Project description:The interaction between the hormone hepcidin and the iron exporter ferroportin (Fpn) regulates plasma iron concentrations. Hepcidin binds to Fpn and induces its internalization and degradation, resulting in decreased iron efflux from cells into plasma. Fpn mutations in N144, Y64N, and C326 residue cause autosomal dominant disease with parenchymal iron overload, apparently due to the resistance of mutant Fpn to hepcidin-mediated internalization. To define the mechanism of resistance, we generated human Fpn constructs bearing the pathogenic mutations. The mutants localized to the cell surface and exported iron normally, but were partially or completely resistant to hepcidin-mediated internalization and continued to export iron despite the presence of hepcidin. The primary defect with exofacial C326 substitutions was the loss of hepcidin binding, which resulted in the most severe phenotype. The thiol form of C326 was essential for interaction with hepcidin, suggesting that C326-SH homology is located in or near the binding site of hepcidin. In contrast, N144 and Y64 residues were not required for hepcidin binding, but their mutations impaired the subsequent internalization of the ligand-receptor complex. Our observations explain why the mutations in C326 Fpn residue produce a severe form of hemochromatosis with iron overload at an early age.
Project description:Open framework materials such as zeolites and metalorganic frameworks are garnering tremendous interest because of their intriguing architecture and attractive functionalities. Thus, new types of open framework materials are highly sought after. Here, we present the discovery of completely new inorganic framework materials, where, in contrast to conventional inorganic open frameworks, the scaffold is not based on tetrahedral EO4 (E = main group element) but octahedral MO6 (M = transition metal) building blocks. These structural features place them closer to polyoxometalates than zeolites. The first representatives of this class of materials are [(R)24(NH4)14(PO(OH)2)6]·[M134(PO3(OH,F))96F120] (M = Co, R = C2Py = 1-ethylpyridinium and M = Ni, R = C4C1Py = 1-butyl-3-methylpyridinium) featuring interlinked fullerene-like nanosphere cavities. Having a transition metal building up the framework brings about interesting properties, for example, spin-glass behavior, and, with this particular topology, a hedgehog-like spin orientation.
Project description:The origin and deep evolution of retroviruses remain largely unclear. It has been proposed that retroviruses might have originated from a Ty3/Gypsy retrotransposon, but all known Ty3/Gypsy retrotransposons are only distantly related to retroviruses. Retroviruses and some plant Athila/Tat elements (within Ty3/Gypsy retrotransposons) independently evolved a dual RNase H domain and an env/env-like gene. Here, we reported the discovery of a novel lineage of retrotransposons, designated Odin retrotransposons, in the genomes of eight sea anemones (order Actinaria) within the Cnidaria phylum. Odin retrotransposons exhibited unique genome features, encoding a dual RNase H domain (like retroviruses) but no env gene (like most Ty3/Gypsy retrotransposons). Phylogenetic analyses based on reverse transcriptase showed that Odin retrotransposons formed a sister group to lokiretroviruses, and lokiretroviruses and Odin retrotransposons together were sister to canonical retroviruses. Moreover, phylogenetic analyses based on RNase H and integrase also supported the hypothesis that Odin retrotransposons were sisters to lokiretroviruses. Lokiretroviruses and canonical retroviruses did not form a monophyletic group, indicating that lokiretroviruses and canonical retroviruses might represent two distinct virus families. Taken together, the discovery of Odin retrotransposons narrowed down the evolutionary gaps between retrotransposons and canonical retroviruses and lokiretroviruses. IMPORTANCE The origin of retroviruses remains largely unclear. In this study, we discovered a novel retrotransposon lineage, Odin retrotransposons, within the genomes of sea anemones (order Actinaria). In contrast to retroviruses and most retrotransposons, Odin retrotransposons encode a dual RNase H domain but no env gene. Phylogenetic analyses showed that Odin retrotransposons were sisters to lokiretroviruses, and lokiretroviruses and Odin retrotransposons were sisters to retroviruses, establishing an evolutionary framework to decipher the origin of retroviruses (canonical retroviruses and lokiretroviruses). Our results provided insights into the diversity and deep evolution of LTR retrotransposons closely related to retroviruses.
