Scientists create mouse that resists cocaine's lure

By biochemically 'hard-wiring' synapses, they prevent drug addiction
Date:February 13, 2017
Source:University of British Columbia
Summary:Scientists have genetically engineered a mouse that resists addiction to cocaine.

This is a diagram showing synapses in the reward circuit of mice when exposed to cocaine: on left, a normal mouse, and on right, a mouse with increased levels of cadherin. Credit: University of British Columbia

This is a diagram showing synapses in the reward circuit of mice when exposed to cocaine: on left, a normal mouse, and on right, a mouse with increased levels of cadherin.

Credit: University of British Columbia

Scientists at the University of British Columbia have genetically engineered a mouse that does not become addicted to cocaine, adding to the evidence that habitual drug use is more a matter of genetics and biochemistry than just poor judgment.

The mice they created had higher levels of a protein called cadherin, which helps bind cells together. In the brain, cadherin helps strengthen synapses between neurons -- the gaps that electrical impulses must traverse to bring about any action or function controlled by the brain, whether it's breathing, walking, learning a new task or recalling a memory.

Learning -- including learning about the pleasure induced by a stimulant drug -- requires a strengthening of certain synapses. So Shernaz Bamji, a Professor in the Department of Cellular and Physiological Sciences, thought that extra cadherin in the reward circuit would make their mice more prone to cocaine addiction.

But she and her collaborators found the opposite to be true, as they explain in an article published today in Nature Neuroscience.

Dr. Bamji and her collaborators injected cocaine into mice over a number of days and immediately placed in a distinctly decorated compartment in a three-room cage, so that they would associate the drug with that compartment. After several days of receiving cocaine this way, the mice were put into the cage and allowed to spend time in any compartments they preferred. The normal mice almost always gravitated to the cocaine-associated compartment, while the mice with extra cadherin spent half as much time there -- indicating that these mice hadn't formed strong memories of the drug.

To understand that unexpected result, Dr. Bamji and her associates in UBC's Life Sciences Institute analyzed the brain tissue of the genetically engineered mice.

They found that extra cadherin prevents a type of neurochemical receptor from migrating from the cell's interior to the synaptic membrane. Without that receptor in place, it's difficult for a neuron to receive a signal from adjoining neurons. So the synapses don't strengthen and the pleasurable memory does not "stick."

"Through genetic engineering, we hard-wired in place the synapses in the reward circuits of these mice," says graduate student Andrea Globa, a co-lead author with former graduate student Fergil Mills. "By preventing the synapses from strengthening, we prevented the mutant mice from 'learning' the memory of cocaine, and thus prevented them from becoming addicted."

Their finding provides an explanation for previous studies showing that people with substance use problems tend to have more genetic mutations associated with cadherin and cell adhesion. As studies such as this one illuminate the biochemical underpinnings of addiction, it could lead to greater confidence in predicting who is more vulnerable to drug abuse -- and enable people to act on that knowledge.

Unfortunately, finding a way of augmenting cadherin as a way of resisting addiction in humans is fraught with pitfalls. In many cases, it's important to strengthen synapses -- even in the reward circuit of the brain.

"For normal learning, we need to be able to both weaken and strengthen synapses," Dr. Bamji says. "That plasticity allows for the pruning of some neural pathways and the formation of others, enabling the brain to adapt and to learn. Ideally, we would need to find a molecule that blocks formation of a memory of a drug-induced high, while not interfering with the ability to remember important things."

Story Source:

Materials provided by University of British ColumbiaNote: Content may be edited for style and length.

Journal Reference:

  1. Fergil Mills, Andrea K Globa, Shuai Liu, Catherine M Cowan, Mahsan Mobasser, Anthony G Phillips, Stephanie L Borgland, Shernaz X Bamji. Cadherins mediate cocaine-induced synaptic plasticity and behavioral conditioningNature Neuroscience, 2017; DOI: 10.1038/nn.4503

Originally published at https://www.sciencedaily.com/releases/2017/02/170213131507.htm

(We do not own this article. Credits go to their respective owners)

CRISPR Applications in Plants

A Report from the Plant and Animal Genomics Conference
DeeAnn Visk, Ph.D.

