Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation

Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence.

Study of phase synchronization in multichannel seizure EEG using nonlinear recurrence measure

Complex biological systems such as the human brain can be expected to be inherently nonlinear and hence difficult to model. Most of the previous studies on investigations of brain function have either used linear models or parametric nonlinear models. In this paper, we propose a novel application of a nonlinear measure of phase synchronization based on recurrences, correlation between probabilities of recurrence (CPR), to study seizures in the brain. The advantage of this nonparametric method is that it makes very few assumptions thus making it possible to investigate brain functioning in a data-driven way. We have demonstrated the utility of CPR measure for the study of phase synchronization in multichannel seizure EEG recorded from patients with global as well as focal epilepsy. For the case of global epilepsy, brain synchronization using thresholded CPR matrix of multichannel EEG signals showed clear differences in results obtained for epileptic seizure and pre-seizure. Brain headmaps obtained for seizure and preseizure cases provide meaningful insights about synchronization in the brain in those states. The headmap in the case of focal epilepsy clearly enables us to identify the focus of the epilepsy which provides certain diagnostic value. Comparative studies with linear correlation have shown that the nonlinear measure CPR outperforms the linear correlation measure. (C) 2014 Elsevier Ltd. All rights reserved.

A three-component protocol for the enantiodifferentiation of amines using triphenyl borate and BINOL: is it an ion pair or an amine-coordinated complex?

The structure of the borate complex responsible for the enantiodifferentiation of amines using a previously reported three-component protocol has been established. The choice between an ion pair and an amine-coordinated complex with the N atom of the amine coordinated to the B atom is favored for the former structure based on the DFT-calculated B-11 NMR chemical shifts. In contrast to expectations, the anisotropies of the quadrupolar B-11 nucleus for the two structures were calculated to be indistinguishable with regard to their effect on the linewidth of the NMR signal. (C) 2014 Elsevier Ltd. All rights reserved.

Mitigating UVA light induced reactivity of 6-thioguanine through formation of a Ru(II) half-sandwich complex

The organometallic complex of (eta(6)-cymene)Ru(II)Br with 6-thioguanine (6-TG) shows better photostability than the biologically active 6-thioguanine which is used as an immunosuppressant and as an anticancer agent.

Influence of the AgrC-AgrA Complex on the Response Time of Staphylococcus aureus Quorum Sensing

The Staphylococcus aureus agr quorum-sensing system plays a major role in the transition from the persistent to the virulent phenotype. S. aureus agr type I to IV strains are characterized by mutations in the sensor domain of the histidine kinase AgrC and differences in the sequences of the secreted autoinducing peptides (AIP). Here we demonstrate that interactions between the cytosolic domain of AgrC (AgrC(Cyto)) and the response regulator domain of AgrA (AgrA(RR)) dictate the spontaneity of the cellular response to AIP stimuli. The crystal structure of AgrC(Cyto) provided a basis for a mechanistic model of AgrC-AgrA interactions. This model enabled an analysis of the biochemical and biophysical parameters of AgrC-AgrA interactions in the context of the conformational features of the AgrC-AgrA complex. This analysis revealed distinct sequence and conformational features that determine the affinity, specificity, and kinetics of the phosphotransfer reaction. This step, which governs the response time for transcriptional reengineering triggered by an AIP stimulus, is independent of the agr type and similar for agonist and antagonist stimuli. These experimental data could serve as a basis on which to validate simulations of the quorum-sensing response and for strategies that employ the agr quorum-sensing system to combat biofilm formation in S. aureus infections.

Frequency-domain stimulated and spontaneous light emission signals at molecular junctions

Using a diagrammatic superoperator formalism we calculate optical signals at molecular junctions where a single molecule is coupled to two metal leads which are held at different chemical potentials. The molecule starts in a nonequilibrium steady state whereby it continuously exchanges electrons with the leads with a constant electron flux. Expressions for frequency domain optical signals measured in response to continuous laser fields are derived by expanding the molecular correlation functions in terms of its many-body states. The nonunitary evolution of molecular states is described by the quantum master equation. (C) 2014 AIP Publishing LLC.

