Phagosomes are competent organelles for antigen cross-presentation

The ability to process microbial antigens and present them at the surface of cells is an important aspect of our innate ability to clear infections. It is generally accepted that antigens in the cytoplasm are loaded in the endoplasmic reticulum and presented at the cell surface on major histocompatibility complex (MHC) class I molecules, whereas peptides present in endo/phagocytic compartments are presented on MHC class II molecules. Despite the apparent segregation of the class I and class II pathways, antigens from intracellular pathogens including mycobacteria, Escherichia coli, Salmonella typhimurium, Brucella abortus and Leishmania, have been shown to elicit an MHC class-I-dependent CD8+ T-cell response, a process referred to as cross-presentation. The cellular mechanisms allowing the cross-presentation pathway are poorly understood. Here we show that phagosomes display the elements and properties needed to be self-sufficient for the cross-presentation of exogenous antigens, a newly ascribed function linked to phagocytosis mediated by the endoplasmic reticulum.     

Mutations in ARFGEF2 implicate vesicle trafficking in neural progenitor proliferation and migration in the human cerebral cortex

Disruption of human neural precursor proliferation can give rise to a small brain (microcephaly), and failure of neurons to migrate properly can lead to an abnormal arrest of cerebral cortical neurons in proliferative zones near the lateral ventricles (periventricular heterotopia). Here we show that an autosomal recessive condition characterized by microcephaly and periventricular heterotopia maps to chromosome 20 and is caused by mutations in the gene ADP-ribosylation factor guanine nucleotide-exchange factor-2 (ARFGEF2). By northern-blot analysis, we found that mouse Arfgef2 mRNA levels are highest during embryonic periods of ongoing neuronal proliferation and migration, and by in situ hybridization, we found that the mRNA is widely distributed throughout the embryonic central nervous system (CNS). ARFGEF2 encodes the large (>200 kDa) brefeldin A (BFA)-inhibited GEF2 protein (BIG2), which is required for vesicle and membrane trafficking from the trans-Golgi network (TGN). Inhibition of BIG2 by BFA, or by a dominant negative ARFGEF2 cDNA, decreases cell proliferation in vitro, suggesting a cell-autonomous regulation of neural expansion. Inhibition of BIG2 also disturbed the intracellular localization of such molecules as E-cadherin and beta-catenin by preventing their transport from the Golgi apparatus to the cell surface. Our findings show that vesicle trafficking is an important regulator of proliferation and migration during human cerebral cortical development.     

Heterozygous TGFBR2 mutations in Marfan syndrome

Marfan syndrome is an extracellular matrix disorder with cardinal manifestations in the eye, skeleton and cardiovascular systems associated with defects in the gene encoding fibrillin (FBN1) at 15q21.1 (ref. 1). A second type of the disorder (Marfan syndrome type 2; OMIM 154705) is associated with a second locus, MFS2, at 3p25-p24.2 in a large French family (family MS1). Identification of a 3p24.1 chromosomal breakpoint disrupting the gene encoding TGF-beta receptor 2 (TGFBR2) in a Japanese individual with Marfan syndrome led us to consider TGFBR2 as the gene underlying association with Marfan syndrome at the MSF2 locus. The mutation 1524G-->A in TGFBR2 (causing the synonymous amino acid substitution Q508Q) resulted in abnormal splicing and segregated with MFS2 in family MS1. We identified three other missense mutations in four unrelated probands, which led to loss of function of TGF-beta signaling activity on extracellular matrix formation. These results show that heterozygous mutations in TGFBR2, a putative tumor-suppressor gene implicated in several malignancies, are also associated with inherited connective-tissue disorders.     

On a General Transformation Making a Dissimilarity Matrix Euclidean

When a dissimilarity matrix cannot be represented in a Euclidean space, it is possible to make it Euclidean by means of suitable transformations of the original dissimilarity values. In this paper we discuss some interesting properties of a class of transformations based on adding a specific squared Euclidean distance to the initial dissimilarity. An erratum to this article is available at .     

