Negative Subtraction Hybridization: An efficient method to isolate large numbers of condition-specific cDNAs

BACKGROUND: The construction of cDNA libraries is a useful tool to understand gene expression in organisms under different conditions, but random sequencing of unbiased cDNA collections is laborious and can give rise to redundant EST collections. We aimed to isolate cDNAs of messages induced by switching Aspergillus nidulans from growth on glucose to growth on selected polysaccharides. Approximately 4,700 contigs from 12,320 ESTs were already available from a cDNA library representing transcripts isolated from glucose-grown A. nidulans during asexual development. Our goals were to expand the cDNA collection without repeated sequencing of previously identified ESTs and to find as many transcripts as possible that are specifically induced in complex polysaccharide metabolism. RESULTS: We have devised a Negative Subtraction Hybridization (NSH) method and tested it in A. nidulans. NSH entails screening a plasmid library made from cDNAs prepared from cells grown under a selected physiological condition with labeled cDNA probes prepared from another physiological condition. Plasmids with inserts that failed to hybridize to cDNA probes through two rounds of screening (i.e. negatives) indicate that they are transcripts present at low concentration in the labeled probe pool. Thus, these transcripts will be predominantly condition-specific, along with some rare transcripts. In a screen for transcripts induced by switching the carbon source from glucose to 12 selected polysaccharides, 3,532 negatives were isolated from approximately 100,000 surveyed colonies using this method. Negative clones were end-sequenced and assembled into 2,039 contigs, of which 1,722 were not present in the previously characterized glucose-grown cDNA library. Single-channel microarray hybridization experiments confirmed that the majority of the negatives represented genes that were differentially induced by a switch from growth in glucose to one or more of the polysaccharides. CONCLUSIONS: The Negative Subtraction Hybridization method described here has several practical benefits. This method can be used to screen any existing cDNA library, including full-length and pooled libraries, and does not rely on PCR or sequence information. In addition, NSH is a cost-effective method for the isolation of novel, full-length cDNAs for differentially expressed transcripts or enrichment of rare transcripts

Coupling between phonons and intrinsic Josephson oscillations in cuprate superconductors

The recently reported subgap structures observed in the current-voltage characteristic of intrinsic Josephson junctions in the high-T_c superconductors Tl_2Ba_2Ca_2Cu_3O_{10+\delta} and Bi_2Sr_2CaCu_2O_{8+\delta} are explained by the coupling between c-axis phonons and Josephson oscillations. A model is developed where c-axis lattice vibrations between adjacent superconducting multilayers are excited by the Josephson oscillations in a resistive junction. The voltages of the lowest structures correspond well to the frequencies of longitudinal c-axis phonons with large oscillator strength in the two materials, providing a new measurement technique for this quantity.Comment: 4 pages, 3 figures, revtex, aps, epsf, psfig. submitted to Physical Review Letters, second version improved in detai

Greenhouse gas emissions of bio-based diapers containing chemically modified protein superabsorbents

Replacing the current mainly fossil-based, disposable, and non-biodegradable sanitary products with sustainable, functional alternatives is an industry priority. Suggested biobased alternatives require evaluation of their actual impact on greenhouse gas (GHG) emissions. We evaluated GHG emissions of biobased baby diapers as the most consumed sanitary product, using a biodegradable functionalized protein superabsorbent polymer (bioSAP) and compared them with currently used fossil-based counterparts. Assessment of the diapers also included estimated GHG emissions from the production of the biobased components, transport, and end-of-life combustion of these items. It was shown that only a few of the biobased diaper alternatives resulted in lower GHG emissions than commercial diapers containing fossil-based materials. At the same time, it was demonstrated that the production of the bioSAP via chemical modification of a protein raw material is the primary GHG contributor, with 78% of the total emissions. Reduction of the GHG contribution of the bioSAP production was achieved via a proposed recycling route of the functionalization agent, reducing the GHG emissions by 13% than if no recycling was carried out. Overall, we demonstrated that reduced and competitive GHG emissions could be achieved in sanitary articles using biobased materials, thereby contributing to a sanitary industry producing disposable products with less environmental pollution while allowing customers to keep their current consumption patterns

