Yos9p assists in the degradation of certain non-glycosylated proteins from the endoplasmic reticulum

The HRD ubiquitin ligase recognizes and ubiquitylates proteins of the endoplasmic reticulum that display structural defects. Here, we apply quantitative proteomics to characterize the substrate spectrum of the HRD complex. Among the identified substrates is Erg3p, a glycoprotein involved in sterol-synthesis. We characterize Erg3p and demonstrate that the elimination of Erg3p requires Htm1p and Yos9p, two proteins that partake in the glycan-dependent turnover of aberrant proteins. We further show that the HRD ligase also mediates the breakdown of Erg3p and CPY* engineered to lack N-glycans. The degradation of these non-glycosylated substrates is enhanced by a mutant variant of Yos9p that has lost its affinity for oligosaccharides, indicating that Yos9p has a previously unrecognized role in the quality control of non-glycosylated proteins

Visual exploration of climate variability changes using wavelet analysis

Due to its nonlinear nature, the climate system shows quite high natural variability on different time scales, including multiyear oscillations such as the El Ni˜no Southern Oscillation phenomenon. Beside a shift of the mean states and of extreme values of climate variables, climate change may also change the frequency or the spatial patterns of these natural climate variations. Wavelet analysis is a well established tool to investigate variability in the frequency domain. However, due to the size and complexity of the analysis results, only few time series are commonly analyzed concurrently. In this paper we will explore different techniques to visually assist the user in the analysis of variability and variability changes to allow for a holistic analysis of a global climate model data set consisting of several variables and extending over 250 years. Our new framework and data from the IPCC AR4 simulations with the coupled climate model ECHAM5/MPI-OM are used to explore the temporal evolution of El Ni˜no due to climate change

Hydrological restoration of Indonesian peatlands to mitigate carbon dioxide emissions

Delta Session DS 9: The lowland deltas of Indonesia. Hydrological restoration of Indonesian peatlands to mitigate carbon dioxide emissions, Henk Wösten (2010). Presented at the international conference Deltas in Times of Climate Change, 29 September - 1 October, Rotterdam, the Netherlands

Genetic bottlenecks in agroforestry systems: results of tree nursery surveys in East Africa

Seedlings sourced through tree nurseries are expected to form an important component of future tree cover on farms. As such, the genetic composition of nursery seedlings is expected to impact on the productivity and sustainability of agroforestry ecosystems. By surveying current practices of nursery managers in five areas from Kenya, Tanzania and Uganda, we quantified parameters associated with the collection, production and distribution of tree germplasm in East Africa. Considerable variation for seed-propagated nursery species was observed in the number of maternal parents (mother trees) sampled to establish nursery lots, the quantity of seedlings raised in nursery lots and the projected number of clients for nursery lots. Current seed collection practice was the most obvious limiting bottleneck in delivering high levels of genetic diversity to farmers. In the 143 cases analysed, seed to establish nursery lots was collected from a mean of only 6.4 maternal parents. In 22% of cases, ursery lots were established from a single maternal parent. On average, each maternal parent produced sufficient progeny to provide all the seedlings received by an individual nursery client. Consequently, the potential impact on farm and landscape genetic diversity of possible non-randomisation of progeny within nurseries is serious. In two instances, pair-wise analysis of transformed data suggested significant differences between geographic areas in the projected number of clients for nursery lots. We discuss improved nursery practices likely to promote genetic diversity, in particular increased maternal parent sampling and germplasm exchang

Scaling property of variational perturbation expansion for general anharmonic oscillator

We prove a powerful scaling property for the extremality condition in the recently developed variational perturbation theory which converts divergent perturbation expansions into exponentially fast convergent ones. The proof is given for the energy eigenvalues of an anharmonic oscillator with an arbitrary $x^p$-potential. The scaling property greatly increases the accuracy of the results

Large Oligomeric Complex Structures Can Be Computationally Assembled by Efficiently Combining Docked Interfaces

Macromolecular oligomeric assemblies are involved in many biochemical processes of living organisms. The benefits of such assemblies in crowded cellular environments include increased reaction rates, efficient feedback regulation, cooperativity and protective functions. However, an atom‐level structural determination of large assemblies is challenging due to the size of the complex and the difference in binding affinities of the involved proteins. In this study, we propose a novel combinatorial greedy algorithm for assembling large oligomeric complexes from information on the approximate position of interaction interfaces of pairs of monomers in the complex. Prior information on complex symmetry is not required but rather the symmetry is inferred during assembly. We implement an efficient geometric score, the transformation match score, that bypasses the model ranking problems of state‐of‐the‐art scoring functions by scoring the similarity between the inferred dimers of the same monomer simultaneously with different binding partners in a (sub)complex with a set of pregenerated docking poses. We compiled a diverse benchmark set of 308 homo and heteromeric complexes containing 6 to 60 monomers. To explore the applicability of the method, we considered 48 sets of parameters and selected those three sets of parameters, for which the algorithm can correctly reconstruct the maximum number, namely 252 complexes (81.8%) in, at least one of the respective three runs. The crossvalidation coverage, that is, the mean fraction of correctly reconstructed benchmark complexes during crossvalidation, was 78.1%, which demonstrates the ability of the presented method to correctly reconstruct topology of a large variety of biological complexes. Proteins 2015; 83:1887–1899. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc