The rockefeller university

Autophagy is a tightly regulated lysosomal degradation pathway for maintaining cellular homeostasis and responding to stresses. Beclin 1 and its interacting proteins, including the class III phosphatidylinositol-3 kinase Vps34, play crucial roles in autophagy regulation in mammals. We identified nuclear receptor binding factor 2 (Nrbf2) as a Beclin 1-interacting protein from Becn1(-/-); Becn1-EGFP/+ mouse liver and brain. We also found that Nrbf2-Beclin 1 interaction required the N terminus of Nrbf2. We next used the human retinal pigment epithelial cell line RPE-1 as a model system and showed that transiently knocking down Nrbf2 by siRNA increased autophagic flux under both nutrient-rich and starvation conditions. To investigate the mechanism by which Nrbf2 regulates autophagy, we demonstrated that Nrbf2 interacted and colocalized with Atg14L, suggesting that Nrbf2 is a component of the Atg14L-containing Beclin 1-Vps34 complex. Moreover, ectopically expressed Nrbf2 formed cytosolic puncta that were positive for isolation membrane markers. These results suggest that Nrbf2 is involved in autophagosome biogenesis. Furthermore, we showed that Nrbf2 deficiency led to increased intracellular phosphatidylinositol-3 phosphate levels and diminished Atg14L-Vps34/Vps15 interactions, suggesting that Nrbf2-mediated Atg14L-Vps34/Vps15 interactions likely inhibit Vps34 activity. Therefore, we propose that Nrbf2 may interact with the Atg14L-containing Beclin 1-Vps34 protein complex to modulate protein-protein interactions within the complex, leading to suppression of Vps34 activity, autophagosome biogenesis, and autophagic flux. This work reveals a novel aspect of the intricate mechanism for the Beclin 1-Vps34 protein-protein interaction network to achieve precise control of autophagy.

Ants have evolved an amazing variety of feeding habits to utilize diverse food sources. However, only one ant species, Euprenolepis pro cera (EMERY, 1900) (Formicidae: Formicinae), has been described as a specialist harvester of wild-growing mushrooms. Mushrooms are a very abundant food source in certain habitats, but utilizing them is expected to require specific adaptations. Here, we report the discovery of another, sympatric, and widespread mushroom harvesting ant, Euprenolepis wittei LAPOLLA, 2009. The similarity in nutritional niches of both species was expected to be accompanied by similarities in adaptive behavior and differences due to competitive avoidance. Similarities were found in mushroom acceptance and harvesting behavior: Both species harvested a variety of wild-growing mushrooms and formed characteristic mushroom piles inside the nest that were processed continuously by adult workers. Euprenolepis procera was apparently dominant at mushroom baits displacing the smaller, less numerous E. wittei foragers. However, interspecific competition for mushrooms is likely relaxed by differences in other niche dimensions, particularly the temporal activity pattern. The discovery of a second, widespread mushroom harvesting ant suggests that this life style is more common than previously thought, at least in Southeast Asia, and has implications for the ecology of tropical rainforests. Exploitation of the reproductive organs of fungi likely impacts spore development and distribution and thus affects the fungal community.

A search for supersymmetry through the direct pair production of top squarks, with Higgs (H) or Z bosons in the decay chain, is performed using a data sample of proton-proton collisions at root s = 8 TeVcollected in 2012 with the CMS detector at the LHC. The sample corresponds to an integrated luminosity of 19.5 fb(-1). The search is performed using a selection of events containing leptons and bottom-quark jets. No evidence for a significant excess of events over the standard model background prediction is observed. The results are interpreted in the context of simplified supersymmetric models with pair production of a heavier top-squark mass eigenstate (t) over tilde (2) decaying to a lighter top-squark mass eigenstate (t) over tilde (1) via either (t) over tilde (2) -> H (t) over tilde (1) or (t) over tilde (2) -> Z (t) over tilde (1), followed in both cases by (t) over tilde (1) -> t (chi) over tilde (0)(1), where (chi) over tilde (0)(1) is an undetected, stable, lightest supersymmetric particle. The interpretation is performed in the region where the mass difference between the (t) over tilde (1) and (chi) over tilde (0)(1) states is approximately equal to the top-quark mass (m((t) over tilde )1) - m((chi) over tilde 10) similar or equal to m(t)) which is not probed by searches for direct (t) over tilde (1) squark pair production. The analysis excludes top squarks with masses m((t) over tilde2) < 575 GeVand m(<(t)over tilde>1) < 400 GeVat a 95% confidence level. (C) 2014 The Authors. Published by Elsevier B.V.

A search for the standard model Higgs boson produced in association with a top-quark pair (t (t) over barH) is presented, using data samples corresponding to integrated luminosities of up to 5.1 fb(-1) and 19.7 fb(-1) collected in pp collisions at center-of-mass energies of 7 TeV and 8 TeV respectively. The search is based on the following signatures of the Higgs boson decay: H -> hadrons, H -> photons, and H -> leptons. The results are characterized by an observed t (t) over barH signal strength relative to the standard model cross section, mu = sigma/sigma(SM), under the assumption that the Higgs boson decays as expected in the standard model. The best fit value is mu = 2.8 +/- 1.0 for a Higgs boson mass of 125.6 GeV.

