News and updates



1/17/2017

Ask Me Anything about synthetic cells
Reddit AMA on synthetic minimal cells, answering questions from the public about our work. AskScience AMA Synthetic Cells.
reddit-ama-adamala


1/6/2017

TEDx Talk on Synthetic life
Kate presented concept of building synthetic minimal cells, with its biotechnological, biomedical and basic science implications, in a TEDx talk .


12/20/2016

New lab member
Welcome Joe Heili to the lab!


11/14/2016

New publication

Engineering genetic circuit interactions within and between synthetic minimal cells;
Katarzyna P. Adamala*, Daniel A. Martin-Alarcon*, Katriona R. Guthrie-Honea, Edward S. Boyden; Nature Chemistry, 2016, doi:10.1038/nchem.2644; *equal contribution
local copy pdf
publisher website link
details, abstract

Engineering genetic circuit interactions within and between synthetic minimal cells;
Katarzyna P. Adamala*, Daniel A. Martin-Alarcon*, Katriona R. Guthrie-Honea, Edward S. Boyden; Nature Chemistry, 2016, doi:10.1038/nchem.2644; *equal contribution

Genetic circuits and reaction cascades are of great importance for synthetic biology, biochemistry and bioengineering. An open question is how to maximize the modularity of their design to enable the integration of different reaction networks and to optimize their scalability and flexibility. One option is encapsulation within liposomes, which enables chemical reactions to proceed in well-isolated environments. Here we adapt liposome encapsulation to enable the modular, controlled compartmentalization of genetic circuits and cascades. We demonstrate that it is possible to engineer genetic circuit-containing synthetic minimal cells (synells) to contain multiple-part genetic cascades, and that these cascades can be controlled by external signals as well as inter-liposomal communication without crosstalk. We also show that liposomes that contain different cascades can be fused in a controlled way so that the products of incompatible reactions can be brought together. Synells thus enable a more modular creation of synthetic biology cascades, an essential step towards their ultimate programmability.


11/09/2016

Masonic Cancer Center
Our lab become affiliated with the Masonic Canter Center. We're proud to become part of this amazing research community.


10/24/2016

Synthetic cells in the news
So we are working on building "simplified cells" now. Associated Press noticed (local copy pdf). So did MPR news (local copy pdf).


10/15/2016

New Lab member
Welcome Jose Gomez-Garcia to the lab!


9/22/2016

Conference
BioHack the Planet!
biohtp-adamala


9/19/2016

New publication

Astrobiology Primer 2.0.;
Domagal-Goldman and Wright et al. (includes chapter editor K.P.Adamala)
Astrobiology, 2016, 16(8):561-653. doi:10.1089/ast.2015.1460.
publisher website link


Astrobiology Primer 2.0.;
Domagal-Goldman and Wright et al. (includes chapter editor K.P.Adamala) Astrobiology, 2016, 16(8):561-653. doi:10.1089/ast.2015.1460.
publisher website link


8/14/2016

HTGAA

How to grow almost Anything?
HTGAA Class is back in 2016. More students, more sites.


8/1/2016

FABLAB 2.0

The theme of the 12th international Fab Lab conference in Shenzhen, China, is fab labs that make fab labs: systems that makes systems, applying the biology concept of self-replicating systems into the fabrication world.

fab12-adamala
Kate is giving a talk on synthetic life during the plenary Symposium.
What if we build life instead of growing?
Or what if we grow machines instead of building?


