Bacterial transformation using micro-shock waves

Shock waves are one of the most competent mechanisms of energy dissipation observed in nature. We have developed a novel device to generate controlled micro-shock waves using an explosive-coated polymer tube. In this study, we harnessed these controlled micro-shock waves to develop a unique bacterial transformation method. The conditions were optimized for the maximum transformation efficiency in Escherichia coli. The maximum transformation efficiency was obtained when we used a 30 cm length polymer tube, 100 mu m thick metal foil, 200 mM CaCl(2), 1 ng/mu l plasmid DNA concentration, and 1 x 10(9) cell density. The highest transformation efficiency achieved (1 x 10(-5) transformants/cell) was at least 10 times greater than the previously reported ultrasound-mediated transformation (1 x 10(-6) transformants/cell). This method was also successfully employed for the efficient and reproducible transformation of Pseudomonas aeruginosa and Salmonella typhimurium. This novel method of transformation was shown to be as efficient as electroporation with the added advantage of better recovery of cells, reduced cost (40 times cheaper than a commercial electroporator), and growth phase independent transformation. (C) 2011 Elsevier Inc. All rights reserved.

A Low ML-Decoding Complexity, Full-Diversity, Full-Rate MIMO Precoder

Precoding for multiple-input multiple-output (MIMO) antenna systems is considered with perfect channel knowledge available at both the transmitter and the receiver. For two transmit antennas and QAM constellations, a real-valued precoder which is approximately optimal (with respect to the minimum Euclidean distance between points in the received signal space) among real-valued precoders based on the singular value decomposition (SVD) of the channel is proposed. The proposed precoder is obtainable easily for arbitrary QAM constellations, unlike the known complex-valued optimal precoder by Collin et al. for two transmit antennas which is in existence for 4-QAM alone and is extremely hard to obtain for larger QAM constellations. The proposed precoding scheme is extended to higher number of transmit antennas on the lines of the E - d(min) precoder for 4-QAM by Vrigneau et al. which is an extension of the complex-valued optimal precoder for 4-QAM. The proposed precoder's ML-decoding complexity as a function of the constellation size M is only O(root M)while that of the E - d(min) precoder is O(M root M)(M = 4). Compared to the recently proposed X- and Y-precoders, the error performance of the proposed precoder is significantly better while being only marginally worse than that of the E - d(min) precoder for 4-QAM. It is argued that the proposed precoder provides full-diversity for QAM constellations and this is supported by simulation plots of the word error probability for 2 x 2, 4 x 4 and 8 x 8 systems.

Collocated and Distributed STBCs with Partial Interference Cancellation Decoding, Part I: Full-Diversity Criterion

Low complexity decoders called Partial Interference Cancellation (PIC) and PIC with Successive Interference Cancellation (PIC-SIC), which include the Zero Forcing (ZF) and ZF-SIC receivers as special cases, were given by Guo and Xia along with sufficient conditions for a Space-Time Block Code (STBC) to achieve full diversity with PIC/PIC-SIC decoding for point-to-point MIMO channels. In Part-I of this two part series of papers, we give new 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. We then show that PIC and PIC-SIC decoders are capable of achieving the full cooperative diversity available in wireless relay networks and give sufficient conditions for a Distributed Space-Time Block Code (DSTBC) to achieve full diversity with PIC and PIC-SIC decoders. In Part-II, we construct new low complexity full-diversity PIC/PIC-SIC decodable STBCs and DSTBCs that achieve higher rates than the known full-diversity low complexity ML decodable STBCs and DSTBCs.

Asymptotically-Optimal, Fast-Decodable, Full-Diversity STBCs

For a family/sequence of Space-Time Block Codes (STBCs) C1, C2,⋯, with increasing number of transmit antennas Ni, with rates Ri complex symbols per channel use (cspcu), i = 1,2,⋯, the asymptotic normalized rate is defined as limi→∞ Ri/Ni. A family of STBCs is said to be asymptotically-good if the asymptotic normalized rate is non-zero, i.e., when the rate scales as a non-zero fraction of the number of transmit antennas, and the family of STBCs is said to be asymptotically-optimal if the asymptotic normalized rate is 1, which is the maximum possible value. In this paper, we construct a new class of full-diversity STBCs that have the least maximum-likelihood (ML) decoding complexity among all known codes for any number of transmit antennas N>;1 and rates R>;1 cspcu. For a large set of (R,N) pairs, the new codes have lower ML decoding complexity than the codes already available in the literature. Among the new codes, the class of full-rate codes (R=N) are asymptotically-optimal and fast-decodable, and for N>;5 have lower ML decoding complexity than all other families of asymptotically-optimal, fast-decodable, full-diversity STBCs available in the literature. The construction of the new STBCs is facilitated by the following further contributions of this paper: (i) Construction of a new class of asymptotically-good, full-diversity multigroup ML decodable codes, that not only includes STBCs for a larger set of antennas, but also either matches in rate or contains as a proper subset all other high-rate or asymptotically-good, delay-optimal, multigroup ML decodable codes available in the literature. (ii) Construction of a new class of fast-group-decodable codes (codes that combine the low ML decoding complexity properties of multigroup ML decodable codes and fast-decodable codes) for all even number of transmit antennas and rates 1 <; R ≤ 5/4.- - (iii) Given a design with full-rank linear dispersion matrices, we show that a full-diversity STBC can be constructed from this design by encoding the real symbols independently using only regular PAM constellations.

