SynBioFromLeukipposInstitute

Cellular phenotypes underpinned by regulatory networks need to respond to evolutionary pressures to allow adaptation, but at the same time be robust to perturbations. This creates a conflict in which mutations affecting regulatory networks must both generate variance but also be tolerated at the phenotype level. Here, we perform mathematical analyses and simulations of regulatory networks to better understand the potential trade-off between robustness and evolvability. Examining the phenotypic effects of mutations, we find an inverse correlation between robustness and evolvability that breaks only with nonlinearity in the network dynamics, through the creation of regions presenting sudden changes in phenotype with small changes in genotype. For genotypes embedding low levels of nonlinearity, robustness and evolvability correlate negatively and almost perfectly. By contrast, genotypes embedding nonlinear dynamics allow expression levels to be robust to small perturbations, while generating high diversity (evolvability) under larger perturbations. Thus, nonlinearity breaks the robustness-evolvability trade-off in gene expression levels by allowing disparate responses to different mutations. Using analytical derivations of robustness and system sensitivity, we show that these findings extend to a large class of gene regulatory network architectures and also hold for experimentally observed parameter regimes. Further, the effect of nonlinearity on the robustness-evolvability trade-off is ensured as long as key parameters of the system display specific relations irrespective of their absolute values. We find that within this parameter regime genotypes display low and noisy expression levels. Examining the phenotypic effects of mutations, we find an inverse correlation between robustness and evolvability that breaks only with nonlinearity in the network dynamics. Our results provide a possible solution to the robustness-evolvability trade-off, suggest an explanation for the ubiquity of nonlinear dynamics in gene expression networks, and generate useful guidelines for the design of synthetic gene circuits.

Legume laboratory discusses a recent effort to introduce an algal carbon concentration mechanism into higher plants for improved photosynthetic efficiency.

Source: Fast-Tracked Photosynthesis

We have previously written on the topic of increasing the efficiency of photosynthesis as a possible method of increasing crop growth and yield. By swapping out the predominant C3 photosynthesis system with the superior C4 system, it was estimated that rice and wheat yields could increase by 50%.

The Long Now Foundation recently published online a talk titled “Radical Ag: C4 and beyond” in which Jane Langdale of the Langdale Lab discusses the 60 odd plant species that have naturally evolved C4 photosynthesis and the efforts to use this knowledge to get C4 photosynthesis into rice.

A different method of supercharging photosynthesis?

And a recent paper in the Plant Biotechnology Journal (which is open access – yay!) investigated the possibility of using a carbon-concentrating mechanism (CCM) commonly found in a number of photosynthetic organisms like cyanobacteria and green algae.

Whilst C3 photosynthesis relies on CO2 passively diffusing to the chloroplasts, resulting in the enzyme which assimilates the carbon into the plant (RuBisCO) not being saturated with CO2, the microbial CCM increases the concentration of CO2 to RuBisCO and thereby increases photosynthetic efficiency.

In algae, the CCM consists of transporters of inorganic carbon at the plasma membrane, chloroplast envelope and carbonic anhydrases. These all work together to deliver the elevated concentration of CO2 to the RuBisCo enzyme.

In this paper, the researchers took a number of steps to check the plausibility of inserting this CCM into tobacco plants:

After choosing 10 critical components of the CCM, these components were tagged with fluorescent markers to determine where they were located within Chlamydomonas reinhardtii.
With the usual location of these proteins confirmed, the proteins were expressed in tobacco leaves to determine whether the same components were located in the same cellular locations.
Focusing on two inorganic carbon transporters within this selection of 10 components, the researchers showed that they both function as such when expressed in the outer membrane of a model single-celled organism (Xenopus oocytes) and when transformed into Arabidopsis thaliana.
Finally, they tested the growth of the Arabidopsis plants against wild-type plants of the same species.

The positives

The location of the 10 components were confirmed within the bacteria and 8 of these were located in the same cellular position when expressed in tobacco leaves. 1 protein was mistargeted whilst the researchers struggled to clearly identify the location of another.

Delving further into this issue, the researchers looked for a way to direct one of the proteins specifically to the chloroplast stroma using a specific transporter found in an online plant membrane protein database. Using this transporter and the tagged protein, they were able to demonstrate the ability to re-target a protein from a single celled organism to a specific part of the cell of a higher plant.

Taking two specific proteins for further study, the proteins were expressed in Arabidopsis plants and the location was confirmed as being the same as in the tobacco plants.

The negatives

Actually, the report specifically states that it wasn’t expected that Arabidopsis plants transformed with the two CCM components would have an altered rate of photosynthesis given the complexity of this machinery and the number of components missing. However, they tested and compared growth rates under normal and reduced CO2 concentrations, finding no difference between the transformed and wild-types. They also measured CO2 assimilation rates, again finding no difference.

