Translation efficiency in humans: tissue specificity,global optimization and differences between developmental stages

Various studies in unicellular and multicellular organisms have shown that codon bias plays a significant role in translation efficiency (TE) by co-adaptation to the tRNA pool. Yet, in humans and other mammals the role of codon bias is still an open question, with contradictory results from different studies. Here we address this question, performing a large-scale tissue-specific analysis of TE in humans, using the tRNA Adaptation Index (tAI) as a direct measure for TE. We find tAI to significantly correlate with expression levels both in tissue-specific and in global expression measures, testifying to the TE of human tissues. Interestingly, we find significantly higher correlations in adult tissues as opposed to fetal tissues, suggesting that the tRNA pool is more adjusted to the adult period. Optimization based analysis suggests that the tRNA pool—codon bias co-adaptation is globally (and not tissue-specific) driven. Additionally, we find that tAI correlates with several measures related to the protein functionally importance, including gene essentiality. Using inferred tissue-specific tRNA pools lead to similar results and shows that tissue-specific genes are more adapted to their tRNA pool than other genes and that related sets of functional gene groups are translated efficiently in each tissue. Similar results are obtained for other mammals. Taken together, these results demonstrate the role of codon bias in TE in humans, and pave the way for future studies of tissue-specific TE in multicellular organisms.     

Network-Free Inference of Knockout Effects in Yeast

Perturbation experiments, in which a certain gene is knocked out and the expression levels of other genes are observed, constitute a fundamental step in uncovering the intricate wiring diagrams in the living cell and elucidating the causal roles of genes in signaling and regulation. Here we present a novel framework for analyzing large cohorts of gene knockout experiments and their genome-wide effects on expression levels. We devise clustering-like algorithms that identify groups of genes that behave similarly with respect to the knockout data, and utilize them to predict knockout effects and to annotate physical interactions between proteins as inhibiting or activating. Differing from previous approaches, our prediction approach does not depend on physical network information; the latter is used only for the annotation task. Consequently, it is both more efficient and of wider applicability than previous methods. We evaluate our approach using a large scale collection of gene knockout experiments in yeast, comparing it to the state-of-the-art SPINE algorithm. In cross validation tests, our algorithm exhibits superior prediction accuracy, while at the same time increasing the coverage by over 25-fold. Significant coverage gains are obtained also in the annotation of the physical network.     

Energy-linked nicotinamide-nucleotide transhydrogenase. Characterization of reconstituted ATP-driven transhydrogenase from beef heart mitochondria

The interaction between pure transhydrogenase and ATPase (Complex V) from beef heart mitochondria was investigated with transhydrogenase-ATPase vesicles in which the two proteins were co-reconstituted by dialysis or dilution procedures. In addition to phosphatidylcholine and phosphatidylethanolamine, reconstitution required phosphatidylserine and lysophosphatidylcholine. Transhydrogenase-ATPase vesicles catalyzed a 20-30-fold stimulation of the reduction of NADP+ or thio-NADP+ by NADH and a 70-fold shift of the apparent equilibrium expressed as the nicotinamide nucleotide ratio [NADPH][NAD+]/[NADP+][NADH]. In both of these respects, the transhydrogenase-ATPase vesicles were severalfold more efficient than beef heart submitochondrial particles. By measuring the ATP-driven transhydrogenase and the oligomycin-sensitive ATPase activities simultaneously and under the same conditions at low ATP concentrations, i.e. below 15 microM, the ATP-driven transhydrogenase/oligomycin-sensitive ATPase activity ratio was found to be about 3. This value is consistent with the stoichiometries of three protons translocated per ATP hydrolyzed and one proton translocated per NADPH formed and with a mechanism where the two enzymes interact through a delocalized proton-motive force.     

The protein substrate binding site of the ubiquitin-protein ligase system

In order to gain insight into the mechanisms that determine the selectivity of the ubiquitin proteolytic pathway, the protein substrate binding site of the ubiquitin-protein ligase system was identified and examined. Previous studies had shown that the ligase system consists of three components: a ubiquitin-activating enzyme (E1), ubiquitin-carrier protein (E2), and a third enzyme, E3, the mode of action of which has not been defined. E3 from rabbit reticulocytes was further purified by a combination of affinity chromatography, hydrophobic chromatography, and gel filtration procedures. A 180-kDa protein was identified as the subunit of E3. Two independent methods indicate that E3 has the protein binding site of the ubiquitin ligase system. These are the chemical cross-linking of 125I-labeled proteins to the E3 subunit and the functional conversion of enzyme-bound labeled proteins to ubiquitin conjugates in pulse-chase experiments. The trapping of E3-bound protein for labeled product formation was allowed by the slow dissociation of E3 X protein complex. The specificity of binding of different proteins to E3, examined by both methods, showed a direct correlation with their susceptibility to degradation by the ubiquitin system. Proteins with free alpha-NH2 groups, which are good substrates, bind better to E3 than corresponding proteins with blocked NH2 termini, which are not substrates. Oxidation of methionine residues to sulfoxide derivatives greatly increases the susceptibility of some proteins to ligation with ubiquitin, with a corresponding increase in their binding to E3. However, a protein derivative which was subjected to both amino group modification and oxidation binds strongly to the enzyme, even though it cannot be ligated to ubiquitin. It thus seems that the substrate binding site of E3 participates in determining the specificity of proteins that enter the ubiquitin pathway of protein degradation.     