Theory for the coupling between longitudinal phonons and intrinsic Josephson oscillations in layered superconductors

In this publication a microscopic theory for the coupling of intrinsic Josephson oscillations in layered superconductors with longitudinal c-axis-phonons is developed. It is shown that the influence of lattice vibrations on the c-axis transport can be fully described by introducing an effective longitudinal dielectric function. Resonances in the I-V-characteristic appear at van Hove singularities of both acoustical and optical longitudinal phonon branches. This provides a natural explanation of the recently discovered subgap structures in the I-V-characteristic of highly anisotropic cuprate superconductors. The effect of the phonon dispersion on the damping of these resonances and the coupling of Josephson oscillations in different resistive junctions due to phonons are discussed in detail.Comment: submitted to Phys. Rev. B, corrections following referee repor

Structure optimization effects on the electronic properties of Bi2_2Sr2_2CaCu2_2O8_8

We present detailed first-principles calculations for the normal state electronic properties of the high T$_C$ superconductor Bi$_2$Sr$_2$CaCu$_2$O$_8$, by means of the linearized augmented plane wave (LAPW) method within the framework of density functional theory (DFT). As a first step, the body centered tetragonal (BCT) cell has been adopted, and optimized regarding its volume, $c/a$ ratio and internal atomic positions by total energy and force minimizations. The full optimization of the BCT cell leads to small but visible changes in the topology of the Fermi surface, rounding the shape of CuO$_2$ barrels, and causing both the BiO bands, responsible for the pockets near the \textit{\=M} 2D symmetry point, to dip below the Fermi level. We have then studied the influence of the distortions in the BiO plane observed in nature by means of a $\sqrt{2}\times\sqrt{2}$ orthorhombic cell (AD-ORTH) with $Bbmb$ space group. Contrary to what has been observed for the Bi-2201 compound, we find that for Bi-2212 the distortion does not sensibly shift the BiO bands which retain their metallic character. As a severe test for the considered structures we present Raman-active phonon frequencies ($q = 0$) and eigenvectors calculated within the frozen-phonon approximation. Focussing on the totally symmetric A$_{g}$ modes, we observe that for a reliable attribution of the peaks observed in Raman experiments, both $c$- and a-axis vibrations must be taken into account, the latter being activated by the in-plane orthorhombic distortion.Comment: 22 pages, 4 figure

From Analogical Proportion to Logical Proportions

International audienceGiven a 4-tuple of Boolean variables (a, b, c, d), logical proportions are modeled by a pair of equivalences relating similarity indicators ( a∧b and a¯∧b¯), or dissimilarity indicators ( a∧b¯ and a¯∧b) pertaining to the pair (a, b), to the ones associated with the pair (c, d). There are 120 semantically distinct logical proportions. One of them models the analogical proportion which corresponds to a statement of the form “a is to b as c is to d”. The paper inventories the whole set of logical proportions by dividing it into five subfamilies according to what they express, and then identifies the proportions that satisfy noticeable properties such as full identity (the pair of equivalences defining the proportion hold as true for the 4-tuple (a, a, a, a)), symmetry (if the proportion holds for (a, b, c, d), it also holds for (c, d, a, b)), or code independency (if the proportion holds for (a, b, c, d), it also holds for their negations (a¯,b¯,c¯,d¯)). It appears that only four proportions (including analogical proportion) are homogeneous in the sense that they use only one type of indicator (either similarity or dissimilarity) in their definition. Due to their specific patterns, they have a particular cognitive appeal, and as such are studied in greater details. Finally, the paper provides a discussion of the other existing works on analogical proportions

Representing uncertainty regarding satisfaction degrees using possibility distributions

Evaluating flexible criteria on data leads to degrees of satisfaction. If a datum is uncertain, it can be uncertain to which degree it satisfies the criterion. This uncertainty can be modelled using a possibility distribution over the domain of possible degrees of satisfaction. In this work, we discuss the meaningfulness thereof by looking at the semantics of such a representation of the uncertainty. More specifically, it is shown that defuzzification of such a representation, towards usability in (multi-criteria) decision support systems, corresponds to expressing a clear attitude towards uncertainty (optimistic, pessimistic, cautious, etc.

