Selective cytotoxic T-lymphocyte targeting of tumor immune escape variants

Defects in major histocompatibility complex (MHC) class I-restricted antigen presentation are frequently observed in human cancers and result in escape of tumors from cytotoxic T lymphocyte (CTL) immune surveillance in mice. Here, we show the existence of a unique category of CTLs that can prevent this escape. The CTLs target an alternative repertoire of peptide epitopes that emerge in MHC class I at the surface of cells with impaired function of transporter associated with antigen processing (TAP), tapasin or the proteasome. These peptides, although derived from self antigens such as the commonly expressed Lass5 protein (also known as Trh4), are not presented by normal cells. This explains why they act as immunogenic neoantigens. The newly discovered epitopes can be exploited for immune intervention against processing-deficient tumors through adoptive T-cell transfer or peptide vaccination.     

Crystal structures of interleukin-2 tyrosine kinase and their implications for the design of selective inhibitors

Interleukin-2 tyrosine kinase, Itk, is an important member of the Tec family of non-receptor tyrosine kinases that play a central role in signaling through antigen receptors such as the T-cell receptor, B-cell receptor, and Fcepsilon. Selective inhibition of Itk may be an important way of modulating many diseases involving heightened or inappropriate activation of the immune system. In addition to an unliganded nonphophorylated Itk catalytic kinase domain, we determined the crystal structures of the phosphorylated and nonphosphorylated kinase domain bound to staurosporine, a potent broad-spectrum kinase inhibitor. These structures are useful for the design of novel, highly potent and selective Itk inhibitors and provide insight into the influence of inhibitor binding and phosphorylation on the conformation of Itk.     

The NeuC protein of Escherichia coli K1 is a UDP N-acetylglucosamine 2-epimerase

The K1 capsule is an essential virulence determinant of Escherichia coli strains that cause meningitis in neonates. Biosynthesis and transport of the capsule, an alpha-2,8-linked polymer of sialic acid, are encoded by the 17-kb kps gene cluster. We deleted neuC, a K1 gene implicated in sialic acid synthesis, from the chromosome of EV36, a K-12-K1 hybrid, by allelic exchange. Exogenously added sialic acid restored capsule expression to the deletion strain (DeltaneuC), confirming that NeuC is necessary for sialic acid synthesis. The deduced amino acid sequence of NeuC showed similarities to those of UDP-N-acetylglucosamine (GlcNAc) 2-epimerases from both prokaryotes and eukaryotes. The NeuC homologue from serotype III Streptococcus agalactiae complements DeltaneuC. We cloned the neuC gene into an intein expression vector to facilitate purification. We demonstrated by paper chromatography that the purified neuC gene product catalyzed the formation of [2-(14)C]acetamidoglucal and [N-(14)C]acetylmannosamine (ManNAc) from UDP-[(14)C]GlcNAc. The formation of reaction intermediate 2-acetamidoglucal with the concomitant release of UDP was confirmed by proton and phosphorus nuclear magnetic resonance spectroscopy. NeuC could not use GlcNAc as a substrate. These data suggest that neuC encodes an epimerase that catalyzes the formation of ManNAc from UDP-GlcNAc via a 2-acetamidoglucal intermediate. The unexpected release of the glucal intermediate and the extremely low rate of ManNAc formation likely were a result of the in vitro assay conditions, in which a key regulatory molecule or protein was absent.     

Old-field secondary succession in SE Spain: can fire divert it?

In the Mediterranean Basin, most cultivated areas were abandoned in the last century and are now in various stages of old-field succession. The aim of this work was to analyse the successional trajectories of these ecosystems, and to assess possible deviations in these pathways due to fire occurrence at high or low recurrence levels. Old-fields abandoned either about 50 or about 100 years ago were selected in SE Spain. Within the 50-year-old abandoned fields, plots were established which had been burned by 1, 2 and 3 fires in the last 25 years. Cover values of vascular species were sampled and then analysed by means of multivariate analysis. Euclidean distances between resulting communities were used as an indicator of the possible deviation from the unburned successional pathway. Our results pointed to the possibility that different successional pathways may exist depending on fire occurrence and recurrence. In the absence of fire, the vegetation is dominated by pioneer species, mainly Pinus. With the passage of time this vegetation will become dominated by later successional tree species (Quercus). However, when early-successional communities are affected by fire, the succession can be diverted. A single fire is enough to change Pinus forests into alternative stable states dominated by Rosmarinus officinalis shrub communities, where the colonisation of species in later successional stages is arrested. This deviation increases in high fire recurrence regimes where the vegetation changes to dwarf shrubs and herbs.     

