Synthetic-Biology

huffingtonpost.com
Hacking Gut Bacteria Could Be The Next Major Class Of Medicines
MIT biologists are reprogramming gut bacteria as "live therapeutics."

“We start with the probiotics that you can literally buy over the counter at your local pharmacy,” Lu explained. “We’re trying to show that probiotics that are really engineered with our technologies can treat serious human diseases. So we take those probiotics and modify them so that we can significantly amplify their beneficial effects.”  

Here’s how it works: Lu and Dr. Jim Collins, Synlogic co-founder and biological engineer, developed “genetic circuits” made of synthetic DNA or RNA that carry instructions for certain bacteria, telling them to seek out and cure infections. Essentially, the researchers are tweaking the genetic codes within the bacteria in order to program them like a computer.

The bacteria can be programmed, for instance, to detect inflammation in the gut and create anti-inflammatory molecules on the spot, as well as producing molecules to boost immune system function.

Bacteriophages: Antibiotic Alternative or Just a Phase?

It is now clear that we are rapidly approaching a post-antibiotic era, and the need for an alternative is more vital than ever. The CDC estimates that approximately 2 million people are infected with antibiotic resistant bacteria each year, and of that 23 000 of them die as a result of the infection [1]. Our antibiotic pipeline is drying up and the development of new antibiotics is both slow and expensive, making antibiotics unappealing investments for pharmaceutical companies. Although alternatives to antibiotics are far from the market, the field is slowly expanding. Amongst the alternatives, bacteriophages (phages) are a potential candidate for both diagnostic and therapeutic medicine.

Quite simply, phages are viruses that infect bacteria. These are the most abundant biological entity on the planet and are thought to outnumber bacteria 10:1. Their sheer abundance has led to a vast diversity that has yet to be exploited by modern medicine. This is in part due to a number of problems with phages that haven’t made them ideal candidates for therapy. This article seeks to look at some of the problems with phages, and what steps are being taken to improve them for application in humans.

Rapid clearance from the host:

Delivery systems for phages have not been thoroughly assessed for systemic phage application. In other words we are still lacking a way of delivering a bacteriophage drug intravenously to ensure that phages have the maximal effect on the patient. Annoyingly, our immune systems are great at rapidly inactivating and removing them from our bodies [2], with animal studies showing that phage can be completely cleared within 24 hours [3]. Early work carried out in germ-free mice in the 70s showed that phages are passively collected in the mononuclear phagocyte system (MPS), where they remain viable until inactivated by immune cells [3].

There have been two solutions developed so far to amend this problem [2]. The first was developed in the late 90s by the National Institute of Health in the US, which involved the serial passage of phage through a living organism. It was hypothesised that some phage would have mutations in their coat proteins that would give them increased protection from the natural filtration systems in the body over wild type phage [3] and by selecting for these phage, you could gradually produce a population of long-circulating phage. When applied, these phage would have longer circulation times, and therefore a greater chance of colliding with their target bacteria. Animal studies have shown far better recovery of animals given long-circulating strains of virus over wild type, when presenting symptoms of otherwise fatal bacteraemia [4].

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Figure 1. Diagram showing a few of the possible receptors for Salmonella sp. phage [5]

Additionally, to prevent degradation or inactivation of phages, polymers can be added to the coatings of phages [1]. The polymer polyethylene glycol (PEG) has been shown to increase systematic circulation and decrease T-helper cell activation in response to phage. It is likely that a combination of these two methods may improve delivery strategies in the future of phage therapeutics.

Altering host range and preventing resistance:

Unlike antibiotics, phages have incredibly refined, narrow host-ranges. This property is in reality a double edged sword: in many cases, phages are only able to target a few strains of a single species, whereas antibiotics relentlessly target multiple branches of the bacterial phylogenetic tree. Antibiotic treatment can lead to disruption of the host’s own microbiota which can permit the colonisation of nastier and less cooperative microorganisms.

In contrast, phages can target their host whilst leaving the surrounding organisms in relative peace. When a patient presents symptoms of infection, the particular species or strain causing the infection would be unknown. Identifying the culprit before selecting the right phage would take time a patient may not have.

