Living GenoChemetics by hyphenating synthetic biology and synthetic chemistry in vivo

Marrying synthetic biology with synthetic chemistry provides a powerful approach toward natural product diversification, combining the best of both worlds: expediency and synthetic capability of biogenic pathways and chemical diversity enabled by organic synthesis. Biosynthetic pathway engineering can be employed to insert a chemically orthogonal tag into a complex natural scaffold affording the possibility of site-selective modification without employing protecting group strategies. Here we show that, by installing a sufficiently reactive handle (e.g., a C–Br bond) and developing compatible mild aqueous chemistries, synchronous biosynthesis of the tagged metabolite and its subsequent chemical modification in living culture can be achieved. This approach can potentially enable many new applications: for example, assay of directed evolution of enzymes catalyzing halo-metabolite biosynthesis in living cells or generating and following the fate of tagged metabolites and biomolecules in living systems. We report synthetic biological access to new-to-nature bromo-metabolites and the concomitant biorthogonal cross-coupling of halo-metabolites in living culture

The ecology and biodiversity of urban ponds

Recent research has demonstrated that ponds contribute a great deal to biodiversity at a regional level as networks of habitat patches that also act as ‘stepping stones’ to facilitate the movement of species through the landscape. Similarly, a great deal of biodiversity persists in urban environments where synanthropic communities are supplemented by species that thrive in disturbed environments. Aquatic urban biodiversity appears to persist despite anthropogenic stressors: an array of anthropogenic pollutants (road salt and heavy metals), invasive species, and active mismanagement—particularly the removal of riparian vegetation. Optimizing urban ponds for different ecosystem services results in conflicting priorities over hydrological, geochemical, ecological, aesthetic, and cultural functions. The socio-ecosystem approach to environmental management opens a path to greater incorporation of biodiversity into town planning and sustainability, while accounting for cultural attitudes to urban ecosystems. I identify a range of research needs: (1) the roles of design and location of urban ponds in influencing biodiversity, (2) the function of urban wetlands for stormwater and pollution management, and (3) public perceptions of urban ecosystems and how those perceptions are influenced by interactions with natural systems. Urban wetlands offer an important opportunity to educate the general public on natural systems and science in general using a resource that is located on their doorstep. In the face of increasing pressures on natural systems and increasing extent and intensity of urbanization, a more comprehensive appreciation of the challenges and opportunities provided by urban ponds could play a substantial role in driving sustainable urban development

Methods for discovering genomic loci exhibiting complex patterns of differential methylation.

BACKGROUND: Cytosine methylation is widespread in most eukaryotic genomes and is known to play a substantial role in various regulatory pathways. Unmethylated cytosines may be converted to uracil through the addition of sodium bisulphite, allowing genome-wide quantification of cytosine methylation via high-throughput sequencing. The data thus acquired allows the discovery of methylation 'loci'; contiguous regions of methylation consistently methylated across biological replicates. The mapping of these loci allows for associations with other genomic factors to be identified, and for analyses of differential methylation to take place. RESULTS: The segmentSeq R package is extended to identify methylation loci from high-throughput sequencing data from multiple experimental conditions. A statistical model is then developed that accounts for biological replication and variable rates of non-conversion of cytosines in each sample to compute posterior likelihoods of methylation at each locus within an empirical Bayesian framework. The same model is used as a basis for analysis of differential methylation between multiple experimental conditions with the baySeq R package. We demonstrate the capability of this method to analyse complex data sets in an analysis of data derived from multiple Dicer-like mutants in Arabidopsis. This reveals several novel behaviours at distinct sets of loci in response to loss of one or more of the Dicer-like proteins that indicate an antagonistic relationship between the Dicer-like proteins at at least some methylation loci. Finally, we show in simulation studies that this approach can be significantly more powerful in the detection of differential methylation than many existing methods in data derived from both mammalian and plant systems. CONCLUSIONS: The methods developed here make it possible to analyse high-throughput sequencing of the methylome of any given organism under a diverse set of experimental conditions. The methods are able to identify methylation loci and evaluate the likelihood that a region is truly methylated under any given experimental condition, allowing for downstream analyses that characterise differences between methylated and non-methylated regions of the genome. Futhermore, diverse patterns of differential methylation may also be characterised from these data

Systems genetics identifies a convergent gene network for cognition and neurodevelopmental disease

