Silencing of toxic gene expression by Fis

Bacteria and bacteriophages have evolved DNA modification as a strategy to protect their genomes. Mom protein of bacteriophage Mumodifies the phage DNA, rendering it refractile to numerous restriction enzymes and in turn enabling the phage to successfully invade a variety of hosts. A strong fortification, a combined activity of the phage and host factors, prevents untimely expression of mom and associated toxic effects. Here, we identify the bacterial chromatin architectural protein Fis as an additional player in this crowded regulatory cascade. Both in vivo and in vitro studies described here indicate that Fisacts as a transcriptional repressor of mom promoter. Further, our data shows that Fis mediates its repressive effect by denying access to RNA polymerase at mom promoter. We propose that a combined repressive effect of Fis and previously characterized negative regulatory factors could be responsible to keep the gene silenced most of the time. We thus present a new facet of Fis function in Mu biology. In addition to bringing about overall downregulation of Mu genome, it also ensures silencing of the advantageous but potentially lethal mom gene.

An approach toward the synthesis of PPAP natural product garsubellin A: construction of the tricyclic core

In a study directed toward the bioactive natural product garsubellin A, an expedient route to the bicyclo 3.3.1]nonan-9-one bearing tricyclic core, with a bridgehead anchored tetrahydrofuran ring, is delineated. The approach emanating from commercially available dimedone involved a DIBAL-H mediated retro aldol/re-aldol cyclization cascade and a PCC mediated oxidative cyclization as the key steps. (C) 2013 Elsevier Ltd. All rights reserved.

A finite-rate-of-innovation signal sampling perspective of the source-filter model of speech production

We consider the speech production mechanism and the asso- ciated linear source-filter model. For voiced speech sounds in particular, the source/glottal excitation is modeled as a stream of impulses and the filter as a cascade of second-order resonators. We show that the process of sampling speech signals can be modeled as filtering a stream of Dirac impulses (a model for the excitation) with a kernel function (the vocal tract response),and then sampling uniformly. We show that the problem of esti- mating the excitation is equivalent to the problem of recovering a stream of Dirac impulses from samples of a filtered version. We present associated algorithms based on the annihilating filter and also make a comparison with the classical linear prediction technique, which is well known in speech analysis. Results on synthesized as well as natural speech data are presented.

IGF-1 stimulated upregulation of cyclin D1 is mediated via STAT5 signaling pathway in neuronal cells

Signal Transducer and Activator of Transcription (STATs) regulate various target genes such as cyclin D1, MYC, and BCL2 in nonneuronal cells which contribute towards progression as well as prevention of apoptosis and are involved in differentiation and cell survival. However, in neuronal cells, the role of STATs in the activation and regulation of these target genes and their signaling pathways are still not well established. In this study, a robust cyclin D1 expression was observed following IGF-1 stimulation in SY5Y cells as well as neurospheres. JAK/STAT pathway was shown to be involved in this upregulation. A detailed promoter analysis revealed that the specific STAT involved was STAT5, which acted as a positive regulatory element for cyclin D1 expression. Overexpression studies confirmed increase in cyclin D1 expression in response to STAT5a and STAT5b constructs when compared to dominant-negative STAT5. siRNA targeting STAT5, diminished the cyclin D1 expression, further confirming that STAT5 specifically regulated cyclin D1 in neuronal cells. Together, these findings shed new light on the mechanism of IGF-1 mediated upregulation of cyclin D1 expression in neural cell lines as well as in neural stem cells via the JAK/STAT5 signaling cascade.

Species importance in a heterospecific foraging association network

There is a growing recognition of the need to integrate non-trophic interactions into ecological networks for a better understanding of whole-community organization. To achieve this, the first step is to build networks of individual non-trophic interactions. In this study, we analyzed a network of interdependencies among bird species that participated in heterospecific foraging associations (flocks) in an evergreen forest site in the Western Ghats, India. We found the flock network to contain a small core of highly important species that other species are strongly dependent on, a pattern seen in many other biological networks. Further, we found that structural importance of species in the network was strongly correlated to functional importance of species at the individual flock level. Finally, comparisons with flock networks from other Asian forests showed that the same taxonomic groups were important in general, suggesting that species importance was an intrinsic trait and not dependent on local ecological conditions. Hence, given a list of species in an area, it may be possible to predict which ones are likely to be important. Our study provides a framework for the investigation of other heterospecific foraging associations and associations among species in other non-trophic contexts.

