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

Geographic and temporal morphological stasis in the latest Cretaceous ammonoid Discoscaphites iris from the U.S. Gulf and Atlantic Coastal Plains

We examine temporal and spatial variation in morphology of the ammonoid cephalopod Discoscaphites iris using a large dataset from multiple localities in the Late Cretaceous (Maastrichtian) of the United States Gulf and Atlantic Coastal Plains, spanning a distance of 2000 km along the paleoshoreline. Our results suggest that the fossil record of D. iris is consistent with no within species net accumulation of phyletic evolutionary change across morphological traits or the lifetime of this species. Correlations between some traits and paleoenvironmental conditions as well as changes in the coefficient of variation may support limited population-scale ecophenotypic plasticity, however where stratigraphic data are available, no directional changes in morphology occur prior to the Cretaceous/Paleogene (K/Pg) boundary. This is consistent with models of 'dynamic' evolutionary stasis. Combined with knowledge of life history traits and paleoecology of scaphitid ammonoids, specifically a short planktonic phase after hatching followed by transition to a nektobenthic adult stage, these data suggest that scaphitids had significant potential for rapid morphological change in conjunction with limited dispersal capacity. It is therefore likely that evolutionary mode in the Scaphitidae (and potentially across the broader ammonoid clade) follows a model of cladogenesis wherein a dynamic morphological stasis is periodically interrupted by more substantial evolutionary change at speciation events. Finally, the lack of temporal changes in our data suggest that global environmental changes (such as those possibly related to the emplacement of the Deccan Traps Large Igneous Province) had a limited effect on the morphology of North American ammonoid faunas during the latest Cretaceous prior to the K/Pg mass extinction event.Missing morphometric values are highlighted with NA in the dataset.Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: 1924807Funding provided by: American Museum of Natural History and Richard Gilder Graduate School*Crossref Funder Registry ID: Award Number:We assembled a large morphometric dataset consisting of 328 individual fossil specimens of the scaphitid ammonoid cephalopod Discoscaphites iris collected from nine localities in Texas, Missouri, Mississippi, and New Jersey, representing a ~2000 km transect from SW to NE and encompassing the full geographic range of this species. Morphometric parameters were measured on well-preserved adult specimens of two dimorphs (Macroconchs - presumably the female, and microconch, presumably the male). We took up to seven morphometric measurements, and calculated ratios that captured the size, shape, and degree of compression of each of these ammonoid shells from each different locality. We evaluated the coefficient of variation (the standard deviation divided by the mean) for size and shape ratios as well as compression ratios at each locality. We used non-parametric statistical tests [Mann-Whitney U] to evaluate the significance of changes in mean morphological trait values between localities. To correct for multiple comparisons we applied a Bonferroni correction and also controlled for the false discovery rate. We also explored relationships between morphological traits and several environmental variables using linear modelling. All analyses were conducted in the R programming environment

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

Cretaceous/Tertiary boundary cephalopods.