Moisture transport across Central America as a positive feedback on abrupt climatic changes

Moisture transport from the Atlantic to the Pacific ocean across Central America leads to relatively high salinities in the North Atlantic Ocean and contributes to the formation of North Atlantic Deep Water. This deep water formation varied strongly between Dansgaard/Oeschger interstadials and Heinrich events-millennial-scale abrupt warm and cold events, respectively, during the last glacial period. Increases in the moisture transport across Central America have been proposed to coincide with northerly shifts of the Intertropical Convergence Zone and with Dansgaard/Oeschger interstadials, with opposite changes for Heinrich events. Here we reconstruct sea surface salinities in the eastern equatorial Pacific Ocean over the past 90,000 years by comparing palaeotemperature estimates from alkenones and Mg/Ca ratios with foraminiferal oxygen isotope ratios that vary with both temperature and salinity. We detect millennial-scale fluctuations of sea surface salinities in the eastern equatorial Pacific Ocean of up to two to four practical salinity units. High salinities are associated with the southward migration of the tropical Atlantic Intertropical Convergence Zone, coinciding with Heinrich events and with Greenland stadials. The amplitudes of these salinity variations are significantly larger on the Pacific side of the Panama isthmus, as inferred from a comparison of our data with a palaeoclimate record from the Caribbean basin. We conclude that millennial-scale fluctuations of moisture transport constitute an important feedback mechanism for abrupt climate changes, modulating the North Atlantic freshwater budget and hence North Atlantic Deep Water formation.     

Quantum jumps of light recording the birth and death of a photon in a cavity

A microscopic quantum system under continuous observation exhibits at random times sudden jumps between its states. The detection of this quantum feature requires a quantum non-demolition (QND) measurement repeated many times during the system's evolution. Whereas quantum jumps of trapped massive particles (electrons, ions or molecules) have been observed, this has proved more challenging for light quanta. Standard photodetectors absorb light and are thus unable to detect the same photon twice. It is therefore necessary to use a transparent counter that can 'see' photons without destroying them. Moreover, the light needs to be stored for durations much longer than the QND detection time. Here we report an experiment in which we fulfil these challenging conditions and observe quantum jumps in the photon number. Microwave photons are stored in a superconducting cavity for times up to half a second, and are repeatedly probed by a stream of non-absorbing atoms. An atom interferometer measures the atomic dipole phase shift induced by the non-resonant cavity field, so that the final atom state reveals directly the presence of a single photon in the cavity. Sequences of hundreds of atoms, highly correlated in the same state, are interrupted by sudden state switchings. These telegraphic signals record the birth, life and death of individual photons. Applying a similar QND procedure to mesoscopic fields with tens of photons should open new perspectives for the exploration of the quantum-to-classical boundary.     

TGFB2 mutations cause familial thoracic aortic aneurysms and dissections associated with mild systemic features of Marfan syndrome

A predisposition for thoracic aortic aneurysms leading to acute aortic dissections can be inherited in families in an autosomal dominant manner. Genome-wide linkage analysis of two large unrelated families with thoracic aortic disease followed by whole-exome sequencing of affected relatives identified causative mutations in TGFB2. These mutations-a frameshift mutation in exon 6 and a nonsense mutation in exon 4-segregated with disease with a combined logarithm of odds (LOD) score of 7.7. Sanger sequencing of 276 probands from families with inherited thoracic aortic disease identified 2 additional TGFB2 mutations. TGFB2 encodes transforming growth factor (TGF)-β2, and the mutations are predicted to cause haploinsufficiency for TGFB2; however, aortic tissue from cases paradoxically shows increased TGF-β2 expression and immunostaining. Thus, haploinsufficiency for TGFB2 predisposes to thoracic aortic disease, suggesting that the initial pathway driving disease is decreased cellular TGF-β2 levels leading to a secondary increase in TGF-β2 production in the diseased aorta.     

Distributions of epistasis in microbes fit predictions from a fitness landscape model

How do the fitness effects of several mutations combine? Despite its simplicity, this question is central to the understanding of multilocus evolution. Epistasis (the interaction between alleles at different loci), especially epistasis for fitness traits such as reproduction and survival, influences evolutionary predictions "almost whenever multilocus genetics matters". Yet very few models have sought to predict epistasis, and none has been empirically tested. Here we show that the distribution of epistasis can be predicted from the distribution of single mutation effects, based on a simple fitness landscape model. We show that this prediction closely matches the empirical measures of epistasis that have been obtained for Escherichia coli and the RNA virus vesicular stomatitis virus. Our results suggest that a simple fitness landscape model may be sufficient to quantitatively capture the complex nature of gene interactions. This model may offer a simple and widely applicable alternative to complex metabolic network models, in particular for making evolutionary predictions.