Synconset Waves and Chains: Spiking Onsets in Synchronous Populations Predict and Are Predicted by Network Structure

Synfire waves are propagating spike packets in synfire chains, which are feedforward chains embedded in random networks. Although synfire waves have proved to be effective quantification for network activity with clear relations to network structure, their utilities are largely limited to feedforward networks with low background activity. To overcome these shortcomings, we describe a novel generalisation of synfire waves, and define `synconset wave' as a cascade of first spikes within a synchronisation event. Synconset waves would occur in `synconset chains', which are feedforward chains embedded in possibly heavily recurrent networks with heavy background activity. We probed the utility of synconset waves using simulation of single compartment neuron network models with biophysically realistic conductances, and demonstrated that the spread of synconset waves directly follows from the network connectivity matrix and is modulated by top-down inputs and the resultant oscillations. Such synconset profiles lend intuitive insights into network organisation in terms of connection probabilities between various network regions rather than an adjacency matrix. To test this intuition, we develop a Bayesian likelihood function that quantifies the probability that an observed synfire wave was caused by a given network. Further, we demonstrate it's utility in the inverse problem of identifying the network that caused a given synfire wave. This method was effective even in highly subsampled networks where only a small subset of neurons were accessible, thus showing it's utility in experimental estimation of connectomes in real neuronal-networks. Together, we propose synconset chains/waves as an effective framework for understanding the impact of network structure on function, and as a step towards developing physiology-driven network identification methods. Finally, as synconset chains extend the utilities of synfire chains to arbitrary networks, we suggest utilities of our framework to several aspects of network physiology including cell assemblies, population codes, and oscillatory synchrony.

Moving to stay in place: behavioral mechanisms for coexistence of African large carnivores

Most ecosystems have multiple predator species that not only compete for shared prey, but also pose direct threats to each other. These intraguild interactions are key drivers of carnivore community structure, with ecosystem-wide cascading effects. Yet, behavioral mechanisms for coexistence of multiple carnivore species remain poorly understood. The challenges of studying large, free-ranging carnivores have resulted in mainly coarse-scale examination of behavioral strategies without information about all interacting competitors. We overcame some of these challenges by examining the concurrent fine-scale movement decisions of almost all individuals of four large mammalian carnivore species in a closed terrestrial system. We found that the intensity of intraguild interactions did not follow a simple hierarchical allometric pattern, because spatial and behavioral tactics of subordinate species changed with threat and resource levels across seasons. Lions (Panthera leo) were generally unrestricted and anchored themselves in areas rich in not only their principal prey, but also, during periods of resource limitation (dry season), rich in the main prey for other carnivores. Because of this, the greatest cost (potential intraguild predation) for subordinate carnivores was spatially coupled with the highest potential benefit of resource acquisition (prey-rich areas), especially in the dry season. Leopard (P. pardus) and cheetah (Acinonyx jubatus) overlapped with the home range of lions but minimized their risk using fine-scaled avoidance behaviors and restricted resource acquisition tactics. The cost of intraguild competition was most apparent for cheetahs, especially during the wet season, as areas with energetically rewarding large prey (wildebeest) were avoided when they overlapped highly with the activity areas of lions. Contrary to expectation, the smallest species (African wild dog, Lycaon pictus) did not avoid only lions, but also used multiple tactics to minimize encountering all other competitors. Intraguild competition thus forced wild dogs into areas with the lowest resource availability year round. Coexistence of multiple carnivore species has typically been explained by dietary niche separation, but our multi-scaled movement results suggest that differences in resource acquisition may instead be a consequence of avoiding intraguild competition. We generate a more realistic representation of hierarchical behavioral interactions that may ultimately drive spatially explicit trophic structures of multi-predator communities.