122 p. : ill. (some col.), maps (some col.); 26 cm.Includes bibliographical references (p. 111-122).Geological investigations in the upper Manasquan River Basin, central Monmouth County, New Jersey, reveal a Cretaceous/Tertiary (= Cretaceous/Paleogene) succession consisting of approximately 2 m of the Tinton Formation overlain by 2 m of the Hornerstown Formation. The top of the Tinton Formation consists of a very fossiliferous unit, approximately 20 cm thick, which we refer to as the Pinna Layer. It is laterally extensive and consists mostly of glauconitic minerals and some angular quartz grains. The Pinna Layer is truncated at the top and is overlain by the Hornerstown Formation, which consists of nearly equal amounts of glauconitic minerals and siderite. The base of the Hornerstown Formation is marked by a concentration of siderite nodules containing reworked fossils. This layer also contains a few fossils of organisms that were living in the environment during the time of reworking. At some downdip sites, there is an additional layer (the Burrowed Unit), which is sandwiched between the top of the Pinna Layer and the concentrated bed of nodules. This unit is very thin and is characterized by large burrows piping down material from above. The Pinna Layer is abundantly fossiliferous and represents a diverse, nearshore marine community. It contains approximately 110 species of bivalves, gastropods, cephalopods, echinoids, sponges, annelids, bryozoans, crustaceans, and dinoflagellates. The cephalopods include Eutrephoceras dekayi (Morton, 1834), Pachydiscus (Neodesmoceras) mokotibensis Collignon, 1952, Sphenodiscus lobatus (Tuomey, 1856), Eubaculites carinatus (Morton, 1834), Eubaculites latecarinatus (Brunnschweiler, 1966), Discoscaphites iris (Conrad, 1858), Discoscaphites sphaeroidalis Kennedy and Cobban, 2000, Discoscaphites minardi Landman et al., 2004b, Discoscaphites gulosus (Morton, 1834), and Discoscaphites jerseyensis, n.sp. The dinoflagellates include Palynodinium grallator Gocht, 1970, Thalassiphora pelagica (Eisenack, 1954) Eisenack & Gocht, 1960, Deflandrea galeata (Lejeune-Carpentier, 1942) Lentin & Williams, 1973, and Disphaerogena carposphaeropsis Wetzel, 1933. These ammonites and dinoflagellates are indicative of the uppermost Maastrichtian, corresponding to the upper part of calcareous nannofossil Subzone CC26b. The mode of occurrence of the fossils in the Pinna Layer suggests an autochthonous accumulation with little or no postmortem transport. Many of the benthic organisms are preserved in life position. For example, specimens of Pinna laqueata Conrad, 1858, are oriented in a vertical position, similar to that of modern members of this genus. The echinoids also occur in aggregations of hundreds of individuals, suggesting gregarious feeding behavior. In addition, there are monospecific clusters of baculites and scaphites. These clusters are biological in origin and could not have been produced by hydraulic means. Scaphite jaws are also present, representing the first reports of these structures in the Upper Cretaceous of the Atlantic Coastal Plain. They occur both as isolated specimens and inside the body chamber, and indicate little or no postmortem transport. The Pinna Layer represents a geologically short interval of time. The fact that most of the animals are mature suggests that the community persisted for at least 5-10 years. If multiple generations of animals are present, perhaps reflecting multiple episodes of colonization and burial, then this unit probably represents more time, amounting to several tens of years. The fact that the Pinna Layer is truncated at the top implies a still longer period of time, amounting to hundreds of years. These age estimates are consistent with observed rates of sedimentation in nearshore environments. Iridium analyses of 37 samples of sediment from three sites in the Manasquan River Basin reveal an elevated concentration of iridium of 520 pg/g, on average, at the base of the Pinna Layer. The iridium profile is aymmetric with an abrupt drop off above the base of this unit and a gradual decline below the base. The elevated concentration of iridium is not as high as that recorded from some other Cretaceous/Tertiary boundary sections. However, it is sufficiently above background level to suggest that it is related to the global Ir anomaly documented at many other localities, and attributed to a bolide impact. The position of the iridium anomaly at the base of the Pinna Layer is inconsistent with the biostratigraphic data, because this anomaly occurs below the unit containing fossils indicative of the uppermost Maastrichtian. We present two alternative hypotheses: (1) If the enriched concentration of iridium is in place, it marks the Cretaceous/Tertiary boundary by reference to the global stratotype section and point at El Kef, Tunisia. The position of the iridium anomaly further implies that the Pinna community was living at the moment of impact and may even have flourished in its immediate wake. Subsequently, the community may have been buried by pulses of mud-rich sediment, possibly associated with enhanced riverine discharge following the impact. The Burrowed Unit may represent a subsequent pulse of riverine discharge that scoured the top of the Pinna Layer. (2) The iridium anomaly was originally located at the top of the Pinna Layer and was displaced downward due to bioturbation and/or chemical diffusion. This hypothesis implies that the Pinna Layer was deposited prior to the deposition of the iridium. The Pinna community may have died before or at the moment of impact. Erosion of the top of the Pinna Layer and deposition of the Burrowed Unit may have been associated with events immediately following the impact. In both hypotheses, the sea floor experienced an extended period of erosion and reworking in the early Danian, which may have lasted for several hundred thousand years, producing a concentrated lag of siderite nodules containing reworked fossils in the basal part of the Hornerstown Formation. This lag deposit is equivalent to the Main Fossiliferous Layer at the base of the Hornerstown Formation elsewhere in New Jersey. This period of erosion and reworking was probably associated with a transgression in the early Danian. The post-impact community was greatly reduced in diversity, with most of the species representing Cretaceous survivors

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Conjunction and Disjunction in Infectious Logics

In this paper we discuss the extent to which conjunction and disjunction can be rightfully regarded as such, in the context of infectious logics. Infectious logics are peculiar many-valued logics whose underlying algebra has an absorbing or infectious element, which is assigned to a compound formula whenever it is assigned to one of its components. To discuss these matters, we review the philosophical motivations for infectious logics due to Bochvar, Halldén, Fitting, Ferguson and Beall, noticing that none of them discusses our main question. This is why we finally turn to the analysis of the truth-conditions for conjunction and disjunction in infectious logics, employing the framework of plurivalent logics, as discussed by Priest. In doing so, we arrive at the interesting conclusion that —in the context of infectious logics— conjunction is conjunction, whereas disjunction is not disjunction

Gene content evolution in the arthropods

Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity

Archive of Darkness:William Kentridge's Black Box/Chambre Noire

Situating itself in histories of cinema and installation art, William Kentridge's Black Box/Chambre Noire (2005) raises questions about screens, exhibition space, site-specificity and spectatorship. Through his timely intervention in a debate on Germany’s colonial past, Kentridge’s postcolonial art has contributed to the recognition and remembrance of a forgotten, colonial genocide. This article argues that, by transposing his signature technique of drawings for projection onto a new set of media, Kentridge explores how and what we can know through cinematic projection in the white cube. In particular, his metaphor of the illuminated shadow enables him to animate archival fragments as shadows and silhouettes. By creating a multi-directional archive, Black Box enables an affective engagement with the spectres of colonialism and provides a forum for the calibration of moral questions around reparation, reconciliation and forgiveness