Conclusion

The paper gives a great insight into complexity involved in demonstrating the plausibility of transforming plants for greater growth rates and, potentially, greater yield from food crops.

The ability to express and redirect proteins is impressive, but also impressive is the catalogue of plant proteins that is continually being built and which can be freely accessed and used for research.

Increasing CO2 sequestration rates is a focal point for many researchers in the quest to grow more food on the agricultural resources we have. Swapping out or supercharging the C3 photosynthesis present in most crops is one method with seeming potential and the detail of the work performed so far gives an exciting insight into the possibility of it coming to fruition.

Bacteria navigate environments full of various chemicals to seek favorable places for survival by controlling the flagella’s rotation using a complicated signal transduction pathway. By influencing the pathway, bacteria can be engineered to search for specific molecules, which has great potential for application to biomedicine and bioremediation. In this study, genetic circuits were constructed to make bacteria search for a specific molecule at particular concentrations in their environment through a synthetic biology method. In addition, by replacing the “brake component” in the synthetic circuit with some specific sensitivities, the bacteria can be engineered to locate areas containing specific concentrations of the molecule. Measured by the swarm assay qualitatively and microfluidic techniques quantitatively, the characteristics of each “brake component” were identified and represented by a mathematical model. Furthermore, we established another mathematical model to anticipate the characteristics of the “brake component”. Based on this model, an abundant component library can be established to provide adequate component selection for different searching conditions without identifying all components individually. Finally, a systematic design procedure was proposed. Following this systematic procedure, one can design a genetic circuit for bacteria to rapidly search for and locate different concentrations of particular molecules by selecting the most adequate “brake component” in the library. Moreover, following simple procedures, one can also establish an exclusive component library suitable for other cultivated environments, promoter systems, or bacterial strains.

Genetically-encoded biosensors offer a wide range of opportunities to develop advanced synthetic biology applications. Circuits with the ability of detecting and quantifying intracellular amounts of a compound of interest are central to whole-cell biosensors design for medical and environmental applications, and they also constitute essential parts for the selection and regulation of high-producer strains in metabolic engineering. However, the number of compounds that can be detected through natural mechanisms, like allosteric transcription factors, is limited; expanding the set of detectable compounds is therefore highly desirable. Here, we present the SensiPath web server, accessible at http://sensipath.micalis.fr. SensiPath implements a strategy to enlarge the set of detectable compounds by screening for multi-step enzymatic transformations converting non-detectable compounds into detectable ones. The SensiPath approach is based on the encoding of reactions through signature descriptors to explore sensing-enabling metabolic pathways, which are putative biochemical transformations of the target compound leading to known effectors of transcription factors. In that way, SensiPath enlarges the design space by broadening the potential use of biosensors in synthetic biology applications.

The CRISPR–Cas systems, as exemplified by CRISPR–Cas9, are RNA-guided adaptive immune systems used by bacteria and archaea to defend against viral infection1, 2, 3, 4, 5, 6, 7. The CRISPR–Cpf1 system, a new class 2 CRISPR–Cas system, mediates robust DNA interference in human cells1, 8, 9, 10. Although functionally conserved, Cpf1 and Cas9 differ in many aspects including their guide RNAs and substrate specificity. Here we report the 2.38 Å crystal structure of the CRISPR RNA (crRNA)-bound Lachnospiraceae bacterium ND2006 Cpf1 (LbCpf1). LbCpf1 has a triangle-shaped architecture with a large positively charged channel at the centre. Recognized by the oligonucleotide-binding domain of LbCpf1, the crRNA adopts a highly distorted conformation stabilized by extensive intramolecular interactions and the (Mg(H2O)6)2+ ion. The oligonucleotide-binding domain also harbours a looped-out helical domain that is important for LbCpf1 substrate binding. Binding of crRNA or crRNA lacking the guide sequence induces marked conformational changes but no oligomerization of LbCpf1. Our study reveals the crRNA recognition mechanism and provides insight into crRNA-guided substrate binding of LbCpf1, establishing a framework for engineering LbCpf1 to improve its efficiency and specificity for genome editing.

At the Karolinska Institute in Stockholm, Fredrik Lanner is preparing to edit genes in human embryos. It’s the kind of research that sparked an international frenzy in April last year, when a Chinese team revealed that it had done the world’s first such experiments1.

