Bootstrapping of gene-expression data improves and controls the false discovery rate of differentially expressed genes

The ordinary-, penalized-, and bootstrap t-test, least squares and best linear unbiased prediction were compared for their false discovery rates (FDR), i.e. the fraction of falsely discovered genes, which was empirically estimated in a duplicate of the data set. The bootstrap-t-test yielded up to 80% lower FDRs than the alternative statistics, and its FDR was always as good as or better than any of the alternatives. Generally, the predicted FDR from the bootstrapped P-values agreed well with their empirical estimates, except when the number of mRNA samples is smaller than 16. In a cancer data set, the bootstrap-t-test discovered 200 differentially regulated genes at a FDR of 2.6%, and in a knock-out gene expression experiment 10 genes were discovered at a FDR of 3.2%. It is argued that, in the case of microarray data, control of the FDR takes sufficient account of the multiple testing, whilst being less stringent than Bonferoni-type multiple testing corrections. Extensions of the bootstrap simulations to more complicated test-statistics are discussed.     

High content analysis to determine cytotoxicity of the antimicrobial peptide, melittin and selected structural analogs

Antimicrobial peptides (AMPs) are naturally occurring entities with potential as pharmaceutical candidates and/or food additives. They are present in many organisms including bacteria, insects, fish and mammals. While their antimicrobial activity is equipotent with many commercial antibiotics, current limitations are poor pharmacokinetics, stability and potential toxicology issues. Most elicit antimicrobial action via perturbation of bacterial membranes. Consequently, associated cytotoxicity in human cells is reflected by their capacity to lyse erythrocytes. However, more rigorous toxicological assessment of AMPs is required in order to predict potential failure at a later stage of development. We describe a high-content analysis (HCA) screening protocol recently established for determination and prediction of safety in pharmaceutical drug discovery. HCA is a powerful, multi-parameter bioanalytical tool that amalgamates the actions of fluorescence microscopy with automated cell analysis software in order to understand multiple changes in cellular health. We describe the application of HCA in assessing cytotoxicity of the cytolytic α-helical peptide, melittin, and selected structural analogs. The data shows that structural modification of melittin reduces its cytotoxic action and that HCA is suitable for rapidly identifying cytotoxicity.     

Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations

The helical hairpin is one of the most ubiquitous and elementary secondary structural motifs in nucleic acids, capable of serving functional roles and participating in long-range tertiary contacts. Yet the self-assembly of these structures has not been well-characterized at the atomic level. With this in mind, the dynamics of nucleic acid hairpin formation and disruption have been studied using a novel computational tool: large-scale, parallel, atomistic molecular dynamics simulation employing an inhomogeneous distributed computer consisting of more than 40,000 processors. Using multiple methodologies, over 500 micro s of atomistic simulation time has been collected for a large ensemble of hairpins (sequence 5'-GGGC[GCAA]GCCU-3'), allowing characterization of rare events not previously observable in simulation. From uncoupled ensemble dynamics simulations in unperturbed folding conditions, we report on 1), competing pathways between the folded and unfolded regions of the conformational space; 2), observed nonnative stacking and basepairing traps; and 3), a helix unwinding-rewinding mode that is differentiated from the unfolding and folding dynamics. A heterogeneous transition state ensemble is characterized structurally through calculations of conformer-specific folding probabilities and a multiplexed replica exchange stochastic dynamics algorithm is used to derive an approximate folding landscape. A comparison between the observed folding mechanism and that of a peptide beta-hairpin analog suggests that although native topology defines the character of the folding landscape, the statistical weighting of potential folding pathways is determined by the chemical nature of the polymer.     

Synthesis and properties of novel 2'-O-alkoxymethyl-modified nucleic acids

Novel 2'-O-modified oligoribonucleotides with alkoxymethyl skeletons were synthesized, and their ability to hybridize complementary nucleic acids and their nuclease resistance were analyzed. The hybridization ability was improved by introducing electron-withdrawing groups and the increases in melting temperature (T(m) value) was particularly high for chlorine-substituted compounds. Nuclease resistance of these 2'-O-alkoxymethylated oligomers was lower than expected, but cyano substitution resulted in a higher nuclease resistance than 2'-O-methylation.     

