Novel insights into the architecture and protein interaction network of yeast eIF3.

Translation initiation in eukaryotes is a multistep process requiring the orchestrated interaction of several eukaryotic initiation factors (eIFs). The largest of these factors, eIF3, forms the scaffold for other initiation factors, promoting their binding to the 40S ribosomal subunit. Biochemical and structural studies on eIF3 need highly pure eIF3. However, natively purified eIF3 comprise complexes containing other proteins such as eIF5. Therefore we have established in vitro reconstitution protocols for Saccharomyces cerevisiae eIF3 using its five recombinantly expressed and purified subunits. This reconstituted eIF3 complex (eIF3(rec)) exhibits the same size and activity as the natively purified eIF3 (eIF3(nat)). The homogeneity and stoichiometry of eIF3(rec) and eIF3(nat) were confirmed by analytical size exclusion chromatography, mass spectrometry, and multi-angle light scattering, demonstrating the presence of one copy of each subunit in the eIF3 complex. The reconstituted and native eIF3 complexes were compared by single-particle electron microscopy showing a high degree of structural conservation. The interaction network between eIF3 proteins was studied by means of limited proteolysis, analytical size exclusion chromatography, in vitro binding assays, and isothermal titration calorimetry, unveiling distinct protein domains and subcomplexes that are critical for the integrity of the protein network in yeast eIF3. Taken together, the data presented here provide a novel procedure to obtain highly pure yeast eIF3, suitable for biochemical and structural analysis, in addition to a detailed picture of the network of protein interactions within this complex

The role of multiplier bounds in fuzzy data envelopment analysis

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.The non-Archimedean epsilon ε is commonly considered as a lower bound for the dual input weights and output weights in multiplier data envelopment analysis (DEA) models. The amount of ε can be effectively used to differentiate between strongly and weakly efficient decision making units (DMUs). The problem of weak dominance particularly occurs when the reference set is fully or partially defined in terms of fuzzy numbers. In this paper, we propose a new four-step fuzzy DEA method to re-shape weakly efficient frontiers along with revisiting the efficiency score of DMUs in terms of perturbing the weakly efficient frontier. This approach eliminates the non-zero slacks in fuzzy DEA while keeping the strongly efficient frontiers unaltered. In comparing our proposed algorithm to an existing method in the recent literature we show three important flaws in their approach that our method addresses. Finally, we present a numerical example in banking with a combination of crisp and fuzzy data to illustrate the efficacy and advantages of the proposed approach

Crystal Structure of the RNA Recognition Motif of Yeast Translation Initiation Factor eIF3b Reveals Differences to Human eIF3b

BACKGROUND: The multi-subunit eukaryotic initiation factor3 (eIF3) plays a central role in the initiation step of protein synthesis in eukaryotes. One of its large subunits, eIF3b, serves as a scaffold within eIF3 as it interacts with several other subunits. It harbors an RNA Recognition Motif (RRM), which is shown to be a non-canonical RRM in human as it is not capable to interact with oligonucleotides, but rather interacts with eIF3j, a sub-stoichiometric subunit of eIF3. PRINCIPAL FINDING: We have analyzed the high-resolution crystal structure of the eIF3b RRM domain from yeast. It exhibits the same fold as its human ortholog, with similar charge distribution on the surface interacting with the eIF3j in human. Thermodynamic analysis of the interaction between yeast eIF3b-RRM and eIF3j revealed the same range of enthalpy change and dissociation constant as for the human proteins, providing another line of evidence for the same mode of interaction between eIF3b and eIF3j in both organisms. However, analysis of the surface charge distribution of the putative RNA-binding β-sheet suggested that in contrast to its human ortholog, it potentially could bind oligonucleotides. Three-dimensional positioning of the so called "RNP1" motif in this domain is similar to other canonical RRMs, suggesting that this domain might indeed be a canonical RRM, conferring oligonucleotide binding capability to eIF3 in yeast. Interaction studies with yeast total RNA extract confirmed the proposed RNA binding activity of yeast eIF3b-RRM. CONCLUSION: We showed that yeast eIF3b-RRM interacts with eIF3j in a manner similar to its human ortholog. However, it shows similarities in the oligonucleotide binding surface to canonical RRMs and interacts with yeast total RNA. The proposed RNA binding activity of eIF3b-RRM may help eIF3 to either bind to the ribosome or recruit the mRNA to the 43S pre-initiation complex

