Signal set design for full-diversity low-decoding-complexity differential scaled-unitary STBCs

The problem of designing high rate, full diversity noncoherent space-time block codes (STBCs) with low encoding and decoding complexity is addressed. First, the notion of g-group encodable and g-group decodable linear STBCs is introduced. Then for a known class of rate-1 linear designs, an explicit construction of fully-diverse signal sets that lead to four-group encodable and four-group decodable differential scaled unitary STBCs for any power of two number of antennas is provided. Previous works on differential STBCs either sacrifice decoding complexity for higher rate or sacrifice rate for lower decoding complexity.

Low PAPR full-diversity space-frequency codes for MIMO-OFDM systems

Use of precoding transforms such as Hadamard Transforms and Phase Alteration for Peak to Average Power Ratio (PAPR) reduction in OFDM systems are well known. In this paper we propose use of Inverse Discrete Fourier Transform (IDFT) and Hadamard transform as precoding transforms in MIMO-OFDM systems to achieve low peak to average power ratio (PAPR). We show that while our approach using IDFT does not disturb the diversity gains of the MIMO-OFDM systems (spatial, temporal and frequency diversity gains), it offers a better trade-off between PAPR reduction and ML decoding complexity compared to that of the Hadamard transform precoding. We study in detail the amount of PAPR reduction achieved for the following two recently proposed full-diversity Space-Frequency coded MIMO-OFDM systems using both the IDFT and the Hadamard transform: (i) W. Su. Z. Safar, M. Olfat, K. J. R. Liu (IEEE Trans. on Signal Processing, Nov. 2003), and (ii) W. Su, Z. Safar, K. J. R. Liu (IEEE Trans. on Information Theory, Jan. 2005).

sRNAscanner: A Computational Tool for Intergenic Small RNA Detection in Bacterial Genomes

Background:Bacterial non-coding small RNAs (sRNAs) have attracted considerable attention due to their ubiquitous nature and contribution to numerous cellular processes including survival, adaptation and pathogenesis. Existing computational approaches for identifying bacterial sRNAs demonstrate varying levels of success and there remains considerable room for improvement. Methodology/Principal Findings: Here we have proposed a transcriptional signal-based computational method to identify intergenic sRNA transcriptional units (TUs) in completely sequenced bacterial genomes. Our sRNAscanner tool uses position weight matrices derived from experimentally defined E. coli K-12 MG1655 sRNA promoter and rho-independent terminator signals to identify intergenic sRNA TUs through sliding window based genome scans. Analysis of genomes representative of twelve species suggested that sRNAscanner demonstrated equivalent sensitivity to sRNAPredict2, the best performing bioinformatics tool available presently. However, each algorithm yielded substantial numbers of known and uncharacterized hits that were unique to one or the other tool only. sRNAscanner identified 118 novel putative intergenic sRNA genes in Salmonella enterica Typhimurium LT2, none of which were flagged by sRNAPredict2. Candidate sRNA locations were compared with available deep sequencing libraries derived from Hfq-co-immunoprecipitated RNA purified from a second Typhimurium strain (Sittka et al. (2008) PLoS Genetics 4: e1000163). Sixteen potential novel sRNAs computationally predicted and detected in deep sequencing libraries were selected for experimental validation by Northern analysis using total RNA isolated from bacteria grown under eleven different growth conditions. RNA bands of expected sizes were detected in Northern blots for six of the examined candidates. Furthermore, the 5'-ends of these six Northern-supported sRNA candidates were successfully mapped using 5'-RACE analysis. Conclusions/Significance: We have developed, computationally examined and experimentally validated the sRNAscanner algorithm. Data derived from this study has successfully identified six novel S. Typhimurium sRNA genes. In addition, the computational specificity analysis we have undertaken suggests that similar to 40% of sRNAscanner hits with high cumulative sum of scores represent genuine, undiscovered sRNA genes. Collectively, these data strongly support the utility of sRNAscanner and offer a glimpse of its potential to reveal large numbers of sRNA genes that have to date defied identification. sRNAscanner is available from: http://bicmku.in:8081/sRNAscanner or http://cluster.physics.iisc.ernet.in/sRNAscanner/.

A Low ML-Decoding Complexity, High Coding Gain, Full-Rate, Full-Diversity STBC for 4 x 2 MIMO System

This paper proposes a full-rate, full-diversity space-time block code(STBC) with low maximum likelihood (ML) decoding complexity and high coding gain for the 4 transmit antenna, 2 receive antenna (4 x 2) multiple-input multiple-output (MIMO) system that employs 4/16-QAM. For such a system, the best code known is the DjABBA code and recently, Biglieri, Hong and Viterbo have proposed another STBC (BHV code) for 4-QAM which has lower ML-decoding complexity than the DjABBA code but does not have full-diversity like the DjABBA code. The code proposed in this paper has the same ML-decoding complexity as the BHV code for any square M-QAM but has full-diversity for 4- and 16-QAM. Compared with the DjABBA code, the proposed code has lower ML-decoding complexity for square M-QAM constellation, higher coding gain for 4- and 16-QAM, and hence a better codeword error rate (CER) performance. Simulation results confirming this are presented.