The opportunity for sampling: the ecological context of female mate choice

Female mate choice decisions, which influence sexual selection, involve complex interactions between the 2 sexes and the environment. Theoretical models predict that male movement and spacing in the field should influence female sampling tactics, and in turn, females should drive the evolution of male movement and spacing to sample them optimally. Theoretically, simultaneous sampling of males using the best-of-n or comparative Bayes strategy should yield maximum mating benefits to females. We examined the ecological context of female mate sampling based on acoustic signals in the tree cricket Oecanthus henryi to determine whether the conditions for such optimal strategies were met in the field. These strategies involve recall of the quality and location of individual males, which in turn requires male positions to be stable within a night. Calling males rarely moved within a night, potentially enabling female sampling strategies that require recall. To examine the possibility of simultaneous acoustic sampling of males, we estimated male acoustic active spaces using information on male spacing, call transmission, and female hearing threshold. Males were found to be spaced far apart, and active space overlap was rare. We then examined female sampling scenarios by studying female spacing relative to male acoustic active spaces. Only 15% of sampled females could hear multiple males, suggesting that simultaneous mate sampling is rare in the field. Moreover, the relatively large distances between calling males suggest high search costs, which may favor threshold strategies that do not require memory.

A versatile ternary ionic complex for chiral discrimination of molecules with diverse functionalities using H-1 NMR

This study reports a simple, efficient and versatile protocol developed for NMR spectroscopic enantiodiscrimination of molecules containing diverse functional -groups, such as amino alcohols, secondary alcohols, cyanohydrins, oxazolidones, diols, thiones and epoxides, using a phosphorous based three component mixture. The simple mixing and shaking of enantiopure 1,1'-binaphthyt-2,2'-diyl hydrogenphosphate (BNPA), 4-(dimethylamino)pyridine (DMAP) and a chiral analyte in the solvent CDCl3 served as a chiral solvating agent and resulted in well dispersed peaks for each enantiomer in the H-1 NMR spectrum. Discrimination could be achieved not only for the proton at the chiral centre, but also for multiple proton sites. The devised approach also permitted the precise measurement of the enantiomeric excess (ee).

Contrasting reactivity behaviour of the RuHCl(CO)(PNP)] complex with electrophilic reagents XOTf (X = H, CH3, Me3Si)

A new ruthenium pincer complex RuHCl(CO)(PNP)] (PNP = PhCH2N(CH2CH2PPh2)(2)) (1) was synthesized and characterized. The reactivity of complex 1 with electrophilic reagents XOTf (X = H, CH3, and Me3Si; OTf = CF3SO3) was studied by variable temperature NMR spectroscopy with an aim to observe and characterize sigma complexes of type Ru(eta(2)-HX)Cl(CO)(PNP)]OTf] (X = H (2), CH3 (3), Me3Si (4)). Reaction of complex 1 with HOTf resulted in the formation of the dihydrogen complex, Ru(eta(2)-H-2)Cl(CO)(PNP)OTf] (2). On the other hand, the reaction between complex 1 and MeOTf and Me3SiOTf resulted in the direct elimination of MeCl and Me3SiCl via a S(N)2 type of reaction without the intermediacy of the respective sigma complexes 3 and 4. This contrasting reactivity behaviour has been rationalized taking into consideration the approach of the relatively bulky electrophites CH3+ and Me3Si+ onto the hydride moiety of the ruthenium fragment, which is sterically hindered.

Phenyl carbohydrazone conjugated 2-oxoindoline as a new scaffold that augments the DNA and BSA binding affinity and anti-proliferative activity of a 1,10-phenanthroline based copper(II) complex

A new type of copper(II) complex, CuL(phen)(2)](NO3) (CuIP), where L ((E)-N'-(2-oxoindolin-3-ylidene) benzohydrazide) is a N donor ligand and phen is the N, N-donor heterocyclic 1,10-phenanthroline, has been synthesized. The phenyl carbohydrazone conjugated isatin-based ligand L and CuIP were characterized by elemental analysis, infrared, UV-Vis, H-1 and C-13 NMR and ESI-mass spectral data, as well as single-crystal X-ray diffraction. The interaction of calf thymus DNA (CT DNA) with L and CuIP has been investigated by absorption, fluorescence and viscosity titration methods. The complex CuIP displays better binding affinity than the ligand L. The observed DNA binding constant (K-b = 4.15(+/- 0.18) x 10(5) M-1) and binding site size (s = 0.19), viscosity data together with molecular docking studies of CuIP suggest groove binding and/or a partial intercalative mode of binding to CT DNA. In addition, CuIP shows good binding propensity to the bovine serum albumin (BSA) protein, giving a K-BSA value of 1.25(+/- 0.24) x 10(6) M-1. In addition, the docking studies on DNA and human serum albumin (HSA) CuIP interactions are consistent with the consequence of binding experiments. The in vitro anti-proliferative study establishes the anticancer potency of the CuIP against the human cervical (HeLa) and breast (MCF7) cancer cells; noncancer breast epithelial (MCF10a) cells have also been investigated. CuIP shows better cytotoxicity and sensitivity towards cancer cells over noncancer ones than L under identical conditions, with the appearance of apoptotic bodies. (C) 2014 Elsevier B.V. All rights reserved.

