DNA Condensation by the Rat Spermatidal Protein TP2 Shows GC-Rich Sequence Preference and Is Zinc Dependent

Transition protein-2 (TP2), isolated from rat testes, was recently shown to be a zinc metalloprotein. We have now carried out a detailed analysis of the DNA condensing properties of TP2 with various polynucleotides using circular dichroism spectroscopy. The condensation of the alternating copolymers by TP2 (incubated with 10 mu M ZnSO4), namely, poly(dG-dC). poly(dG-dC) and poly(dA-dT). poly(dA-dT), was severalfold higher than condensation of either of the homoduplexes poly(dG). poly-(dC) and poly(dA). poly(dT) or rat oligonucleosomal DNA. Between the two alternating copolymers, poly(dG-dC). poly(dG-dC) was condensed 3.2-fold more effectively than poly(dA-dT). poly(dA-dT). Preincubation of TP2 with 5 mM EDTA significantly reduced its DNA-condensing property. Interestingly, condensation of the alternating copolymer poly(dI-dC). poly(dI-dC) by TP2 was much less as compared to that of poly(dG-dC). poly(dG-dC). The V8 protease-derived N-terminal fragment (88 aa) condensed poly(dA-dT). poly(dA-dT) to a very small extent but did not have any effect on poly(dG-dC). poly-(dG-dC). The C-terminal fragment (28 aa) was able to condense poly(dA-dT) . poly(dA-dT) more effectively than poly(dG-dC). poly(dG-dC). These results suggest that TP2 in its zinc-coordinated form condenses GC-rich polynucleotides much more effectively than other types of polynucleotides. Neither the N-terminal two-thirds of TP2 which is the zinc-binding domain nor the C-terminal basic domain are as effective as intact TP2 in bringing about condensation of DNA.

Preferential condensation of SAR-DNA by histone H1 and its SPKK containing octapeptide repeat motif

Linker histone H1 binds preferentially the scaffold associated region (SAR) DNA elements that contain characteristic oligo dA . dT tracts. In the present study, we have compared the condensation brought about by histone H1 of a SAR DNA fragment in the histone spacer region of Drosophila melanogaster with that of a random DNA (pBR322 EcoRI-SalI) fragment by circular dichroism spectroscopy. The condensation of the SAR DNA fragment by histone H1 is 3-4-fold higher than that of the random DNA fragment. A 16-mer peptide, ATPKKSTKKTPKKAKK, the sequence that is present in the C-terminus of histone H1d, which has recently been shown to possess DIVA and chromatin condensing properties, also condenses the SAR DNA fragment preferentially in a highly cooperative manner. We have proposed a model for the dynamics of chromatin structure involving histone H1-SAR DNA interaction through SPKK containing peptide motifs and its competition by AT-hook peptides present in the nonhistone chromosomal proteins like HMG-I and HMG-Y.

Training-Embedded, Single-Symbol ML-Decodable, Distributed STBCs for Relay Networks

Recently, a special class of complex designs called Training-Embedded Complex Orthogonal Designs (TE-CODs) has been introduced to construct single-symbol Maximum Likelihood decodable (SSD) distributed space-time block codes (DSTBCs) for two-hop wireless relay networks using the amplify and forward protocol. However, to implement DSTBCs from square TE-CODs, the overhead due to the transmission of training symbols becomes prohibitively large as the number of relays increase. In this paper, we propose TE-Coordinate Interleaved Orthogonal Designs (TE-CIODs) to construct SSD DSTBCs. Exploiting the block diagonal structure of TE-CIODs, we show that the overhead due to the transmission of training symbols to implement DSTBCs from TE-CIODs is smaller than that for TE-CODs. We also show that DSTBCs from TE-CIODs offer higher rate than those from TE-CODs for identical number of relays while maintaining the SSD and full-diversity properties.