Placozoa and the evolution of Metazoa and intrasomatic cell differentiation

The multicellular Metazoa evolved from single-celled organisms (Protozoa) and usually – but not necessarily – consist of more cells than Protozoa. In all cases, and thus by definition, Metazoa possess more than one somatic cell type, i.e. they show-in sharp contrast to protists–intrasomatic differentiation. Placozoa have the lowest degree of intrasomatic variation; the number of somatic cell types according to text books is four (but see also Jakob W, Sagasser S, Dellaporta S, Holland P, Kuhn K, and Schierwater B. The Trox-2 Hox/ParaHox gene of Trichoplax (Placozoa) marks an epithelial boundary. Dev Genes Evol 2004;214:170–5). For this and several other reasons Placozoa have been regarded by many as the most basal metazoan phylum. Thus, the morphologically most simply organized metazoan animal, the placozoan Trichoplax adhaerens, resembles a unique model system for cell differentiation studies and also an intriguing model for a prominent “urmetazoon” hypotheses—the placula hypothesis. A basal position of Placozoa would provide answers to several key issues of metazoan-specific inventions (including for example different lines of somatic cell differentiation leading to organ development and axis formation) and would determine a root for unraveling their evolution. However, the phylogenetic relationships at the base of Metazoa are controversial and a basal position of Placozoa is not generally accepted (e.g. Schierwater B, DeSalle R. Can we ever identify the Urmetazoan? Integr Comp Biol 2007;47:670–76; DeSalle R, Schierwater B. An even “newer” animal phylogeny. Bioessays 2008;30:1043–47). Here we review and discuss (i) long-standing morphological evidence for the simple placozoan bauplan resembling an ancestral metazoan stage, (ii) some rapidly changing alternative hypotheses derived from molecular analyses, (iii) the surprising idea that triploblasts (Bilateria) and diploblasts may be sister groups, and (iv) the presence of genes involved in cell differentiation and signaling pathways in the placozoan genome.     

Human enhancement and sexual dimorphism

I argue that the existence of sexual dimorphism poses a profound challenge to those philosophers who wish to deny the moral significance of the idea of 'normal human capacities' in debates about the ethics of human enhancement. The biological sex of a child will make a much greater difference to their life prospects than many of the genetic variations that the philosophical and bioethical literature has previously been concerned with. It seems, then, that bioethicists should have something to say about the choice between a male and a female embryo. Either, 1) parents have reason to choose boys over girls; (2) parents have reason to choose girls over boys; or, (3) parents have neither reason to choose girls over boys nor reason to choose boys over girls. Embracing either of the first two alternatives has strongly counterintuitive--and arguably morally repugnant--consequences. To motivate the third option we must either make reference to the idea of 'normal human capacities' or argue that parents should consider the interests of society when thinking about what sort of children they should bring into the world - an implication that should be extremely controversial in debates about the 'new eugenics'. I conclude, then, that the idea of 'normal human capacities' is properly crucial to reasoning about the ethics of shaping future persons.     

Seed storage: maintaining seed viability and vigor for restoration use

Effective seed storage after sourcing (harvesting or purchasing) is critical to restoration practitioners and native seed producers, as it is key to maintaining seed viability. Inadequate seed storage can lead to a waste of both natural and economic resources when seeds of poor quality are sown. When working with native species with unknown storage behavior, general assumptions can be made based on studies on related species, and standard practices may be applied with caution; however, an investigation should be conducted to understand if specific storage requirements are needed and for how long seeds can be stored before they lose significant viability. In this paper of the Special Issue Standards for Native Seeds in Ecological Restoration, we provide an overview of the key concepts in seed storage and the steps to take for effective storage of native seeds for restoration use.     