Recent work by University of North Carolina researchers in the model organism Arabidopsis shows that the CRISPR/Cas9 system correctly targets the desired loci in plant genomes. [AnRo0002/Wikimedia]

Recent work by University of North Carolina researchers in the model organism Arabidopsis shows that the CRISPR/Cas9 system correctly targets the desired loci in plant genomes. [AnRo0002/Wikimedia]

Are you a food label reader?  If so, you may have noticed some of your favorite snacks bear the phrase “partially produced with genetic engineering.” This makes sense, given that the soy lectin and corn syrup used in many foods is probably isolated from plants genetically modified to be resistant to a powerful herbicide, glyphosate. Genes, originally isolated from bacteria, were inserted into crop plants, conferring glyphosate tolerance to the soybeans, corn, and other crops. Then, federal regulations followed: requiring that human food made with these plants be labeled “partially produced with genetic engineering.”

While these genetically modified plants have been around almost 20 years, new tools for plant biologists have yielded new traits for plants. At the Plant and Animal Genomics Conference held recently in San Diego, a topic of great interest was applications of the CRIPSR/Cas9 system to plants.

One brilliant approach to using CRISPR in plants is to edit the family of genes that confers susceptibility to bacterial blight in rice. Bacterial blight in rice, caused by Xanthomonas oryzae pv. oryzae, is a huge problem in Asia and Africa.

“To understand sensitivity to bacterial blight, it is necessary to first understand the biology of the disease process,” explains Bing Yang, Ph.D., associate professor in genetics, development and cell biology at Iowa State University.

“Bacteria that cause the blight have effector proteins (called TALs; transcription activator-like) that transcriptionally activate a family of genes in rice, referred to as SWEET genes. We strategized that by mutating the promoter region of the SWEET family of genes, the bacterial TAL proteins would no long be able to bind to the promoter. Being unable to bind to the promoter DNA, the bacterial TAL proteins cannot induce expression of the SWEET genes. Hence, TAL proteins could no longer bring about a state of disease susceptibility in rice,” explains Dr. Yang.

“CRISPR experiments can be designed to leave no fingerprint, or exogenous DNA in the plants. From a regulatory standpoint, the USDA should accept rice plants with small deletions or mutations in their genomes as safe for field tests,” concludes Dr. Yang.

Using a similar approach, disease-resistant citrus trees have also been developed. In Florida, the citrus industry faces disease challenges from citrus canker and citrus greening disease caused by two bacteria, Xanthomonas citri and Candidatus Liberibacter asiaticus, respectively.

"Citrus canker is also a big problem," asserts Nian Wang, Ph.D., associate professor, department of microbiology and cell science, Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida. "A specific effector protein from the infecting bacteria binds to the promoter region of the canker susceptibility gene CsLOB1 to induce disease symptoms. By utilizing CRISPR techniques, we can target the promoter region or the coding region of the citrus susceptibility gene to mutate it in such a way to prevent binding of bacterial transducers."

The CRISPR/Cas9 system can be applied in a manner that leave no exogenous DNA in the citrus, which is very beneficial in getting USDA approval.

"Applying the same strategy for citrus greening disease, we have begun research to identify the key virulence factors and their targets," continues Dr. Wang. "We are mutating the putative targets using the CRISPR technology. We hope to generate citrus trees resistant to citrus greening disease."

Another talk at the conference was on gene editing in cereals by Ming Luo, Ph.D., of the Commonwealth Scientific and Industrial Research Organisation (CSIRO) in Canberra, Australia. Wheat rust is a huge problem in failure of wheat crops worldwide; finding a solution to the problem would be a milestone in addressing world hunger.

“A pilot study of CRISPR efficacy in rice was successful with a knockout of two closely linked genes. In contrast, the homologous CRISPR experiment in wheat did not lead to any mutations,” declares Dr. Luo. “In contrast, using TALEN in wheat yielded results.

“While CRISPR works in rice and barley, CRISPR editing in wheat has not worked in our hands. We conclude that employing TALENs as a gene-editing tool in wheat is more efficient than CRISPR.”

One drawback to the CRISPR/Cas9 system in plants concerns off-target effects. To assess these effects in plants, whole genome sequencing is the current gold standard.

