Endothelial cells decode VEGF-mediated Ca2+ signaling patterns to produce distinct functional responses

A single extracellular stimulus can promote diverse behaviors among isogenic cells by differentially regulated signaling networks. We examined Ca2+ signaling in response to VEGF (vascular endothelial growth factor), a growth factor that can stimulate different behaviors in endothelial cells. We found that altering the amount of VEGF signaling in endothelial cells by stimulating them with different VEGF concentrations triggered distinct and mutually exclusive dynamic Ca2+ signaling responses that correlated with different cellular behaviors. These behaviors were cell proliferation involving the transcription factor NFAT (nuclear factor of activated T cells) and cell migration involving MLCK (myosin light chain kinase). Further analysis suggested that this signal decoding was robust to the noisy nature of the signal input. Using probabilistic modeling, we captured both the stochastic and deterministic aspects of Ca2+ signal decoding and accurately predicted cell responses in VEGF gradients, which we used to simulate different amounts of VEGF signaling. Ca2+ signaling patterns associated with proliferation and migration were detected during angiogenesis in developing zebrafish

Evaluation of Phage Display Discovered Peptides as Ligands for Prostate-Specific Membrane Antigen (PSMA)

The aim of this study was to identify potential ligands of PSMA suitable for further development as novel PSMA-targeted peptides using phage display technology. The human PSMA protein was immobilized as a target followed by incubation with a 15-mer phage display random peptide library. After one round of prescreening and two rounds of screening, high-stringency screening at the third round of panning was performed to identify the highest affinity binders. Phages which had a specific binding activity to PSMA in human prostate cancer cells were isolated and the DNA corresponding to the 15-mers were sequenced to provide three consensus sequences: GDHSPFT, SHFSVGS and EVPRLSLLAVFL as well as other sequences that did not display consensus. Two of the peptide sequences deduced from DNA sequencing of binding phages, SHSFSVGSGDHSPFT and GRFLTGGTGRLLRIS were labeled with 5-carboxyfluorescein and shown to bind and co-internalize with PSMA on human prostate cancer cells by fluorescence microscopy. The high stringency requirements yielded peptides with affinities KD∼1 μM or greater which are suitable starting points for affinity maturation. While these values were less than anticipated, the high stringency did yield peptide sequences that apparently bound to different surfaces on PSMA. These peptide sequences could be the basis for further development of peptides for prostate cancer tumor imaging and therapy. © 2013 Shen et al

The impact of predation by marine mammals on Patagonian toothfish longline fisheries

Predatory interaction of marine mammals with longline fisheries is observed globally, leading to partial or complete loss of the catch and in some parts of the world to considerable financial loss. Depredation can also create additional unrecorded fishing mortality of a stock and has the potential to introduce bias to stock assessments. Here we aim to characterise depredation in the Patagonian toothfish (Dissostichus eleginoides) fishery around South Georgia focusing on the spatio-temporal component of these interactions. Antarctic fur seals (Arctocephalus gazella), sperm whales (Physeter macrocephalus), and orcas (Orcinus orca) frequently feed on fish hooked on longlines around South Georgia. A third of longlines encounter sperm whales, but loss of catch due to sperm whales is insignificant when compared to that due to orcas, which interact with only 5% of longlines but can take more than half of the catch in some cases. Orca depredation around South Georgia is spatially limited and focused in areas of putative migration routes, and the impact is compounded as a result of the fishery also concentrating in those areas at those times. Understanding the seasonal behaviour of orcas and the spatial and temporal distribution of “depredation hot spots” can reduce marine mammal interactions, will improve assessment and management of the stock and contribute to increased operational efficiency of the fishery. Such information is valuable in the effort to resolve the human-mammal conflict for resources

Physiology of digestion in mango weevil, Sternochetus gravis (Fabr.) (Curculionidae : Coleoptera)

Sternochetus gravis has been proved to be a serious pest of mango fruit in Manipur. The insect during both of its larval and adult stages feed on the fruit pulp where the entire life cycle is completed. Certain physiological parameters of the pest and its food have been revealed significant interaction between them. The hydrogen-ion concentration has been observed to vary from 3.2 to 6.5 in the unripe and ripe fruit pulp and 4.5 to 6.2 in the larval and adult gut respectively. The qualitative estimation of digestive enzymes has revealed the presence of almost all the enzymes in the insect gut namely amylase, maltase, lactase, lipase and invertase to digest the different components of its food. Thus, the pest is host specific and is well adapted both physiologically as well as morphologically inside the growing food

