Interaction of ecoP15I DNA methyltransferase with oligonucleotides containing the asymmetric sequence 5?-CAGCAG-3

EcoP15I DNA methyltransferase (Mtase) recognizes the asymmeteric sequence CAGCAG and catalyzes the transfer of a methyl group from S-adenosyl-L-methionine to the second adenine residue. We have investigated the DNA binding properties of EcoP15I DNA Mtase using gel mobility shift assays. EcoP15I DNA Mtase binds approximately threefold more tightly to DNA containing its recognition sequence, CAGCAG, than to non-specific sequences in the absence or presence of cofactors. Interestingly, in the presence of ATP the discrimination between specific and non-specific sequences increases significantly. These results suggest for the first time a role for ATP in DNA recognition by type III restriction-modification enzymes. In addition, we have shown that bromodeoxyuridine-containing oligonucleotides form complexes with EcoP15I DNA Mtase that are crosslinked upon irradiation. More importantly, we have shown that the crosslink site is at the site of DNA binding, since it can be suppressed by an excess of unmodified oligonucleotide. EcoP15I DNA Mtase exhibited Michaelis-Menten kinetics with both unmodified and bromodeoxyuridine-substituted DNA, with a higher specificity constant for the latter. Furthermore, gel mobility shift assays showed that proteolyzed EcoP15I DNA Mtase formed a specific complex with DNA, which had similar mobility as the native protein-DNA complex. Taken together these results form the basis fora detailed structure-function analysis of EcoP15I DNA Mtase.

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.

Structural proteins of mycobacteriophage I3: cloning, expression and sequence analysis of a gene encoding a 70-kDa structural protein

The structural proteins of mycobacteriophage I3 have been analysed by sodium dodecyl sulfate-polyacrylamide-gel electrophoresis (SDS-PAGE), radioiodination and immunoblotting. Based on their abundance the 34- and 70-kDa bands appeared to represent the major structural proteins. Successful cloning and expression of the 70-kDa protein-encoding gene of phage I3 in Escherichia coli and its complete nucleotide sequence determination have been accomplished, A second (partial) open reading frame following the stop codon for the 70-kDa protein was also identified within the cloned fragment. The deduced amino-acid sequence of the 70-kDa protein and the codon usage patterns indicated the preponderance of codons, as predicted from the high G+C content of the genomic DNA of phage I3.

Structure and stability of human telomeric sequence

Telomeric DNA of a variety of vertebrates including humans contains the tandem repeat d(TTAGGG)(n). We have investigated the structural properties of the human telomeric repeat oligonucleotide models d(T(2)AG(3))(4), d(G(3)T(2)A)(3)G(3), and d(G(3)T(2)AG(3)) using CD, gel electrophoresis, and chemical probing techniques. The sequences d(G(3)T(2)A)(3)G(3) and d(T(2)AG(3))(4) assume an antiparallel G quartet structure by intramolecular folding, while the sequence d(G(3)T(2)AG(3)) also adopts an antiparallel G quartet structure but by dimerization of hairpins. In all the above cases, adenines are in the loop. The TTA loops are oriented at the same end of the G tetrad stem in the case of hairpin dimer. Further, the oligonucleotide D(G(3)T(2)AG(3)) forms a higher order structure by the association of two hairpin dimers via stacking of G tetrad planes. Here we show that N-7 of adenine in the hairpin dimer is Hoogsteen hydrogen-bonded. The partial reactivity of loop adenines with DEPC in d(T(2)AG(3))(4) suggests that the intramolecular G quartet structure is highly polymorphic and structures with different loop orientations and topologies are formed in solution. Intra- and interloop hydrogen bonding schemes for the TTA loops are proposed to account for the observed diethyl pyrocarbonate reactivities of adenines. Sodium-induced G quartet structures differ from their potassium-induced counterparts not only in stability but also in loop conformation and interactions. Thus, the overall structure and stability of telomeric sequences are modulated by the cation present, loop sequence, and the number of G tracts, which might be important for the telomere function.

The cDNA sequence of cytochrome b5 associated with cytokinin-induced haustoria formation in Cuscuta reflexa

A cDNA clone isolated by differentially screening a cytokinin-induced haustorial cDNA library of Cuscuta reflexa was sequenced and identified as the gene coding for cytochrome b(5), based on the similarity of the deduced amino-acid sequence with that of the cauliflower (60% identity) and tobacco (78% identity) proteins. The 5'-UTR is unusually long (720 bp) and contains 14 potential start codons (ATG) and 10 short ORFs.