6/27/2016

New publication


Oligoarginine peptides slow strand annealing and assist non-enzymatic RNA replication;
Tony Z. Jia, Albert C. Fahrenbach, Neha P. Kamat, Katarzyna P. Adamala & Jack W. Szostak; Nature Chemistry, 2016, doi:10.1038/nchem.2551
local copy pdf
publisher website link
details, abstract

Oligoarginine peptides slow strand annealing and assist non-enzymatic RNA replication;
Tony Z. Jia, Albert C. Fahrenbach, Neha P. Kamat, Katarzyna P. Adamala & Jack W. Szostak; Nature Chemistry, doi:10.1038/nchem.2551

The non-enzymatic replication of RNA is thought to have been a critical process required for the origin of life. One unsolved difficulty with non-enzymatic RNA replication is that template-directed copying of RNA results in a double-stranded product. After strand separation, rapid strand reannealing outcompetes slow non-enzymatic template copying, which renders multiple rounds of RNA replication impossible. Here we show that oligoarginine peptides slow the annealing of complementary oligoribonucleotides by up to several thousand-fold; however, short primers and activated monomers can still bind to template strands, and template-directed primer extension can still occur, all within a phase-separated condensed state, or coacervate. Furthermore, we show that within this phase, partial template copying occurs even in the presence of full-length complementary strands. This method to enable further rounds of replication suggests one mechanism by which short non-coded peptides could have enhanced early cellular fitness, and potentially explains how longer coded peptides, that is, proteins, came to prominence in modern biology.


5/2/2016

New publication


Programmable RNA-binding protein composed of repeats of a single modular unit;
Katarzyna P. Adamala*, Daniel A. Martin-Alarcon*, and Edward S. Boyden; PNAS, 2016, 10.1073/pnas.1519368113; *equal contribution
local copy pdf
publisher website link
details, abstract

Programmable RNA-binding protein composed of repeats of a single modular unit;
Katarzyna P. Adamala*, Daniel A. Martin-Alarcon*, and Edward S. Boyden; PNAS, 2016, 10.1073/pnas.1519368113; *equal contribution

The ability to monitor and perturb RNAs in living cells would benefit greatly from a modular protein architecture that targets unmodified RNA sequences in a programmable way. We report that the RNA-binding protein PumHD (Pumilio homology domain), which has been widely used in native and modified form for targeting RNA, can be engineered to yield a set of four canonical protein modules, each of which targets one RNA base. These modules (which we call Pumby, for Pumilio-based assembly) can be concatenated in chains of varying composition and length, to bind desired target RNAs. The specificity of such Pumby - RNA interactions was high, with undetectable binding of a Pumby chain to RNA sequences that bear three or more mismatches from the target sequence. We validate that the Pumby architecture can perform RNA-directed protein assembly and enhancement of translation of RNAs. We further demonstrate a new use of such RNA-binding proteins, measurement of RNA translation in living cells. Pumby may prove useful for many applications in the measurement, manipulation, and biotechnological utilization of unmodified RNAs in intact cells and systems.


3/21/2016

New publication


Collaboration between primitive cell membranes and soluble catalysts;
K. Adamala*, A. E. Engelhart* and J. W. Szostak; Nature Communications, 2016, doi:10.1038/ncomms11041; *equal contribution
local copy pdf
publisher website link
details, abstract

Collaboration between primitive cell membranes and soluble catalysts;
K. Adamala*, A. E. Engelhart* and J. W. Szostak; Nature Communications, 2016, doi:10.1038/ncomms11041; *equal contribution

One widely-held model of early life suggests primitive cells consisted of simple RNA-based catalysts within lipid compartments. One possible selective advantage conferred by an encapsulated catalyst is stabilization of the compartment, resulting from catalyst-promoted synthesis of key membrane components.
Here, we show model protocell vesicles containing an encapsulated enzyme that promotes the synthesis of simple fatty acid derivatives become stabilized to Mg2+, which is required for ribozyme activity and RNA synthesis. Thus, protocells capable of such catalytic transformations would have enjoyed a selective advantage over other protocells in high Mg2+ environments. The synthetic transformation requires both the catalyst and vesicles, which solubilize the water-insoluble precursor lipid.
We suggest that similar modified lipids could have played a key role in early life, and that primitive lipid membranes and encapsulated catalysts, such as ribozymes, may have acted in conjunction with each other, enabling otherwise-impossible chemical transformations within primordial cells.


