The proteasome biogenesis regulator Rpn4 cooperates with the unfolded protein response to promote ER stress resistance

Misfolded proteins in the endoplasmic reticulum (ER) activate the unfolded protein response (U PR), which enhances protein folding to restore homeostasis. Additional pathways respond to ER stress, but how they help counteract protein misfolding is incompletely understood. Here, we develop a titratable system for the induction of ER stress in yeast to enable a genetic screen for factors that augment stress resistance independently of the UPR. We identify the proteasome biogenesis regulator Rpn4 and show that it cooperates with the UPR. Rpn4 abundance increases during ER stress, first by a post-transcriptional, then by a transcriptional mechanism. Induction of RPN4 transcription is triggered by cytosolic mislocalization of secretory proteins, is mediated by multiple signaling pathways and accelerates clearance of misfolded proteins from the cytosol. Thus, Rpn4 and the UPR are complementary elements of a modular cross-compartment response to ER stress

The Pairwise Peculiar Velocity Dispersion of Galaxies: Effects of the Infall

We study the reliability of the reconstruction method which uses a modelling of the redshift distortions of the two-point correlation function to estimate the pairwise peculiar velocity dispersion of galaxies. In particular, the dependence of this quantity on different models for the infall velocity is examined for the Las Campanas Redshift Survey. We make extensive use of numerical simulations and of mock catalogs derived from them to discuss the effect of a self-similar infall model, of zero infall, and of the real infall taken from the simulation. The implications for two recent discrepant determinations of the pairwise velocity dispersion for this survey are discussed.Comment: minor changes in the discussion; accepted for publication in ApJ; 8 pages with 2 figures include

Watershed services of smallholder agriculture in the Eastern Amazon.

Abstract: Several hydrobiogeochemical research activities have been conducted in the Eastern Amazon, contributing to the understanding of how changes in forests and agro-ecosystems affect ecosystem service provision. Findings have demonstrate that good agricultural practices and the presence of natural secondary vegetation favored by smallholder farm management are important factors for hydrobiogeochemical cycling, aquatic ecosystem conservation, soil conservation, and mitigation of trace emissions from biomass burning in Amazonian small catchments. Two challenges for watershed service management arise in this context. First, low population densities and the relatively flat landscape mean that a critical mass of downstream beneficiaries of such services - a prerequisite for public intervention - is more difficult to identify than in more densely populated mountainous areas. Second, although watershed service providers (farmers) are also to considerable extent service beneficiaries, conflicts over land and cultural heterogeneities among settlers inhibit local collective action to safeguard stream water quality. Including smallholders in carbon payment schemes that and other alternatives to slash-and-burn agriculture by compensating farmers for additional watershed services, including forest conservation. The development of payments for watershed services schemes currently hinges on a better understanding of the biophysical determinants of hydrological service provision, especially in the Amazon region

The Simultaneous Evolution of Author and Paper Networks

There has been a long history of research into the structure and evolution of mankind's scientific endeavor. However, recent progress in applying the tools of science to understand science itself has been unprecedented because only recently has there been access to high-volume and high-quality data sets of scientific output (e.g., publications, patents, grants), as well as computers and algorithms capable of handling this enormous stream of data. This paper reviews major work on models that aim to capture and recreate the structure and dynamics of scientific evolution. We then introduce a general process model that simultaneously grows co-author and paper-citation networks. The statistical and dynamic properties of the networks generated by this model are validated against a 20-year data set of articles published in the Proceedings of the National Academy of Science. Systematic deviations from a power law distribution of citations to papers are well fit by a model that incorporates a partitioning of authors and papers into topics, a bias for authors to cite recent papers, and a tendency for authors to cite papers cited by papers that they have read. In this TARL model (for Topics, Aging, and Recursive Linking), the number of topics is linearly related to the clustering coefficient of the simulated paper citation network.Comment: 14 pages, 6 figures, 2 table

Distinct and overlapping roles for AP-1 and GGAs revealed by the "knocksideways" system