This article presents one scientist's perspective on the transition from life at the bench to an editorial career.

A measurement of the cross section for the production of top quark-antiquark pairs (t (t) over bar) in association with a vector boson V (W or Z) in proton-proton collisions at root s = 8 TeV is presented. The results are based on a dataset corresponding to an integrated luminosity of 19.5 fb(-1) recorded with the CMS detector at the LHC. The measurement is performed in three leptonic (e and mu) channels: a same-sign dilepton analysis targeting t (t) over barW events, and trilepton and four-lepton analyses designed for t (t) over barZ events. In the same-sign dilepton channel, the t (t) over barW cross section is measured as sigma(t (t) over barW) = 170(-80)(+90) (stat) +/- 70 (syst) fb, corresponding to a significance of 1.6 standard deviations over the background-only hypothesis. Combining the trilepton and four-lepton channels, a direct measurement of the t (t) over barZ cross section, sigma(t (t) over barZ) = 200(-70)(+80) (stat)(-30)(+40) (syst)fb(-1), is obtained with a significance of 3.1 standard deviations. The measured cross sections are compatible with standard model predictions within their experimental uncertainties. The inclusive t (t) over barV process is observed with a significance of 3.7 standard deviations from the combination of all three leptonic channels.

Motivation: The detection of genomic regions unusually rich in a given pattern is an important undertaking in the analysis of next-generation sequencing data. Recent studies of chromosomal translocations in activated B lymphocytes have identified regions that are frequently translocated to c-myc oncogene. A quantitative method for the identification of translocation hotspots was crucial to this study. Here we improve this analysis by using a simple probabilistic model and the framework provided by scan statistics to define the number and location of translocation breakpoint hotspots. A key feature of our method is that it provides a global chromosome-wide nominal control level to clustering, as opposed to previous methods based on local criteria. While being motivated by a specific application, the detection of unusual clusters is a widespread problem in bioinformatics. We expect our method to be useful in the analysis of data from other experimental approaches such as of ChIP-seq and 4C-seq. Results: The analysis of translocations from B lymphocytes with the method described here reveals the presence of longer hotspots when compared with those defined previously. Further, we show that the hotspot size changes substantially in the absence of DNA repair protein 53BP1. When 53BP1 deficiency is combined with overexpression of activation-induced cytidine deaminase, the hotspot length increases even further. These changes are not detected by previous methods that use local significance criteria for clustering. Our method is also able to identify several exclusive translocation hotspots located in genes of known tumor supressors.

We have previously reported on a unique patient in whom homozygosity for a mutation at IRF8 (IRF8(K108E)) causes a severe immunodeficiency. Laboratory evaluation revealed a highly unusual myeloid compartment, remarkable for the complete absence of CD14(+) and CD16(+) monocytes, absence of CD11c(+) conventional dendritic cells (DCs) and CD11c(+)/CD123(+) plasmacytoid DCs, and striking granulocytic hyperplasia. The patient initially presented with severe disseminated mycobacterial and mucocutaneous fungal infections and was ultimately cured by cord blood transplant. Sequencing RNA from the IRF8(K108E) patient's primary blood cells prior to transplant shows not only depletion of IRF8-bound and IRF8-regulated transcriptional targets, in keeping with the distorted composition of the myeloid compartment, but also a paucity of transcripts associated with activated CD4(+) and CD8(+) T lymphocytes. This suggests that T cells reared in the absence of a functional antigen-presenting compartment in IRF8(K108E) are anergic. Biochemical characterization of the IRF8(K108E) mutant in vitro shows that loss of the positively charged side chain at K108 causes loss of nuclear localization and loss of transcriptional activity, which is concomitant with decreased protein stability, increased ubiquitination, increased small ubiquitin-like modification, and enhanced proteasomal degradation. These findings provide functional insight into the molecular basis of immunodeficiency associated with loss of IRF8.

The drug DMXAA (5,6-dimethylxanthenone-4-acetic acid) showed therapeutic promise against solid tumors in mouse models but subsequently failed in human clinical trials. DMXAA was later discovered to activate mouse, but not human, STING, an adaptor protein in the cyclic dinucleotide cGAMP-mediated signaling pathway, inducing type I interferon expression. To facilitate the development of compounds that target human STING, we combined structural, biophysical, and cellular assays to study mouse and human chimeric proteins and their interaction with DMXAA. We identified a single substitution (G230I) that enables a DMXAA-induced conformational transition of hSTING from an inactive "open" to an active "closed" state. We also identified a substitution within the binding pocket (Q266I) that cooperates with G230I and the previously identified S162A binding-pocket point substitution, rendering hSTING highly sensitive to DMXAA. These findings should facilitate the reciprocal engineering of DMXAA analogs that bind and stimulate wild-type hSTING and their exploitation for vaccine-adjuvant and anticancer drug development.