Synthetic biological networks.

Despite their obvious relationship and overlap, the field of physics is blessed with many insightful laws, while such laws are sadly absent in biology. Here we aim to discuss how the rise of a more recent field known as synthetic biology may allow us to more directly test hypotheses regarding the possible design principles of natural biological networks and systems. In particular, this review focuses on synthetic gene regulatory networks engineered to perform specific functions or exhibit particular dynamic behaviors. Advances in synthetic biology may set the stage to uncover the relationship of potential biological principles to those developed in physics.

Engineered E. coli that detect and respond to gut inflammation through nitric oxide sensing.

Advances in synthetic biology now allow for the reprogramming of microorganisms to execute specific tasks. Here, we describe the development of an engineered strain of E. coli capable of sensing and responding to the presence of a mammalian inflammatory signal. The synthetic gene regulatory circuit is designed to permanently alter gene expression in response to the well characterized inflammatory signal nitric oxide. The detection of nitric oxide initiates the expression of a DNA recombinase, causing the permanent activation of a DNA switch. We demonstrate that E. coli containing this synthetic circuit respond to nitric oxide from both chemical and biological sources, with permanent DNA recombination occurring in the presence of nitric oxide donor compounds or inflamed mouse ileum explants. In the future, this synthetic genetic circuit will be optimized to allow E. coli to reliably detect and respond to inflammation in vivo.

Development of social familiarity in ewes.

We assessed the development of individual discrimination resulting from direct contact/familiarization in ewes. Unfamiliar ewes were introduced during 6, 24 or 72 h in groups of already familiarized ewes. At the end of this contact period, the development of social recognition with the animal that has been introduced was assessed using two different types of tests: a Y-maze preference test and a delayed paired close encounters test where tested ewes are successively and randomly interacting with the familiar animal and an unfamiliar conspecific. The results of both tests showed that ewes developed a recognition of the familiar animal in comparison to a completely unfamiliar female. However, this preference was evidenced after 24 h of contact when using the paired close encounters test whereas it appears only after 72 h when using the Y-maze test, suggesting that the paired close encounters test is a more sensitive methodology to assess the development of social familiarization. The importance of estrogens, in the formation of social familiarization was also evaluated. To this end, social recognition in the paired close encounters test was compared between ovariectomized animals receiving estrogen implants or not. Despite significant high levels of estradiol in estrogen implanted females, no major differences in recognition appeared between groups, suggesting that in our conditions estrogens do not have major influence on social familiarization.

When are genetic methods useful for estimating contemporary abundance and detecting population trends?

The utility of microsatellite markers for inferring population size and trend has not been rigorously examined, even though these markers are commonly used to monitor the demography of natural populations. We assessed the ability of a linkage disequilibrium estimator of effective population size (N(e) ) and a simple capture-recapture estimator of abundance (N) to quantify the size and trend of stable or declining populations (true N = 100-10,000), using simulated Wright-Fisher populations. Neither method accurately or precisely estimated abundance at sample sizes of S = 30 individuals, regardless of true N. However, if larger samples of S = 60 or 120 individuals were collected, these methods provided useful insights into abundance and trends for populations of N = 100-500. At small population sizes (N = 100 or 250), precision of the N(e) estimates was improved slightly more by a doubling of loci sampled than by a doubling of individuals sampled. In general, monitoring N(e) proved a more robust means of identifying stable and declining populations than monitoring N over most of the parameter space we explored, and performance of the N(e) estimator is further enhanced if the N(e) /N ratio is low. However, at the largest population size (N = 10,000), N estimation outperformed N(e) . Both methods generally required ≥ 5 generations to pass between sampling events to correctly identify population trend.

Inhibition of mammalian muscle differentiation by regeneration blastema extract of Sternopygus macrurus.

Tissue regeneration through stem cell activation and/or cell dedifferentiation is widely distributed across the animal kingdom. By comparison, regeneration in mammals is poor and this may reflect a limited dedifferentiation potential of mature cells. Because mammalian myotubes can dedifferentiate in the presence of newt blastema extract, the present study tested the dedifferentiation induction capability of the blastema from the teleost Sternopygus macrurus (SmBE). Our in vitro data showed that SmBE did not induce cell cycle reentry of myonuclei in myotubes. Instead, SmBE caused myotubes to detach and time-lapse imaging analyses characterized the cellular events before their detachment. Furthermore, SmBE enhanced myoblast proliferation and reversibly inhibited their differentiation. These data suggest the presence of protein factors in SmBE that regulate mammalian muscle physiology and differentiation, but do not support the conservation of a dedifferentiation induction capability by the blastema of S. macrurus.

Duplex oligomers defined via covalent casting of a one-dimensional hydrogen-bonding motif.

Hydrogen-bonded tapes comprised of monomeric molecular precursors are used to define structural parameters for the design of related oligomers encoded with predetermined modes of assembly. Application of this "covalent casting" strategy vis-à-vis the one-dimensional H-bonding motif expressed by 2-amino-4,6-dichlorotriazine has enabled the design of high-affinity duplex molecular strands. Dimeric, trimeric, and tetrameric duplex oligomers are prepared through an iterative synthetic protocol involving sequential homologation of the oligo(aminotriazine). The mode of assembly and interstrand affinity of homologous oligomers are established in solution by (1)H NMR dilution experiments, isothermal titration calorimetry (ITC), vapor pressure osmometry (VPO), cross-hybridization experiments involving the analysis of dye-labeled strands via thin-layer chromatography (TLC), and in the solid state by X-ray crystallographic analysis. Binding free energy per unimer (-Delta G degrees/n) increases significantly upon extension from monomer to dimer to trimer, signifying a strong positive cooperative effect. Nanomolar binding affinity (K(d) = 1.44 +/- 0.50 nM) was determined for the duplex trimer by ITC in 1,2-dichloroethane at 20 degrees C. In-register duplex formation is not observed for the tetramer, which appears to adopt an alternative binding mode. These data give insight into the structural and interactional features of the oligomers required for high-affinity, high-specificity binding and define a platform for the design of second-generation systems and related duplex strands for use in nanoscale assembly.