The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.     

Émilie Du Châtelet's interpretation of the laws of motion in the light of 18th century mechanics

Émilie Du Châtelet is well known for her French translation of Newton's Philosophiae Naturalis Principia Mathematica. It is the first and only French translation of Newton's magnum opus. The complete work appeared in 1759 under the title Principes mathématiques de la philosophie naturelle, par feue Madame la Marquise Du Chastellet. Before translating Newton's Principia, Du Châtelet worked on her Institutions de physique. In this book she defended the Leibnizian concept of living forces – vis viva. This paper argues that both of these works were part of a critical transformation and consolidation of post-Newtonian mechanics in the early 18th century, beyond Newton and Leibniz. This will be shown by comparing Du Châtelet's translation of Newton's axioms with her own formulations of the laws of motion in light of Thomas Le Seur's and François Jacquier's Geneva edition which holds a special place among the several editions of the Principia that appeared in the early 18th century.     

The bryozoan genus Conopeum (Electridae) in New Zealand,with description of a new species and discussion of the morphological and genetic characters of Conopeum seurati (Canu, 1928)

ABSTRACT

The status of Conopeum Gray, 1848 in New Zealand is clarified, confirming the presence of three living species – one a naturalised alien, one new to science, and a third that is also known in the Pleistocene. Conopeum seurati (Canu, 1928), a Mediterranean-European species, is naturalised at three localities in New Zealand – Opua, Whangarei Harbour and Whanganui Inlet. Conopeum antipodum n. sp., previously confused with C. seurati, is an estuarine species distributed from Kaipara Harbour to Lyttelton Harbour and is also found in Te Whanga Lagoon at Chatham Island (all New Zealand localities). Conopeum oretiensis Uttley, 1951, first described from Foveaux Strait, is known as far north as Kaipara and Manukau Harbours and is known as a Pleistocene fossil from Napier, New Zealand. There is one other solely fossil New Zealand species – Plio-Pleistocene Electra ongleyi Brown, 1952 is transferred to Conopeum. Sequence data from the 18SrDNA locus confirm that Conopeum antipodum n. sp. is resolved within Conopeum and is distinct from C. seurati.

http://www.zoobank.org/urn:lsid:zoobank.org:act:4FED6730-1C70-4420-B1DA-F1D9046221DF http://www.zoobank.org/urn:lsid:zoobank.org.pub:5C130A99-0869-44A2-885C-338005FBCE07     

Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida

Deuterostomes comprise vertebrates, the related invertebrate chordates (tunicates and cephalochordates) and three other invertebrate taxa: hemichordates, echinoderms and Xenoturbella. The relationships between invertebrate and vertebrate deuterostomes are clearly important for understanding our own distant origins. Recent phylogenetic studies of chordate classes and a sea urchin have indicated that urochordates might be the closest invertebrate sister group of vertebrates, rather than cephalochordates, as traditionally believed. More remarkable is the suggestion that cephalochordates are closer to echinoderms than to vertebrates and urochordates, meaning that chordates are paraphyletic. To study the relationships among all deuterostome groups, we have assembled an alignment of more than 35,000 homologous amino acids, including new data from a hemichordate, starfish and Xenoturbella. We have also sequenced the mitochondrial genome of Xenoturbella. We support the clades Olfactores (urochordates and vertebrates) and Ambulacraria (hemichordates and echinoderms). Analyses using our new data, however, do not support a cephalochordate and echinoderm grouping and we conclude that chordates are monophyletic. Finally, nuclear and mitochondrial data place Xenoturbella as the sister group of the two ambulacrarian phyla. As such, Xenoturbella is shown to be an independent phylum, Xenoturbellida, bringing the number of living deuterostome phyla to four.     

Prediction of central nervous system embryonal tumour outcome based on gene expression.

Embryonal tumours of the central nervous system (CNS) represent a heterogeneous group of tumours about which little is known biologically, and whose diagnosis, on the basis of morphologic appearance alone, is controversial. Medulloblastomas, for example, are the most common malignant brain tumour of childhood, but their pathogenesis is unknown, their relationship to other embryonal CNS tumours is debated, and patients' response to therapy is difficult to predict. We approached these problems by developing a classification system based on DNA microarray gene expression data derived from 99 patient samples. Here we demonstrate that medulloblastomas are molecularly distinct from other brain tumours including primitive neuroectodermal tumours (PNETs), atypical teratoid/rhabdoid tumours (AT/RTs) and malignant gliomas. Previously unrecognized evidence supporting the derivation of medulloblastomas from cerebellar granule cells through activation of the Sonic Hedgehog (SHH) pathway was also revealed. We show further that the clinical outcome of children with medulloblastomas is highly predictable on the basis of the gene expression profiles of their tumours at diagnosis.     

Single mimivirus particles intercepted and imaged with an X-ray laser

X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions. Very short and extremely bright, coherent X-ray pulses can be used to outrun key damage processes and obtain a single diffraction pattern from a large macromolecule, a virus or a cell before the sample explodes and turns into plasma. The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval. Here we show that high-quality diffraction data can be obtained with a single X-ray pulse from a non-crystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source. Calculations indicate that the energy deposited into the virus by the pulse heated the particle to over 100,000?K after the pulse had left the sample. The reconstructed exit wavefront (image) yielded 32-nm full-period resolution in a single exposure and showed no measurable damage. The reconstruction indicates inhomogeneous arrangement of dense material inside the virion. We expect that significantly higher resolutions will be achieved in such experiments with shorter and brighter photon pulses focused to a smaller area. The resolution in such experiments can be further extended for samples available in multiple identical copies.