Blueprint for a high-performance biomaterial: full-length spider dragline silk genes.

Spider dragline (major ampullate) silk outperforms virtually all other natural and manmade materials in terms of tensile strength and toughness. For this reason, the mass-production of artificial spider silks through transgenic technologies has been a major goal of biomimetics research. Although all known arthropod silk proteins are extremely large (>200 kiloDaltons), recombinant spider silks have been designed from short and incomplete cDNAs, the only available sequences. Here we describe the first full-length spider silk gene sequences and their flanking regions. These genes encode the MaSp1 and MaSp2 proteins that compose the black widow's high-performance dragline silk. Each gene includes a single enormous exon (>9000 base pairs) that translates into a highly repetitive polypeptide. Patterns of variation among sequence repeats at the amino acid and nucleotide levels indicate that the interaction of selection, intergenic recombination, and intragenic recombination governs the evolution of these highly unusual, modular proteins. Phylogenetic footprinting revealed putative regulatory elements in non-coding flanking sequences. Conservation of both upstream and downstream flanking sequences was especially striking between the two paralogous black widow major ampullate silk genes. Because these genes are co-expressed within the same silk gland, there may have been selection for similarity in regulatory regions. Our new data provide complete templates for synthesis of recombinant silk proteins that significantly improve the degree to which artificial silks mimic natural spider dragline fibers

Dramatic expansion of the black widow toxin arsenal uncovered by multi-tissue transcriptomics and venom proteomics.

BackgroundAnimal venoms attract enormous interest given their potential for pharmacological discovery and understanding the evolution of natural chemistries. Next-generation transcriptomics and proteomics provide unparalleled, but underexploited, capabilities for venom characterization. We combined multi-tissue RNA-Seq with mass spectrometry and bioinformatic analyses to determine venom gland specific transcripts and venom proteins from the Western black widow spider (Latrodectus hesperus) and investigated their evolution.ResultsWe estimated expression of 97,217 L. hesperus transcripts in venom glands relative to silk and cephalothorax tissues. We identified 695 venom gland specific transcripts (VSTs), many of which BLAST and GO term analyses indicate may function as toxins or their delivery agents. ~38% of VSTs had BLAST hits, including latrotoxins, inhibitor cystine knot toxins, CRISPs, hyaluronidases, chitinase, and proteases, and 59% of VSTs had predicted protein domains. Latrotoxins are venom toxins that cause massive neurotransmitter release from vertebrate or invertebrate neurons. We discovered ≥ 20 divergent latrotoxin paralogs expressed in L. hesperus venom glands, significantly increasing this biomedically important family. Mass spectrometry of L. hesperus venom identified 49 proteins from VSTs, 24 of which BLAST to toxins. Phylogenetic analyses showed venom gland specific gene family expansions and shifts in tissue expression.ConclusionsQuantitative expression analyses comparing multiple tissues are necessary to identify venom gland specific transcripts. We present a black widow venom specific exome that uncovers a trove of diverse toxins and associated proteins, suggesting a dynamic evolutionary history. This justifies a reevaluation of the functional activities of black widow venom in light of its emerging complexity

Inelastic Displacement Ratios of SSI Systems

This paper presents the effect of soil-structure interaction on seismic inelastic displacement ratios of Single Degree of Freedom (SDOF) systems. Existing methods used in the past assumes the soil to be rigid. Through simplified equivalent fixed-base methods, the effect of soil-structure interaction (SSI) on the inelastic behaviour of structures is evaluated for different soil parameters using effective period and damping values. Using a degrading modified Clough model, the influence of different types of degradation is accounted for, for SDOF systems with periods ranging from 0.2 to 1.4 s. In total 300 different earthquake motions recorded on firm soil condition with magnitudes greater than 5 and peak ground acceleration (PGA) values greater than 0.08 g were selected. These records were scaled to the same hazard level and applied on five experimentally-tested reinforced concrete columns selected from the Pacific Earthquake Engineering Research Centre database. A total of 384,000 dynamic analyses were conducted. The results of the soil interacting systems are compared with the fixed-base case for different strength reduction factors (R) and foundation aspect ratios (h/r) for a range of NEHRP soil types C and D properties. These results show that the maximum inelastic displacements for soil type D are greater than those of soil type C and the fixed-base case. Particularly for periods less than 0.6 s with large aspect ratios, the effects of soil-structure interaction should be accounted for. Finally, the collected data was used to derive mathematical expressions for inelastic displacement ratios of SSI systems, suitable for use in performance-based seismic evaluation of structures

Ancient properties of spider silks revealed by the complete gene sequence of the prey-wrapping silk protein (AcSp1).