Modulation Diversity in Fading Channels with a Quantized Receiver

In this paper, we address the design of codes which achieve modulation diversity in block fading single-input single-output (SISO) channels with signal quantization at the receiver. With an unquantized receiver, coding based on algebraic rotations is known to achieve maximum modulation coding diversity. On the other hand, with a quantized receiver, algebraic rotations may not guarantee gains in diversity. Through analysis, we propose specific rotations which result in the codewords having equidistant component-wise projections. We show that the proposed coding scheme achieves maximum modulation diversity with a low-complexity minimum distance decoder and perfect channel knowledge. Relaxing the perfect channel knowledge assumption we propose a novel channel training/estimation technique to estimate the channel. We show that our coding/training/estimation scheme and minimum distance decoding achieves an error probability performance similar to that achieved with perfect channel knowledge.

Surface chemical and adsorption studies using Thiobacillus ferrooxidans with reference to bacterial adhesion to sulfide minerals

Adhesion of Thiobacillus ferrooxidans to pyrite and chalcopyrite in relation to its importance in bioleaching and bioflotation has been studied. Electrokinetic studies as well as FT-IR spectra suggest that the surface chemistry of Thiobacillus ferrooxidans depends on bacterial growth conditions. Sulfur-,Pyrite- and chalcopyrite-grown Thiobacillus ferrooxidans were found to be relatively more hydrophobic. The altered surface chemistry of Thiobacillus ferrooxidans was due to secretion of newer and specific proteinaceous compounds. The adsorption density corresponds to a monolayer coverage in a horizontal orientation of the cells. The xanthate flotation of pyrite in presence of Thiobacillus ferrooxidans is strongly depressed where as the cells have insignificant effect on chalcopyrite flotation. This study demonstrate that: (a)Thiobacillus ferrooxidans cells can be used for selective flotation of chalcopyrite from pyrite and importantly at natural pH values. (b)Sulfur-grown cells exhibits higher leaching kinetics than ferrous ion-grown cells.

Deorphanization of Malonyl CoA:ACP Transacylase Drug Target in Plasmodium falciparum (PfFabD) Using Bacterial Antagonists: A Piggyback' Approach for Antimalarial Drug Discovery

Quest for new drug targets in Plasmodium sp. has underscored malonyl CoA:ACP transacylase (PfFabD) of fatty acid biosynthetic pathway in apicoplast. In this study, a piggyback approach was employed for the receptor deorphanization using inhibitors of bacterial FabD enzymes. Due to the lack of crystal structure, theoretical model was constructed using the structural details of homologous enzymes. Sequence and structure analysis has localized the presence of two conserved pentapeptide motifs: GQGXG and GXSXG and five key invariant residues viz., Gln109, Ser193, Arg218, His305 and Gln354 characteristic of FabD enzyme. Active site mapping of PfFabD using substrate molecules has disclosed the spatial arrangement of key residues in the cavity. As structurally similar molecules exhibit similar biological activities, signature pharmacophore fingerprints of FabD antagonists were generated using 0D-3D descriptors for molecular similarity-based cluster analysis and to correlate with their binding profiles. It was observed that antagonists showing good geometrical fitness score were grouped in cluster-1, whereas those exhibiting high binding affinities in cluster-2. This study proves important to shed light on the active site environment to reveal the hotspot for binding with higher affinity and to narrow down the virtual screening process by searching for close neighbors of the active compounds.

