A Hypothesis-Based Approach to Landscape Change in Suðuroy,Faroe Islands

Hovsdalur, an area delimited by the great cirques of upland central Suðuroy, draining into the valley of the Hovsá and terminating in the east at the coastal amphitheatre of Hovsfjø rdur, is a microcosm of the Faroes. The area contains the physical and economic features which characterize the greater part of the island group—mountain, valley, and coast, and marine, cultivation, and grazing environments. Data comprising mainly geomorphological, palynological, and pedological evidence, covering the period prior to and subsequent to the initial Norse settlement (landnám), are used to test a series of hypotheses which exemplify the human ecology of the area. Not all the hypotheses, or aspects of them, proved acceptable—the Norse period clearly coincided with a number of vegetational and pedological changes, but this must be set partly against a backdrop of long-term geomorphological activity.     

Saccharomyces cerevisiae MutLalpha is a mismatch repair endonuclease

MutL homologs are crucial for mismatch repair and genetic stability, but their function is not well understood. Human MutLalpha (MLH1-PMS2 heterodimer) harbors a latent endonuclease that is dependent on the integrity of a PMS2 DQHA(X)2E(X)4E motif (Kadyrov, F. A., Dzantiev, L., Constantin, N., and Modrich, P. (2006) Cell 126, 297-308). This sequence element is conserved in many MutL homologs, including the PMS1 subunit of Saccharomyces cerevisiae MutLalpha, but is absent in MutL proteins from bacteria like Escherichia coli that rely on d(GATC) methylation for strand directionality. We show that yeast MutLalpha is a strand-directed endonuclease that incises DNA in a reaction that depends on a mismatch, yMutSalpha, yRFC, yPCNA, ATP, and a pre-existing strand break, whereas E. coli MutL is not. Amino acid substitution within the PMS1 DQHA(X)2E(X)4E motif abolishes yMutLalpha endonuclease activity in vitro and confers strong genetic instability in vivo, but does not affect yMutLalpha ATPase activity or the ability of the protein to support assembly of the yMutLalpha.yMutSalpha.heteroduplex ternary complex. The loaded form of yPCNA may play an important effector role in directing yMutLalpha incision to the discontinuous strand of a nicked heteroduplex.     

N-glycans on Nipah virus fusion protein protect against neutralization but reduce membrane fusion and viral entry

Nipah virus (NiV) is a deadly emerging paramyxovirus. The NiV attachment (NiV-G) and fusion (NiV-F) envelope glycoproteins mediate both syncytium formation and viral entry. Specific N-glycans on paramyxovirus fusion proteins are generally required for proper conformational integrity and biological function. However, removal of individual N-glycans on NiV-F had little negative effect on processing or fusogenicity and has even resulted in slightly increased fusogenicity. Here, we report that in both syncytium formation and viral entry assays, removal of multiple N-glycans on NiV-F resulted in marked increases in fusogenicity (>5-fold) but also resulted in increased sensitivity to neutralization by NiV-F-specific antisera. The mechanism underlying the hyperfusogenicity of these NiV-F N-glycan mutants is likely due to more-robust six-helix bundle formation, as these mutants showed increased fusion kinetics and were more resistant to neutralization by a fusion-inhibitory reagent based on the C-terminal heptad repeat region of NiV-F. Finally, we demonstrate that the fusogenicities of the NiV-F N-glycan mutants were inversely correlated with the relative avidities of NiV-F's interactions with NiV-G, providing support for the attachment protein "displacement" model of paramyxovirus fusion. Our results indicate that N-glycans on NiV-F protect NiV from antibody neutralization, suggest that this "shielding" role comes together with limiting cell-cell fusion and viral entry efficiencies, and point to the mechanisms underlying the hyperfusogenicity of these N-glycan mutants. These features underscore the varied roles that N-glycans on NiV-F play in the pathobiology of NiV entry but also shed light on the general mechanisms of paramyxovirus fusion with host cells.     

The biological effects of syngeneic and allogeneic cytokine-expressing prophylactic whole cell vaccines and the influence of irradiation in a murine melanoma model

Allogeneic whole tumour cell vaccines are inherently practical compared with autologous vaccines. Cell lines are derived from allogeneic tumour, grown in bulk and then administered as a vaccine to the patient, following irradiation, which not only prevents any replication but also enhances antigen presentation. Protection is believed to occur through the presentation of antigens shared between the syngeneic and allogeneic tumours. Although cytokine-transfected tumour whole cell vaccines have been used clinically, little data is available comparing the effects of immunomodulatory cytokine-transfection directly on the same cells when used as both an allogeneic and autologous vaccine. To address this, weakly immunogenic B16-F10 (H-2^b) murine melanoma was transfected to secrete either GM-CSF, IL-4 or IL-7. Prophylactic vaccination of both syngeneic C57/BL6 (H-2^b) (B6) and allogeneic C3H/Hej (H-2^k) (C3H) mice showed the effects of transfected cytokine varied between models. Both GM-CSF and IL-7 significantly (P<0.05) increased the levels of protection within syngeneic B6 mice, but had a diminished effect (P>0.05) within C3H allogeneic mice. Allogeneic B16-F10 cells and syngeneic K1735 cells generated CTL against K1735 suggesting cross-reactive immunity. Using cells labeled with fluorescent dye we demonstrate that irradiated vaccines, of either syngeneic or allogeneic origin, appear to generate potent immune responses and fragments of either vaccine remain at the injection site for up to 9 days. This study shows that protection can be enhanced in vivo by using transfected cytokine, but suggests that irradiated whole cell vaccines, of either tissue-type, are rapidly processed. This leads to the conclusion that the cytokine effects are transient and thus transfection with cytokine may be of limited long-term use in situ.     

