Selection for Catalytic Function with Nucleic Acids

For in vitro selection of catalytic polynucleotides, each new protocol must be designed to harness the desired catalytic activity to help propel the selection process itself. This unit gives guidelines for design of in vitro selection experiments for catalytic function. It outlines several representative protocols as examples of successful selection experiments, providing a conceptual basis for the design and implementation of new selective‐amplification protocols for nucleic acids.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143687/1/cpnc0904.pd

How robust is a 2SC quark matter phase under compact star constraints?

We study the phase structure and equation of state for two-flavor quark matter at low temperature under compact star constraints within a nonlocal chiral quark model. We find that the occurence of a two-flavor color superconducting (2SC) phase is sensitive to variations of both the formfactor of the interaction and the ratio \eta between the coupling constants in the diquark and the scalar meson channels. Our study suggests that for standard values of the coupling ratio 0.5<\eta<0.75 either the 2SC phase does not occur (Gaussian formfactor) or it exists only in a mixed phase with normal quark matter (NQ-2SC) with a volume fraction less than 20 - 40 %, occuring at high baryon chemical potentials \mu_B >1200 MeV and most likely not relevant for compact stars. We also present the relevant region of the phase diagram for compact star applications and obtain that no gapless 2SC occurs at low temperatures.Comment: 19 pages, 9 figures, Subsec.2.5: "Phase diagram" adde

SUSY Intertwining Relations of Third Order in Derivatives

The general solution of the intertwining relations between a pair of Schr\"odinger Hamiltonians by the supercharges of third order in derivatives is obtained. The solution is expressed in terms of one arbitrary function. Some properties of the spectrum of the Hamiltonian are derived, and wave functions for three energy levels are constructed. This construction can be interpreted as addition of three new levels to the spectrum of partner potential: a ground state and a pair of levels between successive excited states. Possible types of factorization of the third order supercharges are analysed, the connection with earlier known results is discussed.Comment: 17

A tissue-specific knockout reveals that Gata1 is not essential for Sertoli cell function in the mouse

The transcription factor Gata1 is essential for the development of erythroid cells. Consequently, Gata1 null mutants die in utero due to severe anaemia. Outside the haematopoietic system, Gata1 is only expressed in the Sertoli cells of the testis. To elucidate the function of Gata1 in the testis, we made a Sertoli cell-specific knockout of the Gata1 gene in the mouse. We deleted a normally functioning 'floxed' Gata1 gene in pre-Sertoli cells in vivo through the expression of Cre from a transgene driven by the Desert Hedgehog promoter. Surprisingly, Gata1 null testes developed to be morphologically normal, spermatogenesis was not obviously affected and expression levels of putative Gata1 target genes, and other Gata factors, were not altered. We conclude that expression of Gata1 in Sertoli cells is not essential for testis development or spermatogenesis in the mouse

Comparison of Spectra in Unsequenced Species

International audienceWe introduce a new algorithm for the mass spectromet- ric identication of proteins. Experimental spectra obtained by tandem MS/MS are directly compared to theoretical spectra generated from pro- teins of evolutionarily closely related organisms. This work is motivated by the need of a method that allows the identication of proteins of unsequenced species against a database containing proteins of related organisms. The idea is that matching spectra of unknown peptides to very similar MS/MS spectra generated from this database of annotated proteins can lead to annotate unknown proteins. This process is similar to ortholog annotation in protein sequence databases. The difficulty with such an approach is that two similar peptides, even with just one mod- ication (i.e. insertion, deletion or substitution of one or several amino acid(s)) between them, usually generate very dissimilar spectra. In this paper, we present a new dynamic programming based algorithm: Packet- SpectralAlignment. Our algorithm is tolerant to modications and fully exploits two important properties that are usually not considered: the notion of inner symmetry, a relation linking pairs of spectrum peaks, and the notion of packet inside each spectrum to keep related peaks together. Our algorithm, PacketSpectralAlignment is then compared to SpectralAlignment [1] on a dataset of simulated spectra. Our tests show that PacketSpectralAlignment behaves better, in terms of results and execution tim

Ferromagnetism and Canted Spin Phase in AlAs/GaMnAs Single Quantum Wells: Monte Carlo Simulation

The magnetic order resulting from a confinement-adapted Ruderman-Kittel-Kasuya-Yosida indirect exchange between magnetic moments in the metallic phase of a AlAs/Ga(1-x)Mn(x)As quantum well is studied by Monte Carlo simulation. This coupling mechanism involves magnetic moments and carriers (holes), both coming from the same Mn(2+) ions. It leads to a paramagnetic, a ferromagnetic, or a canted spin phase, depending on the carrier concentration, and on the magnetic layer width. It is shown that high transition temperatures may be obtained.Comment: 7 figure

How not to describe a species: lessons from a tangle of anacondas (Boidae: Eunectes Wagler, 1830)

A recent revision of the anacondas (Serpentes: Boidae: Eunectes), with the description of a new species of green anaconda, generated extensive publicity, but also provoked considerable controversy due to inadequacies of the evidence used and errors in nomenclature. We here use the case of this problematic publication to: (i) highlight common issues affecting species delimitations, especially an over-reliance on mitochondrial DNA data, and reiterate best practices; (ii) reanalyse the data available for anacondas to establish the true current state of knowledge and to highlight lines of further research; and (iii) analyse the nomenclatural history and status of the genus. While our analysis reveals significant morphological variation in both green and yellow anacondas, denser sampling and an analysis of informative nuclear markers are required for meaningful species delimitation in Eunectes. Tracing the history of name-bearing types establishes Trinidad as the type locality for Boa murina Linnaeus, 1758 and allows identification of the extant lectotype for the species. Finally, we emphasize the responsibility of both journals and authors to ensure that published taxonomic work meets the burden of evidence required to substantiate new species descriptions and that species are named in compliance with the rules of zoological nomenclature

Manganites at Quarter Filling: Role of Jahn-Teller Interactions

We have analyzed different correlation functions in a realistic spin-orbital model for half-doped manganites. Using a finite-temperature diagonalization technique the CE phase was found in the charge-ordered phase in the case of small antiferromagnetic interactions between $t_{2g}$ electrons. It is shown that a key ingredient responsible for stabilization of the CE-type spin and orbital-ordered state is the cooperative Jahn-Teller (JT) interaction between next-nearest Mn$^{+3}$ neighbors mediated by the breathing mode distortion of Mn$^{+4}$ octahedra and displacements of Mn$^{+4}$ ions. The topological phase factor in the Mn-Mn hopping leading to gap formation in one-dimensional models for the CE phase as well as the nearest neighbor JT coupling are not able to produce the zigzag chains typical for the CE phase in our model.Comment: 16 pages with 16 figures, contains a more detailed parameter estimate based on the structural data by Radaelli et al. (accepted for publication in Phys. Rev. B

Relation Between Chiral Susceptibility and Solutions of Gap Equation in Nambu--Jona-Lasinio Model

We study the solutions of the gap equation, the thermodynamic potential and the chiral susceptibility in and beyond the chiral limit at finite chemical potential in the Nambu--Jona-Lasinio (NJL) model. We give an explicit relation between the chiral susceptibility and the thermodynamic potential in the NJL model. We find that the chiral susceptibility is a quantity being able to represent the furcation of the solutions of the gap equation and the concavo-convexity of the thermodynamic potential in NJL model. It indicates that the chiral susceptibility can identify the stable state and the possibility of the chiral phase transition in NJL model.Comment: 21 pages, 6 figures, misprints are correcte