Receptors on the bacterial cell surface are what determine which phage are able to bind to the cell. A wide variety of receptors are used by phage, but many still remain a mystery. To curtail these issues and ensure that as many receptors can be targeted for a particular bacterium, phage cocktails are used [6]. These are mixtures containing a number of different phage strains. In theory, the cocktail should be designed so that the phages together should be able to target all the known clinically relevant strains of a particular species of bacteria.

Creating phage cocktails from natural sources can be laborious [7], however viral DNA provides a platform for genetically engineering phages with desired properties. Improving phage cocktails with modified phages expressing structures that could target a wide variety of receptors on a bacterial cell could ensure that a cocktail could target the maximum number of strains, whilst reducing the selection pressure on a sole receptor. Resistance to the phage cocktail would then also be avoided.

Much of this work looks at genetically engineering phage tail fibres [7, 8]. These ‘spider-leg’ like components regulate the initial binding step between a phage and a target cell. It has been shown by Mahichi et al, 2009 and Ando et al, 2015 that switching tail fibres between phages with different host ranges can confer host-range specificity from one phage to another. Hopefully, modular engineering of phages will push phage technology forwards, offering new strategies for developing phages for therapeutic purposes.

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Figure 2. Diagram showing how the modular shuffling of tail fibres between viral strains can confer host range of parental strain [7].

Preventing the release of cellular toxins

A major health risk of phage, is that like β-lactam antibiotics, they interfere with the bacterial cell wall integrity and ultimately lead to cell lysis. Lysing cells prevents further replication, but also releases all the cell’s content. This may include but not be limited to superantigens and lipopolysaccharides (LPS) [2]. These toxins will trigger the inflammatory response, and in extreme cases cause organ failure and death.

Phages have a simple dual-lysis system consisting of a holin and endolysin. The holin is a pore-forming membrane protein that creates an exit from the cytoplasm for the endolysin. The endolysin is then able to attack the peptidoglycan of the bacterial cell wall, resulting in its rupture. To generate phage incapable of lysing a cell, the dual lysis system simply needs to be inactivated.

To restore killing power to the phage in the absense of the dual lysis system, a bacterial toxin needs to be incorporated into the phage genome. Hagens et al, 2004 has shown that by engineering the filamentous phage M13 to encode a non-native restriction enzyme, antimicrobial activity can be restored through the generation of double stranded breaks in chromosomal DNA. Upon infecting Psuedomonas aeruginosa with this phage, there was a 99% drop in viable cell counts over the time course [9]. Other research has looked into other uses for the non-lytic killing of bacteria, including proteins that interfere with regulatory systems and other bacterial toxins.

Conclusions:

Phage therapy has shown promise in recent years as being a good candidate for either working in synergy with or replacing antibiotics. The appalling lack of human based clinical trials haven’t helped to expose their potential for human use. Although this is the case, a significant amount of work has been done on improving phage therapy in preparation for further studies with human application. The past 15 years have seen an improved outcome for this technology as obstacles with phages are gradually manoeuvred by intelligent reengineering. With hindsight we have now acquired through our experiences with antibiotics, hopefully we will not make the same mistakes with phages as we have done with antibiotics.

1. CDC (2013) Antibiotic resistance threats. US Dep Heal Hum Serv 22–50

2. Lu TK, Koeris MS (2011) The next generation of bacteriophage therapy. Curr Opin Microbiol 14:524–531

3. Carlton RM (1999) Phage therapy: past history and future prospects. Arch Immunol Ther Exp (Warsz) 47:267–274

4. Merril CR, Biswas B, Carlton R, Jensen NC, Creed GJ, Zullo S, Adhya S (1996) Long-circulating bacteriophage as antibacterial agents. Proc Natl Acad Sci U S A 93:3188–3192

5. Chaturongakul S, Ounjai P (2014) Phage host interplay: examples from tailed phages and Gram-negative bacterial pathogens. Front Microbiol 5:1–8

6. Moradpour Z, Ghasemian A (2011) Modified phages: Novel antimicrobial agents to combat infectious diseases. Biotechnol Adv 29:732–738

7. Ando H, Lemire S, Pires DP, Lu TK (2015) Engineering Modular Viral Scaffolds for Targeted Bacterial Population Editing. Cell Syst 1:187–196