Although adaptor protein complex 1 (AP-1) and Golgi-localized, γ ear-containing, ADP-ribosylation factor-binding proteins (GGAs) are both adaptors for clathrin-mediated intracellular trafficking, the pathways they mediate and their relationship to each other remain open questions [1]. To tease apart the functions of AP-1 and GGAs, we rapidly inactivated each adaptor using the “knocksideways” system [2] and then compared the protein composition of clathrin-coated vesicle (CCV) fractions from control and knocksideways cells. The AP-1 knocksideways resulted in a dramatic and unexpected loss of GGA2 from CCVs. Over 30 other peripheral membrane proteins and over 30 transmembrane proteins were also depleted, including several mutated in genetic disorders, indicating that AP-1 acts as a linchpin for intracellular CCV formation. In contrast, the GGA2 knocksideways affected only lysosomal hydrolases and their receptors. We propose that there are at least two populations of intracellular CCVs: one containing both GGAs and AP-1 for anterograde trafficking and another containing AP-1 for retrograde trafficking. Our study shows that knocksideways and proteomics are a powerful combination for investigating protein function, which can potentially be used on many different types of proteins

5-Fluorouracil as protracted continuous intravenous infusion can be added to full-dose docetaxel (Taxotere®)-cisplatin in advanced gastric carcinoma: a phase I-II trial

Background: A phase I-II multicenter trial was conducted to define the maximum tolerated dose (MTD) according to tolerance and toxicity (primary objective), as well as to describe the clinical activity, in terms of response and survival (secondary objectives), of a combination of 5-fluorouracil (5-FU) in protracted continuous intravenous infusion (p.i.v.) with docetaxel and cisplatin for patients with advanced gastric cancer. Patients and methods: Patients with measurable unresectable and/or metastatic gastric carcinoma, World Health Organization performance status ≤1, normal hematological and renal functions, adequate hepatic function and not pretreated for advanced disease by chemotherapy, received up to eight cycles of a combination of docetaxel on day 1, cisplatin on day 1 and 5-FU p.i.v. on days 1-14 (TCF) every 3 weeks, which was escalated up to the MTD, defined by the occurrence of dose-limiting toxicity in two patients in one dose level. Results: Fifty-two patients were accrued and treated (43 in the phase I part of the trial and nine additional at the recommended dose level). A median of five cycles/patient was given. The recommended dose of TCF was docetaxel 85 mg/m2 on day 1, cisplatin 75 mg/m2 on day 1 and 5-FU p.i.v. 300 mg/m2/day on days 1-14. Grade ≥3 toxicities were neutropenia 79%, alopecia 46%, fatigue 23%, mucositis 10%, diarrhea 19%, nausea/vomiting 13%, neurological 4% and palmar-plantar 2%. Ten non-fatal febrile neutropenia episodes were recorded in eight patients. There were no treatment-related deaths. Among 41 patients with measurable disease (79%), we observed one complete and 20 partial responses for an overall intent-to-treat response rate of 51% (95% confidence interval 35-67%). Five patients (20%) had stable disease for ≥12 weeks (four cycles). The median overall survival was 9.3 months. Conclusions: 5-FU p.i.v. at 300 mg/m2/day for 2 weeks out of three could be safely added to the docetaxel-cisplatin (TC) combination, but the dose of docetaxel had to be reduced to 75 mg/m2 in a subsequent phase II trial. This drug regimen seems to be very active in advanced gastric cancer. Comparison with both TC and ECF in a randomized SAKK trial is ongoin

Molecular Maps in Cereals: Methodology and Progress

Cereals provide for our major food crops, and therefore have been a subject of detailed genetic and cytogenetic studies during major part of the last century. These studies led to the preparation of linkage maps, which were also assigned to individual chromosomes, thus leading to the construction of chromosome maps in all major cereals. In some cases, the availability of cytogenetic stocks (e.g. deletion stocks in bread wheat) also allowed construction of physical maps. In the past, a major limitation in the construction of genetic maps has been the non-availability of mutants for majority of individual genes, so that only handful of genes could be mapped. However, during 1980s, the availability of molecular markers and the high level of DNA polymorphism, which they detect, led to renewed emphasis on genetic and physica.......