Spider silk fibers have impressive mechanical properties and are primarily composed of highly repetitive structural proteins (termed spidroins) encoded by a single gene family. Most characterized spidroin genes are incompletely known because of their extreme size (typically >9 kb) and repetitiveness, limiting understanding of the evolutionary processes that gave rise to their unusual gene architectures. The only complete spidroin genes characterized thus far form the dragline in the Western black widow, Latrodectus hesperus. Here, we describe the first complete gene sequence encoding the aciniform spidroin AcSp1, the primary component of spider prey-wrapping fibers. L. hesperus AcSp1 contains a single enormous (∼19 kb) exon. The AcSp1 repeat sequence is exceptionally conserved between two widow species (∼94% identity) and between widows and distantly related orb-weavers (∼30% identity), consistent with a history of strong purifying selection on its amino acid sequence. Furthermore, the 16 repeats (each 371-375 amino acids long) found in black widow AcSp1 are, on average, >99% identical at the nucleotide level. A combination of stabilizing selection on amino acid sequence, selection on silent sites, and intragenic recombination likely explains the extreme homogenization of AcSp1 repeats. In addition, phylogenetic analyses of spidroin paralogs support a gene duplication event occurring concomitantly with specialization of the aciniform glands and the tubuliform glands, which synthesize egg-case silk. With repeats that are dramatically different in length and amino acid composition from dragline spidroins, our L. hesperus AcSp1 expands the knowledge base for developing silk-based biomimetic technologies

H5N1 Clade 2.2 Polymorphism Tracing Identifies Influenza Recombination and Potential Vaccine Targets

Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997 1. The number of confirmed human cases now exceeds 300 and the associated Case Fatality Rate exceeds 60% 2. The genetic diversity of the serotype continues to increase. Four distinct clades or sub-clades have been linked to human cases 3.4. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift 5. We traced polymorphism acquisition in Clade 2.2 sequences. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, Clade 2.2 sub-clades in Egypt, Russia and Ghana. These changes are not easily explained by the current theory of “random mutation” through copy error, and are more easily explained by recombination with a common source. This conclusion is supported by additional polymorphisms shared by Clade 2.2 isolates in Egypt, Nigeria and Germany including aggregation of regional polymorphisms from each of these areas into a single Nigerian human hemagglutinin gene

Compositional Variations in Sands of the Bagnold Dunes, Gale Crater, Mars, from Visible-Shortwave Infrared Spectroscopy and Comparison to Ground-Truth from the Curiosity Rover

During its ascent up Mount Sharp, the Mars Science Laboratory Curiosity rover traversed the Bagnold Dune Field. We model sand modal mineralogy and grain size at four locations near the rover traverse, using orbital shortwave infrared single-scattering albedo spectra and a Markov chain Monte Carlo implementation of Hapke's radiative transfer theory to fully constrain uncertainties and permitted solutions. These predictions, evaluated against in situ measurements at one site from the Curiosity rover, show that X-ray diffraction-measured mineralogy of the basaltic sands is within the 95% confidence interval of model predictions. However, predictions are relatively insensitive to grain size and are nonunique, especially when modeling the composition of minerals with solid solutions. We find an overall basaltic mineralogy and show subtle spatial variations in composition in and around the Bagnold Dunes, consistent with a mafic enrichment of sands with cumulative aeolian-transport distance by sorting of olivine, pyroxene, and plagioclase grains. Furthermore, the large variations in Fe and Mg abundances (~20 wt %) at the Bagnold Dunes suggest that compositional variability may be enhanced by local mixing of well-sorted sand with proximal sand sources. Our estimates demonstrate a method for orbital quantification of composition with rigorous uncertainty determination and provide key constraints for interpreting in situ measurements of compositional variability within Martian aeolian sandstones

Reversible 1,2-Alkyl Migration to Carbene and Ammonia Activation in an N-Heterocyclic Carbene–Zirconium Complex

Addition of trimethylphosphine to a bis(phenolate)benzylimidazolylidene(dibenzyl)zirconium complex induces migration of a benzyl ligand from the metal center to the C_(carbine) atom. This process may be reversed, resulting in C_(sp)^3–C_(sp)^3 activation, by abstraction of the phosphine, an example of regulated, reversible alkyl migration. Addition of ammonia to the dibenzyl complex results in migration of one benzyl group and protonolysis of the other to generate a bis(NH_2)-bridged dimer via an NMR-observable intermediate NH_3 adduct