Project description:BackgroundFunctional traits are the primary biotic component driving organism influence on ecosystem functions; in consequence, traits are widely used in ecological research. However, most animal trait-based studies use easy-to-measure characteristics of species that are at best only weakly associated with functions. Animal-mediated pollination is a key ecosystem function and is likely to be influenced by pollinator traits, but to date no one has identified functional traits that are simple to measure and have good predictive power.MethodsHere, we show that a simple, easy to measure trait (hairiness) can predict pollinator effectiveness with high accuracy. We used a novel image analysis method to calculate entropy values for insect body surfaces as a measure of hairiness. We evaluated the power of our method for predicting pollinator effectiveness by regressing pollinator hairiness (entropy) against single visit pollen deposition (SVD) and pollen loads on insects. We used linear models and AICC model selection to determine which body regions were the best predictors of SVD and pollen load.ResultsWe found that hairiness can be used as a robust proxy of SVD. The best models for predicting SVD for the flower species Brassica rapa and Actinidia deliciosa were hairiness on the face and thorax as predictors (R2 = 0.98 and 0.91 respectively). The best model for predicting pollen load for B. rapa was hairiness on the face (R2 = 0.81).DiscussionWe suggest that the match between pollinator body region hairiness and plant reproductive structure morphology is a powerful predictor of pollinator effectiveness. We show that pollinator hairiness is strongly linked to pollination-an important ecosystem function, and provide a rigorous and time-efficient method for measuring hairiness. Identifying and accurately measuring key traits that drive ecosystem processes is critical as global change increasingly alters ecological communities, and subsequently, ecosystem functions worldwide.
Project description:Reinforcement learning systems usually assume that a value function is defined over all states (or state-action pairs) that can immediately give the value of a particular state or action. These values are used by a selection mechanism to decide which action to take. In contrast, when humans and animals make decisions, they collect evidence for different alternatives over time and take action only when sufficient evidence has been accumulated. We have previously developed a model of memory processing that includes semantic, episodic and working memory in a comprehensive architecture. Here, we describe how this memory mechanism can support decision making when the alternatives cannot be evaluated based on immediate sensory information alone. Instead we first imagine, and then evaluate a possible future that will result from choosing one of the alternatives. Here we present an extended model that can be used as a model for decision making that depends on accumulating evidence over time, whether that information comes from the sequential attention to different sensory properties or from internal simulation of the consequences of making a particular choice. We show how the new model explains both simple immediate choices, choices that depend on multiple sensory factors and complicated selections between alternatives that require forward looking simulations based on episodic and semantic memory structures. In this framework, vicarious trial and error is explained as an internal simulation that accumulates evidence for a particular choice. We argue that a system like this forms the "missing link" between more traditional ideas of semantic and episodic memory, and the associative nature of reinforcement learning.
Project description:A minor electrophoretically fast component was found in ferritin from iron-loaded rat liver in addition to a major electrophoretically slow ferritin similar to that observed in control rats. The electrophoretically fast ferritin showed immunological identity with the slow component, but on electrophoresis in SDS it gave a peptide of 17.3 kDa, in contrast with the electrophoretically slow ferritin, which gave a major band corresponding to the L-subunit (20.7 kDa). Thus the electrophoretically fast ferritin resembles that reported by Massover [(1985) Biochim. Biophys. Acta 829, 377-386] in livers of mice with short-term parenteral iron overload. The electrophoretically fast ferritin had a lower iron content (2000 Fe atoms/molecule) than the electrophoretically slow ferritin (3000 Fe atoms/molecule). Removal and re-incorporation of iron was possible without effect on the electrophoretic mobility of either ferritin species. On subcellular fractionation the electrophoretically fast ferritin was enriched in pellet fractions and was the sole soluble ferritin isolated from iron-laden secondary lysosomes (siderosomes). The amount and relative proportion of the electrophoretically fast species increased with iron loading. Haemosiderin isolated from siderosomes was found to contain a peptide reactive to anti-ferritin serum and corresponding to the 17.3 kDa peptide of the electrophoretically fast ferritin species. Unlike the electrophoretically slow ferritin, the electrophoretically fast ferritin did not become significantly radioactive in a 1 h biosynthetic labelling experiment. We conclude that the minor ferritin is not, as has been suggested for mouse liver ferritin, 'a completely new species of smaller holoferritin that represents a shift in the ferritin phenotype' in response to siderosis, but a precursor of haemosiderin, in agreement with the proposal by Richter [(1984) Lab. Invest. 50, 26-35] concerning siderosomal ferritin.
