A palaeontological and phylogenetical analysis of squaliform sharks (Chondrichthyes: Squaliformes) based on dental characters

Squaliformes comprise the major proportion of modern deep-water sharks, yet their fossil history and phylogenetic relationships are still poorly understood. New analyses have been undertaken, however, and new living and fossil species have been discovered during the past 10 years. A cladistic analysis involving 29 dental characters has been made and most living and fossil genera are included. On the basis of their dental morphology, the monophyly of the Squaliformes can be supported if the fossil genus Protospinax is excluded. The traditional phylogenetic positions of most living genera, Protosqualus, Cretascymnus and Eoetmopterus, are confirmed despite the fact that the Oxynotidae, Etmopterinae, Palaeomicroides, Proetmopterus and Microetmopterus have some atypical phylogenetic relationships within the Squaliformes. The addition of the palaeontological data in a phylogenetic tree including fossil and living Squaliformes demonstrates some gaps in the fossil record. Nevertheless, and as a consequence of that stratigraphy-phylogeny inference, two particular events can be pinpointed in the history of the Squaliformes: the first one occurs after the major Cenomanian-Turonian anoxic event and the second one after the Cretaceous/Tertiary crisis. The first radiation involves the majority of the living Squaliformes (Somniosinae, Centrophorinae, most of the Etmopterinae, Oxynotinae) in deep-sea waters, the second, the more epipelagic sharks (most of the Dalatiidae), suggesting a secondary adaptation to more shallow environments.     

Lapworthellids and other skeletonised microfossils from the Cambrian Stage 3 of the northern Montagne Noire,southern France

The Montagne Noire (southern France) possesses one of the most complete Cambrian successions in the western peri-Gondwana margin and might provide a good stratigraphic reference for both regional charts and international correlations. However, to date, the lower Cambrian succession of the northern Montagne Noire has been supposed to be devoid of biostratigraphically significant fossils. The complex tectonostratigraphic framework of the area (a range divided into Axial Zone, northern and southern Montagne Noire) exacerbated problems related to regional correlations and palaeogeographic reconstructions. As a result, the chronostratigraphic context of the lower Cambrian of northern Montagne Noire is still uncertain and stratigraphic reports have broadly relied on putative lithostratigraphic correlations with the southern Montagne Noire. The purpose of this study is to characterise, for the first time, the fossil record of carbonate beds and lenses of the northern Montagne Noire occurring at the top of the siliciclastic-dominated Marcory Formation, in order to provide regional bio- and chronostratigraphic constraints on lower Cambrian strata. Moreover, this study is aimed at improving international chronostratigraphic correlation. Carbonate beds and lenses cropping out along the Orque Cliff, in the Mélagues thrust slice, were investigated. They yielded a faunal assemblage constituted of molluscs (Igorella cf. ungulata and Igorella moncereti n. sp.), hyoliths (Conotheca brevica), chancelloriids (Archiasterella cf. pentactina and Allonnia sp.) and tommotiids (Lapworthella rete). L. rete is recorded in upper Meishucunian (Cambrian Stage 3) strata of the Yangtze Platform (South China) where it is used as index fossil of the Cambrian Stage 3 Sinosachites flabelliformis–Tannuolina zhangwentangi Assemblage Zone. Therefore, the presence of this tommotiid provides evidence that the studied carbonate beds and lenses are Cambrian Age 3 (Atdabanian according to the Siberian chart). The upper part of the Marcory Formation in the Mélagues slice, dated as Cambrian Stage 3, might represent a lateral equivalent of the mixed (carbonate-siliciclastic) Pardailhan Formation defined in the southern Montagne Noire.     

Ultrastructure and Composition of the Nannochloropsis gaditana Cell Wall

Marine algae of the genus Nannochloropsis are promising producers of biofuel precursors and nutraceuticals and are also harvested commercially for aquaculture feed. We have used quick-freeze, deep-etch electron microscopy, Fourier transform infrared spectroscopy, and carbohydrate analyses to characterize the architecture of the Nannochloropsis gaditana (strain CCMP 526) cell wall, whose recalcitrance presents a significant barrier to biocommodity extraction. The data indicate a bilayer structure consisting of a cellulosic inner wall (∼75% of the mass balance) protected by an outer hydrophobic algaenan layer. Cellulase treatment of walls purified after cell lysis generates highly enriched algaenan preparations without using the harsh chemical treatments typically used in algaenan isolation and characterization. Nannochloropsis algaenan was determined to comprise long, straight-chain, saturated aliphatics with ether cross-links, which closely resembles the cutan of vascular plants. Chemical identification of >85% of the isolated cell wall mass is detailed, and genome analysis is used to identify candidate biosynthetic enzymes.     

A Coarray Fortran implementation to support data-intensive application development

In this paper, we describe our experiences in implementing and applying Coarray Fortran (CAF) for the development of data-intensive applications in the domain of Oil and Gas exploration. The successful porting of reverse time migration (RTM), a data-intensive algorithm and one of the largest uses of computational resources in seismic exploration, is described, and results are presented demonstrating that the CAF implementation provides comparable performance to an equivalent MPI version. We then discuss further language extensions for supporting scalable parallel I/O operating on the massive data sets that are typical of applications used in seismic exploration.     

The Intrinsically Disordered Domain of the Antitoxin Phd Chaperones the Toxin Doc against Irreversible Inactivation and Misfolding

The toxin Doc from the phd/doc toxin-antitoxin module targets the cellular translation machinery and is inhibited by its antitoxin partner Phd. Here we show that Phd also functions as a chaperone, keeping Doc in an active, correctly folded conformation. In the absence of Phd, Doc exists in a relatively expanded state that is prone to dimerization through domain swapping with its active site loop acting as hinge region. The domain-swapped dimer is not capable of arresting protein synthesis in vitro, whereas the Doc monomer is. Upon binding to Phd, Doc becomes more compact and is secured in its monomeric state with a neutralized active site.     

Mechanism of cholesterol‐assisted oligomeric channel formation by a short Alzheimer β‐amyloid peptide

Alzheimer β‐amyloid (Aβ) peptides can self‐organize into oligomeric ion channels with high neurotoxicity potential. Cholesterol is believed to play a key role in this process, but the molecular mechanisms linking cholesterol and amyloid channel formation have so far remained elusive. Here, we show that the short Aβ22‐35 peptide, which encompasses the cholesterol‐binding domain of Aβ, induces a specific increase of Ca²⁺ levels in neural cells. This effect is neither observed in calcium‐free medium nor in cholesterol‐depleted cells, and is inhibited by zinc, a blocker of amyloid channel activity. Double mutations V24G/K28G and N27R/K28R in Aβ22‐35 modify cholesterol binding and abrogate channel formation. Molecular dynamic simulations suggest that cholesterol induces a tilted α‐helical topology of Aβ22‐35. This facilitates the establishment of an inter‐peptide hydrogen bond network involving Asn‐27 and Lys‐28, a key step in the octamerization of Aβ22‐35 which proceeds gradually until the formation of a perfect annular channel in a phosphatidylcholine membrane. Overall, these data give mechanistic insights into the role of cholesterol in amyloid channel formation, opening up new therapeutic options for Alzheimer's disease.