Biophysical Measurement of the Balance of Influenza A Hemagglutinin and Neuraminidase Activities

The interaction of influenza A viruses with the cell surface is controlled by the surface glycoproteins hemagglutinin (HA) and neuraminidase (NA). These two glycoproteins have opposing activities: HA is responsible for binding the host receptor (sialic acid) to allow infection, and NA is responsible for cleaving the receptor to facilitate virus release. Several studies have demonstrated that compatible levels of HA and NA activity are required for a virus to replicate efficiently. This is consequently of great interest for determining virus transmissibility. The concurrent role of these two proteins in receptor binding has never been directly measured. We demonstrate a novel biophysical approach based on bio-layer interferometry to measure the balance of the activities of these two proteins in real time. This technique measures virus binding to and release from a surface coated with either the human-like receptor analog α2,6-linked sialic acid or the avian-like receptor analog α2,3-linked sialic acid in both the presence and absence of NA inhibitors. Bio-layer interferometry measurements were also carried out to determine the effect of altering HA receptor affinity and NA stalk length on receptor binding.     

Evolution of ecospace occupancy by Mesozoic marine tetrapods

Ecology and morphology are different, and yet in comparative studies of fossil vertebrates the two are often conflated. The macroevolution of Mesozoic marine tetrapods has been explored in terms of morphological disparity, but less commonly using ecological‐functional categories. Here we use ecospace modelling to quantify ecological disparity across all Mesozoic marine tetrapods. We document the explosive radiation of marine tetrapod groups in the Triassic and their rapid attainment of high ecological disparity. Late Triassic extinctions led to a marked decline in ecological disparity, and the recovery of ecospace and ecological disparity was sluggish in the Early Jurassic. High levels of ecological disparity were again achieved by the Late Jurassic and maintained during the Cretaceous, when the ecospace became saturated by the Late Cretaceous. Sauropterygians, turtles and ichthyosauromorphs were the largest contributors to ecological disparity. Throughout the Mesozoic, we find that established groups remained ecologically conservative and did not explore occupied or vacant niches. Several parts of the ecospace remained vacant for long spans of time. Newly evolved, radiating taxa almost exclusively explored unoccupied ecospace, suggesting that abiotic releases are needed to empty niches and initiate diversification. In the balance of evolutionary drivers in Mesozoic marine tetrapods, abiotic factors were key to initiating diversification events, but biotic factors dominated the subsequent generation of ecological diversity.     

The hierarchy of directional interactions in visual motion processing

It is well known that context influences our perception of visual motion direction. For example, spatial and temporal context manipulations can be used to induce two well-known motion illusions: direction repulsion and the direction after-effect (DAE). Both result in inaccurate perception of direction when a moving pattern is either superimposed on (direction repulsion), or presented following adaptation to (DAE), another pattern moving in a different direction. Remarkable similarities in tuning characteristics suggest that common processes underlie the two illusions. What is not clear, however, is whether the processes driving the two illusions are expressions of the same or different neural substrates. Here we report two experiments demonstrating that direction repulsion and the DAE are, in fact, expressions of different neural substrates. Our strategy was to use each of the illusions to create a distorted perceptual representation upon which the mechanisms generating the other illusion could potentially operate. We found that the processes mediating direction repulsion did indeed access the distorted perceptual representation induced by the DAE. Conversely, the DAE was unaffected by direction repulsion. Thus parallels in perceptual phenomenology do not necessarily imply common neural substrates. Our results also demonstrate that the neural processes driving the DAE occur at an earlier stage of motion processing than those underlying direction repulsion.     

The outcome of poliovirus infections in K562 cells is cytolytic rather than persistent after hemin-induced differentiation.

K562-Mu erythroleukemia cells readily establish a long-term persistent poliovirus infection characterized by continuous virus production in the absence of complete p220 cleavage and host translation shutoff (R. E. Lloyd and M. Bovee, Virology 194:200-209, 1993). The mechanism of resistance appears to be modulated at the intracellular level and to be related to decreased virus-mediated cytopathic effects (P. A. Benton, J. W. Murphy, and R. E. Lloyd Virology 213:7-18, 1995). It is well documented that hemin induces the differentiation of K562 cells and alters the expression of several host proteins. We report here that growth of K562 cells in hemin prior to poliovirus infection results in a dose-dependent increase in virus-induced cell lysis and thereby alters the normally persistent outcome of infection to a more lytic phenotype. K562 cells infected after hemin treatment displayed increased host translation shutoff, p220 cleavage, viral protein synthesis, and viral RNA accumulation compared with nontreated cells. Since hemin treatment of K562 cells also induced the increased expression of several heat shock proteins (Hsp70, Hsc70, Hsp90, and cohort p60), we tested the hypothesis that their increased expression may play a role in altering poliovirus infection in hemin-treated K562 cells. However, neither heat stress nor oxidative stress, inducers of heat shock protein synthesis, altered the outcome (of virus infections. In addition, we report the novel finding that subunits of two translation initiation factors, p220 (eIF-4G) and eIF-2alpha, are cleaved as a result of hemin treatment of K562 cells. It is proposed that hemin alters the expression of specific host proteins in K562 cells, probably other than heat shock proteins, which changes the initial response to poliovirus infections from persistent to lytic.     