“Recent work in the model organism Arabidopsis, shows that the CRISPR/Cas9 system correctly targets the desired loci in plant genomes,” states Cara Soyars, University of North Carolina doctoral candidate. “This finding contrasts with off-target CRISPR effects in animals where off-target effects are a serious concern. Extrapolating this to other genera of plants, we postulate that modifications to the Cas9 protein to increase specificity of the binding site is not necessary in plants.”

“Plant genomes have many redundant genes. Hence, to effectively knockout a particular pathway of interest, many genes need to be knocked out,” continues Soyars. “Our lab, the Zachary Nimchuk lab, has developed a system that allows entire families of genes to be targeted in one experiment. While the system is predicted to increase the risk of off-target effects, we have shown with whole genome sequencing that there are very few or no off-target effects in Arabidopsis.

“One of our studies necessitated the targeting of 14 genomic loci at once. Using the multiplexed CRISPR/Cas9 system, we had a 33­–92% success rate. Whole genome sequencing also revealed that chromosomal translocation events are extremely rare after genome manipulation in Arabidopsis via CRISPR/Cas9.

“We really do not know why there is such a lower rate of off-target effects in plants when compared to animals,” clarifies Soyars. “Speculatively, plants use nonhomologous recombination; whereas animals employ homologous recombination when joining double DNA breaks. Perhaps differences in these repair mechanisms explain the difference in off target effects?”

One advantage of the CRISPR/Cas9 system is the applicability across a wide range of organisms. Editing carried out for research purposes does not require the same level of stringency as those for therapeutic applications. However, any plants or animals undergoing genome editing will need to be carefully vetted.

The regulatory body overseeing this is the Animal and Plant Health Inspection Service (APHIS), which is part of the USDA. APHIS released for comment a policy suggesting a path forward. For now, very small changes [like single base insertion or deletions (2–10 base pairs removed)] do not seem to be of much interest to APHIS.

“The ability to make these tiny changes at a very specific place in the genome is the result of using CRISPR/Cas9 technology in plants,” affirms Jeff Wolt, Ph.D., professor of agronomy at Iowa State University. “In the past, genetic additions to plants included either exogenous genes or even some of the machinery to get the modifications incorporated.

“Dr. Bing screened plants to select the edited gene of interest, while selecting against the inclusion of the CRISPR machinery. Dr. Bing confirmed this with lots of sequencing. His letter of inquiry to APHIS posed the question: will these rice plants be subject to regulation? APHIS responded that the material can be used without regulatory oversight.

“Plant researchers are moving forward cautiously, as the all the wonderful technology from previous methods of transgenic manipulation was not fully realized due to public push-back. We need to ensure that what we are doing is well-communicated and transparent,” expounds Dr. Wolt.

“Plant sciences have lagged behind in adopting new technologies for genome editing for a couple of reasons,” he continues. “First, funding levels are generally lower for plant researchers than studies involving animals. Second, the techniques used to change the genome must go through the cell walls of plants; in animals, especially cell lines, it is much simpler to get the components of CRISPR/Cas9 into the cells.”

 “Another reason many of the exciting applications of CRISPR in plants are not discussed as often as medical applications,” explains Mark Behlke, M.D, Ph.D., CSO of Integrated DNA Technologies, “is that the development of agricultural applications done by industry is confidential and is not published quickly, or at all. Also, working with crop plant genomes can be more complex than mammalian cells; as these species are often polyploid, which makes manipulation of their genomes more complicated.  Furthermore, plant genomes often have huge repetitive content.

“On the other hand,” Dr. Behlke continues, “advances in CRISPR/Cas9 technology has made genome manipulation accessible for just about any research lab in the world. One method that is especially promising is the use of a DNA-free system to perform genome engineering in plants. In this sort of system, the RNA guide is bound to recombinant Cas9 protein and added directly into cells as a ribonucleoprotein (RNP) complex, with no use of plasmids or other DNA-based expression cassettes.

“A delivery method of coating gold nanoparticles with plasmids and shooting them into whole animals has worked in cattle vaccinations (‘biolistics’). This approach is already being applied to plants, to get the Cas9 RNP complexes into cells through their tough cell walls,” concludes Dr. Behlke.

