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

Developing a partcipatory approach to seed production and varietal selection

The performance of UK winter wheat varieties was tested under organic conditions involving farmer participation. Three breadmaking varieties (Hereward, Solstice and Xi19) and their mixture (1:1:1) were grown at 19 UK farms in 2003/04 and 2004/05. The variability of productivity on organic farms was illustrated with more variation among farm sites than among varieties. Seed health was generally high over all sites. Although the trials were successful, more time was needed at project initiation to improve farmer involvement. Some farmers expected more researcher visits, and were reticent about assessing the trials themselves. In contrast, some participants valued the variety performance data on their farms particularly when related to that of other growers. The balance between the goals of the researchers relative to the farmers needs to be defined at project initiation

MOTMOT:Models of trait macroevolution on trees (an update)

The disparity in species’ traits arises through variation in the tempo and mode of evolution over time and between lineages. Understanding these patterns is a core goal in evolutionary biology. Here we present the comprehensively updated r package MOTMOT: Models Of Trait Macroevolution On Trees that contains methods to fit and test models of continuous trait evolution on phylogenies of extant and extinct species. MOTMOT provides functions to investigate a range of evolutionary hypotheses, including flexible approaches to investigate heterogeneous rates and modes of evolution, models of trait change under interspecific competition and patterns of trait change across significant evolutionary transitions such as mass extinctions. We introduce and test novel algorithms of heterogeneous tempo and mode of evolution that allow for phylogeny-wide shifts in evolution at specific times on a tree. We use these new MOTMOT functions to highlight an exceptionally high rate of mammalian body mass evolution for 10 million years following the Cretaceous–Palaeogene mass extinction. These methods provide biologists and palaeontologists with the tools to analyse continuous trait data on phylogenies, including large trees of up to thousands of species.</p

MDS_IES_DB: a database of macronuclear and micronuclear genes in spirotrichous ciliates

Ciliated protozoa have two kinds of nuclei: Macronuclei (MAC) and Micronuclei (MIC). In some ciliate classes, such as spirotrichs, most genes undergo several layers of DNA rearrangement during macronuclear development. Because of such processes, these organisms provide ideal systems for studying mechanisms of recombination and gene rearrangement. Here, we describe a database that contains all spirotrich genes for which both MAC and MIC versions are sequenced, with consistent annotation and easy access to all the features. An interface to query the database is available at http://oxytricha.princeton.edu/dimorphism/database.htm

Model Checking CTL is Almost Always Inherently Sequential

The model checking problem for CTL is known to be P-complete (Clarke, Emerson, and Sistla (1986), see Schnoebelen (2002)). We consider fragments of CTL obtained by restricting the use of temporal modalities or the use of negations---restrictions already studied for LTL by Sistla and Clarke (1985) and Markey (2004). For all these fragments, except for the trivial case without any temporal operator, we systematically prove model checking to be either inherently sequential (P-complete) or very efficiently parallelizable (LOGCFL-complete). For most fragments, however, model checking for CTL is already P-complete. Hence our results indicate that, in cases where the combined complexity is of relevance, approaching CTL model checking by parallelism cannot be expected to result in any significant speedup. We also completely determine the complexity of the model checking problem for all fragments of the extensions ECTL, CTL+, and ECTL+

Verifying Temporal Regular Properties of Abstractions of Term Rewriting Systems

The tree automaton completion is an algorithm used for proving safety properties of systems that can be modeled by a term rewriting system. This representation and verification technique works well for proving properties of infinite systems like cryptographic protocols or more recently on Java Bytecode programs. This algorithm computes a tree automaton which represents a (regular) over approximation of the set of reachable terms by rewriting initial terms. This approach is limited by the lack of information about rewriting relation between terms. Actually, terms in relation by rewriting are in the same equivalence class: there are recognized by the same state in the tree automaton. Our objective is to produce an automaton embedding an abstraction of the rewriting relation sufficient to prove temporal properties of the term rewriting system. We propose to extend the algorithm to produce an automaton having more equivalence classes to distinguish a term or a subterm from its successors w.r.t. rewriting. While ground transitions are used to recognize equivalence classes of terms, epsilon-transitions represent the rewriting relation between terms. From the completed automaton, it is possible to automatically build a Kripke structure abstracting the rewriting sequence. States of the Kripke structure are states of the tree automaton and the transition relation is given by the set of epsilon-transitions. States of the Kripke structure are labelled by the set of terms recognized using ground transitions. On this Kripke structure, we define the Regular Linear Temporal Logic (R-LTL) for expressing properties. Such properties can then be checked using standard model checking algorithms. The only difference between LTL and R-LTL is that predicates are replaced by regular sets of acceptable terms

A participatory methodology for large scale field trials in the UK

Farmer participation was essential in developing a uniquely useful set of wheat variety trials data on a wide range of organic farms over two years. Although the trials were successful, it became clear that some of the participating farmers felt there were some limitations in the process. These included a lack of ownership in the project and a concern for more researcher help. It was clear that a greater time in-vestment was needed at the start of the project to help with farmer understanding and ownership. De-spite the negative comments, farmers appreciated their involvement, particularly in contrasting their own views and information with that from the wider scene. Farmer participation is essential for systems-level research and this project helped to develop a small core of trained farmers and researchers

An Eocene fossil scarab beetle (Coleoptera: Scarabaeoidea) from Tanzania

A fossil scarabaeoid (Coleoptera: Scarabaeoidea) Mahengea mckayi new genus, new species – the only well-preserved insect fossil and one of only a few insects found at the site – is described from an otherwise rich Eocene (~ 45.6 mya) maar Lagerstätte at Mahenge in central northern Tanzania. Numerous fossil fishes and plants have been recovered from this site and described. The dearth of insect fossils is surprising considering their richness in other deposits of similar origin and age. We suggest that the rich fish fauna present in the oxygen-rich parts of the water in the former volcanic crater lake may have scavenged most of the terrestrial insects that fell into the water. Although the fossil described here is undoubtedly that of a member of the Scarabaeoidea, the family placement remains unsure. Significance: We describe the first Eocene fossil scarab from Africa. It is one of only a few scarab fossils from the continent and one of the best-preserved insect (invertebrate) fossils from the deposit