But Lanner doesn’t expect his work, which will explore early human development, to cause such a fuss. A year of discussion about the ethics of embryo-editing research, and perhaps simply the passage of time, seems to have blunted its controversial edge — although such work remains subject to the same ethical anxieties that surround other reproductive-biology experiments. “At least in the scientific community, I sense more support for basic-research applications,” says Lanner, who gained approval for his experiments last June.

His instinct seems to be borne out by the fairly muted reaction to a 6 April report2 of an experiment to edit human embryos — only the second to be published. A team led by Yong Fan at Guangzhou Medical University in China used the gene-editing technology CRISPR–Cas9 to try to introduce a mutation that makes humans resistant to HIV infection.

The US Department of Agriculture (USDA) will not regulate a mushroom genetically modified with the gene-editing tool CRISPR–Cas9.

The long-awaited decision means that the mushroom can be cultivated and sold without passing through the agency's regulatory process — making it the first CRISPR-edited organism to receive a green light from the US government.

“The research community will be very happy with the news,” says Caixia Gao, a plant biologist at the Chinese Academy of Sciences’s Institute of Genetics and Developmental Biology in Beijing, who was not involved in developing the mushroom. “I am confident we'll see more gene-edited crops falling outside of regulatory authority.”

Twist Bioscience, a startup making and using synthetic DNA to store digital data, just struck a contract with Microsoft and the University of Washington to encode vast amounts of information on synthetic genes.

Big data means business and the company able to gather a lot of it is very valuable to investors and stockholders. But that data needs to be stored somewhere and can cost a lot for the upkeep.

Digital data stored on media also has a finite shelf life. But researchers have discovered new ways to stuff digital information over the last few years – including in our DNA, which can last thousands of years intact.

Just how much data can you store in your genes? According to Harvard scientists, about 700 terabytes can go on a single gram.

Or, to put it in layman’s terms, “[Using DNA,] you could fit all the knowledge in the whole world inside the trunk of your car,” Twist Bioscience CEO Emily Leproust told TechCrunch.

The cost of genetic sequencing has also plummeted recently, going from $2.7 billion to map out just one whole human genome in 2003 to now the ability to pull up your entire genome on your smartphone for under $1,000.

We don’t know what exactly Microsoft plans to put inside tiny strands of DNA but the new technology presents an interesting way to keep a lot of data in a small amount of space for a really long time.

Twist Bioscience recently acquired the Israel-based Genome Compiler Corporation and announced a teeny tiny funding round of $2.6 million this month – an odd contrast to the $81 million raised earlier in January to build out its synthetic DNA manufacturing platform.

“If I had only learned science the way it was taught to me in the classroom, I probably never would have become a scientist,” says Natalie Kuldell, a faculty member in MIT’s Department of Biological Engineering. “It was only in high school when I had a chance to work in an investigative lab that I realized how creative and fun science could be.”

"As summer approaches we are edging closer to the start of the 2016 iGEM competition. Here the Leiden iGEM team introduce their project which aims to use E. coli to convert a toxic compound found in Martian soil into oxygen. This research could aid ongoing efforts to make life on the red planet possible. We’re looking forward to seeing how things develop!

by  Leiden iGEM 2016

Colonising Mars

It’s just a matter of time before Mars is colonised, but before that can happen there are some problems that first need to be resolved, problems that the students are well aware of.  The prime problem is that there has to be a sustainable and self-maintaining atmosphere that can support human life. The students have come up with an idea for creating such an atmosphere and have developed the idea into a workable plan.

Natural products are a group of bioactive structurally diverse chemicals produced by microorganisms and plants. These molecules and their derivatives have contributed to over a third of the therapeutic drugs produced in the last century. However, over the last few decades traditional drug discovery pipelines from natural products have become far less productive and far more expensive. One recent development with promise to combat this trend is the application of synthetic biology to therapeutic natural product biosynthesis. Synthetic biology is a young discipline with roots in systems biology, genetic engineering, and metabolic engineering. In this review, we discuss the use of synthetic biology to engineer improved yields of existing therapeutic natural products. We further describe the use of synthetic biology to combine and express natural product biosynthetic genes in unprecedented ways, and how this holds promise for opening up completely new avenues for drug discovery and production.

When the medical charity Médecins Sans Frontières called the worldwide shortage of snake antivenom a public-health crisis last September, Brazilian biochemist Paulo Lee Ho wasn’t surprised. He has spent his career at São Paulo’s Butantan Institute searching for better ways to create antivenom to treat bites from coral snakes.

Conventional methods rely on natural coral-snake venom, which is hard to come by: the snakes produce only small amounts with each bite and are hard to raise in captivity. So Ho and others have turned to proteomics and synthetic biology in the hope of improving the quality and availability of antivenom. “We need a new way to meet the demand for antivenom from the Ministry of Health,” he says.