Automated Additive Construction (AAC) for Earth and Space Using In-situ Resources

Using Automated Additive Construction (AAC), low-fidelity large-scale compressive structures can be produced out of a wide variety of materials found in the environment. Compressionintensive structures need not utilize materials that have tight specifications for internal force management, meaning that the production of the building materials do not require costly methods for their preparation. Where a certain degree of surface roughness can be tolerated, lower-fidelity numerical control of deposited materials can provide a low-cost means for automating building processes, which can be utilized in remote or extreme environments on Earth or in Space. For space missions where every kilogram of mass must be lifted out of Earth’s gravity well, the promise of using in-situ materials for the construction of outposts, facilities, and installations could prove to be enabling if significant reduction of payload mass can be achieved. In a 2015 workshop sponsored by the Keck nstitute for Space Studies, on the topic of Three Dimensional (3D) Additive Construction For Space Using In-situ Resources, was conducted with additive construction experts from around the globe in attendance. The workshop explored disparate efforts, methods, and technologies and established a proposed framework for the field of Additive Construction Using In-situ Resources. This paper defines the field of Automated Additive Construction Using In-situ Resources, describes the state-of-the-art for various methods, establishes a vision for future efforts, identifies gaps in current technologies, explores investment opportunities, and proposes potential technology demonstration missions for terrestrial, International Space Station (ISS), lunar, deep space zero-gravity, and Mars environments

From Architectured Materials to Large-Scale Additive Manufacturing

The classical material-by-design approach has been extensively perfected by materials scientists, while engineers have been optimising structures geometrically for centuries. The purpose of architectured materials is to build bridges across themicroscale ofmaterials and themacroscale of engineering structures, to put some geometry in the microstructure. This is a paradigm shift. Materials cannot be considered monolithic anymore. Any set of materials functions, even antagonistic ones, can be envisaged in the future. In this paper, we intend to demonstrate the pertinence of computation for developing architectured materials, and the not-so-incidental outcome which led us to developing large-scale additive manufacturing for architectural applications

SME efficiency in transforming regional business research and innovation investments into innovative sales output

Based on data provided by the Regional Innovation Scoreboard on 23 capital and 184 non-capital regions in Europe, slacks-based models of data envelopment analysis (DEA) reveal that the efficiency by which business research and innovation inputs are converted at regional-level aggregated innovative sales output in small and medium-sized enterprises was significantly lower in capital regions in the period 2006–14. In view of efficiency maximization, a majority of the capital regions overinvest in non-research and development innovation activities, are over-specialized in knowledge-intensive industries, and fall behind in converting research and innovation inputs in intermediary intellectual property outcomes

Performance evaluation of R&D active firms

The Publisher's final version can be found by following the DOI link.This study focuses on the allocation of R&D resources in R&D active firms. We utilize the input oriented constant (CRS) and variable (VRS) returns to scale data efficiency analysis models to evaluate the efficiency of firms. Scale efficiency and the respective types of returns to scale have been examined by using DEA models with ratio inputs and outputs. We pay attention to the global frontier and the firm's own sector and size frontiers. We highlight the sources of inefficiency and suggestions are proposed to improve efficiencies of R&D resources allocation. The analysis is based on a representative set of (quasi-) permanent R&D active firms in Belgium. We consider R&D related inputs in the year 2009 and include firm performance in terms of turnover and net added value per employee in a four year time span. The paper highlights that on average, R&D active firms suffer from both technical inefficiency and scale size problems since the average of the CRS and the VRS efficiency are low, and also the average of scale efficiency is modest. According to firm size, small-sized firms suffer from scale and technical inefficiency. Medium-sized firms endure scale inefficiency rather than technical inefficiency. Large firms present a higher average scale efficiency and technical efficiency. According to sector of activity, firms in specialized supplier industries tend to outperform other firms in terms of average scale efficiency and average technical efficiency. Firms in science based industries are found to underperform on average in terms of VRS and scale efficiency

Evaluation of research, technology development and innovation using data envelopment analysis.

status: publishe