Compressive Nonparametric Graphical Model Selection For Time Series

We propose a method for inferring the conditional indepen- dence graph (CIG) of a high-dimensional discrete-time Gaus- sian vector random process from finite-length observations. Our approach does not rely on a parametric model (such as, e.g., an autoregressive model) for the vector random process; rather, it only assumes certain spectral smoothness proper- ties. The proposed inference scheme is compressive in that it works for sample sizes that are (much) smaller than the number of scalar process components. We provide analytical conditions for our method to correctly identify the CIG with high probability.Comment: to appear in Proc. IEEE ICASSP 201

Light-Activatable Nucleic Acids 'Caged' at the Nucleobases

The attachment of photolabile groups to biologically active molecules offers a very versatile way to put a biological effect under the control of an external trigger signal and thus confers spatiotemporal and dose control to this effect. Over the last years we have prepared a number of oligonucleotide derivatives that are modified in such a way. These derivatives are usually referred to as 'caged compounds' and in particular our photolabile 'caging groups' are located at the nucleobases of oligonucleotides so that the Watson–Crick interaction is temporarily impossible. Thus several nucleic acid-based applications have now become controllable with light

Dependence of aptamer activity on opposed terminal extensions : improvement of light-regulation efficiency

Aptamers that can be regulated with light allow precise control of protein activity in space and time and hence of biological function in general. In a previous study, we showed that the activity of the thrombin-binding aptamer HD1 can be turned off by irradiation using a light activatable "caged" intramolecular antisense-domain. However, the activity of the presented aptamer in its ON state was only mediocre. Here we studied the nature of this loss in activity in detail and found that switching from 5'- to 3'-extensions affords aptamers that are even more potent than the unmodified HD1. In particular we arrived at derivatives that are now more active than the aptamer NU172 that is currently in phase 2 clinical trials as an anticoagulant. As a result, we present light-regulatable aptamers with a superior activity in their ON state and an almost digital ON/OFF behavior upon irradiation

Test of the isotropy of the speed of light using a continuously rotating optical resonator

We report on a test of Lorentz invariance performed by comparing the resonance frequencies of one stationary optical resonator and one continuously rotating on a precision air bearing turntable. Special attention is paid to the control of rotation induced systematic effects. Within the photon sector of the Standard Model Extension, we obtain improved limits on combinations of 8 parameters at a level of a few parts in $10^{-16}$. For the previously least well known parameter we find $\tilde \kappa_{e-}^{ZZ} =(-1.9 \pm 5.2)\times 10^{-15}$. Within the Robertson-Mansouri-Sexl test theory, our measurement restricts the isotropy violation parameter $\beta -\delta -\frac 12$ to $(-2.1\pm 1.9)\times 10^{-10}$, corresponding to an eightfold improvement with respect to previous non-rotating measurements.Comment: 4 pages, 3 figures, to appear in Phys. Rev. Let

Life-stage specific environments in a cichlid fish: implications for inducible maternal effects

Through environmentally induced maternal effects females may fine-tune their offspring's phenotype to the conditions offspring will encounter after birth. If juvenile and adult ecologies differ, the conditions mothers experienced as juveniles may better predict their offspring's environment than the adult females' conditions. Maternal effects induced by the environment experienced by females during their early ontogeny should evolve when three ecological conditions are met: (1) Adult ecology does not predict the postnatal environmental conditions of offspring; (2) Environmental conditions for juveniles are correlated across successive generations; and (3) Juveniles occasionally settle in conditions that differ from the juvenile habitat of their mothers. By combining size-structured population counts, ecological surveys and a genetic analysis of population structure we provide evidence that all three conditions hold for Simochromis pleurospilus, a cichlid fish in which mothers adjust offspring quality to their own juvenile ecology. In particular we show (1) that the spatial niches and the habitat quality differ between juveniles and adults, and we provide genetic evidence (2) that usually fish of successive generations grow up in similar habitats, and (3) that occasional dispersal in populations with a different habitat quality is likely to occur. As adults of many species cannot predict their offspring's environment from ambient cues, life-stage specific maternal effects are likely to be common in animals. It will therefore be necessary to incorporate parental ontogeny in the study of parental effects when juveniles and adults inhabit different environment

