts towards delivering disease-resistant cassava varieties.VIRCA Plus builds on the success of two predecessor projects: VIRCA project and BioCassava Plus project. The VIRCA project successfully developed varieties with strong and stable CBSD resistance in Kenya and Uganda. The two projects applied genetic engineering in developing these particular lines.

This is the second major project financed by the Gates Foundation to attack these deadly viruses. Another variety for Nigeria with elevated levels of iron and zinc, and resistant to viruses is also under research. But tests so far show the African BioCassava Plus project has developed cassava plants that accumulate greater than 10 times more iron and zinc than comparable varieties in Nigeria. In January, Gates himself outlinedthis project:

In the developed world, most people eat the root vegetable cassava only in tapioca pudding or bubble tea. But in Africa, its the primary staple for half a billion people and the continents most popular crop. Thats why Im super excited that scientists are using the most advanced hybridization techniques for the benefit of cassava farmers and those who depend on the crop. With the support of UK Department for International Development and our foundation, scientists are making great progress developing hybrids that are resistant to the major virus that cuts down on cassava yields (cassava mosaic virus). At the same time, these scientists are breeding strains that have more nutrients than the strains under cultivation today.

The joint efforts will not only involve partner institutions but will bring together conventional plant breeders and biotechnologists. One of the VIRCA Plus product development pathways is crossing the transgene resistant to brown streak virus with non transgenic varieties resistant to the mosaic virus in order to have a product resistant to both viruses. This decision meant VIRCA plus would need to employ the services of so-called human pollinators.

Human bees: Applying both conventional and genetic engineering breeding techniques

Some of the new breeding techniques that are being used on the transgenic crops are revolutionary. If breeding is the art and science of developing a new variety, thena special category of those involved in breeding, the pollinators or the human bees, fit in the art category.Unlike bees that visit flowers for nectar to feed the brood and carry along pollen that accidentally fertilize another flower, human pollinators are intentional. They must know the time of the day the female flower opens up to receive pollen. This time must not be missed as the gametes would eventually become nonviable. Pollinators ensure the male and the female flower about the same time to guarantee success. This, depending on the varieties under crossing, may require synchronized planting of the parental lines. Pollinators also keep records of where the pollen is coming from in order to maintain the integrity of the crosses.

Transgenic cassava is pollinated with a traditional variety.

Conventional breeding is more challenging for cassava pollinators because once they miss the chance of pollinating the flowers, either because the plants have flowered at different times or not flowered at all, they would have to wait for another flowering cycle or replant. Worse still, with one of the parents being transgenic, the research team might have to reapply again to government authorities for requisite permissions. This is costly in terms of time, deferred farmers expectations for solution, and additional financial burden on funding partners. A pollinator bears a big portion of these expectations and the pressure of making no mistakes.

14 years pollinating cassava

Solomon Agenoga is one of these human bees whose dream of a cassava variety resistant to cassava brown streak virus could be realized. He has been actively involved in the conventional breeding attempts that delivered different varieties to fight cassava brown streak disease at Ugandas national cassava program based in Namulonge.

Solomon grew up seeing a cassava crop grow up healthy without any major problems. He has eaten cassava for over 40 years. He recalls the emergence of CMD that threatened to wipe out cassava in his village. Scientists eventually developed CMD-resistant varieties but before longCBSD struck and up to today no resistant variety has beenreleased to farmers.

Solomon recalls, when I was young, It never crossed my mind that one day I would get directly involved in improving my main staple for yield, pests and diseases. For 14 years, Solomon has seen five different varieties released to farmers: NASE 14, NASE 16, NASE 19, NARO CAS1, NARO CAS2. To hisdisappointment, none of these varieties was resistant to bothviruses. All of themare tolerant but not resistant.His full satisfaction willonly come, he says, when a variety resistant to both mosaic virus and brown streak virus is developed. Following several conventional breeding attempts, only incorporating genetic engineering and conventional breeding approaches together could bring Solomons dream of a brown streak virus resistant variety into reality.

When the VIRCA project started in Solomons institution, there seemed to be irreconcilable differences between conventional breeding and genetic engineering. In fact, this technology that could do without flowers had a potential of rendering this experienced pollinator jobless. Solomon recalls, as a pollinator, in his mind, he could not imagine playing a role in this initiative that could help him save his childhood crop.

