Month: November 2017

A semi-synthetic organism that stores and retrieves increased genetic information

Since at least the last common ancestor of all life on Earth, genetic information has been stored in a four-letter alphabet that is propagated and retrieved by the formation of two base pairs. The central goal of synthetic biology is to create new life forms and functions, and the most general route to this goal is the creation of semi-synthetic organisms whose DNA harbours two additional letters that form a third, unnatural base pair. Previous efforts to generate such semi-synthetic organisms culminated in the creation of a strain of Escherichia colithat, by virtue of a nucleoside triphosphate transporter from Phaeodactylum tricornutum, imports the requisite unnatural triphosphates from its medium and then uses them to replicate a plasmid containing the unnatural base pair dNaM–dTPT3. Although the semi-synthetic organism stores increased information when compared to natural organisms, retrieval of the information requires in vivotranscription of the unnatural base pair into mRNA and tRNA, aminoacylation of the tRNA with a non-canonical amino acid, and efficient participation of the unnatural base pair in decoding at the ribosome. Here we report the in vivo transcription of DNA containing dNaM and dTPT3 into mRNAs with two different unnatural codons and tRNAs with cognate unnatural anticodons, and their efficient decoding at the ribosome to direct the site-specific incorporation of natural or non-canonical amino acids into superfolder green fluorescent protein. The results demonstrate that interactions other than hydrogen bonding can contribute to every step of information storage and retrieval. The resulting semi-synthetic organism both encodes and retrieves increased information and should serve as a platform for the creation of new life forms and functions.


A semi-synthetic organism that stores and retrieves increased genetic information
Yorke Zhang, Jerod L. Ptacin, Emil C. Fischer, Hans R. Aerni, Carolina E. Caffaro, Kristine San Jose, Aaron W. Feldman, Court R. Turner & Floyd E. Romesberg
Nature 551, 644–647 (30 November 2017)


Strains, functions and dynamics in the expanded Human Microbiome Project

The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, diversity, biogeography, and molecular function. The National Institutes of Health Human Microbiome Project has provided one of the broadest such characterizations so far. Here we introduce a second wave of data from the study, comprising 1,631 new metagenomes (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. We applied updated profiling and assembly methods to provide new characterizations of microbiome personalization. Strain identification revealed subspecies clades specific to body sites; it also quantified species with phylogenetic diversity under-represented in isolate genomes. Body-wide functional profiling classified pathways into universal, human-enriched, and body site-enriched subsets. Finally, temporal analysis decomposed microbial variation into rapidly variable, moderately variable, and stable subsets. This study furthers our knowledge of baseline human microbial diversity and enables an understanding of personalized microbiome function and dynamics.


Strains, functions and dynamics in the expanded Human Microbiome Project
Jason Lloyd-Price, Anup Mahurkar, Gholamali Rahnavard, Jonathan Crabtree, Joshua Orvis, A. Brantley Hall, Arthur Brady, Heather H. Creasy, Carrie McCracken, Michelle G. Giglio, Daniel McDonald, Eric A. Franzosa, Rob Knight, Owen White & Curtis Huttenhower
Nature 550, 61–66 (05 October 2017)


How the news media activate public expression and influence national agendas

We demonstrate that exposure to the news media causes Americans to take public stands on specific issues, join national policy conversations, and express themselves publicly—all key components of democratic politics—more often than they would otherwise. After recruiting 48 mostly small media outlets, we chose groups of these outlets to write and publish articles on subjects we approved, on dates we randomly assigned. We estimated the causal effect on proximal measures, such as website pageviews and Twitter discussion of the articles’ specific subjects, and distal ones, such as national Twitter conversation in broad policy areas. Our intervention increased discussion in each broad policy area by ~62.7% (relative to a day’s volume), accounting for 13,166 additional posts over the treatment week, with similar effects across population subgroups.


How the news media activate public expression and influence national agendas
Gary King, Benjamin Schneer, Ariel White

Science  10 Nov 2017:
Vol. 358, Issue 6364, pp. 776-780
DOI: 10.1126/science.aao1100


A Fantastic Voyage in Genomics

Imagine being able to shrink down to a small enough size to peer into the human body at the single-cell level. Now take a deep breath and plunge into that cell to see all of the ongoing biological processes, including the full complement of molecules and their locations within the cell. This has long been the realm of science fiction, but not for much longer. Recent technological advances now allow us to identify and visualize RNA transcripts, proteins, and other cellular components at the single-cell level. This has led to discoveries about the immune system, brain, and developmental processes and is poised to revolutionize our understanding of the entire human body.


A Fantastic Voyage in Genomics
Laura M. Zahn

Science  06 Oct 2017:
Vol. 358, Issue 6359, pp. 56-57
DOI: 10.1126/science.358.6359.56