ELLIPSE FITTING USING FINITE RATE OF INNOVATION PRINCIPLES

We address the problem of parameter estimation of an ellipse from a limited number of samples. We develop a new approach for solving the ellipse fitting problem by showing that the x and y coordinate functions of an ellipse are finite-rate-of-innovation (FRI) signals. Uniform samples of x and y coordinate functions of the ellipse are modeled as a sum of weighted complex exponentials, for which we propose an efficient annihilating filter technique to estimate the ellipse parameters from the samples. The FRI framework allows for estimating the ellipse parameters reliably from partial or incomplete measurements even in the presence of noise. The efficiency and robustness of the proposed method is compared with state-of-art direct method. The experimental results show that the estimated parameters have lesser bias compared with the direct method and the estimation error is reduced by 5-10 dB relative to the direct method.

NESTED SPARSE BAYESIAN LEARNING FOR BLOCK-SPARSE SIGNALS WITH INTRA-BLOCK CORRELATION

In this work, we address the recovery of block sparse vectors with intra-block correlation, i.e., the recovery of vectors in which the correlated nonzero entries are constrained to lie in a few clusters, from noisy underdetermined linear measurements. Among Bayesian sparse recovery techniques, the cluster Sparse Bayesian Learning (SBL) is an efficient tool for block-sparse vector recovery, with intra-block correlation. However, this technique uses a heuristic method to estimate the intra-block correlation. In this paper, we propose the Nested SBL (NSBL) algorithm, which we derive using a novel Bayesian formulation that facilitates the use of the monotonically convergent nested Expectation Maximization (EM) and a Kalman filtering based learning framework. Unlike the cluster-SBL algorithm, this formulation leads to closed-form EMupdates for estimating the correlation coefficient. We demonstrate the efficacy of the proposed NSBL algorithm using Monte Carlo simulations.

Anthrapyrazolone analogues intercept inflammatory JNK signals to moderate endotoxin induced septic shock

Severe sepsis or septic shock is one of the rising causes for mortality worldwide representing nearly 10% of intensive care unit admissions. Susceptibility to sepsis is identified to be mediated by innate pattern recognition receptors and responsive signaling pathways of the host. The c-Jun N-terminal Kinase (JNK)-mediated signaling events play critical role in bacterial infection triggered multi-organ failure, cardiac dysfunction and mortality. In the context of kinase specificities, an extensive library of anthrapyrazolone analogues has been investigated for the selective inhibition of c-JNK and thereby to gain control over the inflammation associated risks. In our comprehensive biochemical characterization, it is observed that alkyl and halogen substitution on the periphery of anthrapyrazolone increases the binding potency of the inhibitors specifically towards JNK. Further, it is demonstrated that hydrophobic and hydrophilic interactions generated by these small molecules effectively block endotoxin-induced inflammatory genes expression in in vitro and septic shock in vivo, in a mouse model, with remarkable efficacies. Altogether, the obtained results rationalize the significance of the diversity oriented synthesis of small molecules for selective inhibition of JNK and their potential in the treatment of severe sepsis.

Exact Phase Retrieval for a Class of 2-D Parametric Signals

We address the problem of two-dimensional (2-D) phase retrieval from magnitude of the Fourier spectrum. We consider 2-D signals that are characterized by first-order difference equations, which have a parametric representation in the Fourier domain. We show that, under appropriate stability conditions, such signals can be reconstructed uniquely from the Fourier transform magnitude. We formulate the phase retrieval problem as one of computing the parameters that uniquely determine the signal. We show that the problem can be solved by employing the annihilating filter method, particularly for the case when the parameters are distinct. For the more general case of the repeating parameters, the annihilating filter method is not applicable. We circumvent the problem by employing the algebraically coupled matrix pencil (ACMP) method. In the noiseless measurement setup, exact phase retrieval is possible. We also establish a link between the proposed analysis and 2-D cepstrum. In the noisy case, we derive Cramer-Rao lower bounds (CRLBs) on the estimates of the parameters and present Monte Carlo performance analysis as a function of the noise level. Comparisons with state-of-the-art techniques in terms of signal reconstruction accuracy show that the proposed technique outperforms the Fienup and relaxed averaged alternating reflections (RAAR) algorithms in the presence of noise.