Tag Archives: synthetic biology

more on gene circuits

This is pretty dense, but what it is talking about is the idea of programming genes like circuits.

Enzyme-free nucleic acid dynamical systems

Abstract chemical reaction networks have been proposed as a programming language for complex dynamics, along with their systematic implementation using short synthetic DNA molecules. We developed this technology for dynamical systems by identifying critical design principles and codifying them into a compiler automating the design process. Using this approach, we built an oscillator containing only DNA components, establishing that Watson-Crick base-pairing interactions alone suffice for complex chemical dynamics and that autonomous molecular systems can be designed via molecular programming languages.

Gene Editing 2.0

Before CRISPR even becomes a household word (er, acronym?), it is already being replaced by newer and more precise methods, according to Wired.

Usually, when we’ve referred to Crispr, we’ve really meant Crispr/Cas9—a riboprotein complex composed of a short strand of RNA and an efficient DNA-cutting enzyme. It did for biology and medicine what the Model T did for manufacturing and transportation; democratizing access to a revolutionary technology and disrupting the status quo in the process. Crispr has already been used to treat cancer in humans, and it could be in clinical trials to cure genetic diseases like sickle cell anemia and beta thalassemia as soon as next year...

But this year, newer, flashier gene editing tools began rolling off the production line, promising to outshine their first-generation cousin. So if you were just getting your head around Crispr, buckle up. Because gene-editing 2.0 is here.


What are the trends in ecology and evolution for 2018?

The journal Trends in Ecology and Evolution does an annual “Horizon Scan of Emerging Issues for Global Conservation and Biological Diversity”. I can only see the abstract so here is the one sentence describing the trends:

The issues highlighted span a wide range of fields and include thiamine deficiency in wild animals, the geographic expansion of chronic wasting disease, genetic control of invasive mammal populations and the effect of culturomics on conservation science, policy and action.

I was new to the term culturomics, and thought it might have something to do with synthesizing new compounds in giant vats of yogurt. But no, according to Wikipedia it is not that kind of culture, but relates to search and synthesis algorithms for scientific articles, which does indeed seem to be a recurring theme on this blog lately.

Culturomics is a form of computational lexicology that studies human behavior and cultural trends through the quantitative analysis of digitized texts.[1][2] Researchers data mine large digital archives to investigate cultural phenomena reflected in language and word usage.[3] The term is an American neologism first described in a 2010 Science article called Quantitative Analysis of Culture Using Millions of Digitized Books, co-authored by Harvard researchers Jean-Baptiste Michel and Erez Lieberman Aiden.[4]

At that point, I just needed to figure out what a neologism was, so I looked it up in Webster’s 1913 which some people say is the most artfully written dictionary:

Ne*ol”o*gism (?), n. [Cf. F. néologisme.]

1. The introduction of new words, or the use of old words in a new sense. Mrs. Browning.

2. A new word, phrase, or expression.

3. A new doctrine; specifically, rationalism.

Mrs. Browning? Elizabeth Barrett Browning wrote a long poem called Aurora Leigh which contains the word. And no, I wouldn’t have learned that if I had looked up neologism in the New Oxford American Dictionary.

I learnt my complement of classic French
(Kept pure of Balzac and neologism,)
And German also, since she liked a range
Of liberal education,–tongues, not books.
I learnt a little algebra, a little
Of the mathematics,–brushed with extreme flounce
The circle of the sciences, because
She misliked women who are frivolous.

It goes on like that. Forever.

Oh okay, one more, here is the definition of flounce in Webster’s 1913:

Flounce, v. t. To deck with a flounce or flounces; as, to flounce a petticoat or a frock.

Flounce, n. [Cf. G. flausflausch, a tuft of wool or hair; akin to vliess, E.fleece; or perh. corrupted fr. rounce.] An ornamental appendage to the skirt of a woman’s dress, consisting of a strip gathered and sewed on by its upper edge around the skirt, and left hanging.

Flounce (?), v. i. [imp. & p. p.Flounced (flounst); p. pr. & vb. n.Flouncing(?).] [Cf. OSw. flunsa to immerge.] To throw the limbs and body one way and the other; to spring, turn, or twist with sudden effort or violence; to struggle, as a horse in mire; to flounder; to throw one’s self with a jerk or spasm, often as in displeasure.

To flutter and flounce will do nothing but batter and bruise us.


With his broad fins and forky tail he laves
The rising sirge, and flounces in the waves.


“Sirge” I think is an old-timey spelling of “surge”. And if you look up “surge” in this dictionary, its usage is quite interesting and you want to go on. But that’s it for me.


silicon-based life

Scientists can now synthesize proteins that could be incorporated in silicon-based life forms.

Directed evolution of cytochrome c for carbon–silicon bond formation: Bringing silicon to life

Enzymes that catalyze carbon–silicon bond formation are unknown in nature, despite the natural abundance of both elements. Such enzymes would expand the catalytic repertoire of biology, enabling living systems to access chemical space previously only open to synthetic chemistry. We have discovered that heme proteins catalyze the formation of organosilicon compounds under physiological conditions via carbene insertion into silicon–hydrogen bonds. The reaction proceeds both in vitro and in vivo, accommodating a broad range of substrates with high chemo- and enantioselectivity. Using directed evolution, we enhanced the catalytic function of cytochrome c from Rhodothermus marinus to achieve more than 15-fold higher turnover than state-of-the-art synthetic catalysts. This carbon–silicon bond-forming biocatalyst offers an environmentally friendly and highly efficient route to producing enantiopure organosilicon molecules.

designing genetic circuits

This article in Science describes design of circuits that can be translated directly to DNA sequences, which when built will perform the function of the circuit.
Programming circuitry for synthetic biology

As synthetic biology techniques become more powerful, researchers are anticipating a future in which the design of biological circuits will be similar to the design of integrated circuits in electronics. Nielsen et al. describe what is essentially a programming language to design computational circuits in living cells. The circuits generated on plasmids expressed in Escherichia coli required careful insulation from their genetic context, but primarily functioned as specified. The circuits could, for example, regulate cellular functions in response to multiple environmental signals. Such a strategy can facilitate the development of more complex circuits by genetic engineering.

making chemotherapy “a thing of the past”

From the BBC, this caught my eye:

Prime Minister David Cameron has said it “will see the UK lead the world in genetic research within years”.

The first genetic codes of people with cancer or rare diseases, out of a target of 100,000, have been sequenced.

Experts believe it will lead to targeted therapies and could make chemotherapy “a thing of the past”…

The project has now passed the 100 genome mark, with the aim of reaching 1,000 by the end of the year and 10,000 by the end of 2015