High-yield bacterial expression and structural characterization of recombinant human insulin-like growth factor binding protein-2

The diverse biological activities of the insulin-like growth factors (IGF-1 and IGF-2) are mediated by the IGF-1 receptor (IGF-1R). These actions are modulated by a family of six IGF-binding proteins (ICFBP-1-6; 22-31 kDa) that via high affinity binding to the IGFs (K-D similar to 300-700 pM) both protect the IGFs in the circulation and attenuate IGF action by blocking their receptor access In recent years, IGFBPs have been implicated in a variety of cancers However, the structural basis of their interaction with IGFs and/or other proteins is not completely understood A critical challenge in the structural characterization of full-length IGFBPs has been the difficulty in expressing these proteins at levels suitable for NMR/X-ray crystallography analysis Here we describe the high-yield expression of full-length recombinant human IGFBP-2 (rhIGFBP-2) in Eschericha coli Using a single step purification protocol, rhIGFBP-2 was obtained with >95% purity and structurally characterized using NMR spectroscopy. The protein was found to exist as a monomer at the high concentrations required for structural studies and to exist in a single conformation exhibiting a unique intra-molecular disulfide-bonding pattern The protein retained full biologic activity. This study represents the first high-yield expression of wild-type recombinant human IGFBP-2 in E coli and first structural characterization of a full-length IGFBP (C) 2010 Elsevier Inc. All rights reserved

High-quality annotation of promoter regions for 913 bacterial genomes

Motivation: The number of bacterial genomes being sequenced is increasing very rapidly and hence, it is crucial to have procedures for rapid and reliable annotation of their functional elements such as promoter regions, which control the expression of each gene or each transcription unit of the genome. The present work addresses this requirement and presents a generic method applicable across organisms. Results: Relative stability of the DNA double helical sequences has been used to discriminate promoter regions from non-promoter regions. Based on the difference in stability between neighboring regions, an algorithm has been implemented to predict promoter regions on a large scale over 913 microbial genome sequences. The average free energy values for the promoter regions as well as their downstream regions are found to differ, depending on their GC content. Threshold values to identify promoter regions have been derived using sequences flanking a subset of translation start sites from all microbial genomes and then used to predict promoters over the complete genome sequences. An average recall value of 72% (which indicates the percentage of protein and RNA coding genes with predicted promoter regions assigned to them) and precision of 56% is achieved over the 913 microbial genome dataset.

DNA Binding, Coprotease, and Strand Exchange Activities of Mycobacterial RecA Proteins: Implications for Functional Diversity among RecA Nucleoprotein Filaments

One of the fundamental questions concerning homologous recombination is how RecA or its homologues recognize several DNA sequences with high affinity and catalyze all the diverse biological activities. In this study, we show that the extent of single-stranded DNA binding and strand exchange (SE) promoted by mycobacterial RecA proteins with DNA substrates having various degrees of GC content was comparable with that observed for Escherichia coli RecA. However, the rate and extent of SE promoted by these recombinases showed a strong negative correlation with increasing amounts of sequence divergence embedded at random across the length of the donor strand. Conversely, a positive correlation was seen between SE efficiency and the degree of sequence divergence in the recipient duplex DNA. The extent of heteroduplex formation was not significantly affected when both the pairing partners contained various degrees of sequence divergence, although there was a moderate decrease in the case of mycobacterial RecA proteins with substrates containing larger amounts of sequence divergence. Whereas a high GC content had no discernible effect on E. coli RecA coprotease activity, a negative correlation was apparent between mycobacterial RecA proteins and GC content. We further show clear differences in the extent of SE promoted by E. coli and mycobacterial RecA proteins in the presence of a wide range of ATP:ADP ratios. Taken together, our findings disclose the existence of functional diversity among E. coli and mycobacterial RecA nucleoprotein filaments, and the milieu of sequence divergence (i.e., in the donor or recipient) exerts differential effects on heteroduplex formation, which has implications for the emergence of new genetic variants.