Detecting growth under environmental extremes: Spatial and temporal patterns in nucleic acid ratios in two Antarctic bivalves

Growth of Antarctic benthic organisms is very slow due to temperature and food availability, and subtle differences in growth rate may be difficult to detect. Nucleic acid ratios (RNA/DNA, RNA/protein or total RNA concentration) are measures of protein synthesis potential and may be used to assess short-term growth rate in a range of marine organisms. We quantified nucleic acid ratios in the scallop Adamussium colbecki and the clam Laternula elliptica at five locations in the Ross Sea, Antarctica. We were able to detect species-specific, habitat-specific, and seasonal differences in nucleic acid ratios and related these to associated differences in primary productivity. By using nucleic acid ratios, future studies could relatively easily obtain a measure of growth rate from a multitude of locations with contrasting habitat characteristics, food availability and temperature regimes around the Antarctic continent. This would yield a unique understanding of spatial and temporal patterns in bivalve growth in this extreme environment.     

Cumulative t-link threshold models for the genetic analysis of calving ease scores

In this study, a hierarchical threshold mixed model based on a cumulative t-link specification for the analysis of ordinal data or more, specifically, calving ease scores, was developed. The validation of this model and the Markov chain Monte Carlo (MCMC) algorithm was carried out on simulated data from normally and t₄ (i.e. a t-distribution with four degrees of freedom) distributed populations using the deviance information criterion (DIC) and a pseudo Bayes factor (PBF) measure to validate recently proposed model choice criteria. The simulation study indicated that although inference on the degrees of freedom parameter is possible, MCMC mixing was problematic. Nevertheless, the DIC and PBF were validated to be satisfactory measures of model fit to data. A sire and maternal grandsire cumulative t-link model was applied to a calving ease dataset from 8847 Italian Piemontese first parity dams. The cumulative t-link model was shown to lead to posterior means of direct and maternal heritabilities (0.40 ± 0.06, 0.11 ± 0.04) and a direct maternal genetic correlation (-0.58 ± 0.15) that were not different from the corresponding posterior means of the heritabilities (0.42 ± 0.07, 0.14 ± 0.04) and the genetic correlation (-0.55 ± 0.14) inferred under the conventional cumulative probit link threshold model. Furthermore, the correlation (> 0.99) between posterior means of sire progeny merit from the two models suggested no meaningful rerankings. Nevertheless, the cumulative t-link model was decisively chosen as the better fitting model for this calving ease data using DIC and PBF.     

Isolation and structural analysis of ajugose from Vigna mungo L

The hexasaccharide ajugose, alpha-D-galactopyranosyl-(1-->6)-alpha-D-galactopyranosyl-(1-->6)-O-alpha-D-galactopyranosyl-(1-->6)-alpha-D-galactopyranosyl-(1-->6)-alpha-D-glucopyranosyl-(1<-->2)-beta-D-fructofuranoside, generally uncommon in legumes, was detected in the seeds of Vigna mungo L. by TLC and paper chromatography. Ajugose was then isolated by silica gel chromatography and its structure was established by acid and enzymatic hydrolysis, fast atom bombardment mass spectrometry and both one- and two-dimensional 1H and 13C NMR techniques.     

Sialic acid-binding dwarf elder four-chain lectin displays nucleic acid N-glycosidase activity

Sialic acid-binding dwarf elder agglutinin (SEA) present only in rhizomes of the medicinal plant Sambucus ebulus L., was found to be a tetrameric glycoprotein consisting of two covalently-associated dimers of an enzymic A chain with rRNA N-glycosidase activity (EC 3.2.2.22) linked to a B chain with agglutinin properties. The lectin inhibited protein synthesis by a cell-free system and depurinated ribosomes. Cloning of the corresponding gene and molecular modeling of the deduced amino acid sequence demonstrated that SEA has a three-dimensional structure which resembles that reported for other two tetrameric type 2 RIPs from Sambucus (SNAI and SSA). The lectin agglutinated red blood cells and displayed sugar affinity for sialic acid residues apart from d-galactose, binding to the mucin-producing gut goblet cells. Since sialic acid is present in animal cells, especially in epithelial lining gut cells, but not in plants, SEA could play a role in the defense against insect attack.     

Computational structural and functional analysis of hypothetical proteins of Staphylococcus aureus

Genome sequencing projects has led to an explosion of large amount of gene products in which many are of hypothetical proteinswith unknown function. Analyzing and annotating the functions of hypothetical proteins is important in Staphylococcus aureuswhich is a pathogenic bacterium that cause multiple types of diseases by infecting various sites in humans and animals. In thisstudy, ten hypothetical proteins of Staphylococcus aureus were retrieved from NCBI and analyzed for their structural and functionalcharacteristics by using various bioinformatics tools and databases. The analysis revealed that some of them possessed functionallyimportant domains and families and protein-protein interacting partners which were ABC transporter ATP-binding protein,Multiple Antibiotic Resistance (MAR) family, export proteins, Helix-Turn-helix domains, arsenate reductase, elongation factor,ribosomal proteins, Cysteine protease precursor, Type-I restriction endonuclease enzyme and plasmid recombination enzymewhich might have the same functions in hypothetical proteins. The structural prediction of those proteins and binding sitesprediction have been done which would be useful in docking studies for aiding in the drug discovery.     