Methionine down-regulates TLR4/MyD88/NF-kappa B signalling in osteoclast precursors to reduce bone loss during osteoporosis

Background and PurposeStudies have demonstrated that a moderate intake of amino acids is associated with development of bone health. Methionine, a sulphur-containing essential amino acid, has been largely implicated for improving cartilage formation, however its physiological significance on bone integrity and functionality have not been elucidated. We investigated whether methionine can prevent osteoporotic bone loss. Experimental ApproachThe anti-resorptive effect of methionine, (250mgkg(-1) body wt administered in drinking water for 10 weeks), was evaluated in ovariectomized (OVX) rats by monitoring changes in bone turnover, formation of osteoclasts from blood-derived mononuclear cells and changes in the synthesis of pro-osteoclastogenic cytokines. Key resultsMethionine improved bone density and significantly decreased the degree of osteoclast development from blood mononuclear cells in OVX rats, as indicated by decreased production of osteoclast markers tartarate resistant acid phosphatase b (TRAP5b) and MIP-1. siRNA-mediated knockdown of myeloid differentiation primary response 88 MyD88], a signalling molecule in the toll-like receptor (TLR) signalling cascade, abolished the synthesis of both TRAP5b and MIP-1 in developing osteoclasts. Methionine supplementation disrupted osteoclast development by inhibiting TLR-4/MyD88/NF-B pathway. Conclusions and ImplicationsTLR-4/MyD88/NF-B signalling pathway is integral for osteoclast development and this is down-regulated in osteoporotic system on methionine treatment. Methionine treatment could be beneficial for the treatment of postmenopausal osteoporosis.

Imaging cellular signalling: many `moving tales' in MAP kinase odyssey

Cellular signalling events are at the core of every adaptive response. Signalling events link environmental changes to physiological responses, consequently allowing cellular and organismal sustenance and survival. Classical approaches to study cellular signalling have relied on a variety of cell disruptive techniques which yield limited kinetic information, while the underlying events are much more complex. In this article, we discuss how modern live cell imaging microscopy has found increasing utilization in revealing spatio temporal dynamics of various signalling pathways. Utilizing the well studied mitogen-activated protein kinase (MAPK) signalling cascade as a template, the design, construction and utilization of `mobile' (translocation proficient) biosensors, suitable for studying MAPK signalling in living cells are described in detail. Experimental setup and results obtained from these biosensors, based on different proteins involved in the MAPK signalling cascade, have been described along with the setup of a microscope optimal for live cell imaging applications. Utilizing the ability to activate or deactivate signalling pathways using defined activators and specific pharmacological inhibitors, we also show how these sensors can yield unique spatial and temporal kinetic information of signalling in living cells.

An Approach to a Bislactone Skeleton: A Scalable Total Synthesis of (+/-)-Penifulvin A

An efficient and scalable total synthesis of the architecturally challenging sesquiterpenoid (+/-)-penifulvin A has been accomplished via a 12-step sequence with an overall yield of 16%. For the construction of this structurally complex tetracyclic molecule, the key steps used included 1,4-conjugate addition, a Pd(0) catalyzed cross-coupling reaction between an enol phosphate and trimethyl aluminum, Claisen rearrangement using the Johnson orthoester protocol, Ti(III)-mediated reductive epoxide opening-cyclization, Lewis acid catalyzed epoxy-aldehyde rearrangement, and finally a substrate controlled oxidative cascade lactonization process.

Critical cysteines in Akt1 regulate its activity and proteasomal degradation: implications for neurodegenerative diseases

Impaired Akt1 signaling is observed in neurodegenerative diseases, including Parkinson's disease (PD). In PD models oxidative modification of Akt1 leads to its dephosphorylation and consequent loss of its kinase activity. To explore the underlying mechanism we exposed Neuro2A cells to cadmium, a pan inhibitor of protein thiol disulfide oxidoreductases, including glutaredoxin 1 (Grx1), or downregulated Grx1, which led to dephosphorylation of Akt1, loss of its kinase activity, and also decreased Akt1 protein levels. Mutation of cysteines to serines at 296 and 310 in Akt1 did not affect its basal kinase activity but abolished cadmium- and Grx1 downregulation-induced reduction in Akt1 kinase activity, indicating their critical role in redox modulation of Akt1 function and turnover. Cadmium-induced decrease in phosphorylated Akt1 correlated with increased association of wild-type (WT) Akt1 with PP2A, which was absent in the C296-310S Akt1 mutant and was also abolished by N-acetylcysteine treatment. Further, increased proteasomal degradation of Akt1 by cadmium was not seen in the C296-310S Akt1 mutant, indicating that oxidation of cysteine residues facilitates degradation of WT Akt1. Moreover, preventing oxidative modification of Akt1 cysteines 296 and 310 by mutating them to serines increased the cell survival effects of Akt1. Thus, in neurodegenerative states such as PD, maintaining the thiol status of cysteines 296 and 310 in Akt1 would be critical for Akt1 kinase activity and for preventing its degradation by proteasomes. Preventing downregulation of Akt signaling not only has long-range consequences for cell survival but could also affect the multiple roles that Ala plays, including in the Akt-mTOR signaling cascade. (C) 2014 Elsevier Inc. All rights reserved.