Originally Published at http://www.genengnews.com/gen-exclusives/crispr-applications-in-plants/77900846

(We do not own this article. Credits go to their respective owners)

GEN Introduces Biotechnology Dictionary

Reader Contributions Are Encouraged So We Can Compile an Even More Valuable Resource

The GEN Dictionary is composed of 100 definitions at this time. We are inviting GEN readers to submit their own definitions to add to our dictionary. [Oktay Ortakcioglu/Getty]

The GEN Dictionary is composed of 100 definitions at this time. We are inviting GEN readers to submit their own definitions to add to our dictionary. [Oktay Ortakcioglu/Getty]

Faith in the wisdom of crowds and even democracy itself has been shaken—not just by an unlikely presidential candidate or a disruptive referendum result, but by Boaty McBoatface, the most popular submission in a highly publicized name-our-ship contest. Alas, Boaty was scuttled by the contest’s organizers, who ultimately launched a more dignified name. But a meme—Blank·y McBlank·face—steamed full speed ahead. Still foundering in its wake is the idea that anything “crowdsourced” could have enduring value.

Eager to recover this flotsam, GEN is launching an initiative of its own: the GEN Dictionary. This resource already comprises 100 definitions, the GEN editorial staff’s “Top 100” terms in biotechnology. The fitting-out of this resource will be left to GEN’s readers, who are invited to submit their own definitions (or improved versions of existing definitions) by emailing them to this address:dictionary@genengnews.com or send a tweet to @GENbio  using hashtag #GENDictionary.

As proud as we are of our definitions, we know that our knowledge is severely limited compared to the knowledge that could be supplied by contributing readers. And so our hope is to stimulate reader contributions that we may compile into an ever-richer resource.

This approach—partly directed, partly crowdsourced—is in the best “wisdom of crowds” tradition. According to James Surowiecki, the man who literally wrote the book on the subject, a wise crowd has four elements: diversity of opinion, independence, decentralization, and aggregation. The first three elements will be met by GEN’s readership. The last element, which amounts to a mechanism for turning private judgments into a collective decision, will be supplied by GEN’s editors.

Unlike the boat-naming contest, which became top-heavy with Boaty McBoatface whimsy, the GEN Dictionary will be kept on an even keel. The initial definitions, we think you’ll agree, are shipshape. And since overhauled versions of the GEN Dictionary will continue to be freely available, all fitting-out operations will remain above board.

 

Originally published at http://www.genengnews.com/insight-and-intelligence/gen-introduces-biotechnology-dictionary/77900697/

Carnegie Mellon builds new algorithm for analyzing the cancer genome

Extra copies of normally paired chromosomes. Variations in chromosome color show where DNA has become rearranged and duplicated within and between chromosomes.

Extra copies of normally paired chromosomes. Variations in chromosome color show where DNA has become rearranged and duplicated within and between chromosomes.

A cancer genome can be insanely complicated, making the disease difficult to study and treat. Large chunks of DNA — including millions of base pairs or even whole chromosomes — can get yanked from their original locations and moved elsewhere, duplicated or even flipped. But an algorithm, named Weaver, developed by researchers at Carnegie Mellon University, may offer new ways to break down some of that complexity.

Named for a character called Weaver in the video game Defense of the Ancients, Weaver also describes the algorithm’s function: weaving together disparate pieces of genomic information.

“The cancer genome is reshuffled and scrambled compared to the normal genome” said associate professor of computational biology Jian Ma, whose Computational Comparative Genomics Lab is leading the project. “Weaver’s goal is to interlace genomic pieces and keep things in the right order.”

To accomplish this, Weaver analyzes two major classes of mutations in tumor DNA. The first are copy number variations and aneuploidy, in which chromosomes get duplicated. The other is structural rearrangements, such as DNA insertions, deletions, duplications or rearrangements. The algorithm uses a model called the Markov Random Field, which allows researchers to visualize interrelationships in complex data.

Until now, no tool has been able to simultaneously analyze genomic sequencing data for both types of variations. It’s like being able to identify how furniture is aligned in a room, or how many rooms are in the house, but not both. Understanding how the rooms are arranged adds context to the furniture.

“The goal is to look at the sequencing data from the cancer genome and recognize these complex alterations,” said Ma. “None of the current structural variant detection methods are specifically designed for genomes with aneuploidy, a hallmark of cancer. Our algorithm can more precisely quantify complex rearrangement structure variants in the context of aneuploidy.”