Performance analysis of single-symbol maximum likelihood decodable linear STBCs

Performance of space-time block codes can be improved using the coordinate interleaving of the input symbols from rotated M-ary phase shift keying (MPSK) and M-ary quadrature amplitude modulation (MQAM) constellations. This paper is on the performance analysis of coordinate-interleaved space-time codes, which are a subset of single-symbol maximum likelihood decodable linear space-time block codes, for wireless multiple antenna terminals. The analytical and simulation results show that full diversity is achievable. Using the equivalent single-input single-output model, simple expressions for the average bit error rates are derived over flat uncorrelated Rayleigh fading channels. Optimum rotation angles are found by finding the minimum of the average bit error rate curves.

Single real-symbol decodable, high-rate, distributed space-time block codes

A scheme to apply the rate-1 real orthogonal designs (RODs) in relay networks with single real-symbol decodability of the symbols at the destination for any arbitrary number of relays is proposed. In the case where the relays do not have any information about the channel gains from the source to themselves, the best known distributed space time block codes (DSTBCs) for k relays with single real-symbol decodability offer an overall rate of complex symbols per channel use. The scheme proposed in this paper offers an overall rate of 2/2+k complex symbol per channel use, which is independent of the number of relays. Furthermore, in the scenario where the relays have partial channel information in the form of channel phase knowledge, the best known DSTBCs with single real-symbol decodability offer an overall rate of 1/3 complex symbols per channel use. In this paper, making use of RODs, a scheme which achieves the same overall rate of 1/3 complex symbols per channel use but with a decoding delay that is 50 percent of that of the best known DSTBCs, is presented. Simulation results of the symbol error rate performance for 10 relays, which show the superiority of the proposed scheme over the best known DSTBC for 10 relays with single real-symbol decodability, are provided.

Pruned Universal Symbol Sequences for LZW based Language identification

We present a improved language modeling technique for Lempel-Ziv-Welch (LZW) based LID scheme. The previous approach to LID using LZW algorithm prepares the language pattern table using LZW algorithm. Because of the sequential nature of the LZW algorithm, several language specific patterns of the language were missing in the pattern table. To overcome this, we build a universal pattern table, which contains all patterns of different length. For each language it's corresponding language specific pattern table is constructed by retaining the patterns of the universal table whose frequency of appearance in the training data is above the threshold.This approach reduces the classification score (Compression Ratio [LZW-CR] or the weighted discriminant score[LZW-WDS]) for non native languages and increases the LID performance considerably.

The advection-condensation model and water-vapour probability density functions

The statistically steady humidity distribution resulting from an interaction of advection, modelled as an uncorrelated random walk of moist parcels on an isentropic surface, and a vapour sink, modelled as immediate condensation whenever the specific humidity exceeds a specified saturation humidity, is explored with theory and simulation. A source supplies moisture at the deep-tropical southern boundary of the domain and the saturation humidity is specified as a monotonically decreasing function of distance from the boundary. The boundary source balances the interior condensation sink, so that a stationary spatially inhomogeneous humidity distribution emerges. An exact solution of the Fokker-Planck equation delivers a simple expression for the resulting probability density function (PDF) of the wate-rvapour field and also the relative humidity. This solution agrees completely with a numerical simulation of the process, and the humidity PDF exhibits several features of interest, such as bimodality close to the source and unimodality further from the source. The PDFs of specific and relative humidity are broad and non-Gaussian. The domain-averaged relative humidity PDF is bimodal with distinct moist and dry peaks, a feature which we show agrees with middleworld isentropic PDFs derived from the ERA interim dataset. Copyright (C) 2011 Royal Meteorological Society

Training-Symbol Embedded, High-Rate, Single-Symbol ML-Decodable, Distributed STBCs for Relay Networks