U-Pin polyamide motif for recognition of the DNA minor groove

Abstract: DNA-binding hairpin pyrrole ± imidazole polyamides with g-aminobutyric acid as a turn-forming residue tolerate A ¥ T or T¥ A base pairs under the turn. U-pins-polyamides with a different turn-have been synthesized and their DNA binding properties were studied. The two turn-forming residues are connected via the ring nitrogens using variable length aliphatic linkers ((CH 2 ) n , n 3 ± 6). Through optimization of the linker length and the substituents at the 2-position of the pyrrole residue on the U-turn, polyamides with G ¥ C/C ¥ G tolerant turns could be found, which bind to DNA in a predictable manner

Dynamics of Boolean networks - an exact solution

The dynamics of Boolean networks (BN) with quenched disorder and thermal noise is studied via the generating functional method. A general formulation, suitable for BN with any distribution of Boolean functions, is developed. It provides exact solutions and insight into the evolution of order parameters and properties of the stationary states, which are inaccessible via existing methodology. We identify cases where the commonly used annealed approximation is valid and others where it breaks down. Broader links between BN and general Boolean formulas are highlighted

Dependence of aptamer activity on opposed terminal extensions: improvement of light-regulation efficiency

Aptamers that can be regulated with light allow precise control of protein activity in space and time and hence of biological function in general. In a previous study, we showed that the activity of the thrombin-binding aptamer HD1 can be turned off by irradiation using a light activatable ‘caged’ intramolecular antisense-domain. However, the activity of the presented aptamer in its ON state was only mediocre. Here we studied the nature of this loss in activity in detail and found that switching from 5′- to 3′-extensions affords aptamers that are even more potent than the unmodified HD1. In particular we arrived at derivatives that are now more active than the aptamer NU172 that is currently in phase 2 clinical trials as an anticoagulant. As a result, we present light-regulatable aptamers with a superior activity in their ON state and an almost digital ON/OFF behavior upon irradiation

Dependence of aptamer activity on opposed terminal extensions: improvement of light-regulation efficiency

Aptamers that can be regulated with light allow precise control of protein activity in space and time and hence of biological function in general. In a previous study, we showed that the activity of the thrombin-binding aptamer HD1 can be turned off by irradiation using a light activatable ‘caged’ intramolecular antisense-domain. However, the activity of the presented aptamer in its ON state was only mediocre. Here we studied the nature of this loss in activity in detail and found that switching from 5′- to 3′-extensions affords aptamers that are even more potent than the unmodified HD1. In particular we arrived at derivatives that are now more active than the aptamer NU172 that is currently in phase 2 clinical trials as an anticoagulant. As a result, we present light-regulatable aptamers with a superior activity in their ON state and an almost digital ON/OFF behavior upon irradiation

Sialome of a Generalist Lepidopteran Herbivore: Identification of Transcripts and Proteins from Helicoverpa armigera Labial Salivary Glands

Although the importance of insect saliva in insect-host plant interactions has been acknowledged, there is very limited information on the nature and complexity of the salivary proteome in lepidopteran herbivores. We inspected the labial salivary transcriptome and proteome of Helicoverpa armigera, an important polyphagous pest species. To identify the majority of the salivary proteins we have randomly sequenced 19,389 expressed sequence tags (ESTs) from a normalized cDNA library of salivary glands. In parallel, a non-cytosolic enriched protein fraction was obtained from labial salivary glands and subjected to two-dimensional gel electrophoresis (2-DE) and de novo peptide sequencing. This procedure allowed comparison of peptides and EST sequences and enabled us to identify 65 protein spots from the secreted labial saliva 2DE proteome. The mass spectrometry analysis revealed ecdysone, glucose oxidase, fructosidase, carboxyl/cholinesterase and an uncharacterized protein previously detected in H. armigera midgut proteome. Consistently, their corresponding transcripts are among the most abundant in our cDNA library. We did find redundancy of sequence identification of saliva-secreted proteins suggesting multiple isoforms. As expected, we found several enzymes responsible for digestion and plant offense. In addition, we identified non-digestive proteins such as an arginine kinase and abundant proteins of unknown function. This identification of secreted salivary gland proteins allows a more comprehensive understanding of insect feeding and poses new challenges for the elucidation of protein function