VIRCA Plus made a decision to incorporate conventional breeding techniques in its product development pathways. This decision elevated Solomon from being another pollinator to the key person who the project relied upon to deliver seeds of transgenic and non transgenic crosses. He rubbedshoulders with these modern scientists who transfer genes rather thanpollen. He left his home in Uganda for the first time to pollinate cassava across the border. It then occurred to him that he was playing an important role in ensuring that millions of African farmers get to have a variety that is resistant to the deadly CBSD.

Solomon has donehis best in leading a team of pollinators who, for the first time in their lives, make crosses involving a genetically modified parent working with a hybrid of con
ventional breeders and biotechnologists. According to Solomon, other than the additional regulatory procedures associated with transgenic crops, the steps involved were basically similar to the usual conventional breeding practices.

The Gates grant will not only unite scientists in rescuing millions of farm families from hunger due to crop failures, but could grant Solomon an opportunity to have a hand in saving his childhood crop from the viruses.

Isaac Ongu is an agriculturist, science writer and an advocate for science based interventions in solving agricultural challenges in Africa. Follow Isaac on twitter@onguisaac

For more background on the Genetic Literacy Project, read GLP on Wikipedia.

Read the rest here:
How 'human bees', biotechnologists and Gates Foundation are rescuing the African cassava staple - Genetic Literacy Project

The tech world has embraced Machine Learning (ML) for its powerful intuitive capabilitiesto increase click-through rates on ads, sell more books, and help you keep in touch with mom. Despite being increasingly common as a classification tool in applications ranging from transcriptomics, metabolomics, and neuronal synaptic activities, ML is still almost absent in the area of bioengineering. Why is that and what can we do to increase ML use in bioengineering?

Machine Learning algorithms that date back half a century are now commonly used for pattern-based analysis, including Decision Trees, Nearest Neighbors, Neural Nets, and more recently with significant success Deep Learninga version of Neural Net with more layers and more nodesreceived significant attention when it won against the best human in the ancient Chinese game of Go. Deep Learning has been enabled by access to new powerful computational hardware, in particular the graphical processing units (GPUs) originally developed for the gaming industry. These gaming GPUs allow for massively parallel computations, which is perfect for ML applications. Its comforting to know that Call of Duty brought something of value to this world. In recent years we have seen ML flourishing in a broad range of applications where there is sufficient amounts of data to digest and classify; from self-driving cars to Barcelona FC soccer strategy, to deciding if you get the bank loan.

But think instead about a common diabetes complication, diabetic retinopathy, which results in irreversible blindness if not caught early. There are today >400 million diabetic patients at risk, many in underserved areas with limited access to clinical diagnosis. In a recent JAMA publication, Google Research applied Deep Learning to diagnose diabetic retinopathy patients from photographs of their retina. An initial set of 128,000 retina images was analyzed and scored by trained ophthalmologists for signs of onset of diabetic retinopathy. The images and the scoring were then processed by Googles Deep Learning software to identify patterns in the images that correlated with the clinical scoring. The resulting algorithm was subsequently validated with a separate set of ~12,000 images that the software had not seen before.

Not only did the Deep Learning image analysis software recognize early signs of the disease just as well as the human experts, it did so much more consistently. Its easy to see a day in the not too distant future when anyone with a smartphone will be able to diagnose this disease accurately and save millions of people from going blind. It will be exciting to see how fast this and similar algorithms will transform medical image based diagnosis in the areas of radiology, pathology, and dermatology.

Small molecule drug discovery is another arena where ML is rapidly gaining traction. Companies ranging from GSK and Pfizer to Atomwise, Numerate, and InSilico Medicine are compiling large datasets of ligands, targets, and associated biological functions to identify and quantify the patterns of ligand-target interactions using Deep Learning. Atomwise has an undisclosed, previously approved drug candidate that blocks Ebola infection as well as another promising lead molecule to treat multiple sclerosis. Both were identified using Deep Learning to find patterns among thousands (in the case of Ebola) and millions (in the case of multiple sclerosis) of related molecules and their physicochemical properties.

So if we understand the powerful and intuitive nature of ML, what has limited its application in bioengineering?

Is it just too new an idea? Probably not, seeing as early as the 1990s, thought leaders like David Haussler at UCSC and Tim Hunkapiller at Caltech were publishing papers using hidden Markov models to capture patterns in DNA and protein datasets. These patterns have subsequently propagated into PFAM and other well-established databases to classify enzymes from protein sequences. So its not a new idea.

