MVF Sensor Enables Analysis of Nucleic Acids with Stable Secondary Structures

One major challenge in nucleic acids analysis by hybridization probes is a compromise between the probe's tight binding and sequence‐selective recognition of nucleic acid targets folded into stable secondary structures. We have been developing a four‐way junction (4WJ)‐based sensor that consists of a universal stem‐loop (USL) probe immobilized on an electrode surface and two adaptor strands (M and F). The sensor was shown to be highly selective towards single base mismatches at room temperature, able to detect multiple targets using the same USL probe, and have improved ability to detect folded nucleic acids. However, some nucleic acid targets, including natural RNA, are folded into very stable secondary and tertiary structures, which may represent a challenge even for the 4WJ sensors. This work describes a new sensor, named MVF since it uses three probe stands M, V and F, which further improves the performance of 4WJ sensors with folded targets. The MVF sensor interrogating a 16S rRNA NASBA amplicon with calculated folding energy of ?32.82 kcal/mol has demonstrated 2.5‐fold improvement in a signal‐to‐background ratio in comparison with a 4WJ sensor lacking strand V. The proposed design can be used as a general strategy in the analysis of folded nucleic acids including natural RNA.     

Ergodic decomposition of a topological space

Given a positive contraction,P, onC(X) we define the conservative and dissipative parts ofP and establish divergence of ΣP ⁿf(x) on the conservative part ofX.     

On order preserving contractions

Let (Ω,Σ,μ) be a measure space and letP be an operator onL ₂(Ω,Σ,μ) with ‖P‖≦1,Pf≧0 a.e. wheneverf≧0. If the subspaceK is defined byK={x| ||P ⁿ x||=||P ^*n x||=||x||,n=1,2,...} thenK=L ₂(Ω,Σ₁,μ), where Σ₁ ⊂ Σ and onK the operatorP is “essentially” a measure preserving transformation. Thus the eigenvalues ofP of modulus one, form a group under multiplication. This last result was proved by Rota for finiteμ here finiteness is not assumed) and is a generalization of a theorem of Frobenius and Perron on positive matrices. The research reported in this document has been sponsored in part by Air Force Office of Scientific Research, OAR through the European Office, Aerospace Research, United States Air Force.     

Identification of archaeal proteins that affect the exosome function in vitro

Background  

The archaeal exosome is formed by a hexameric RNase PH ring and three RNA binding subunits and has been shown to bind and degrade RNA in vitro. Despite extensive studies on the eukaryotic exosome and on the proteins interacting with this complex, little information is yet available on the identification and function of archaeal exosome regulatory factors.     

The effect of structural variation of alcohols on water solubilization in nonionic microemulsions 1. From linear to branched amphiphiles--general considerations

This article is the first part of a two-part study that exemplifies how to treat the solubilization of water in multicomponent surfactant-based systems. In particular, it aims at clarifying the role of cosurfactants in water solubilization in these systems. The judicious selection of the components in such systems to maximize water solubilization is occasionally thought to be dictated by the chain length compatibility principle, which may be expressed quantitatively by the BSO (Bansal, Shah, O'Connell) equation. Here we demonstrate some limitations of the equation. For example, in our best model system, C12(EO)8/dodecane+pentanol=1:1 (by weight)/water at 27+/-0.2 degrees C, the BSO equation predicts that no alcohol is needed for maximum water solubilization, contrary to our experimental findings. We discuss how to optimize the alcohol/oil weight ratio needed for stabilizing four-component microemulsions. In our model systems C12(EO)8 or C(18:1)(EO)10/pentanol/dodecane/water, this optimal weight ratio is 1:1. We also highlight the difference between the effect of normal alcohols on water solubilization-which passes via a maximum-and their effect on percolation processes and structured changes of proteins, which depends solely upon the alcohol hydrophobicity. For the investigation of the effect of branching on phase behavior the utilization of an extended form of the geometrical branching factor F(b) is suggested. The meaning of this factor is elucidated by comparing it with topological indices.     

Direct measurement of the flow field around swimming microorganisms

Swimming microorganisms create flows that influence their mutual interactions and modify the rheology of their suspensions. While extensively studied theoretically, these flows have not been measured in detail around any freely-swimming microorganism. We report such measurements for the microphytes Volvox carteri and Chlamydomonas reinhardtii. The minute (～0.3%) density excess of V. carteri over water leads to a strongly dominant Stokeslet contribution, with the widely-assumed stresslet flow only a correction to the subleading source dipole term. This implies that suspensions of V. carteri have features similar to suspensions of sedimenting particles. The flow in the region around C. reinhardtii where significant hydrodynamic interaction is likely to occur differs qualitatively from a puller stresslet, and can be described by a simple three-Stokeslet model.     

A Note On Subloop Lattices

Pálfy and Pudlák (Algebra Universalis 11, 22–27, 1980) posed the question: is every finite lattice isomorphic to an interval sublattice of the lattice of subgroups of a finite group? in this paper we will look at examples of lattices that can be realized as subloop lattices but not as subgroup lattices. This is a first step in answering a new question: is every finite lattice isomorphic to an interval sublattice of the subloop lattice of a finite loop?     

Invariant subspaces of a measure preserving transformation

We consider, in this note, some invariant subspaces of a unitary operator induced by a measure preserving transformation. For these subspaces two problems are studied:

1. a.
   Is the subspace generated by characteristic functions?