Diversity in Functional Organization of Class I and Class II Biotin Protein Ligase

The cell envelope of Mycobacterium tuberculosis (M. tuberculosis) is composed of a variety of lipids including mycolic acids, sulpholipids, lipoarabinomannans, etc., which impart rigidity crucial for its survival and pathogenesis. Acyl CoA carboxylase (ACC) provides malonyl-CoA and methylmalonyl-CoA, committed precursors for fatty acid and essential for mycolic acid synthesis respectively. Biotin Protein Ligase (BPL/BirA) activates apo-biotin carboxyl carrier protein (BCCP) by biotinylating it to an active holo-BCCP. A minimal peptide (Schatz), an efficient substrate for Escherichia coli BirA, failed to serve as substrate for M. tuberculosis Biotin Protein Ligase (MtBPL). MtBPL specifically biotinylates homologous BCCP domain, MtBCCP87, but not EcBCCP87. This is a unique feature of MtBPL as EcBirA lacks such a stringent substrate specificity. This feature is also reflected in the lack of self/promiscuous biotinylation by MtBPL. The N-terminus/HTH domain of EcBirA has the selfbiotinable lysine residue that is inhibited in the presence of Schatz peptide, a peptide designed to act as a universal acceptor for EcBirA. This suggests that when biotin is limiting, EcBirA preferentially catalyzes, biotinylation of BCCP over selfbiotinylation. R118G mutant of EcBirA showed enhanced self and promiscuous biotinylation but its homologue, R69A MtBPL did not exhibit these properties. The catalytic domain of MtBPL was characterized further by limited proteolysis. Holo-MtBPL is protected from proteolysis by biotinyl-59 AMP, an intermediate of MtBPL catalyzed reaction. In contrast, apo-MtBPL is completely digested by trypsin within 20 min of co-incubation. Substrate selectivity and inability to promote self biotinylation are exquisite features of MtBPL and are a consequence of the unique molecular mechanism of an enzyme adapted for the high turnover of fatty acid biosynthesis.

A Low-Complexity, Full-Rate, Full-Diversity 2 x 2 STBC with Golden Code's Coding Gain

This paper presents a low-ML-decoding-complexity, full-rate, full-diversity space-time block code (STBC) for a 2 transmit antenna, 2 receive antenna multiple-input multiple-output (MIMO) system, with coding gain equal to that of the best and well known Golden code for any QAM constellation. Recently, two codes have been proposed (by Paredes, Gershman and Alkhansari and by Sezginer and Sari), which enjoy a lower decoding complexity relative to the Golden code, but have lesser coding gain. The 2 x 2 STBC presented in this paper has lesser decoding complexity for non-square QAM constellations, compared with that of the Golden code, while having the same decoding complexity for square QAM constellations. Compared with the Paredes-Gershman-Alkhansari and Sezginer-Sari codes, the proposed code has the same decoding complexity for non-rectangular QAM constellations. Simulation results, which compare the codeword error rate (CER) performance, are presented.

On the improvement of diversity-multiplexing gain tradeoff in a training based TDD-simo system

This paper investigates the diversity-multiplexing gain tradeoff (DMT) of a time-division duplex (TDD) single-input multiple-output (SIMO) system with perfect channel state information (CSI) at the receiver (CSIR) and partial CSI at the transmitter (CSIT). The partial CSIT is acquired through a training sequence from the receiver to the transmitter. The training sequence is chosen in an intelligent manner based on the CSIR, to reduce the training length by a factor of r, the number of receive antennas. We show that, for the proposed training scheme and a given channel coherence time, the diversity order increases linearly with r for nonzero multiplexing gain. This is a significant improvement over conventional orthogonal training schemes.

Detection of nif genes in nitrogen-fixing bacterial isolate from tomato (Lycopersicon esculentum Mill cv Pusa ruby)

Nitrogen-fixing bacterial isolate from the intercellular spaces of tomato root cortical cells was studied for the location of nif genes on the chromosomal or plasmid DNA. The bacterial isolate showed two plasmids of approximate molecular sizes of 220 and 120 kb. Klebsiella pneumoniae nif HDK probe hybridized with the chromosomal DNA and not with the plasmid DNA thereby showing that nif genes are localised on the chromosomal DNA.

Role of bacterial growth conditions and adhesion in the bioleaching of chalcopyrite by Thiobacillus ferrooxidans

The role of growth conditions and adhesion of Thiobacillus ferrooxidans on the leaching of chalcopyrite was investigated. Thiobacillus ferrooxidans grown on sulfur, thiosulfate and ferrous ion substrates was used in this comparative study. Growth on sulfur, a solid substrate, requires bacterial adhesion unlike that required in the presence of soluble thiosulfate and ferrous ion in a mineral-salts medium. Solid substrate-grown cells showed higher rates of leaching than those grown in liquid media. An initial lag period noticed during leaching by solution-grown cells was absent when solid substrate-grown cells were used. Such a behavior is attributed to the presence of an inducible proteinaceous cell-surface appendage on the sulfur-grown cells. This appendage aids in bacterial adhesion onto the mineral surfaces. Such an appendage is absent in solution-grown cells, as substantiated by electrophoretic measurements. The importance of bacterial adhesion and the direct mechanism in leaching by Thiobacillus ferrooxidans are demonstrated.