Genetic determinants of cognition are poorly characterized, and their relationship to genes that confer risk for neurodevelopmental disease is unclear. Here we performed a systems-level analysis of genome-wide gene expression data to infer gene-regulatory networks conserved across species and brain regions. Two of these networks, M1 and M3, showed replicable enrichment for common genetic variants underlying healthy human cognitive abilities, including memory. Using exome sequence data from 6,871 trios, we found that M3 genes were also enriched for mutations ascertained from patients with neurodevelopmental disease generally, and intellectual disability and epileptic encephalopathy in particular. M3 consists of 150 genes whose expression is tightly developmentally regulated, but which are collectively poorly annotated for known functional pathways. These results illustrate how systems-level analyses can reveal previously unappreciated relationships between neurodevelopmental disease–associated genes in the developed human brain, and provide empirical support for a convergent gene-regulatory network influencing cognition and neurodevelopmental disease

Principles of genetic circuit design

Cells navigate environments, communicate and build complex patterns by initiating gene expression in response to specific signals. Engineers seek to harness this capability to program cells to perform tasks or create chemicals and materials that match the complexity seen in nature. This Review describes new tools that aid the construction of genetic circuits. Circuit dynamics can be influenced by the choice of regulators and changed with expression 'tuning knobs'. We collate the failure modes encountered when assembling circuits, quantify their impact on performance and review mitigation efforts. Finally, we discuss the constraints that arise from circuits having to operate within a living cell. Collectively, better tools, well-characterized parts and a comprehensive understanding of how to compose circuits are leading to a breakthrough in the ability to program living cells for advanced applications, from living therapeutics to the atomic manufacturing of functional materials.National Institute of General Medical Sciences (U.S.) (Grant P50 GM098792)National Institute of General Medical Sciences (U.S.) (Grant R01 GM095765)National Science Foundation (U.S.). Synthetic Biology Engineering Research Center (EEC0540879)Life Technologies, Inc. (A114510)National Science Foundation (U.S.). Graduate Research FellowshipUnited States. Office of Naval Research. Multidisciplinary University Research Initiative (Grant 4500000552

Product multiplet branching in the O(1D) + H2-->OH(2Pi) + H reaction.

The statistical model of atom-diatom insertion reactions is combined with coupled-states capture theory and used to calculate product multiplet-resolved integral cross sections for the title reaction. This involves an ab initio determination of the four electronic potential energy surfaces that correlate with the products ((1,3)A(') and (1,3)A(")), and an accurate description of the electronic and spin-orbit couplings between them. The dependence of the resulting cross sections on the final-state rotational quantum number shows a statistical behavior similar to that observed in earlier studies of the reaction in which only the lowest ((1)A(')) potential was retained. In addition, however, the present calculations provide information on the branching between the OH((2)Pi) multiplet levels. Although the two spin-orbit manifolds are predicted to be equally populated, we find a strong propensity for the formation of the Pi(A(')) Lambda-doublet states. These two predictions confirm the experimental results of Butler, Wiesenfeld, Gericke, Brouard, and their co-workers. The nonstatistical population of the OH Lambda-doublet levels is a consequence of the bond breaking in the intermediate H(2)O complex and is preserved through the multiple curve crossings as the products separate. This exit-channel coupling is correctly described by the present theory

Product multiplet branching in the O(1D) + H2-->OH(2Pi) + H reaction.

The statistical model of atom-diatom insertion reactions is combined with coupled-states capture theory and used to calculate product multiplet-resolved integral cross sections for the title reaction. This involves an ab initio determination of the four electronic potential energy surfaces that correlate with the products ((1,3)A(') and (1,3)A(")), and an accurate description of the electronic and spin-orbit couplings between them. The dependence of the resulting cross sections on the final-state rotational quantum number shows a statistical behavior similar to that observed in earlier studies of the reaction in which only the lowest ((1)A(')) potential was retained. In addition, however, the present calculations provide information on the branching between the OH((2)Pi) multiplet levels. Although the two spin-orbit manifolds are predicted to be equally populated, we find a strong propensity for the formation of the Pi(A(')) Lambda-doublet states. These two predictions confirm the experimental results of Butler, Wiesenfeld, Gericke, Brouard, and their co-workers. The nonstatistical population of the OH Lambda-doublet levels is a consequence of the bond breaking in the intermediate H(2)O complex and is preserved through the multiple curve crossings as the products separate. This exit-channel coupling is correctly described by the present theory

Coupled-channel statistical theory of the N(D-2)+H-2 and O(D-1)+H-2 insertion reactions

A detailed statistical theory of atom-diatom insertion reactions is derived by combining the early statistical ideas of Pechukas and Light with the coupled-channel capture theory of Clary and Henshaw. The theory is applied to the N(2D)+H2 and O(1D)+H2 reactions and found to give results in good agreement with the exact quantum mechanical integral cross sections reported recently by Honvault and Launay. © 2001 Elsevier Science B.V