Parasite abundance and diversity in mammals: correlates with host ecology

Fecally dispersed parasites of 12 wild mammal species in Mudumalai Sanctuary, southern India, were studied, Fecal propagule densities and parasite diversity measures were correlated with host ecological variables. Host species with higher predatory pressure had lower parasite loads and parasite diversity. Host body weight, home range, population density, gregariousness, and diet did not show predicted effects on parasite loads. Measures of a! diversity were positively correlated with parasite abundance and were negatively correlated with beta diversity, Based on these data, hypotheses regarding determinants of parasite community are discussed.

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.

Isomerisation of 4-aryl-4-methylhex-5-en-2-ones to 5-aryl-4-methylhex-5-en-2-ones by an intramolecular ene-retro ene reaction sequence

Acid-catalysed thermal rearrangement of 4-aryl-4-methylhex-5-en-2-ones (products of the Claisen rearrangement of beta-methylcinnamyl alcohols and 2-methoxypropene) to isomeric 5-aryl-4-methylhex-5-en-2-ones via an intramolecular ene reaction of the enol tautomer followed by a retro ene reaction of the resultant acetylcyclopropane is described. Formation of the known diketone 13 via the ozonolysis of the rearrangement product 10, confirmed the structures of the rearranged enones, whereas formation of the enone 15 containing an extra methyl group on the styrene double bond confirmed the proposed mechanism. Finally, the rearrangement has been extended to the formal synthesis of beta-cuparenone 20 via the enones 22 and 23.

Stochastic dynamics modeling of the protein sequence length distribution in genomes: implications for microbial evolution

In this paper, we report an analysis of the protein sequence length distribution for 13 bacteria, four archaea and one eukaryote whose genomes have been completely sequenced, The frequency distribution of protein sequence length for all the 18 organisms are remarkably similar, independent of genome size and can be described in terms of a lognormal probability distribution function. A simple stochastic model based on multiplicative processes has been proposed to explain the sequence length distribution. The stochastic model supports the random-origin hypothesis of protein sequences in genomes. Distributions of large proteins deviate from the overall lognormal behavior. Their cumulative distribution follows a power-law analogous to Pareto's law used to describe the income distribution of the wealthy. The protein sequence length distribution in genomes of organisms has important implications for microbial evolution and applications. (C) 1999 Elsevier Science B.V. All rights reserved.

A New Full-diversity Criterion and Low-complexity STBCs with Partial Interference Cancellation Decoding

Recently, Guo and Xia gave sufficient conditions for an STBC to achieve full diversity when a PIC (Partial Interference Cancellation) or a PIC-SIC (PIC with Successive Interference Cancellation) decoder is used at the receiver. In this paper, we give alternative conditions for an STBC to achieve full diversity with PIC and PIC-SIC decoders, which are equivalent to Guo and Xia's conditions, but are much easier to check. Using these conditions, we construct a new class of full diversity PIC-SIC decodable codes, which contain the Toeplitz codes and a family of codes recently proposed by Zhang, Xu et. al. as proper subclasses. With the help of the new criteria, we also show that a class of PIC-SIC decodable codes recently proposed by Zhang, Shi et. al. can be decoded with much lower complexity than what is reported, without compromising on full diversity.

On the diversity and complexity of Zero Forcing receivers for MIMO Zero Padded systems

Zero padded systems with linear receivers are shown to be robust and amenable to fast implementations in single antenna scenarios. In this paper, properties of such systems are investigated when multiple antennas are present at both ends of the communication link. In particular, their diversity and complexity are evaluated for precoded transmissions. The linear receivers are shown to exploit multipath and receive diversities, even in the absence of any coding at the transmitter. Use of additional redundancy to improve performance is considered and the effect of transmission rate on diversity order is analyzed. Low complexity implementations of Zero Forcing receivers are devised to further enhance their applicability.

On the Impact of MIMO Diversity on Higher Layer Performance

In this paper, we shed light on the cross-layer interactions between the PHY, link and routing layers in networks with MIMO links operating in the diversity mode. Many previous studies assume an overly simplistic PHY layer model that does not sufficiently capture these interactions. We show that the use of simplistic models can in fact lead to misleading conclusions with regards to the higher layer performance with MIMO diversity. Towards understanding the impact of various PHY layer features on MIMO diversity, we begin with a simple but widely-used model and progressively incorporate these features to create new models. We examine the goodness of these models by comparing the simulated performance results with each, with measurements on an indoor 802.11 n testbed. Our work reveals several interesting cross-layer dependencies that affect the gains due to MIMO diversity. In particular, we observe that relative to SISO links: (a) PHY layer gains due to MIMO diversity do not always carry over to the higher layers, (b) the use of other PHY layer features such as FEC codes significantly influence the gains due to MIMO diversity, and (c) the choice of the routing metric can impact the gains possible with MIMO.