Project description:Optical resonators are structures that utilize wave interference and feedback to confine light in all three dimensions. Depending on the feedback mechanism, resonators can support either standing- or traveling-wave modes. Over the years, the distinction between these two different types of modes has become so prevalent that nowadays it is one of the main characteristics for classifying optical resonators. Here, we show that an intermediate link between these two rather different groups exists. In particular, we introduce a new class of photonic resonators that supports a hybrid optical mode, i.e. at one location along the resonator the electromagnetic fields associated with the mode feature a purely standing-wave pattern, while at a different location, the fields of the same mode represent a pure traveling wave. The proposed concept is general and can be implemented using chip-scale photonics as well as free-space optics. Moreover, it can be extended to other wave phenomena such as microwaves and acoustics.
Project description:The genetic basis of most traits is highly polygenic and dominated by non-coding alleles. It is widely assumed that such alleles exert small regulatory effects on the expression of cis-linked genes. However, despite the availability of gene expression and epigenomic datasets, few variant-to-gene links have emerged. It is unclear whether these sparse results are due to limitations in available data and methods, or to deficiencies in the underlying assumed model. To better distinguish between these possibilities, we identified 220 gene-trait pairs in which protein-coding variants influence a complex trait or its Mendelian cognate. Despite the presence of expression quantitative trait loci near most GWAS associations, by applying a gene-based approach we found limited evidence that the baseline expression of trait-related genes explains GWAS associations, whether using colocalization methods (8% of genes implicated), transcription-wide association (2% of genes implicated), or a combination of regulatory annotations and distance (4% of genes implicated). These results contradict the hypothesis that most complex trait-associated variants coincide with homeostatic expression QTLs, suggesting that better models are needed. The field must confront this deficit and pursue this 'missing regulation.'
Project description:The HFE gene (OMIM 235200), most commonly associated with the genetic iron overload disorder Hemochromatosis, was identified by Feder et al. in 1996, as a major histocompatibilty complex (MHC) class I like gene, first designated human leukocyte antigen-H (HLA-H). This discovery was thus accomplished 20 years after the realization of the first link between the then "idiopathic" hemochromatosis and the human leukocyte antigens (HLA). The availability of a good genetic marker in subjects homozygous for the C282Y variant in HFE (hereditary Fe), the reliability in serum markers such as transferrin saturation and serum ferritin, plus the establishment of noninvasive methods for the estimation of hepatic iron overload, all transformed hemochromatosis into a unique age related disease where prevention became the major goal. We were challenged by the finding of iron overload in a 9-year-old boy homozygous for the C282Y HFE variant, with two brothers aged 11 and 5 also homozygous for the mutation. We report a 20 year follow-up during which the three boys were seen yearly with serial determinations of iron parameters and lymphocyte counts. This paper is divided in three sections: Learning, applying, and questioning. The result is the illustration of hemochromatosis as an age related disease in the transition from childhood to adult life and the confirmation of the inextricable link between iron overload and the cells of the immune system.
Project description:F(1)F(o)-ATP synthase is the enzyme responsible for most of the ATP synthesis in living systems. The catalytic domain F(1) of the F(1)F(o) complex, F(1)-ATPase, has the ability to hydrolyze ATP. A fundamental problem in the development of a detailed mechanism for this enzyme is that it has not been possible to determine experimentally the relation between the ligand binding affinities measured in solution and the different conformations of the catalytic beta subunits (beta(TP), beta(DP), beta(E)) observed in the crystal structures of the mitochondrial enzyme, MF(1). Using free energy difference simulations for the hydrolysis reaction ATP+H(2)O --> ADP+P(i) in the beta(TP) and beta(DP) sites and unisite hydrolysis data, we are able to identify beta(TP) as the "tight" (K(D) = 10(-12) M, MF(1)) binding site for ATP and beta(DP) as the "loose" site. An energy decomposition analysis demonstrates how certain residues, some of which have been shown to be important in catalysis, modulate the free energy of the hydrolysis reaction in the beta(TP) and beta(DP) sites, even though their structures are very similar. Combined with the recently published simulations of the rotation cycle of F(1)-ATPase, the present results make possible a consistent description of the binding change mechanism of F(1)-ATPase at an atomic level of detail.