Is it because we lack sufficiently large datasets? Maybe. Most curated sequence datasets that include quantified biological function are tiny (in the hundreds) and nonsystematic in that variables are rarely tested in more than one context. On the other hand, Genbank and WGS today encompass ~2 x1012 bp of naturally existing biological sequences and are growing very rapidly. This enormous dataset is however inherently highly correlated because of its evolutionary origin, making it difficult to separate causality from correlation and thus limiting its use for identifying sequence-function relationships. Also, only a vanishingly small part of the data is associated with quantified biological function. Despite these limitations, the Genbank and WGS datasets are extremely informative for e.g. protein engineering as they can readily be used to tell us where not to go. Sequences, elements, or amino acid combinations that never or rarely occurred in biology below some statistical threshold can be assumed to not fold and to not generate new biological functions.

Is it because of differing philosophy of science? Thats part of it. Machine Learning is based on inductive reasoning, i.e. pattern recognition. The system learns from making many observations and finding patterns that can be generalized to a conclusion/hypothesis. Contrary to the inductive reasoning so abundantly and so successfully used by tech companies such as Google, biotechnology has historically been a discovery-based research field led by deductive reasoning. In deductive reasoning we start from a theory and make predictions about what the corresponding observations should be if the theory is correct. Then we look for those observations. However, biology is a gooey and redundant complex megadimensional mess of synergy and antagonism, and an abundance of variables that just came along for the 4 billion year ride of evolution. It quickly becomes humanly impossible to build complex hypotheses that explain biological observation in accordance with deductive reasoning. This instead is the type of data that inductive ML thrives on.

Is it because the cost of making specific observations? Yes and No. The medicinal chemist assessing structure-activity relationships has to independently make and characterize each molecule in the dataset at a large cost. There is thus a significant incentive for the chemist to design and test molecules as efficiently as possible using all available toolsincluding MLto ensure success. This is in stark contrast to the molecular biologist who can make large semi-random datasets through methods like error-prone PCR or DNA shuffling at basically no cost. These gene libraries at sizes of 107-109 can be screened for e.g. binding using phage display or similar high-throughput procedures. Accordingly, the cost of finding a binder is small, diminishing the perceived need for tools such as ML. However, finding a binder is still a long way from making a protein pharmaceutical.

Biotechnology is implicitly well set up for ML applications. Contrary to medicinal chemistry and image-based diagnosis, there are a defined number of available options at each residue and any sequence can be made and tested for function. If we can complement our historical dependence on deductive reasoning with the inductive inference from ML, and increasingly look at biology as something to be engineered instead of a discovery-based science, ML has a bright future in bioengineering.

After all, if we can see our way to a future where ML and a smart phone can diagnose anyone for diabetes-induced blindness, why not use the same methodology perfected over click-through ads and playing Go to make improved antibodies, better vaccines, and novel diagnostic sensors?

Original post:
Building Biology with Machine Learning - Genetic Engineering & Biotechnology News

Dr. Luhan Yang, chief scientific officer at eGenesis, says she wants to pay back to society with her work in genetic engineering.

CAMBRIDGE Where other people see bacon, biologist Luhan Yang sees lifesaving organs hundreds and thousands of them, pig livers and pig kidneys and diabetes-curing pancreases, and possibly hearts and lungs, all growing inside droves of pampered swine.

More established scientists than Yang have dreamed of creating animal organs that are suitable for transplantation into people waiting for a human donor. But until recently, experts said it would take decades to genetically alter pig organs to make them work safely in people. Most dreamers gave up.

Advertisement

Giving up is not in Yangs lexicon. Urgency is. In her native China, she told STAT, 2 million people need organ transplants, and people are dying before they get one.

The intensely driven 31-year-old has a few things going for her that other would-be pioneers did not. As a Harvard graduate student, Yang was a lead author of a breakthrough 2013 study on the genome-editing technology CRISPR-Cas9. And in 2015, she cofounded the biotech company eGenesis with her mentor, legendary Harvard bioengineer George Church, with whom shes also worked on trying to resurrect the Ice Age wooly mammoth through genetic legerdemain. From eGenesiss tiny headquarters in Kendall Square, she intends to use CRISPR to accomplish what the worlds largest drug companies failed to do despite investing billions of dollars: create designer pigs whose organs can be transplanted into people.

Get Talking Points in your inbox:

An afternoon recap of the days most important business news, delivered weekdays.

Luhan is a remarkable person, Church said, and a force of nature.

She better be. Daunting hurdles stand between where biology is now and where it needs to be to make transplantable pig organs. The old problems of infection and rejection of another species organs seem almost quaint compared to those facing eGenesis.

Theres the challenge of CRISPRing an unprecedented number of genes without compromising the viability of the designer pigs and without introducing aberrant edits. And of optimizing mammalian cloning, which is how the company creates the pigs. And of persuading investors and doctors that xenotransplantation, as the process is called, is safe, effective, ethical and lucrative.