8. Mahichi F, Synnott AJ, Yamamichi K, Osada T, Tanji Y (2009) Site-specific recombination of T2 phage using IP008 long tail fiber genes provides a targeted method for expanding host range while retaining lytic activity. FEMS Microbiol Lett 295:211–217

9. Hagens S, Habel A, Ahsen U Von, Gabain A Von (2004) Therapy of Experimental Pseudomonas Infections with a Nonreplicating Genetically Modified Phage Therapy of Experimental Pseudomonas Infections with a Nonreplicating Genetically Modified Phage. Antimicrob Agents Chemother 46:3817–3822

theguardian.com
Organisms created with synthetic DNA pave way for entirely new life forms
E coli microbes have been modified to carry an expanded genetic code which researchers say will ultimately allow them to be programmed
By Ian Sample

Scientists in the US modified common E coli microbes to carry a beefed-up payload of genetic material which, they say, will ultimately allow them to program how the organisms operate and behave.

The work is aimed at making bugs that churn out new kinds of proteins which can be harvested and turned into drugs to treat a range of diseases. But the same technology could also lead to new kinds of materials, the researchers say.

In a report published on Monday, the scientists describe the modified microbes as a starting point for efforts to “create organisms with wholly unnatural attributes and traits not found elsewhere in nature.” The cells constitute a “stable form of semi-synthetic life” and “lay the foundation for achieving the central goal of synthetic biology: the creation of new life forms and functions,” they add.

First life with ‘alien’ DNA

An engineered bacterium is able to copy DNA that contains unnatural genetic letters.

For billions of years, the history of life has been written with just four letters — A, T, C and G, the labels given to the DNA subunits contained in all organisms. That alphabet has just grown longer, researchers announce, with the creation of a living cell that has two 'foreign’ DNA building blocks in its genome.

Hailed as a breakthrough by other scientists, the work is a step towards the synthesis of cells able to churn out drugs and other useful molecules. It also raises the possibility that cells could one day be engineered without any of the four DNA bases used by all organisms on Earth.

Continue Reading

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Synthetic Cells Move On Their Own

What look like animated illustrations that could easily spring from a child’s imagination are actually newly unveiled artificial cells under a microscope.

Biophysicists at Germany’s Technical University of Munich along with an international team developed simple self-propelled biomachines in a quest to create cell models that display biomechanical functions.

The researchers say their work represents the first time a movable cytoskeleton membrane has been fabricated.

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A Bay Area Startup Spins Lab-Grown Silk

“The company has developed a synthetic alternative to spider silk by engineering proteins identical to the natural threads stretched across the nooks in your basement. It’s raised $40 million from Silicon Valley venture capital firms Foundation Capital, Formation 8, and Founders Fund to commercialize its technology and turn those proteins into fabric. “Over the past few decades, as clothing companies squeezed on price, they’ve taken the innovation out of apparel,” says Dan Widmaier, a graduate of the UCSF Ph.D. program in chemical biology and Bolt’s chief executive officer. Widmaier and co-founders Ethan Mirsky, Bolt’s vice president for operations, and David Breslauer, its chief scientific officer, are genetically modifying yeast, single-cell organisms that convert simple carbohydrates to proteins through fermentation, and getting them to excrete silk-like proteins. “What would have been done in cells of spiders is now being done by yeast in our lab,” Widmaier says.”

Life is an astonishingly conservative system: DNA is the same in all species, the letters of the code are all the same; the encryption in the code is the same, even the orientation of the molecules is the same. What’s true in bacteria is true in a blue whale. Only a system with a single root could display such conservation.
— 

Adam Rutherford in “Creation: How Science is Reinventing Life Itself”, from a review in the Los Angeles Times.

The second to last sentence is patently untrue.

Edit: It’s so wrong that it’s giving me a headache.

buzzfeed.com
25 Scientists Just Made A $1 Billion Pitch To Build A Human Genome From...
Some big-name scientists have proposed a lofty plan to build a human genome from scratch. But some pillars of the field say it’s a premature and dangerous idea.
By Nidhi Subbaraman

While ethics is cited as the main reason against the this project, what about the cost? Is this really a good use of research money?