By identifying and quantifying both types of alterations, Weaver provides a more comprehensive view of the cancer genome, as well as shedding light on how these different variations interact.

“In cancer, we can see that certain regions are frequently amplified,” said Ma. “Typically, we don’t know why that amplification is happening. By applying this method, we should at least be able to get a sense that the amplification is due to a specific type of structural variation.”

There’s also the possibility of putting these genomic shifts into temporal context, which might cast light on tumor evolution and generate a better understanding of genomic cause and effect.

“Which variation happened first?” asked Ma. “Did the structural variants or deletion happen before or after the chromosome duplication? This approach could give us a better picture of how these copy number alterations and structural variants are connected.”

While this approach has more immediate applications in research, Ma envisions a possible future for Weaver in the clinic, as these structural mutations could directly impact cancer behavior.

“I think this method to view the genome globally, and in an unbiased fashion, can find complementary information for us to understand the cancer,” said Ma.

Ma’s team has successfully test-driven Weaver in a variety of cancer cell lines (HeLa, MCF-7) and samples from the National Institutes of Health’s Cancer Genome Atlasprogram, research that was recently published in the journal Cell Systems. The next step will be to study specific tumors.

“We would like to apply this to more samples and identify patterns in the same types of cancer, such as breast, ovarian, glioblastoma,” said Ma. “Do these structural changes have an impact on gene expression or phenotypes? If we have a better understanding of the structure of the genome, we’ll be better able to interpret functional genomic information.”

Image: Ella Marushchenko via Carnegie Mellon University

Originally published at http://medcitynews.com/2016/07/carnegie-mellon-algorithm-cancer-genome/

The Synthetic Biology Era Is Here—How We Can Make the Most of It

We are entering an era of directed design in which we will expand the limited notion that biology is only the ‘study of life and living things’ and see biology as the ultimate distributed, manufacturing platform (as Stanford bioengineer, Drew Endy, often says). This new mode of manufacturing will offer us unrivaled personalization and functionality. 

New foods. New fuels. New materials. New drugs.

We’re already taking our first steps in this direction. Joule Unlimited has engineered bacteria to convert CO2 into fuels in a single-step, continuous process. Others are engineering yeast to produce artemisinin — a potent anti-malarial compound used by millions of people globally. Still other microbes are being reprogrammed to produce industrial ingredients, like those used in synthetic rubber.

 

If we look far enough, future bio-based industries will discard expensive, complicated industrial chemical syntheses that use high temperatures, high pressures and toxic catalysts in favor of cheaper, more resource-efficient and less toxic biochemical syntheses. 

We will do these things, and then we will exceed them. Or at least, that’s one (perhaps shamelessly optimistic) version of the future. Alternate perspectives, both pessimistic and realistic, ought to be considered too. There are many opportunities here — billion-dollar companies to be built, billion-person problems to be solved, critical ethical debates to be discussed in public, and policy prescriptions to be scrutinized.

So, how should we view the new world of synthetic biology? Let’s take a look. 

The Optimists 

For the optimists and dreamers amongst us, it’s tempting to believe that synthetic biology will surely usher in a fantastic world of abundance.

The optimists dream of longer, healthier lives enabled by intelligent systems that diagnose our diseases before symptoms appear. They long for truly personalized medicine. They anticipate CRISPR-enabled cures for genetic diseases, cancer and beyond. 

The optimists see synthetic biology as a burgeoning field with unmatched potential for human good — potential that’s only comparable to that of artificial intelligence. 

The Pessimists 

The pessimists and the cautious quietly quiver at this perspective. Because we humans identify very strongly with biology, some consider ‘engineering life’ to be unnatural, unethical and arrogant. 

The pessimists worry about how synthetic biology will affect our jobs, our sense of humanity and our ecosystems. They imagine a day when bio-terrorists can fabricate synthetic pathogens that can survive, multiply and cause deliberate harm to us.

The pessimists are concerned about unintended consequences . They feel that the potential for misuse and abuse is so great that the risks of synthetic biology (synbio) outweigh the benefits.

The Realists

The realists sit somewhere in the middle.