The Puromycin Route to Assess Stereo- and Regiochemical Constraints on Peptide Bond Formation in Eukaryotic Ribosomes

We synthesized a series of puromycin analogues to probe the chemical specificity of the ribosome in an intact eukaryotic translation system. These studies reveal that both d-enantiomers and β-amino acid analogues can be incorporated into protein, and provide a quantitative means to rank natural and unnatural residues. Modeling of a d-amino acid analogue into the 50S ribosomal subunit indicates that steric clash may provide part of the chiral discrimination. The data presented provide one metric of the chiral and regiospecificity of mammalian ribosomes

Isospin Physics in Heavy-Ion Collisions at Intermediate Energies

In nuclear collisions induced by stable or radioactive neutron-rich nuclei a transient state of nuclear matter with an appreciable isospin asymmetry as well as thermal and compressional excitation can be created. This offers the possibility to study the properties of nuclear matter in the region between symmetric nuclear matter and pure neutron matter. In this review, we discuss recent theoretical studies of the equation of state of isospin-asymmetric nuclear matter and its relations to the properties of neutron stars and radioactive nuclei. Chemical and mechanical instabilities as well as the liquid-gas phase transition in asymmetric nuclear matter are investigated. The in-medium nucleon-nucleon cross sections at different isospin states are reviewed as they affect significantly the dynamics of heavy ion collisions induced by radioactive beams. We then discuss an isospin-dependent transport model, which includes different mean-field potentials and cross sections for the proton and neutron, and its application to these reactions. Furthermore, we review the comparisons between theoretical predictions and available experimental data. In particular, we discuss the study of nuclear stopping in terms of isospin equilibration, the dependence of nuclear collective flow and balance energy on the isospin-dependent nuclear equation of state and cross sections, the isospin dependence of total nuclear reaction cross sections, and the role of isospin in preequilibrium nucleon emissions and subthreshold pion production.Comment: 101 pages with embedded epsf figures, review article for "International Journal of Modern Physics E: Nuclear Physics". Send request for a hard copy to 1/author

Blood dynamics of mercury and selenium in northern elephant seals during the lactation period

The effects of reproduction and maternal investment (i.e., milk transfer) on trace element levels remain poorly understood in marine mammals. We examined the blood dynamics of mercury (Hg) and selenium (Se) during lactation in the northern elephant seal (Mirounga angustirostris), a top predator from the North Pacific Ocean. Total Hg and Se levels were measured in whole blood and milk of 10 mother-pup pairs on days 5 and 22 of lactation. Both Hg and Se were transferred to offspring through the milk. Results suggested that the maternal transfer of Se was prominent during lactation, whereas the Hg transfer was larger during gestation. The lactation period affected Hg and Se levels in the blood of elephant seal mothers and pups. Physiological processes and their relationship to body condition should be considered carefully when interpreting trace element levels in the framework of biomonitoring.Peer reviewe

Prospective identification of parasitic sequences in phage display screens

Phage display empowered the development of proteins with new function and ligands for clinically relevant targets. In this report, we use next-generation sequencing to analyze phage-displayed libraries and uncover a strong bias induced by amplification preferences of phage in bacteria. This bias favors fast-growing sequences that collectively constitute <0.01% of the available diversity. Specifically, a library of 10[superscript 9] random 7-mer peptides (Ph.D.-7) includes a few thousand sequences that grow quickly (the ‘parasites’), which are the sequences that are typically identified in phage display screens published to date. A similar collapse was observed in other libraries. Using Illumina and Ion Torrent sequencing and multiple biological replicates of amplification of Ph.D.-7 library, we identified a focused population of 770 ‘parasites’. In all, 197 sequences from this population have been identified in literature reports that used Ph.D.-7 library. Many of these enriched sequences have confirmed function (e.g. target binding capacity). The bias in the literature, thus, can be viewed as a selection with two different selection pressures: (i) target-binding selection, and (ii) amplification-induced selection. Enrichment of parasitic sequences could be minimized if amplification bias is removed. Here, we demonstrate that emulsion amplification in libraries of ~10[superscript 6] diverse clones prevents the biased selection of parasitic clones

Biocatalytic Synthesis of Polymers of Precisely Defined Structures

The fabrication of functional nanoscale devices requires the construction of complex architectures at length scales characteristic of atoms and molecules. Currently microlithography and micro-machining of macroscopic objects are the preferred methods for construction of small devices, but these methods are limited to the micron scale. An intriguing approach to nanoscale fabrication involves the association of individual molecular components into the desired architectures by supramolecular assembly. This process requires the precise specification of intermolecular interactions, which in turn requires precise control of molecular structure