I don’t believe we know enough about the human genome to build one from scratch, as we are continually finding regions previously thought to be “junk” to have important regulatory function (such as lncRNAs). My prediction is this effort will fall flat, wasting a lot of important funding that could be used in more helpful ways. 

youtube

Virus Engineering and Beyond: Andrew Hessel

7

The Art of Deception
Using a decellularizing technique we have taken a pig heart and manipulated it into a material. Decellularization marks a new era of synthetic biology – organs are stripped of their cellular contents, leaving behind a sterile scaffold that can be repopulated with stemcells. While the medical utilization of this resource is being realised, the artistic and creative value of ghost organs represents unexplored territory. Can the ghost organ be a blank canvas for designers? Can organs be objects of design? Will humans be able to manipulate organs for aesthetic purposes?The goal of this project is to further explore how biological interventions and aesthetic manipulation can be used as tools for the ultimate deception: the transformation of inner beauty, from grotesque to perfect. The ghost organs in this case work as a metaphor for regenerated artificial life. The discarded dead hearts will not function as canonical organs, but rather as a representation of how far science can manipulate the human body. In collaboration with Professor Toby Kiers (Free University Amsterdam)   Commissioned by Bio Art & Design Awards, with the support of ZonMw (The Netherlands Organisation for Health Research and Development).
Project assistant: Iza Stepska & Elise Marcus

youtube

Why Bio is the New Digital - Joi Ito keynote

3

Creating a better biofuel from poop

When it comes to liquid fuels, the market is dominated by gasoline, diesel and jet fuel—all compounds derived from crude oil. These fuels are highly energy dense, cheap and (for now) abundant.

But for years, scientists have been working toward a secure and sustainable alternative to fossil fuels.

Ethanol, one of the earliest biofuel that’s largely derived from corn, hasn’t been able to compete with liquid fossil fuels. It isn’t particularly energy-dense and you need special modifications on your car to use ethanol or similar biofuels.

But researchers at UCLA are working on the next generation of advanced biofuels like Isobutanol.

“We try to produce branched-chain alcohols, that are a little larger, more energy dense and burn more like real gasoline,” explains UCLA researcher David Wernick.

Unlike ethanol, these biofuels are compatible with current fuel infrastructure, which means that you could use them with your current car.

By engineering bacteria (Bacillus subtilis), Wernick and his UCLA cohorts have enabled these tiny organisms to break down manure and other protein-rich waste like wastewater algae and byproducts from fermenting wine and beer.  

Once the protein is broken down, the bacteria convert it into biofuel and ammonia, which can be used for fertilizer. The next step is scaling up the process and improving the amount of biofuel produced.

Learn more about the lab and their process of transforming poop and protein waste into fuel:

Camphor Tree Helps Bacteria Make Biofuel Chemically Identical to Petroleum

by Michael Keller

Scientists working to make exact chemical copies of fossil fuels from living microbes say they have scored a major victory in the lab. Merging genes from the camphor tree, soil- and gut-dwelling bacteria, and a microorganism that is lethal to insects, researchers have produced molecular replicas of petroleum-based fuels.

The team, composed of researchers from Exeter University in the United Kingdom and Shell, engineered the DNA of E. coli, a bacterium commonly found in the gut of mammals, to alter how it metabolizes its food so that it excretes the fossil-fuel replicas.

The new fuel doesn’t need to be heavily processed after it’s produced to work in combustion engines, says study coauthor John Love. It could be a solution that bypasses a major hurdle for conventional biofuels, which are not fully compatible with vehicles already out on the road.

“Modern engines are not suited to using these biofuels without major modifications and/or loss of performance,” Love, an associate professor of plant and industrial biotechnology at the University of Exeter, tells Txchnologist. “Ideally, you’d want to replace the fossil fuel with a biofuel that matches it exactly in chemical structure.  We have engineered bacteria to produce such a fuel: biological gasoline or bio-alkanes. These hydrocarbons can be added directly to any engine, including a jet engine.”

Keep reading

buckminsterfullerene, AKA C60
CAS#: 99685-96-8 

I have a friend who is trying to get me to help him find a supplier of this compound because he said he read somewhere it doubled the lifetime of mice and wasn’t carcinogenic. Searching Pubmed has shown a few articles on its use to treat asthma, but I’ve mostly found articles on its applicability in industrial uses. Does anyone have any data on this compound?