WNT-Inflammasome Signaling Mediates NOD2-Induced Development of Acute Arthritis in Mice

In addition to its role in innate immunity, the intracellular pathogen sensor nucleotide-binding oligomerization domain 2 (NOD2) has been implicated in various inflammatory disorders, including the development of acute arthritis. However, the molecular mechanisms involved in the development of NOD2-responsive acute arthritis are not clear. In this study, we demonstrate that NOD2 signals to a cellular protein, Ly6/PLAUR domain-containing protein 6, in a receptor-interacting protein kinase 2-TGF-beta-activated kinase 1-independent manner to activate the WNT signaling cascade. Gain- or loss-of-function of the WNT signaling pathway in an in vivo experimental mouse arthritis model or in vitro systems established the role for WNT-responsive X-linked inhibitor of apoptosis during the development of acute arthritis. Importantly, WNT-stimulated X-linked inhibitor of apoptosis mediates the activation of inflammasomes. The subsequent caspase-1 activation and IL-1 beta secretion together contribute to the phenotypic character of the inflammatory condition of acute arthritis. Thus, identification of a role for WNT-mediated inflammasome activation during NOD2 stimulation serves as a paradigm to understand NOD2-associated inflammatory disorders and develop novel therapeutics.

A Multi-phase Approach for Improving Information Diffusion in Social Networks

For maximizing influence spread in a social network, given a certain budget on the number of seed nodes, we investigate the effects of selecting and activating the seed nodes in multiple phases. In particular, we formulate an appropriate objective function for two-phase influence maximization under the independent cascade model, investigate its properties, and propose algorithms for determining the seed nodes in the two phases. We also study the problem of determining an optimal budget-split and delay between the two phases.

Two-dimensional homogeneous isotropic fluid turbulence with polymer additives

We carry out an extensive and high-resolution direct numerical simulation of homogeneous, isotropic turbulence in two-dimensional fluid films with air-drag-induced friction and with polymer additives. Our study reveals that the polymers (a) reduce the total fluid energy, enstrophy, and palinstrophy; (b) modify the fluid energy spectrum in both inverse-and forward-cascade regimes; (c) reduce small-scale intermittency; (d) suppress regions of high vorticity and strain rate; and (e) stretch in strain-dominated regions. We compare our results with earlier experimental studies and propose new experiments.

A Generalist Predator Regulating Spread of a Wildlife Disease: Exploring Two Infection Transmission Scenarios

Ecoepidemiology is a well-developed branch of theoretical ecology, which explores interplay between the trophic interactions and the disease spread. In most ecoepidemiological models, however, the authors assume the predator to be a specialist, which consumes only a single prey species. In few existing papers, in which the predator was suggested to be a generalist, the alternative food supply was always considered to be constant. This is obviously a simplification of reality, since predators can often choose between a number of different prey. Consumption of these alternative prey can dramatically change their densities and strongly influence the model predictions. In this paper, we try to bridge the gap and explore a generic ecoepidemiological system with a generalist predator, where the densities of all prey are dynamical variables. The model consists of two prey species, one of which is subject to an infectious disease, and a predator, which consumes both prey species. We investigate two main scenarios of infection transmission mode: (i) the disease transmission rate is predator independent and (ii) the transmission rate is a function of predator density. For both scenarios we fulfil an extensive bifurcation analysis. We show that including a second dynamical prey in the system can drastically change the dynamics of the single prey case. In particular, the presence of a second prey impedes disease spread by decreasing the basic reproduction number and can result in a substantial drop of the disease prevalence. We demonstrate that with efficient consumption of the second prey species by the predator, the predator-dependent disease transmission can not destabilize interactions, as in the case with a specialist predator. Interestingly, even if the population of the second prey eventually vanishes and only one prey species finally remains, the system with two prey species may exhibit different properties to those of the single prey system.