They see the world-changing potential of synthetic biology, yet they are aware of the hurdles that must be overcome before the fun stuff starts happening. They may ascribe to the optimist’s portrait of the future, but they remind us that first, we need to make biology easier to engineer and program . We need to develop standards for engineering life, abstractions for biological code and better ways of sharing experimental procedures so that reliable lab results can be replicated in labs around the world.

All three agree on one thing—we are moving fast into the synbio era. They’ve formed their opinion based on this simple fact. And they’re right. 

Forward Momentum Is Undeniable

 Predicting the trajectory of technology is riddled with complexity, but we are seeing movement on a number of different interrelated fronts in synthetic biology.

  • The development of the first programming language for living cells.
  • The arrival of CRISPR — a game-changing tool for cheap, easy genetic manipulation.
  • The colossal drop in the cost of reading DNA.
  • The emergence of IndieBio — the world’s first biotech accelerator that’s tempting postgrads away from academia into the startup world.
  • The explosion of iGem — an annual global student competition where students design, build and test biological devices that do useful things like biosensors that screen drinking water for pathogens or toxic metals.
  • The growth of the iGem Registry — a growing catalog of standard biological parts that engineers can lean on when designing biological circuits.
  • The formation of BioBricks — which works to make synbio an open and collaborative science that serves the public interest.
  • Startups like Amino Labs and Bento Labs that are developing easy-to-use, portable, laptop-size mini-labs equipped for real science — reading DNA and culturing friendly bacteria to make perfumes.
  • The broad maker movement that’s causing technical disciplines — from bioengineering to programming — to be more accessible, more inviting and less mysterious to everyone.

Beyond this, the increased media attention —both the sensationalist headlines and the useful pragmatic discussions are symptomatic of the upward trajectory of this field.

Collectively, all of these trends point to a future in which synthetic biology could be truly transformative in energy, healthcare, manufacturing, agriculture and beyond. But they also illustrate the fact that synthetic biology is still a young field.

This is where the realists have a point—we’re not there quite yet. And the more widely available and powerful the tech gets, the more we’ll want to sort out the rules of the road.

How hard we work today may well determine whether the future tends toward the immensely positive visions of the optimists or those scary pessimistic outcomes.

What Still Needs Doing to Make the Most of Synbio?

Here’s some of the work we still need to do.

  • We need to automate the process of designing and optimizing microbial strains.
  • We need to fully engage the public about the implications of these technologies.
  • We need to decide what our new relationship with biology will look like.
  • We need to explore which applications are acceptable and which are not.
  • We need to fully consider the effects certain synbio applications could have on issues like inequality and discrimination.

Like all powerful technologies, synthetic biology is inherently dual use — it can be used for human good or to threaten human safety. And because biology is involved, there is an added threat of multiplication and self-replication associated with certain biological weapons.

So yes, there is immense potential, and we should be excited about what this future might look like. And yes, we need the dreamers and the technical experts to push the boundaries of what is considered possible from a technical perspective (in a safe way). But in our quest for a better tomorrow, we must not overlook or evade the necessary ethical questions today. 

 

Originally published at http://singularityhub.com/2016/08/19/the-synthetic-biology-era-is-here-how-we-can-make-the-most-of-it/

Raphaël Laurenceau | Truffle Hacking Project | BosLabs

Hack the truffle - select & find its inner microbes - produce its flavors - do DIYbio!

Raphaël Laurenceau is a postdoctoral fellow at MIT and he is one of the co-founders/co-organizers at BosLab. He is leading the Truffle hacking project.

Kindly tell us more about your project?

We have called this project ‘Truffle hacking’. The idea is to produce the delicious truffle aroma molecules from bacteria instead of from the fungus. This idea came after a publication in 2015 showing that bacteria and yeast living in symbiosis within the truffle are the main contributors to making the final aromatic molecules that we humans perceive as tasting delicious. The way we proceed is by isolating bacteria and yeasts from truffles, then cultivate them in a wide range of conditions to detect some aroma producer strains. Our next goal is to identify the aroma molecules, sequence the producer strains and possibly move the enzymes responsible for this production to E. coli, or boost the truffle aroma production in the wild strain.

Who is/are part of this project (people, company etc.)?

