177 research outputs found
Synthetic Physiology
Optogenetic tools are DNA-encoded molecules that, when genetically targeted to cells, enable the control of specific physiological processes within those cells through exposure to light. These tools can pinpoint how these specific processes affect the emergent properties of a complex biological system, such as a mammalian organ or even an entire animal. They can also allow control of a biological system for therapeutic or bioengineering purposes. Many of the optical control tools explored to date are single-component reagents containing a photoactive signaling domain. An interesting question is raised by comparing optogenetics to synthetic biology. In the latter, interchangeable and modular DNA-encoded parts are assembled into complex biological circuits, thus enabling sophisticated logic and computation as well as the production of biologics and reagents (1, 2). Is it possible to devise strategies for the temporally precise cell-targeted optical control of complex engineered biological computational or chemical-synthetic pathways? Such a marriage of optogenetics and synthetic biology—which one might call synthetic physiology—would open up the ability to use optogenetics to trigger and regulate engineered synthetic biology systems, which in turn could execute computational and biological programs of great complexity (3). On page 1565 of this issue, Ye et al. (4) explore such a hybrid approach to controlling a biological system, as well as the bioengineering and preclinical capabilities opened up by such an approach
Creativity and Autonomy in Swarm Intelligence Systems
This work introduces two swarm intelligence algorithms -- one mimicking the behaviour of one species of ants (\emph{Leptothorax acervorum}) foraging (a `Stochastic Diffusion Search', SDS) and the other algorithm mimicking the behaviour of birds flocking (a `Particle Swarm Optimiser', PSO) -- and outlines a novel integration strategy exploiting the local search properties of the PSO with global SDS behaviour. The resulting hybrid algorithm is used to sketch novel drawings of an input image, exploliting an artistic tension between the local behaviour of the `birds flocking' - as they seek to follow the input sketch - and the global behaviour of the `ants foraging' - as they seek to encourage the flock to explore novel regions of the canvas. The paper concludes by exploring the putative `creativity' of this hybrid swarm system in the philosophical light of the `rhizome' and Deleuze's well known `Orchid and Wasp' metaphor
The Role of PAS Kinase in PASsing the Glucose Signal
PAS kinase is an evolutionarily conserved nutrient responsive protein kinase that regulates glucose homeostasis. Mammalian PAS kinase is activated by glucose in pancreatic beta cells, and knockout mice are protected from obesity, liver triglyceride accumulation, and insulin resistance when fed a high-fat diet. Yeast PAS kinase is regulated by both carbon source and cell integrity stress and stimulates the partitioning of glucose toward structural carbohydrate biosynthesis. In our current model for PAS kinase regulation, a small molecule metabolite binds the sensory PAS domain and activates the enzyme. Although bona fide PAS kinase substrates are scarce, in vitro substrate searches provide putative targets for exploration
Swarmic sketches and attention mechanism
This paper introduces a novel approach deploying the mechanism of ‘attention’ by adapting a swarm intelligence algorithm – Stochastic Diffusion Search – to selectively attend to detailed areas of a digital canvas. Once the attention of the swarm is drawn to a certain line within the canvas, the capability of another swarm intelligence algorithm – Particle Swarm Intelligence – is used to produce a ‘swarmic sketch’ of the attended line. The swarms move throughout the digital canvas in an attempt to satisfy their dynamic roles – attention to areas with more details – associated to them via their fitness function. Having associated the rendering process with the concepts of attention, the performance of the participating swarms creates a unique, non-identical sketch each time the ‘artist’ swarms embark on interpreting the input line drawings. The detailed investigation of the ‘creativity’ of such systems have been explored in our previous work; nonetheless, this papers provides a brief account of the ‘computational creativity’ of the work through two prerequisites of creativity within the swarm intelligence’s two infamous phases of exploration and exploitation; these phases are described herein through the attention and tracing mechanisms respectively
Swarmic paintings and colour attention
Swarm-based multi-agent systems have been deployed in non-photorealistic rendering for many years. This paper introduces a novel approach in adapting a swarm intelligence algorithm – Stochastic Diffusion Search – for producing non-photorealistic images. The swarm-based system is presented with a digital image and the agents move throughout the digital canvas in an attempt to satisfy the dynamic roles – attention to different colours - associated to them via their fitness function. Having associated the rendering process with the concepts of ‘attention’ in general and colour attention in particular, this papers briefly discusses the ‘computational creativity’ of the work through two prerequisites of creativity (i.e. freedom and constraints) within the swarm intelligence’s two infamous phases of exploration and exploitation
Characterization of the Blue-Light-Activated Adenylyl Cyclase mPAC by Flash Photolysis and FTIR Spectroscopy
The recently discovered photo-activated adenylyl cyclase (mPAC from
Microcoleus chthonoplastes) is the first PAC that owes a light-, oxygen- and
voltage-sensitive (LOV) domain for blue-light sensing. The photoreaction of