C-axis lattice dynamics in Bi-based cuprate superconductors

We present results of a systematic study of the c axis lattice dynamics in single layer Bi2Sr2CuO6 (Bi2201), bilayer Bi2Sr2CaCu2O8 (Bi2212) and trilayer Bi2Sr2Ca2Cu3O10 (Bi2223) cuprate superconductors. Our study is based on both experimental data obtained by spectral ellipsometry on single crystals and theoretical calculations. The calculations are carried out within the framework of a classical shell model, which includes long-range Coulomb interactions and short-range interactions of the Buckingham form in a system of polarizable ions. Using the same set of the shell model parameters for Bi2201, Bi2212 and Bi2223, we calculate the frequencies of the Brillouin-zone center phonon modes of A2u symmetry and suggest the phonon mode eigenvector patterns. We achieve good agreement between the calculated A2u eigenfrequencies and the experimental values of the c axis TO phonon frequencies which allows us to make a reliable phonon mode assignment for all three Bi-based cuprate superconductors. We also present the results of our shell model calculations for the Gamma-point A1g symmetry modes in Bi2201, Bi2212 and Bi2223 and suggest an assignment that is based on the published experimental Raman spectra. The superconductivity-induced phonon anomalies recently observed in the c axis infrared and resonant Raman scattering spectra in trilayer Bi2223 are consistently explained with the suggested assignment.Comment: 29 pages, 13 figure

Systematics of c-axis Phonons in the Thallium and Bismuth Based Cuprate Superconductors

We present grazing incidence reflectivity measurements in the far infrared region at temperatures above and below Tc for a series of thallium (Tl2Ba2CuO6, Tl2Ba2CaCu2O8) and bismuth (Bi2Sr2CuO6, Bi2Sr2CaCu2O8, and Bi(2-x)Pb(x)Sr2CaCu2O8) based cuprate superconductors. From the spectra, which are dominated by the c-axis phonons, longitudinal frequencies (LO) are directly obtained. The reflectivity curves are well fitted by a series of Lorentz oscillators. In this way the transverse (TO) phonon frequencies were accurately determined. On the basis of the comparative study of the Bi and Tl based cuprates with different number of CuO2 layers per unit cell, we suggest modifications of the assignment of the main oxygen modes. We compare the LO frequencies in Bi2Sr2CaCu2O8 and Tl2Ba2Ca2Cu3O10 obtained from intrinsic Josephson junction characteristics with our measurements, and explain the discrepancy in LO frequencies obtained by the two different methods.Comment: 8 pages Revtex, 6 eps figures, 3 tables, to appear in Phys. Rev.

Correlation between the Josephson coupling energy and the condensation energy in bilayer cuprate superconductors

We review some previous studies concerning the intra-bilayer Josephson plasmons and present new ellipsometric data of the c-axis infrared response of almost optimally doped Bi_{2}Sr_{2}CaCu_{2}O_{8}. The c-axis conductivity of this compound exhibits the same kind of anomalies as that of underdoped YBa_{2}Cu_{3}O_{7-delta}. We analyze these anomalies in detail and show that they can be explained within a model involving the intra-bilayer Josephson effect and variations of the electric field inside the unit cell. The Josephson coupling energies of different bilayer compounds obtained from the optical data are compared with the condensation energies and it is shown that there is a reasonable agreement between the values of the two quantities. We argue that the Josephson coupling energy, as determined by the frequency of the intra-bilayer Josephson plasmon, represents a reasonable estimate of the change of the effective c-axis kinetic energy upon entering the superconducting state. It is further explained that this is not the case for the estimate based on the use of the simplest ``tight-binding'' sum rule. We discuss possible interpretations of the remarkable agreement between the Josephson coupling energies and the condensation energies. The most plausible interpretation is that the interlayer tunneling of the Cooper pairs provides the dominant contribution to the condensation energy of the bilayer compounds; in other words that the condensation energy of these compounds can be accounted for by the interlayer tunneling theory. We suggest an extension of this theory, which may also explain the high values of T_{c} in the single layer compounds Tl_{2}Ba_{2}CuO_{6} and HgBa_{2}CuO_{4}, and we make several experimentally verifiable predictions.Comment: 16 pages (including Tables) and 7 figures; accepted for publication in Physical Review