A rabdomiólise está associada à febre dengue em um paciente lúpico

ResumoEsse relato descreve o caso de uma mulher com lúpus eritematoso sistêmico (LES) que sofreu rabdomiólise em seguida à sua infecção pelo vírus da dengue. Foram relatados apenas alguns casos de LES com manifestação de rabdomiólise, nenhum deles associados à febre dengue.A princípio, a paciente apresentava‐se com febre alta, mialgia, astenia muscular, leve cefaleia, poliartralgia e trombocitopenia, lembrando uma exacerbação lúpica, mas considerando que o número de pessoas infectadas pela dengue na época era alto e tendo em vista que os sintomas das duas condições são parecidos, foi solicitada sorologia para dengue. Trans‐corridos alguns dias, a paciente apresentou rabdomiólise, tendo então sido tratada com medicamentos imunossupressivos, alcalinização urinária e hidratação vigorosa, medidas que melhoraram seus danos musculares e a condição inflamatória. A sorologia positiva para dengue nos foi disponibilizada apenas depois da instauração do tratamento descrito acima. A paciente recebeu alta em estado assintomático.Esse caso demonstra a grande semelhança entre a febre dengue e uma exacerbação lúpica; isso deve alertar o clínico para que, especialmente durante uma epidemia, faça uma cuidadosa diferenciação entre essas doenças, de forma a estabelecer uma terapia correta e eficiente.AbstractThis report describes the case of a woman with systemic lupus erythematous (SLE) that developed rhabdomyolysis after being infected by dengue virus. There are only a few cases of SLE accompanied by rhabdomyolysis, none of them associated with dengue fever.Initially, the woman presented high fever, myalgia, muscular weakness, mild headache, polyarthralgia and thrombocytopenia reminding a lupus flare, but since the number of people infected by dengue at that time was high and the symptoms from both conditions are similar, a dengue serology was requested. After a few days, the patient developed rhabdomyolysis. She was then submitted to immunosuppressive drugs, urinary alkalization and vigorous hydration, which improved her muscle damage and inflammatory condition. The positive dengue serology was only available after the therapy above had been established. She was discharged in an asymptomatic state.This case demonstrates how alike dengue fever and a lupus flare are, warning clinicians that, especially during an epidemic, both diseases should be carefully differentiated in order to establish a correct and efficient therapy

Role of clathrin in dense core vesicle biogenesis

The dense-core vesicles (DCVs) of neuroendocrine cells are a rich source of bioactive molecules such as peptides, hormones, and neurotransmitters, but relatively little is known about how they are formed. Using fractionation profiling, a method that combines subcellular fractionation with mass spectrometry, we identified ∼1200 proteins in PC12 cell vesicle-enriched fractions, with DCV-associated proteins showing distinct profiles from proteins associated with other types of vesicles. To investigate the role of clathrin in DCV biogenesis, we stably transduced PC12 cells with an inducible shRNA targeting clathrin heavy chain, resulting in ∼85% protein loss. DCVs could still be observed in the cells by electron microscopy, but mature profiles were ∼4-fold less abundant than in mock-treated cells. By quantitative mass spectrometry, DCV-associated proteins were found to be reduced ∼2-fold in clathrin-depleted cells as a whole and ∼5-fold in vesicle-enriched fractions. Our combined datasets enabled us to identify new candidate DCV components. Secretion assays revealed that clathrin depletion causes a near-complete block in secretagogue-induced exocytosis. Taken together, our data indicate that clathrin has a function in DCV biogenesis beyond its established role in removing unwanted proteins from the immature vesicle.This work was funded by grants from the Wellcome Trust: 086598 (to M.S.R.), 100140 (Wellcome Trust Strategic Award), and 093026 (for the FEI Tecnai G2 Spirit BioTWIN transmission EM); and by a National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Diseases grant (R01DK102496) to A.B

Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein-protein interactions.

We developed "fractionation profiling," a method for rapid proteomic analysis of membrane vesicles and protein particles. The approach combines quantitative proteomics with subcellular fractionation to generate signature protein abundance distribution profiles. Functionally associated groups of proteins are revealed through cluster analysis. To validate the method, we first profiled >3500 proteins from HeLa cells and identified known clathrin-coated vesicle proteins with >90% accuracy. We then profiled >2400 proteins from Drosophila S2 cells, and we report the first comprehensive insect clathrin-coated vesicle proteome. Of importance, the cluster analysis extends to all profiled proteins and thus identifies a diverse range of known and novel cytosolic and membrane-associated protein complexes. We show that it also allows the detailed compositional characterization of complexes, including the delineation of subcomplexes and subunit stoichiometry. Our predictions are presented in an interactive database. Fractionation profiling is a universal method for defining the clathrin-coated vesicle proteome and may be adapted for the analysis of other types of vesicles and particles. In addition, it provides a versatile tool for the rapid generation of large-scale protein interaction maps