the mPAC receptor was studied by time-resolved UV/vis and light-induced
Fourier transform infrared (FTIR) absorption difference spectroscopy. The
photocycle comprises of the typical triplet state LOV715 and the thio-adduct
state LOV390. While the adduct state decays with a time constant of 8 s, the
lifetime of the triplet state is with 656 ns significantly shorter than in all
other reported LOV domains. The light-induced FTIR difference spectrum shows
the typical bands of the LOV390 and LOV450 intermediates. The negative S-H
stretching vibration at 2573 cm−1 is asymmetric suggesting two rotamer
configurations of the protonated side chain of C194. A positive band at 3632
cm−1 is observed, which is assigned to an internal water molecule. In contrast
to other LOV domains, mPAC exhibits a second positive feature at 3674 cm−1
which is due to the O-H stretch of a second intrinsic water molecule and the
side chain of Y476. We conclude that the latter might be involved in the
dimerization of the cyclase domain which is crucial for ATP binding
BLUF Domain Function Does Not Require a Metastable Radical Intermediate State
BLUF
(blue light using flavin) domain proteins are an important
family of blue light-sensing proteins which control a wide variety
of functions in cells. The primary light-activated step in the BLUF
domain is not yet established. A number of experimental and theoretical
studies points to a role for photoinduced electron transfer (PET)
between a highly conserved tyrosine and the flavin chromophore to
form a radical intermediate state. Here we investigate the role of
PET in three different BLUF proteins, using ultrafast broadband transient
infrared spectroscopy. We characterize and identify infrared active
marker modes for excited and ground state species and use them to
record photochemical dynamics in the proteins. We also generate mutants
which unambiguously show PET and, through isotope labeling of the
protein and the chromophore, are able to assign modes characteristic
of both flavin and protein radical states. We find that these radical
intermediates are not observed in two of the three BLUF domains studied,
casting doubt on the importance of the formation of a population of
radical intermediates in the BLUF photocycle. Further, unnatural amino
acid mutagenesis is used to replace the conserved tyrosine with fluorotyrosines,
thus modifying the driving force for the proposed electron transfer
reaction; the rate changes observed are also not consistent with a
PET mechanism. Thus, while intermediates of PET reactions can be observed
in BLUF proteins they are not correlated with photoactivity, suggesting
that radical intermediates are not central to their operation. Alternative
nonradical pathways including a keto–enol tautomerization induced
by electronic excitation of the flavin ring are considered
Femtosecond Stimulated Raman Study of the Photoactive Flavoprotein AppABLUF
Femtosecond stimulated Raman Spectroscopy (FSRS) is applied to study the photocycle of a blue light using flavin (BLUF) domain photoreceptor, AppABLUF. It is shown that FSRS spectra are sensitive to the light adapted state of the protein and probe its excited state dynamics. The dominant contribution to the most sensitive excited state Raman active modes is from flavin ring modes. However, TD-DFT calculations for excited state structures indicate that reproduction and assignment of the experimentally observed spectral shift will require high level calculations on the flavin in its specific protein environment
On the Dynamic Stability of Cool Supergiant Atmospheres
We have developed a new formalism to compute the thermodynamic coefficient
Gamma1 in the theory of stellar and atmospheric stability. We generalize the
classical derivation of the first adiabatic index, which is based on the
assumption of thermal ionization and equilibrium between gas and radiation
temperature, towards an expression which incorporates photo-ionization due to
radiation with a temperature T_rad different from the local kinetic gas
temperature.Our formalism considers the important non-LTE conditions in the
extended atmospheres of supergiant stars. An application to the Kurucz grid of
cool supergiant atmospheres demonstrates that models with T_rad =~ T_eff
between 6500 K and 7500 K become most unstable against dynamic perturbations,
according to Ledoux' stability integral . This results from Gamma1 and
acquiring very low values, below 4/3, throughout the entire stellar
atmosphere, which causes very high gas compression ratios around these
effective temperatures. Based on detailed NLTE-calculations, we discuss
atmospheric instability of pulsating massive yellow supergiants, like the
hypergiant rho Cas (Ia+), which exist in the extension of the Cepheid
instability strip, near the Eddington luminosity limit.Comment: 54 pages including figures and the Appendix, 7 figures, Accepted for
The Astrophysical Journal, Main Journal, 558, Sept. 200
Information sharing impact of stochastic diffusion search on differential evolution algorithm
This work details the research aimed at applying the powerful resource allocation mechanism deployed in stochastic diffusion search (SDS) to the differential evolution (DE), effectively merging a nature inspired swarm intelligence algorithm with a biologically inspired evolutionary algorithm. The results reported herein suggest that the hybrid algorithm, exploiting information sharing between the population elements, has the potential to improve the optimisation capability of classical DE algorithms. This claim is verified by running several experiments using state-of-the-art benchmarks. Additionally, the significance of the frequency within which SDS introduces communication and information exchange is also investigated
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