3/14/2016

New publication


floating fablab

11/12/2015

The FabLab Lima and Konrad Adenauer Foundation organised workshop Floating FAB LAB Amazon.
We discussed the opportunities for using synthetic minimal cells as biosensors in the Floating FabLab on the Amazon river.



9/06/2015

Fab Academy meets synthetic biology.
Introducing How To Grow (Almost) Anything
The first synth bio FabLab Academy includes unit on synthetic minimal cells.


8/12/2015

adamala

Moving to Minnesota!
Next year, I'm starting as an assistant professor at the Department of Genetics, Cell Biology, and Development at the University of Minnesota.


7/9/2015

New publication


Generation of Functional RNAs from Inactive Oligonucleotide Complexes by Non-enzymatic Primer Extension;
K. Adamala*, A. E. Engelhart* and J. W. Szostak; J. Am. Chem. Soc., 2015, 137 (1), pp 483 - 489, DOI: 10.1021/ja511564d; *equal contribution
publisher website link
local copy pdf
details, abstract

Generation of Functional RNAs from Inactive Oligonucleotide Complexes by Non-enzymatic Primer Extension;
K. Adamala*, A. E. Engelhart* and J. W. Szostak; J. Am. Chem. Soc., 2015, 137 (1), pp 483 - 489, DOI: 10.1021/ja511564d; *equal contribution

The earliest genomic RNAs had to be short enough for efficient replication, while simultaneously serving as unfolded templates and effective ribozymes. A partial solution to this paradox may lie in the fact that many functional RNAs can self-assemble from multiple fragments. Therefore, in early evolution, genomic RNA fragments could have been significantly shorter than unimolecular functional RNAs. Here, we show that unstable, nonfunctional complexes assembled from even shorter 3' - truncated oligonucleotides can be stabilized and gain function via non-enzymatic primer extension. Such short RNAs could act as good templates due to their minimal length and complex-forming capacity, while their minimal length would facilitate replication by relatively inefficient polymerization reactions. These RNAs could also assemble into nascent functional RNAs and undergo conversion to catalytically active forms, by the same polymerization chemistry used for replication that generated the original short RNAs. Such phenomena could have substantially relaxed requirements for copying efficiency in early nonenzymatic replication systems.


2/12/2015

New publication.


Construction of a Liposome Dialyzer for preparation of high-value, small-volume liposome formulations;
K. Adamala*, A. E. Engelhart*, N. Kamat, L. Jin and J. W. Szostak; Nature Protocols, 2015, 10(6), pp 927-938; *equal contribution
publisher website link
local copy pdf
details, abstract

Construction of a Liposome Dialyzer for preparation of high-value, small-volume liposome formulations;
K. Adamala, A. E. Engelhart, N. Kamat, L. Jin and J. W. Szostak; Nature Protocols, 2015, 10(6), pp 927-938;

The liposome dialyzer is a small-volume equilibrium dialysis device, built from commercially available materials, that is designed for the rapid exchange of small volumes of an extraliposomal reagent pool against a liposome preparation. The dialyzer is prepared by modification of commercially available dialysis cartridges (Slide-A-Lyzer cassettes), and it consists of a reactor with two 300-μl chambers and a 1.56 - cm2 dialysis surface area. The dialyzer is prepared in three stages: (i) disassembling the dialysis cartridges to obtain the required parts, (ii) assembling the dialyzer and (iii) sealing the dialyzer with epoxy. Preparation of the dialyzer takes approx 1.5 h, not including overnight epoxy curing. Each round of dialysis takes 1 - 24 h, depending on the analyte and membrane used. We previously used the dialyzer for small-volume non-enzymatic RNA synthesis reactions inside fatty acid vesicles. In this protocol, we demonstrate other applications, including removal of unencapsulated calcein from vesicles, remote loading and vesicle microscopy.



©2016 kate adamala