Advertisement

Yang, eGenesiss chief scientific officer, has already made enormous strides, both scientific and financial. In 2015, she and colleagues in Churchs lab used CRISPR to eliminate from pig cells 62 genes so potentially dangerous their very existence nixed previous efforts to turn pigs into organ donors. Last month, eGenesis announced that it had raised $38 million from investors. The next hurdle: get the surrogate-mother sows that are pregnant with genetically altered embryos to give birth to healthy piglets.

Her work has the potential to change the face of transplantation and to save countless lives, said Dr. James Markmann, chief of transplant surgery at Massachusetts General Hospital.

Yang is not only confident of success, she also sees eGenesiss xeno work as a sort of trial run for even bolder goals. In 2016, she helped conceive Genome Project-write, whose aims include assembling a synthetic human genome from off-the-shelf parts and because, really, as long as youre making a human genome, why not? doing it better than nature.

By starting from scratch, she wonders, could we make the human genome cancer-resistant? ... Or make it virus-resistant? ... There is a great opportunity that xeno can tell us what would happen in humans after dramatic genome engineering.

But if eGenesis is to succeed in making designer pigs, let alone paving the way for new and improved humans, Yang will need to fix the miscarriage problem.

On a frigid March morning, Yang is holding her monthly meeting with Church and the companys half-dozen employees, getting updates on the designer-pig pipeline and lighting a fire under her team. The big conference table in the windowless basement room is strewn with 8.5-ounce cans of Wild Jujube Drink and snacks that Yang brought back from her Lunar New Year visit to China, where she spent five days with her parents and visited eGenesiss pig colony.

The highlight of the month, biologist Marc Guell tells Yang, is that surrogate mother pigs didnt reinfect fetuses with PERVs. Thats crucial, because the memorably named infectious agents, short for porcine endogenous retroviruses, could cause tumors, leukemia, and neuronal degeneration if transplanted into patients. To make xenotransplantation succeed, PERVs have to go.

PERV genes are interwoven into the genome of pig cells, so eGenesis scientists start their work with CRISPR-Cas9, which has made editing organisms genomes so simple high-schoolers can do it. It takes far more expertise, however, to remove dozens of PERV genes at once, as eGenesis does in pig fibroblasts, which are connective-tissue cells.

EGenesis ships batches of these cells to China, where each de-PERVed pig cell is fused with a pig ovum whose own DNA has been removed. The ova, which now contain only the PERV-free genome, start dividing and multiplying, beginning the journey to becoming pig fetuses. The embryos are implanted into surrogate mothers and, if all goes well, born 114 days later. (Yang wont say how many sows are or have been pregnant.) Unfortunately, all has not gone well.

The anti-PERV work is only the start of the changes eGenesis is making to pig genomes. Its scientists are also slipping into the pig ova up to 12 human genes to make the pig organs more human-like, Yang said in an interview. One gene, she said, would shield its organs from attack by the human immune system; another would revamp its coagulation system to reduce the risk of clots.

Thats a ton of genetic handiwork for one little pig to handle, and early signs are it might be too much.

One batch of embryos all died, Yang said, possibly because their chromosomes had gotten scrambled by either the genetic changes or the lab manipulations. Another batch had a lot of miscarriage, she said.

There are other concerns, scientists noted at the March meeting. Sometimes PERVs are found in the embryos before theyre implanted into surrogate mothers. The problem, Yang says as she leaps to the front of the conference room, is that removing the DNA-containing nuclei from pig ova isnt always complete; occasionally some of an ovums own PERV-infested genes remain behind, so the embryo created from it also has PERVs, genetic analyses showed.

Yang grills her team. How prevalent is this? May I see the genetic profile again? What can we do quickly to correct the protocol? A gene that was inserted to protect other genes is the problem, she says with finality. Maybe we should pause this one and look for other solutions. Its better to figure out where the problem comes from, then we dont have the problem anymore.

A clue to how Yangs mind works is that she counts. Ask her about the ethical issues around xenotransplantation and she will immediately tell you there are three, then elaborate on them. Ask her what characteristics make up the entrepreneurial spirit and she will say there are four, then reel them off. Colleagues say she has an uncanny knack for working backward from an ultimate goal and breaking it into a manageable sequence of steps.

She darts down corridors, speaks quickly, hates waiting, and expects others to move at her speed. Some colleagues call her impatient. Biologist Dong Niu, who worked in the Church lab and is now at eGenesis, joined Yang on a recent blitz of apartment hunting. Yang set such a breakneck pace, Niu said, I couldnt even watch.