Negative selection of Plasmodium falciparum reveals targeted gene deletion by double crossover recombination.

The genome sequence of Plasmodium falciparum, the causative agent of the most severe form of malaria in humans, rapidly approaches completion, but our ability to genetically manipulate this organism remains limited. Chromosomal integration has only been achieved following the prolonged maintenance of circularised episomal plasmids which selects for single crossover recombinants. It has not been possible to construct genetic deletions via double crossover recombination, presumably due to the low frequency of this event. We have used the Herpes simplex virus thymidine kinase gene and the Escherichia coli cytosine deaminase gene for negative selection of P. falciparum. Parasites were transformed with plasmids expressing the thymidine kinase and cytosine deaminase genes by positive selection for the human dihydrofolate reductase gene. Parasites expressing thymidine kinase are susceptible to the pro-drug ganciclovir while those expressing cytosine deaminase are sensitive to 5-fluorocytosine. Parental parasites were inherently resistant to these drugs. A significant 'bystander effect' was evident in cultures with either ganciclovir or 5-fluorocytosine. Positive and negative selection of the thymidine kinase transformants with both ganciclovir and WR99210 resulted in the selection of parasites containing a genetic deletion of the Pfrh3 gene, the first targeted double crossover deletions in P. falciparum. The use of negative selection for gene disruptions via double crossover recombination will dramatically improve our ability to analyse protein function and opens the possibility of using this strategy for a variety of gene deletion and modification experiments in the analysis of this important infectious agent.     

Modulation of i-motif thermodynamic stability by the introduction of UNA (unlocked nucleic acid) monomers

The influence of acyclic RNA derivatives, UNA (unlocked nucleic acid) monomers, on i-DNA thermodynamic stability has been investigated. The 22 nt human telomeric fragment was chosen as the model sequence for stability studies. UNA monomers modulate i-motif stability in a position-depending manner. The largest destabilization is observed for position C14, while UNA placed in position A12 causes significant increase of i-DNA thermodynamic stability. CD curves of UNA-modified variants imply no structural changes relative to the native i-motif.     

Comparative structural analysis of oxidized and reduced thioredoxin from Drosophila melanogaster

Thioredoxins (Trx) participate in essential antioxidant and redox-regulatory processes via a pair of conserved cysteine residues. In dipteran insects like Drosophila and Anopheles, which lack a genuine glutathione reductase (GR), thioredoxins fuel the glutathione system with reducing equivalents. Thus, characterizing Trxs from these organisms contributes to our understanding of redox control in GR-free systems and provides information on novel targets for insect control. Cytosolic Trx of Drosophila melanogaster (DmTrx) is the first thioredoxin that was crystallized for X-ray diffraction analysis in the reduced and in the oxidized form. Comparison of the resulting structures shows rearrangements in the active-site regions. Formation of the C32-C35 disulfide bridge leads to a rotation of the side-chain of C32 away from C35 in the reduced form. This is similar to the situation in human Trx and Trx m from spinach chloroplasts but differs from Escherichia coli Trx, where it is C35 that moves upon change of the redox state. In all four crystal forms that were analysed, DmTrx molecules are engaged in a non-covalent dimer interaction. However, as demonstrated by gel-filtration analyses, DmTrx does not dimerize under quasi in vivo conditions and there is no redox control of a putative monomer/dimer equilibrium. The dimer dissociation constants K(d) were found to be 2.2mM for reduced DmTrx and above 10mM for oxidized DmTrx as well as for the protein in the presence of reduced glutathione. In human Trx, oxidative dimerization has been demonstrated in vitro. Therefore, this finding may indicate a difference in redox control of GR-free and GR-containing organisms.     

Mutational analysis and a structural model of methyl-directed restriction enzyme Mrr

The Mrr protein of Escherichia coli K12 is a cryptic Type IV restriction endonuclease whose activity appears to be triggered by high pressure stress. In this report we used high pressure to isolate and analyze several Mrr mutants, and generated a new structural model of the Mrr protein. The activity of a number of spontaneous and strategically constructed Mrr mutants is discussed in the light of this model, providing a first insight into the structure-function relationships of the Mrr enzyme.     