Targeted tandem affinity purification of PSD‐95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins

The molecular complexity of mammalian proteomes demands new methods for mapping the organization of multiprotein complexes. Here, we combine mouse genetics and proteomics to characterize synapse protein complexes and interaction networks. New tandem affinity purification (TAP) tags were fused to the carboxyl terminus of PSD‐95 using gene targeting in mice. Homozygous mice showed no detectable abnormalities in PSD‐95 expression, subcellular localization or synaptic electrophysiological function. Analysis of multiprotein complexes purified under native conditions by mass spectrometry defined known and new interactors: 118 proteins comprising crucial functional components of synapses, including glutamate receptors, K⁺ channels, scaffolding and signaling proteins, were recovered. Network clustering of protein interactions generated five connected clusters, with two clusters containing all the major ionotropic glutamate receptors and one cluster with voltage‐dependent K⁺ channels. Annotation of clusters with human disease associations revealed that multiple disorders map to the network, with a significant correlation of schizophrenia within the glutamate receptor clusters. This targeted TAP tagging strategy is generally applicable to mammalian proteomics and systems biology approaches to disease.     

The ecology of 3-D space use in a sexually dimorphic mammal

The distribution of animals is the result of habitat selection according to sex, reproductive status and resource availability. Little is known about how marine predators investigate their 3-dimensional space along both the horizontal and vertical axes and how temporal variation affects space use. In this study, we assessed the spatio-temporal movement of a sexually dimorphic marine mammal, the grey seal Halichoerus grypus by 1) determining seasonal home range size, 2) testing whether space use of seals was affected by water depth, and 3) investigating the vertical movement of seals according to the maximum depth of each dive. Between 1993 and 2005, we fitted 49 grey seals in the Gulf of St. Lawrence with satellite transmitters. We estimated seasonal 95% fixed-kernel home ranges for each individual. For each seal, we tested for selectivity and preference for 4 water depth classes at the home range scale and within the home range. We also evaluated the proportional number of dives made in each water depth classes according to the maximum depth of each dive. Home ranges were 10 times larger in winter than in summer. Seals generally selected habitats <50 m deep. They also mainly dove to depths of 40 m or less. At both scales of selection, preference for shallow areas decreased in winter. We also observed that adults used shallow habitats more than juveniles to establish their home range. A spatial segregation based on sex also occurred at the finer scale of selection where females were more concentrated in the shallowest parts of their home range than males. Segregation in space use according to age and sex classes occurred at both the horizontal and vertical scales. Our results emphasise the importance of studying habitat selection of marine predators in 3-dimensional space, in addition to the temporal scale.     

Ladderane phospholipids in anammox bacteria comprise phosphocholine and phosphoethanolamine headgroups

Anammox bacteria present in wastewater treatment systems and marine environments are capable of anaerobically oxidizing ammonium to dinitrogen gas. This anammox metabolism takes place in the anammoxosome which membrane is composed of lipids with peculiar staircase-like 'ladderane' hydrocarbon chains that comprise three or four linearly concatenated cyclobutane structures. Here, we applied high-performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to elucidate the full identity of these ladderane lipids. This revealed a wide variety of ladderane lipid species with either a phosphocholine or phosphoethanolamine polar headgroup attached to the glycerol backbone. In addition, in silico analysis of genome data gained insight into the machinery for the biosynthesis of the phosphocholine and phosphoethanolamine phospholipids in anammox bacteria.     

Diversity distribution and floristic differentiation of the coastal lowland vegetation: implications for the conservation of the Brazilian Atlantic Forest

Floristic differentiation and vegetation definition is an important step to recognize biome distribution and for biodiversity conservation. Here, we aim to verify if the distribution of the costal lowland vegetation in Brazilian littoral is congruent with climatic gradient and the previous vegetation definitions. Additionally we discussed the importance of terms for the Atlantic Forest conservation. Our study was based on floristic and geo-climatic data from 58 published surveys. We generate a checklist of 1088 woody species and verified species distribution according to environmental gradient using a Detrended Correspondence Analysis (DCA). We compared DCA??s groups with the a priori vegetation definition and generate an a posteriori classification using TWINSPAN. DCA and TWINSPAN resulted in groups determined mainly by rainfall (r = ?0.65) and soil sandiness (r = ?0.71). Those groups were not congruent with both the previous vegetation definitions. The coastal lowland vegetation comprises two distinctive floristic groups representing forests and scrubs that occur in wetter climates (Ombrophilous lowland forests) in the Brazilian states of Santa Catarina, Paraná and São Paulo and in drier climates of Espírito Santo, Rio de Janeiro (Restinga-Northern group) and Rio Grande do Sul (Restinga-Southern group) states. The floristic and historical relationships between Ombrophylous lowland forests and Restingas suggest that conservation initiatives should be more conservative and treat collectively all coastal lowland vegetation as a biodiversity hotspot.     

How can immunopathology shape the evolution of parasite virulence?

Immunopathology (immune-mediated pathology) is a ubiquitous cause of disease during infection, but how will parasite exploitation strategies evolve in its presence? Immunopathology can act to increase parasite fitness if it increases transmission rate, but can equally act to decrease parasite fitness if it increases host mortality. The focus here is on understanding how immunopathology, mediated through different immune mechanisms, can influence parasite fitness and how experimental manipulations of the immune system can be carried out to examine this. A better understanding of how parasite fitness scales with, or responds to, immunopathology is crucial to understanding the nature of selection acting on parasite virulence traits and will allow more informed predictions to be made regarding the trajectory of parasite virulence evolution.