Influence of livestock grazing on meadow pipit foraging behaviour in upland grassland

Changes in grazing management are believed to be responsible for declines in populations of birds breeding in grassland over the last decades. The relationships between grazing management regimes, vegetation structure and composition and the availability of invertebrate food resources to passerine birds remain poorly understood. In this study, we investigated the foraging site selection of meadow pipits (Anthus pratensis L.) breeding in high intensity sheep-grazed plots or low intensity mixed (i.e. sheep and cattle)-grazed plots. We sampled above-ground invertebrates, measured vegetation height and density and conducted a vegetation survey in areas where meadow pipits were observed to forage and areas that were randomly selected. Birds foraged in areas with a lower vegetation height and density and in areas containing a lower proportion of the dominant, tussock-forming grass species Molinia caerulea. They did not forage in areas with a total higher invertebrate biomass but at areas with preferred vegetation characteristics invertebrate biomass tended to be higher in foraging sites than random sites. The foraging distance of meadow pipits was higher in the intensively grazed plots. Our findings support the hypothesis that resource-independent factors such as food accessibility and forager mobility may determine patch selection and are of more importance as selection criteria than food abundance per se. Food accessibility seems to become an even more important selection criterion under high grazing intensity, where prey abundance and size decrease. In our upland grazing system, a low intensity, mixed grazing regime seems to provide a more suitable combination of sward height, plant diversity, structural heterogeneity and food supply for meadow pipit foraging activity compared to a more intensive grazing regime dominated by sheep.     

Are We Losing the Best Parts of Our Protected Areas in Tropical Mountains?

Protected areas (PAs) on tropical mountains undergo greater forest destruction in their lower altitudes. We compared the extent of forested, nonforested, and fragmented areas between lowland (<1000 m asl) and montane zones of the Blue Mountains inside the Blue and John Crow Mountains National Park established in Jamaica in 1993. We found that in 2008, inside the montane zone, only 4 percent of forest was cleared, and forest fragmentation was minimal. In the lowland zone, however, the percentage of forest cleared was seven times as high, and the density of fragments was 11-fold higher. We established twenty-five 0.04 ha lowland plots; ordination of tree species composition in these plots reflected a rainfall gradient, showing that plots on the wetter northern side of the Blue Mountains were floristically different from those on the drier southern side. The conservation value of the remaining lowland forest is high because of its high endemism (18% of species in our plots) and beta diversity. In addition, IUCN Red List data show that about 71 percent of threatened tree species in the Blue Mountains grow in the lowland region, 92 percent of which are endemic. From these findings, we identify a ‘protected area hotspot zone’, which lies between the PA boundary and the core high-altitude zone, and which should be instituted in IUCN categories I and II PAs.     

Temporal instability in tree-growth/climate response in the Lower Bavarian Forest region: implications for dendroclimatic reconstruction

This paper explores the temporal stability of growth/climate relationships in ring-width chronologies of Norway spruce [ Picea abies (L.) Karst] and silver fir ( Abies alba Mill) in the Lower Bavarian Forest region in southern Germany. These chronologies were compiled, using both historic and living tree-ring data, with the main aim of developing a dendroclimatic reconstruction for the region covering the last 500 years. Moving window correlation analysis shows that prior to the twentieth century, both species co-vary in a similar way (1480–1899 mean r =0.66). There is no significant correlation between the species chronologies since ca. 1930, which partly reflects anomalous growth trends in the fir chronology since ca. 1960. Multiple regression analysis was utilised to assess the ability of both species chronologies to model March–August precipitation. The precipitation signal of the spruce data was found to be both stronger than the fir data (1872–1930 calibration: r ²=0.45 vs 0.25) and more time stable. After ca. 1930, the fir chronology loses it ability to model March–August precipitation until there is no climate signal at all in the fir data in recent decades. The spruce data also express a later weakening in their climate signal in the mid 1970s. We present compelling evidence indicating that the anomalous trends observed in the fir data, since the mid 1960s, appear to be predominantly related to local SO₂ emissions from power plants and refineries. It is also likely that this local anthropogenic forcing is the cause of the weakening of the climate signal in the spruce data since the mid 1970s. The conclusions from this study are: (1) The fir tree-ring data cannot be used for traditional dendroclimatic calibration, although prior to the twentieth century the decadal variability in the fir data is very similar to spruce and so these data could be used to extend potential reconstructions in the future; (2) The recent decline and recovery event in the fir data appears to be unique to the twentieth century and is not part of a natural episodic phenomenon; (3) Traditional dendroclimatic calibration of March–August precipitation will be made using solely the spruce ring-width data. However, due to SO₂ forcing in recent decades, the calibration period will be shortened to the 1871–1978 period.