Neoselachian (Chondrichthyes, Elasmobranchii) diversity across the Cretaceous-Tertiary boundary

Fishes are often thought to have passed through mass extinctions, including the Cretaceous-Tertiary (KT) event, relatively unscathed. We show that neoselachian sharks suffered a major extinction at the K/T boundary. Out of 41 families, 7 became extinct (17±12%). The proportional measure increases at lower taxic levels: 56±10% loss of genera (loss of 60 out of 107) and 84±5% loss of species (loss of 182 out of 216). However, the Maastrichtian and Danian are characterized by a high number of singleton taxa. Excluding singletons we have calculated a 34±11% loss of genera and a 45±9% loss of species. The simple completeness metric (SCM) for genera displays a decrease from the Maastrichtian (94%) to the Danian (85%) indicating a rather complete fossil record of neoselachian genera. The extinctions were heavy among both sharks and batoids (skates and rays), but most severe among batoids, which lost almost all identifiable species. There were equal losses among open marine apex predators (loss of Anacoracidae, Cretoxyrhinidae, and Scapanorhynchidae) and durophagous demersal forms from the continental shelf and shallow seas (Hypsobatidae, Parapaleobatidae, Sclerorhynchidae, Rhombodontidae). Benthopelagic and deep-sea forms were apparently little affected. New families with similar ecological roles (Carcharhinidae, Isuridae, Torpedinidae) replaced these families in the Danian, and full diversity of the different shark and batoid groups had been recovered by the end of the Paleocene or early Eocene. Sharks and rays suffered levels of extinction entirely in line with other groups of organisms at the K/T extinction event.     

Increased initiation and growth of tumor cell lines, cancer stem cells and biopsy material in mice using basement membrane matrix protein (Cultrex or Matrigel) co-injection

This protocol requires 2-4 h and presents a method for injecting tumor cells, cancer stem cells or dispersed biopsy material into subcutaneous or orthotopic locations within recipient mice. The tumor cells or biopsy are mixed with basement membrane matrix proteins (CultrexBME or Matrigel) at 4 °C and then injected into recipient animals at preferred anatomical sites. Tumor cells can also be co-injected with additional cell types, such as fibroblasts, stromal cells, endothelial cells and so on. Details are given on appropriate cell numbers, handling and concentration of the basement membrane proteins, recipient animals, injection location and techniques. This procedure enables the growth of tumors from cells or biopsy material (tumor graft) with greater efficiency of take and growth, and with retention of the primary tumor phenotype based on histology. Co-injection with additional cell types provides more physiological models of human cancers for use in drug screening and studying cancer biology.     

Dinosaurs and other tetrapods in an Early Cretaceous bauxite-filled fissure, northwestern Romania

The bauxite mine at Cornet near Oradea in northwestern Romania produced thousands of bones in an excavation in 1978, mainly from ornithopod dinosaurs and rarer pterosaurs. Bird specimens reported previously from this fauna are equivocal. The fossils are disarticulated bones in good condition which occur highly concentrated in lenses within bauxite clays, which are dated as Berriasian (earliest Cretaceous). The bauxite represents detrital material washed into deep fissures and caves formed within a karst of uplifted Tithonian (latest Jurassic) marine limestones. The bones are generally uniform in size and shape, and they are abraded, evidence for considerable transport and for winnowing of the deposit. The area was one of several islands on the northern shore of Tethys, and it was inundated by the sea later in the Early Cretaceous. There is evidence for insular adaptations in the dinosaur faunas. The ornithopod dinosaurs may include several taxa, but they are smaller on average than an assemblage of typical Wealden ornithopods, perhaps because of dwarfing on the island. In addition, sauropods are absent and theropods are barely represented in the fauna. The fauna is geographically significant since it shows relationships with western Europe and with Asia.     

The Luoping biota: exceptional preservation, and new evidence on the Triassic recovery from end-Permian mass extinction

The timing and nature of biotic recovery from the devastating end-Permian mass extinction (252 Ma) are much debated. New studies in South China suggest that complex marine ecosystems did not become re-established until the middle–late Anisian (Middle Triassic), much later than had been proposed by some. The recently discovered exceptionally preserved Luoping biota from the Anisian Stage of the Middle Triassic, Yunnan Province and southwest China shows this final stage of community assembly on the continental shelf. The fossil assemblage is a mixture of marine animals, including abundant lightly sclerotized arthropods, associated with fishes, marine reptiles, bivalves, gastropods, belemnoids, ammonoids, echinoderms, brachiopods, conodonts and foraminifers, as well as plants and rare arthropods from nearby land. In some ways, the Luoping biota rebuilt the framework of the pre-extinction latest Permian marine ecosystem, but it differed too in profound ways. New trophic levels were introduced, most notably among top predators in the form of the diverse marine reptiles that had no evident analogues in the Late Permian. The Luoping biota is one of the most diverse Triassic marine fossil Lagerstätten in the world, providing a new and early window on recovery and radiation of Triassic marine ecosystems some 10 Myr after the end-Permian mass extinction.