In Significant Advance for Artificial Photosynthesis, a Machine and Living Bacteria Work Together to Make Fuel

Scientists say they have merged living organisms with nanotechnology to mimic the photosynthesis plants use to make energy.  

Blending chemistry, biology and materials science, the team from the University of California, Berkeley and Lawrence Berkeley National Laboratory created a living-synthetic hybrid system. The process brings together nanowires and bacteria (seen in the image above) to convert sunlight, water and carbon dioxide in the air into valuable chemicals like liquid fuel, plastics and pharmaceuticals.

Like plants, the system uses solar power to make complex molecules from simple ones. In contrast to the carbohydrates and oxygen that are the product of natural photosynthesis, the new device converts CO2 into acetate, which is the building block for a number of industrially useful chemicals.

“We believe our system is a revolutionary leap forward in the field of artificial photosynthesis,” said Peidong Yang, a Berkeley Lab chemist who was one of the project leaders. “Our system has the potential to fundamentally change the chemical and oil industry in that we can produce chemicals and fuels in a totally renewable way, rather than extracting them from deep below the ground.”

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  • Degree: MA+PhD Combined Program (Year 1 of MA)
  • Subject: International Relations - Counter terrorism Studies - concentrating more on Indo-African and Indo-European relations.
  • Other Degrees: Bachelor of Medicine in Psychiatry + Language Certs

➾ Nicole

  • Blog: omnia-est-vanitas
  • Degree: PhD
  • Subject: Art History (focus on medieval, minor in Renaissance Art)
  • Other Degrees: B.A. Art History and Museum Studies

➾ Katie

  • Blog: commgradblr
  • Degree: PhD (3rd Year)
  • Subject: Communication
  • Other Degrees: MA, Communication and BS, Communication Disorders

➾ Caitlin

  • Blog: crimefighterphd
  • Degree: PhD (1st Year)
  • Subject: Criminal Justice (minor in Statistics)
  • Other Degrees: BS, Psych; BA, Asian Studies, MSc, Psych; MSc, Forensic Psych

➾ Academic Mermaid

  • Blog: academicmermaid
  • Degree: PhD, 2016 (6th Year)
  • Subject: Religion and Politics

➾ Protagonistanormal

  • Blog: protagonistanormal
  • Degree: PhD, 2018
  • Subject: 21st Century Spanish Literature & Culture
  • Other Degrees: MA in Spanish; BA in English & Spanish

➾ The History Grad

➾ A Blonde Bibliophile

➾ Curious Grad Student

  • Blog: curiousgradstudent
  • Degree: PhD, 2019
  • Subject: Art History
  • Other Degrees: B.A. Medieval Studies & French

PsyD

➾ Murphy

  • Blog: onemoresoultothecall
  • Degree: PsyD (5th Year)
  • Subject: Clinical Psychology (Forensic, Child/Family & Trauma Studies)
  • Other Degrees: Two Master Degrees (Clinical Psych)

➾ Abby

➾ Once Upon a PsyD Student

➾ Kitty-Wine

  • Blog: kitty-wine
  • Degree: PsyD (2nd Year)
  • Subject: Clinical Psychology

➾ Jayropa

  • Blog: jayropa
  • Degree: PsyD (5th Year)
  • Subject: Clinical Psychology

➾ Balance and Blessings

  • Blog: balanceandblessings
  • Degree: PsyD (2nd Year)
  • Subject: Clinical Psychology
  • Other Degrees: BA, Psychology & Mindfulness/Meditation

Other

➾ Kari

  • Blog: kari-and-kaffeine
  • Degree: JD (2nd Year)
  • Other Degrees: BA, Philosophy & English Lit

➾ Another Something The Same

➾ Nureshka

  • Blog: nureska
  • Subject: Math
  • Other Degrees: BS, 2017 (soon!)

Equipping Insects for Special Service

The smallest aerial drones mimic insects in many ways, but none can match the efficiency and maneuverability of the dragonfly. Now, engineers at Draper are creating a new kind of hybrid drone, DRAGONFLEYE,  by combining miniaturized navigation, synthetic biology and neurotechnology to guide dragonfly insects. 

A dragonfly modeling the full backpack

close up of the backpack board and components before being folded and fitted to the dragonfly 

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credit : draper