Multi-tissue transcriptomics of the black widow spider reveals expansions, co-options, and functional processes of the silk gland gene toolkit

Background: Spiders (Order Araneae) are essential predators in every terrestrial ecosystem largely because they have evolved potent arsenals of silk and venom. Spider silks are high performance materials made almost entirely of proteins, and thus represent an ideal system for investigating genome level evolution of novel protein functions. However, genomic level resources remain limited for spiders. Results: We de novo assembled a transcriptome for the Western black widow (Latrodectus hesperus) from deeply sequenced cDNAs of three tissue types. Our multi-tissue assembly contained ~100,000 unique transcripts, of which > 27,000 were annotated by homology. Comparing transcript abundance among the different tissues, we identified 647 silk gland-specific transcripts, including the few known silk fiber components (e.g. six spider fibroins, spidroins). Silk gland specific transcripts are enriched compared to the entire transcriptome in several functions, including protein degradation, inhibition of protein degradation, and oxidation-reduction. Phylogenetic analyses of 37 gene families containing silk gland specific transcripts demonstrated novel gene expansions within silk glands, and multiple co-options of silk specific expression from paralogs expressed in other tissues. Conclusions: We propose a transcriptional program for the silk glands that involves regulating gland specific synthesis of silk fiber and glue components followed by protecting and processing these components into functional fibers and glues. Our black widow silk gland gene repertoire provides extensive expansion of resources for biomimetic applications of silk in industry and medicine. Furthermore, our multi-tissue transcriptome facilitates evolutionary analysis of arachnid genomes and adaptive protein systems. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-365) contains supplementary material, which is available to authorized users

C3G mediated suppression of malignant transformation involves activation of PP2A phosphatases at the subcortical actin cytoskeleton

In previous work, we demonstrated that C3G suppresses Ras oncogenic transformation by a mechanism involving inhibition of ERK phosphorylation. Here we present evidences indicating that this suppression mechanism is mediated, at least in part, by serine/threonine phosphatases of the PP2A family. Thus: (i) ectopic expression of C3G or C3GΔCat (mutant lacking the GEF activity) increases specific ERK-associated PP2A phosphatase activities; (ii) C3G and PP2A interact, as demonstrated by immunofluorescence and co-immunoprecipitation experiments; (iii) association between PP2A and MEK or ERK increases in C3G overexpressing cells; (iv) phosphorylated-inactive PP2A level decreases in C3G expressing clones and, most importantly, (v) okadaic acid reverts the inhibitory effect of C3G on ERK phosphorylation. Moreover, C3G interacts with Ksr-1, a scaffold protein of the Ras-ERK pathway that also associates with PP2A. The fraction of C3G involved in transformation suppression is restricted to the subcortical actin cytoskeleton where it interacts with actin. Furthermore, the association between C3G and PP2A remains stable even after cytoskeleton disruption with cytochalasin D, suggesting that the three proteins form a complex at this subcellular compartment. Finally, C3G- and C3GΔCat-mediated inhibition of ERK phosphorylation is reverted by incubation with cytochalasin D. We hypothesize that C3G triggers PP2A activation and binding to MEK and ERK at the subcortical actin cytoskeleton, thus favouring ERK dephosphorylation. © 2007 Elsevier Inc. All rights reserved.This work was supported by grants SAF2003-04177 andGEN2003- 20239-C06-02 from MEC, Spain, FIS-FEDERPI030651, PI041324 and PI061274 from ISCIII,MSC, Spain, as well as institutional support from Redes Temáticas (C03/10 and RD06/0020/0000) de investigación en cáncer from ISCIII, MSC, Spain. S. M-E is a postodoctoral fellow supported by grant GEN2003-20239-C06-02. C.G. was supported by the Ramón y Cajal Program from the Spanish Ministry of Education.Peer Reviewe

Unexpected rearrangements in the synthesis of an unsymmetrical tridentate dianionic N-heterocyclic carbene

Starting from the same ethylenediamine species, three valuable carbene precursors were synthesized under differing conditions: a tridentate dianionic N-heterocyclic carbene bearing an aniline, a phenol and a central dihydroimidazolium salt, its benzimidazolium isomer by intramolecular rearrangement and a dicationic benzimidazolium-benzoxazolium salt by changing the Brønsted acid from HCl to HBF_4. A DFT study was performed to understand the rearrangement pathway. The structure of a bis[(NCO)carbene] zirconium complex was determined