She pushes colleagues to accomplish tasks now, if not sooner, and when she asks a coworker to explain a scientific detail, she says, Were short of time; just get to the point.

Yet colleagues sing her prais
es, saying she motivates them and brings extraordinary passion and a laser focus to her work. Whenever you have a question, she has an answer, almost before you get it out, said Niu.

Yang was born and grew up in a small town in a mountainous region of southwest China. Her parents were ordinary working-class people, she said, her father a government employee and her mother an accountant.

In 2004, as a high school senior, she was chosen for Chinas four-person team in the 15th International Biology Olympiad, held in Australia. Yang was one of 16 contestants to win a gold medal, coming in 13th.

After majoring in psychology at Peking University, Yang entered graduate school at Harvard, where she rotated through three labs before joining Churchs. It was a crash course not only in biological engineering but also in what success means.

I think my generation of Chinese, we are very aggressive and very optimistic, Yang said. Sometimes I think we all want to be successful and to find a shortcut to be successful, because the competition [for academic success in China] is so fierce.

The different worldviews and value systems she saw at Harvard, she said, made me open my eyes and reassess what kind of person I want to be. I want to pay back to society.

Yang stumbled out of the gate in Churchs lab, nearly failing her PhD qualifying exams because her English was so poor. It was her first academic setback, but in relating the story, Yang betrayed no more emotion over the experience than if it had been another gene she had to CRISPR. George asked the committee to let me pass with the condition that he would spend more time with me for English training, Yang said.

She played point on some of the labs most important experiments. In 2012, she and postdoctoral fellow Prashant Mali teamed up on CRISPR-Cas9, a molecular complex that bacteria use as a primitive immune system; other scientists had recently gotten it to cut specific locations on DNA floating in test tubes. Mali and Yang got a single cluster of CRISPR molecules to edit multiple genes in human and mouse cells in one fell swoop, a breakthrough published in early 2013. Although Mali and Yang had equal billing as first authors, the paper is always referred to as Mali et al. Yang said that doesnt bother her.

Soon after, physicians approached Church about using CRISPR to alter the genomes of pigs so their organs would not be rejected by the human immune system. The very question was a triumph of hope over experience. In the 1990s, a handful of drug companies, including Novartis, had collectively spent north of $2 billion to use genetic manipulation to make human-friendly pig organs.

She said she feels a strong sense of responsibility to help the millions waiting for organs in her homeland: I regard myself as a Chinese scientist. Something that can potentially solve a huge health care and social problem for China and for the world? I feel it is a privilege to work on that.

With hundreds of labs catching CRISPR fever since 2013, most experiments have altered one or two genes at a time, maxing out at five. Yangs challenge was audacious: To knock out all the PERVs would require a tenfold improvement.

But if we could make it work, she said, the impact would be huge.

They did, and it has been. In 2015 the Church lab announced it had CRISPRd out 62 PERV genes in pig kidney cells growing in lab dishes. It was a record, and it still stands.

George always encouraged me to think bigger, Yang said.

Determined as she is to make xenotransplantation succeed, Yang also sees it as opening a back door for me to push the limit of [genomic] technology. For one thing, xenotransplantation requires large-scale genome engineering, she said. In addition to knocking out PERVs, which is relatively easy, making organ-donor pigs requires inserting large chunks of human DNA into the pig genome.

Our ability to knock in a large fragment of DNA is still limited, Yang said.

Working out how to do it in the pigs would point the way toward, say, adding copies of the cancer-fighting gene p53 into a persons genome.

Thats why I love xeno, she said. Its a platform to help us assess technology.

Yang has immersed herself in the ethical issues around xenotransplantation, but they havent slowed her pursuit of transplantable pig organs.

Some scholars argue that it is morally wrong to value human life more than animals, but so many people are eating pork every day, Yang said. As for playing God the argument that it is unethical to change a pig in the way that genome-editing does she retorts that the highest moral standard is human life. I think its a personal choice whether you use a pig organ or die. But you shouldnt prevent other people from using it.

As of early March, two of eGenesiss cloned and CRISPRd pig fetuses were just a few weeks from delivery, Yang said. We checked the genotype and were surprised but also delighted to see that the fetuses [in one surrogate mother] are 100 percent PERV-free.

Yang is more than ready to be a proud mother: I feel its our time.

Read more here:
Cambridge company is making designer pigs with transplantable (to people) organs. - The Boston Globe