We are a team of four people on this project: one microbiologist and three true DIY biologists that are learning all the microbiology techniques along the way. 

What are the challenges you encountered?

The main challenge is time. We are not in a hurry and we do this project in our spare time as a hobby, however cells don’t wait! Very often it is necessary to start a culture for working on it a few days after, and planning all of this in extra work hours can be difficult.

How did you get the funding of this project?

For now Boslab memberships fees have paid for all the materials necessary (mostly plates, media and truffle for the beginning!), however quite soon we will definitely need to find some funding (Mass spectrometry analysis of the compounds produced, sequencing the genome of a strain, etc…). We’re confident that we will find some support for the project. Some companies have already proposed to help us.

BosLabs

What motivates you to create this project?

My personal motivation is for the thrill of playing with microbes, understanding how they work, and tweaking them so that they work for me. Another main motivation comes from the interaction with other DIY biologists. Whether they have experience or not, the common trait among all of us is a lot of curiosity, a fascination for biology, and all technologies coming out of it. 

What equipments did you use/are using?

The first essential piece of equipment for us is the autoclave. We also use an incubator, a PCR machine, and a freezer to store our strains.

When did you started this project and when do you think it will be finished/when did you finished it?

We started almost two months ago, and we have no idea when it will finish!

What are your plans after this project?

Start another one.

(If project is not yet done) Do you think your project would be successful and useful?

I am pretty confident we will be successful in identifying truffle producing microbes. Whether we will be able to turn this finding into an easier way to produce ‘natural’ truffle aromas from microbes, that’s very hard to say. We’ll see! 

Vegan shrimp is tackling sustainability and human rights

By Eva Lampert

Vegan shrimp could put an end to disrupted marine life and slave labour.

The Atlantic reports that algae based, synthetic shrimp is on it’s way to replacing America’s most popular seafood. New Wave Foods, a startup that recently graduated from a biotech accelerator called IndieBio, is set on eliminating overfishing, pollution, and slavery with a single product. Founder and marine conservationist Dominique Barnes and her partner Michelle Wolf, a materials scientist, are taking sustainability and human rights seriously, one vegan popcorn shrimp at a time.

The devastation of fulfilling our appetites for shrimp starts in the ocean. With the average American consuming four pounds of shrimp yearly, the amount of aquatic life lost is unimaginable. On dry land, the practices around shrimp preparation are no better. An AP investigation found that in production, hundreds of migrant workers are kept in warehouses in Thailand, forced to peel shrimp in unclean conditions with shifts of up to 15 hours, for only $4 each day. AP found that the result of this slave labour is on store shelves in popular retail chains like Whole Foods, Wal-Mart, Red Lobster, and Olive Garden. It’s about time this corrupted industry sought change. 

The aptly named New Wave Foods team have figured out how to use plant based protein powders, along with the same pink algae that shrimp eat to create their alternative. The algae helps replicate the colour and flavour we expect, and taste-testers say it has a similar elastic texture, too. Pair that with a mirrored protein and fat content to real shrimp, and there’s absolutely no argument that lab-grown is not the way to go.

New Wave has already been asked for 200 pounds of shrimp from Google for their cafeterias, and a San Francisco kosher sushi company has shown demand as well. Whether or not vegan and non-vegan consumers will be as open to mock shrimp as they have been faux burgers, chicken strips, and bacon is up for evaluation. Until I can get my hands on New Wave shrimp, I’ll be busy perfecting my vegan cocktail sauce. 

Source: www.ecorazzi.com/

 

San Francisco Start-Up Working on Vegan Gelatin

Little do most consumers know that marshmallows and gummy bears aren’t the innocuous treats they appear to be. Like so many other common products, the traditional versions contain gelatin, a macabre ingredient derived from skin, tendons, ligaments, and/or bones of cows and pigs.

Thankfully for animals and consumers alike, a new start-up, Gelzen, is working on creating vegan gelatin.

The San Francisco-based company was founded by partners Alex Lorestani and Nick Ouzounov. Lorestani was in a physician-scientist training program, and quickly learned about the growing risk of infectious disease thanks to antibiotic resistant bacteria (fueled by antiobiotic use in farm animals). Ouzounov earned his PhD in Molecular Biology at Princeton University, and as a vegetarian was frustrated by the lack of an animal-free gelatin alternative.