Hydration dynamics of protein molecules in aqueous solution: Unity among diversity

Dielectric dispersion and NMRD experiments have revealed that a significant fraction of water molecules in the hydration shell of various proteins do not exhibit any slowing down of dynamics. This is usually attributed to the presence of the hydrophobic residues (HBR) on the surface, although HBRs alone cannot account for the large amplitude of the fast component. Solvation dynamics experiments and also computer simulation studies, on the other hand, repeatedly observed the presence of a non-negligible slow component. Here we show, by considering three well-known proteins (lysozyme, myoglobin and adelynate kinase), that the fast component arises partly from the response of those water molecules that are hydrogen bonded with the backbone oxygen (BBO) atoms. These are structurally and energetically less stable than those with the side chain oxygen (SCO) atoms. In addition, the electrostatic interaction energy distribution (EIED) of individual water molecules (hydrogen bonded to SCO) with side chain oxygen atoms shows a surprising two peak character with the lower energy peak almost coincident with the energy distribution of water hydrogen bonded to backbone oxygen atoms (BBO). This two peak contribution appears to be quite general as we find it for lysozyme, myoglobin and adenylate kinase (ADK). The sharp peak of EIED at small energy (at less than 2 k(B)T) for the BBO atoms, together with the first peak of EIED of SCO and the HBRs on the protein surface, explain why a large fraction (similar to 80%) of water in the protein hydration layer remains almost as mobile as bulk water Significant slowness arises only from the hydrogen bonds that populate the second peak of EIED at larger energy (at about 4 k(B)T). Thus, if we consider hydrogen bond interaction alone, only 15-20% of water molecules in the protein hydration layer can exhibit slow dynamics, resulting in an average relaxation time of about 5-10 ps. The latter estimate assumes a time constant of 20-100 ps for the slow component. Interestingly, relaxation of water molecules hydrogen bonded to back bone oxygen exhibit an initial component faster than the bulk, suggesting that hydrogen bonding of these water molecules remains frustrated. This explanation of the heterogeneous and non-exponential dynamics of water in the hydration layer is quantitatively consistent with all the available experimental results, and provides unification among diverse features.

The Contribution of Rare Species to Community Phylogenetic Diversity across a Global Network of Forest Plots

Niche differentiation has been proposed as an explanation for rarity in species assemblages. To test this hypothesis requires quantifying the ecological similarity of species. This similarity can potentially be estimated by using phylogenetic relatedness. In this study, we predicted that if niche differentiation does explain the co-occurrence of rare and common species, then rare species should contribute greatly to the overall community phylogenetic diversity (PD), abundance will have phylogenetic signal, and common and rare species will be phylogenetically dissimilar. We tested these predictions by developing a novel method that integrates species rank abundance distributions with phylogenetic trees and trend analyses, to examine the relative contribution of individual species to the overall community PD. We then supplement this approach with analyses of phylogenetic signal in abundances and measures of phylogenetic similarity within and between rare and common species groups. We applied this analytical approach to 15 long-term temperate and tropical forest dynamics plots from around the world. We show that the niche differentiation hypothesis is supported in six of the nine gap-dominated forests but is rejected in the six disturbance-dominated and three gap-dominated forests. We also show that the three metrics utilized in this study each provide unique but corroborating information regarding the phylogenetic distribution of rarity in communities.

A Rhodanine Derivative CCR-11 Inhibits Bacterial Proliferation by Inhibiting the Assembly and GTPase Activity of FtsZ

A perturbation of FtsZ assembly dynamics has been shown to inhibit bacterial cytokinesis. In this study, the antibacterial activity of 151 rhodanine compounds was assayed using Bacillus subtilis cells. Of 151 compounds, eight strongly inhibited bacterial proliferation at 2 mu M. Subsequently, we used the elongation of B. subtilis cells as a secondary screen to identify potential FtsZ-targeted antibacterial agents. We found that three compounds significantly increased bacterial cell length. One of the three compounds, namely, CCR-11 (E)-2-thioxo-5-({3-(trifluoromethyl)phenyl]furan-2-yl}methylene) thiazolidin-4-one], inhibited the assembly and GTPase activity of FtsZ in vitro. CCR-11 bound to FtsZ with a dissociation constant of 1.5 +/- 0.3 mu M. A docking analysis indicated that CCR-11 may bind to FtsZ in a cavity adjacent to the T7 loop and that short halogen oxygen, H-bonding, and hydrophobic interactions might be important for the binding of CCR-11 with FtsZ. CCR-11 inhibited the proliferation of B. subtilis cells with a half-maximal inhibitory concentration (IC50) of 1.2 +/- 0.2 mu M and a minimal inhibitory concentration of 3 mu M. It also potently inhibited proliferation of Mycobacterium smegmatis cells. Further, CCR-11 perturbed Z-ring formation in B. subtilis cells; however, it neither visibly affected nucleoid segregation nor altered the membrane integrity of the cells. CCR-11 inhibited HeLa cell proliferation with an IC50 value of 18.1 +/- 0.2,mu M (similar to 15 x IC50 of B. subtilis cell proliferation). The results suggested that CCR-11 inhibits bacterial cytokinesis by inhibiting FtsZ assembly, and it can be used as a lead molecule to develop FtsZ-targeted antibacterial agents.