Distributed space-time block codes (DSTBCs) from complex orthogonal designs (CODs) (both square and nonsquare), coordinate interleaved orthogonal designs (CIODs), and Clifford unitary weight designs (CUWDs) are known to lose their single-symbol ML decodable (SSD) property when used in two-hop wireless relay networks using amplify and forward protocol. For such networks, in this paper, three new classes of high rate, training-symbol embedded (TSE) SSD DSTBCs are constructed: TSE-CODs, TSE-CIODs, and TSE-CUWDs. The proposed codes include the training symbols inside the structure of the code which is shown to be the key point to obtain the SSD property along with the channel estimation capability. TSE-CODs are shown to offer full-diversity for arbitrary complex constellations and the constellations for which TSE-CIODs and TSE-CUWDs offer full-diversity are characterized. It is shown that DSTBCs from nonsquare TSE-CODs provide better rates (in symbols per channel use) when compared to the known SSD DSTBCs for relay networks. Important from the practical point of view, the proposed DSTBCs do not contain any zeros in their codewords and as a result, antennas of the relay nodes do not undergo a sequence of switch on/off transitions within every codeword, and, thus, avoid the antenna switching problem.

Maximum rate of 3- and 4-real-symbol ML decodable unitary weight STBCs

It has been shown recently that the maximum rate of a 2-real-symbol (single-complex-symbol) maximum likelihood (ML) decodable, square space-time block codes (STBCs) with unitary weight matrices is 2a/2a complex symbols per channel use (cspcu) for 2a number of transmit antennas [1]. These STBCs are obtained from Unitary Weight Designs (UWDs). In this paper, we show that the maximum rates for 3- and 4-real-symbol (2-complex-symbol) ML decodable square STBCs from UWDs, for 2a transmit antennas, are 3(a-1)/2a and 4(a-1)/2a cspcu, respectively. STBCs achieving this maximum rate are constructed. A set of sufficient conditions on the signal set, required for these codes to achieve full-diversity are derived along with expressions for their coding gain.

Maximum Rate of Unitary-Weight, Single-Symbol Decodable STBCs

It is well known that the space-time block codes (STBCs) from complex orthogonal designs (CODs) are single-symbol decodable/symbol-by-symbol decodable (SSD). The weight matrices of the square CODs are all unitary and obtainable from the unitary matrix representations of Clifford Algebras when the number of transmit antennas n is a power of 2. The rate of the square CODs for n = 2(a) has been shown to be a+1/2(a) complex symbols per channel use. However, SSD codes having unitary-weight matrices need not be CODs, an example being the minimum-decoding-complexity STBCs from quasi-orthogonal designs. In this paper, an achievable upper bound on the rate of any unitary-weight SSD code is derived to be a/2(a)-1 complex symbols per channel use for 2(a) antennas, and this upper bound is larger than that of the CODs. By way of code construction, the interrelationship between the weight matrices of unitary-weight SSD codes is studied. Also, the coding gain of all unitary-weight SSD codes is proved to be the same for QAM constellations and conditions that are necessary for unitary-weight SSD codes to achieve full transmit diversity and optimum coding gain are presented.

Single-Molecule DNA Analysis Reveals That Yeast Hop1 Protein Promotes DNA Folding and Synapsis: Implications for Condensation of Meiotic Chromosomes

During meiosis, long-range interaction between homologous chromosomes is thought to be crucial for homology recognition, exchange of DNA strands, and production of normal haploid gametes. However, little is known about the identity of the proteins involved and the actual molecular mechanism(s) by which chromosomes recognize and recombine with their appropriate homologous partners. Single-molecule analyses have the potential to provide insights into our understanding of this fascinating and long-standing question. Using atomic force microscopy and magnetic tweezers techniques, we discovered that Hop1 protein, a key structural component of Saccharomyces cerevisiae synaptonemal complex, exhibits the ability to bridge noncontiguous DNA segments into intramolecular stem-loop structures in which the DNA segments appear to be fully synapsed within the filamentous protein stems. Additional evidence suggests that Hop1 folds DNA into rigid protein DNA filaments and higher-order nucleoprotein structures. Importantly, Hop1 promotes robust intra- and intermolecular synapsis between double-stranded DNA molecules, suggesting that juxtaposition of DNA sequences may assist in strand exchange between homologues by recombination-associated proteins. Finally, the evidence from ensemble experiments is consistent with the notion that Hop1 causes rigidification of DNA molecules. These results provide the first direct evidence for long-range protein-mediated DNA DNA synapsis, independent of crossover recombination, which is presumed to occur during meiotic recombination.