Alex Lorestani and Nick Ouzounov

Alex Lorestani and Nick Ouzounov

As far as the science, the whole process revolves around microbes. “We make gelatin from scratch by programming microbes to build it for us,” explains Lorestani. “It’s the same approach that humans use to brew beer, make insulin, and many other animal-free products.”

Gelzen’s version of gelatin will be cruelty-free, sustainable, and safer for human consumption.

“We have taken the machinery that builds collagen in animals, and moved it into microbes. These microbes can produce animal-free gelatin at massive scales. Building gelatin from scratch also eliminates the risk of pathogens that can be transmitted from animal material to humans, greatly improves the efficiency of protein production by using fewer land and water inputs, and allows us to precisely engineer its key properties like stiffness.”

Considering that gelatin is in a countless number of products, from gel-caps to Jello, the market for a better version has the potential to be huge. As The New Omnivore put it: “With its special versatility, stability, and more predictable quality, as well as the fact that conventional gelatin is a by-product of the hugely wasteful factory farming system, Gelzen’s new gelatin represents another bright step forward to animal-free food production.”

So where does production currently stand? “We built the collagen-producing microbial factories,” explains Lorestani. “Now, we’re focusing on scaling production up and making prototypes for customers to test. We are thrilled by how supportive the vegan community has been. There’s a real and urgent need for animal-free gelatin, and we’re working hard to get it out there!”

Source: LatestVeganNews.com

Amino’s Cool Bio Kit Is Like the Easy-Bake Oven of Bioreactors

MOST PEOPLE WOULDN’T consider themselves biological engineers. In fact, most people have never worn a lab coat in their lives. Biology is complicated, and often restricted to a lab environment. But at an increasing rate, biology—and our ability to manipulate it—is becoming democratized, to the point that it’s now possible to hack DNA in your own home.

A new kit, called Amino, is like the Easy-Bake Oven of bioreactors. The pretty set of modular parts is a small-scale bio lab that enables you to grow organisms and bend bits of DNA to your will.

You could think of Amino as a beginners guide to biological engineering. The kit (starting at $700) comes with everything you need to grow and tinker with a microorganism: the main bacterial culture, DNA, pipettes, incubators, agar plates and various sensors for monitoring the growth and health of your culture. All of this is built into a color-coded, design-centric plywood dashboard.

Its creator, Julie Legualt, is a designer and graduate of the MIT Media Lab, who herself had no laboratory experience before coming up with the idea while at MIT. “I don’t have a science background—I kind of hated science all the way through school,” she says. “So I wanted to make sure that people who don’t like science don’t feel like this isn’t for them.”

Legualt, who first fell in love with synthetic biology while attending a workshop with the wetware company Synbiota, says she thinks it’s the role of a designer to make a complex subject like synthetic biology more accessible and understandable to the general public. “I thought it was really important to be able to understand it beyond the fear mongering that’s currently the most viewed opinion on it,” she says. The trick is getting people to not just read about synthetic biology, but make something with it. “The hands-on part makes it less scary,” she says.

In that way, Amino is a lot like tinkering with an Arduino, only instead of playing with wires, circuit boards, and programming languages, it’s bacteria, DNA, and incubators. The Amino kit centers around “apps,” which are step-by-step guides to making certain products with DNA. They walk users through how to insert the DNA into untransformed bacteria cells, and how to incubate, grow, and maintain the altered microorganisms. The first app, Living Nightlight, teaches users how E. coli can be reprogrammed to glow like a firefly.The second, Amino Explorer, teaches users to optimize the metabolic pathways responsible for the production of violacein, an anti-parasitic compound used in cancer research. Legault says the company plans to introduce more apps that will let people make scents, brew beer, and make art with the Amino.

The goal is to make synthetic biology feel less like a science experiment shrouded in mystery and more like something that even the most science-averse person can take part in. Because as insular as the world of biological engineering might seem today, Legault believes it’s only a matter of time before it’s as common in our everyday lives as electronics. As she sees it, giving everyday people the tools to create something starts them down the path toward understand how this technology can and should be used in the future. “Once you start making something, you feel like you can take part in the discussion,” she says.

Source: Wired.com