Phylogeny-directed structural analysis of the Arabidopsis PsbS protein

Plant psbS proteins are essential for regulated thermal dissipation of excess light referred to as non-photochemical quenching of chlorophyll fluorescence yield (NPQ). Amino acid sequences derived from 65 psbS genes from 44 species were aligned to reveal extensive conservation consistent with of motifs that underlie intrinsic aspects of the NPQ mechanism. Site-directed mutagenesis was employed to block presumptive zeaxanthin or chlorophyll-binding sites in Arabidopsis psbS by disrupting ion-bonding between two pairs of non-adjacent glutamate and arginine residues. Transgenic Arabidopsis lines synthesizing only the altered psbS forms exhibited severely impaired NPQ capacity. In addition, the phylogenetic depth of the psbS database permitted identification of cryptic sites of adaptive evolution. Instances of localized positive selection were rare and largely limited to the family Poaceae (grasses). Specifically, adaptive evolution was detected in a hydrophilic stroma-exposed region and was correlated with the presence of the C4 pathway of carbon fixation.     

Quadruplex-forming properties of FRAXA (CGG) repeats interrupted by (AGG) triplets

The (CGG) repeats associated with X-chromosome fragility are generally believed to form quadruplexes. This notion has persisted although it had been shown that only very short (CGG)_n sequences form quadruplexes and that this quadruplex formation occurs in conditions far from physiological. We have now studied, using CD and absorption spectroscopies, quadruplex formation of (CGG)_n (n = 4, 7, 8, or 16) and their analogs interrupted by (AGG) triplets under various solvent conditions. In healthy individuals, (AGG) triplets are interspersed throughout the (CGG) repeat regions and appear to hinder (CGG)_n motif expansion. Here we show that (CGG) repeats do not form quadruplexes under physiological conditions in aqueous solution but, interestingly, quadruplexes are readily formed in water–ethanol solutions. The presence of (AGG) triplets markedly stabilized quadruplex formation. Quadruplexes may thus hinder rather than support (CGG)_n motif expansion.     

Heme-heme communication during the alkaline-induced structural transition in cytochrome c oxidase

Alkaline-induced conformational changes at pH 12.0 in the oxidized as well as the reduced state of cytochrome c oxidase have been systematically studied with time-resolved optical absorption and resonance Raman spectroscopies. In the reduced state, the heme a(3) first converts from the native five-coordinate configuration to a six-coordinate bis-histidine intermediate as a result of the coordination of one of the Cu(B) ligands, H290 or H291, to the heme iron. The coordination state change in the heme a(3) causes the alteration in the microenvironment of the formyl group of the heme a(3) and the disruption of the H-bond between R38 and the formyl group of the heme a. This structural transition, which occurs within 1min following the initiation of the pH jump, is followed by a slower reaction, in which Schiff base linkages are formed between the formyl groups of the two hemes and their nearby amino acid residues, presumably R38 and R302 for the heme a and a(3), respectively. In the oxidized enzyme, a similar Schiff base modification on heme a and a(3) was observed but it is triggered by the coordination of the H290 or H291 to heme a(3) followed by the breakage of the native proximal H378-iron and H376-iron bonds in heme a and a(3), respectively. In both oxidation states, the synchronous formation of the Schiff base linkages in heme a and a(3) relies on the structural communication between the two hemes via the H-bonding network involving R438 and R439 and the propionate groups of the two hemes as well as the helix X housing the two proximal ligands, H378 and H376, of the hemes. The heme-heme communication mechanism revealed in this work may be important in controlling the coupling of the oxygen and redox chemistry in the heme sites to proton pumping during the enzymatic turnover of CcO.     

Angiostrongylus cantonensis: experimental study on the susceptibility of apple snails, Pomacea canaliculata compared to Pila polita

Six groups (15 snails/group) of Pomacea canaliculata and Pila polita were infected orally with 0 (control), 200, 400, 800, 1600 and 3200 first-stage Angiostrongylus cantonensis larvae (L1). The respective mean+/-SD third stage larvae (L3) worm recovery 1-month post-infection (p.i.) for P. canaliculata was 0, 1.4+/-5.42 (0.7%), 0.13+/-0.35 (0.03%), 0.07+/-0.26 (0.009%), 0.07+/-0.26 (0.004%), 0, and for P. polita 0, 64.33+/-21.38 (32.25%), 115.36+/-36.82 (28.93%), 265.33+/-90.01 (33.27%), 471.33+/-92.98 (29.60%) and 849.00+/-243.23 (26.61%). The susceptibility of A. cantonensis in P. polita was dose-dependent (p<0.001). In the three groups (nine snails/group) of P. polita given 500 L1, we studied the distribution of L3 in the internal organs (i.e., foot, head+esophagus, kidney, albumin gland, mantle, intestine, digestive gland) and found the highest density after 1, 2 and 3 months p.i. in the mantle at 29.37%, 31.09% and 37.45%. The infection rate in P. canaliculata was too low to study distribution rates.