Friday, November 7, 2014

A Return to Blogging: The Year in Review



After a nearly year absence, Just Me and Eubacteria is back! The past year has been a busy one, not only for science but also for this humble author: I have moved from adjunct positions at several institutions to a full-time professor position at Kingsborough Community College, where I teach several courses (including Microbiology in Health and Disease). I am also engaging in starting my own research projects at the College, with a focus towards translation, synthetic biology, and iGEM. On a personal note, I am now engaged and will be married before the end of the year.


All of these changes unfortunately necessitated a break from blogging, from which I am only now settled enough to begin again. To re-open this blog, I have designed its appearance, and for the first post in almost a year, I will review some of the more interesting papers that have been published in synthetic biology and microbiology in 2014.

In the remainder of this post, you can find the citation, link, and summary from a number of selected publications from PubMed Central (PMC) that I found to be particularly interesting. In the coming months, I will provide a more detailed analysis of some of these papers (among others). In addition, you can continue to look forward to articles about synthetic biology, microbiology education. For example, I will soon be posting my impressions of the giant iGEM jamboree this year, which I again attended as a volunteer. 

Here are some of the articles of interest from 2014:

A Rapid and Simple Method for DNA Engineering Using Cycled Ligation Assembly
Roth, T., Milenkovic, L., and Scott, M. (2014) PLoS One 9(9):e107329
PMC4167330

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information
Ovchinnikov, S., Kamisetty, H., Baker, D. (2014) eLife 3: e02030
PMC4034769

Programmed Allee effect in bacteria causes a tradeoff between population spread and survival
Smith, R., et al (2014) PNAS 111(5); 1969-1974
PMC3918787

Cell-surface receptor control that depends on the size of a synthetic equilateral RNA-protein complex
Fujita, et al (2014) Science Reports 4:6422
PMC4168268

See Stay tuned for more great blog posts! I should be posting about once a week, except for a break in mid-December. Select read more to find links and summaries for more interesting articles from 2014! Think of a paper I missed? Feel free to comment below.




Selected Publications from the Past Year on PMC, Summarized

Below are several papers of interest (in no particular order) in the fields of synthetic biology and microbiology in the past year. All of the below were also selected because they are freely available to the public from Pub Med Central (PMC), and represent an interesting mix of synthetic biology, translation, microbiology, and the like (A paper-roll, if you will - to contrast with the more typical blog-roll).


A Rapid and Simple Method for DNA Engineering Using Cycled Ligation Assembly
Roth, T., Milenkovic, L., and Scott, M. (2014) PLoS One 9(9):e107329
PMC4167330

An interesting alternative to cloning procedures that I wish I had available as a graduate student, if only to try. The authors suggest their method, which relies on short oligos to bridge two sequences and 'stitch' them together, as an alternative to Gibson assembly. The recently developed Gibson assembly approach is useful, but has limitations, particularly for short sequences (as suggested by the authors). The CLA approach is similar to stitching together two PCR products, however only one stitching oligo is necessary, with sequence matching the other two fragments (regards of how they were produced, provided the 5' end of each is phosphorylated). I highly recommend any 'clone rangers' in molecular biology labs to read this article, particularly if you have encountered problems in making your desired construct. 



Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information
Ovchinnikov, S., Kamisetty, H., Baker, D. (2014) eLife 3: e02030
PMC4034769

Another great study from the same group that developed FoldIt and other important advances in bioinformatics. This paper features some impressive bioinformatic work to identify, among several different bacterial protein complexes, the interacting residues through analyzing sequence coevolution (covariance). This analysis requires generating multiple sequence alignments, and analyzing them in pairs (while keeping track of the organism from which the pair is derived). In addition to providing further validation for their methods and the utility of looking at coevolution in general, they use this approach to identify potential protein-protein interactions in several different bacterial complexes. Their data, as well as a web server for carrying out the calculations for your own proteins of interest, is freely available at the Baker Lab website. This paper aligns closely with some of my own research goals, and I will be sure to post a more detailed analysis of this work in the near future.



Programmed Allee effect in bacteria causes a tradeoff between population spread and survival
Smith, R., et al (2014) PNAS 111(5); 1969-1974
PMC3918787

The You lab at Duke University has produced a number of important papers in the field of synthetic biology (indeed, I may one day dedicate a entire blog post to this lab's work). This study follows that tradition, demonstrating the Allee effect in E. coli by artificially programming one into the bacteria. The Allee effect describes the phenomenon wherein the fitness of the individual is increased beyond a certain population threshold; this has implications for the growth and dispersal of different strains of bacteria. The effect was programmed in using the plasmid-addiction toxin and rescue proteins ccdB and ccdA (respectively). Expression of the rescue protein is tied to quorum sensing, and thus dependent on population density.




Cell-surface receptor control that depends on the size of a synthetic equilateral RNA-protein complex
Fujita, et al (2014) Science Reports 4:6422
PMC4168268

Creation of a triangular RNA / protein scaffold to precisely position membrane protein complexes a particular distance from each other. The positioning and interaction between different membrane complexes in mammalian cells is known to active certain signaling cascades. The scaffold created controls the positioning, and thus provides the synthetic biologist a tool for controlling this spatially regulated signaling mechanism. Depending on the size of the scaffold, the signaling cascade was either activated (to induce apoptosis in this study), or even to block association of the membrane complexes, and to repress the signal (The stoichiometry of the competition is interesting).


Other Publications of Interest in 2014


Structural Insights into Higher Order Assembly and Function of the Bacterial Microcompartment Protein PduA
Pang, A., et al (2014) J Biol Chem 289(32) 22377-22384
PMC4139245


A unified design space of synthetic stripe-forming networks
Schaerli, Y., et al (2014) Nature Commun. 5: 4905
PMC4172969

Large Chromosomal Rearrangements during a Long-Term Evolution Experiment with Escherichia coli
Raeside, C., et al (2014) mBio Sep-Oct 5(5): e01377-14
PMC4173774

Optimizing Metabolite Production Using Periodic Oscillations
Sowa, S., Baldea, M., Contreras, L (2014) PLoS Comput. Biol. 10(6): e103658
PMC4046915

Phenotypic Signatures Arising from Unbalanced Bacterial Growth

Tan C., et al (2014) PLoS Comput. Biol. 10(8): e1003751
PMC4125075

Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis
Dam J., et al (2014) BMC Syst Biol. 8(1): 111
PMC4181829

Non-stop mRNA decay: a special attribute of trans-translation mediated ribosome rescue

Venkataraman, K., et al (2014) Front Microbiol. 5:93
PMC3949413

Synthesizing genetic sequential logic circuit with clock pulse generator
Chuang, CH., and Lin, CL (2014) BMC Syst Biol. 8:63
PMC4049394

Engineered recombinant bacterial collagen as an alternative collagen-based biomaterial for tissue engineering
An, B., Kaplan, D., and Brodsky B. (2014) Front Chem. 2:40
PMC4066190

HomeRun Vector Assembly System: A Flexible and Standardized Cloning System for Assembly of Multi-Modular DNA Constructs
Li., M., Shukla, D., Largaespada, D. (2014) PLoS One 9(6):e100948
PMC4069157

“NiCo Buster”: engineering E. coli for fast and efficient capture of cobalt and nickel
Duprey, et al (2014) J Biol Eng. 8:19
PMC4124493

Bacterial Sigma Factors as Targets for Engineered or Synthetic Transcriptional Control
Tripathi, L., Zhang, Y., Li, Z. (2014) Front Bioeng Biotech 2:33
PMC4153023

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