Optimal firing in sparsely-connected low-activity attractor networks

We examine the performance of Hebbian-like attractor neural networks, recalling stored memory patterns from their distorted versions. Searching for an activation (firing-rate) function that maximizes the performance in sparsely connected low-activity networks, we show that the optimal activation function is a threshold-sigmoid of the neuron's input field. This function is shown to be in close correspondence with the dependence of the firing rate of cortical neurons on their integrated input current, as described by neurophysiological recordings and conduction-based models. It also accounts for the decreasing-density shape of firing rates that has been reported in the literature. Received:9 December 1994 / Accepted in revised form: 9 January 1996     

Steroidal glycosides from the bulbs of Lilium dauricum.

The bulbs of Lilium dauricum yielded 11 compounds, including six new steroidal glycosides. The structures have been determined by spectral analysis and hydrolysis to be (25R,26R)-26-methoxyspirost-5-en-3 beta-ol 3-O-alpha-L-rhamnopyranosyl-(1----2)-O-[alpha-L-arabinopyranosyl-( 1----3)]- beta-D-glucopyranoside, (25R,26R)-26-methoxyspirost-5-en-3 beta-ol 3-O-alpha-L-rhamnopyranosyl-(1----2)-O-[beta-D-glucopyranosyl-(1----4)]- beta-D-glucopyranoside, (25R)-spirost-5-en-3 beta-ol (diosgenin) 3-O-alpha-L-rhamnopyranosyl-(1----2)-O-[alpha-L-arabinopyranosyl- (1----3)]-beta-D-glucopyranoside, (25R)-3 beta,17 alpha-dihydroxy-5 alpha-spirostan-6-one 3-O-alpha-L-rhamnopyranosyl-(1----2)-beta-D-glucopyranoside, (25R)-3 beta, 17 alpha-dihydroxy-5 alpha-spirostan-6-one 3-O-alpha-L-rhamnopyranosyl-(1----2)-O-[alpha-L- arabinopyranosyl-(1----3)]-beta-D-glucopyranoside and (20R,22R)-3 beta,20,22-trihydroxy-5 alpha-cholestan-6-one (tenuifoliol) 3-O-alpha-L-rhamnopyranosyl-(1----2)-beta-D-glucopyranoside. The absolute configurations of C-20 and C-22 of tenuifoliol were further confirmed by detailed analysis of the NOE difference spectrum of the corresponding isopropylidene derivative. Several known compounds were also isolated and identified.     

Hypothetical Outcome Plots Outperform Error Bars and Violin Plots for Inferences about Reliability of Variable Ordering

Many visual depictions of probability distributions, such as error bars, are difficult for users to accurately interpret. We present and study an alternative representation, Hypothetical Outcome Plots (HOPs), that animates a finite set of individual draws. In contrast to the statistical background required to interpret many static representations of distributions, HOPs require relatively little background knowledge to interpret. Instead, HOPs enables viewers to infer properties of the distribution using mental processes like counting and integration. We conducted an experiment comparing HOPs to error bars and violin plots. With HOPs, people made much more accurate judgments about plots of two and three quantities. Accuracy was similar with all three representations for most questions about distributions of a single quantity.     

Perception of Graphical Virtual Environments by Blind Users via Sensory Substitution

Graphical virtual environments are currently far from accessible to blind users as their content is mostly visual. This is especially unfortunate as these environments hold great potential for this population for purposes such as safe orientation, education, and entertainment. Previous tools have increased accessibility but there is still a long way to go. Visual-to-audio Sensory-Substitution-Devices (SSDs) can increase accessibility generically by sonifying on-screen content regardless of the specific environment and offer increased accessibility without the use of expensive dedicated peripherals like electrode/vibrator arrays. Using SSDs virtually utilizes similar skills as when using them in the real world, enabling both training on the device and training on environments virtually before real-world visits. This could enable more complex, standardized and autonomous SSD training and new insights into multisensory interaction and the visually-deprived brain. However, whether congenitally blind users, who have never experienced virtual environments, will be able to use this information for successful perception and interaction within them is currently unclear.We tested this using the EyeMusic SSD, which conveys whole-scene visual information, to perform virtual tasks otherwise impossible without vision. Congenitally blind users had to navigate virtual environments and find doors, differentiate between them based on their features (Experiment1:task1) and surroundings (Experiment1:task2) and walk through them; these tasks were accomplished with a 95% and 97% success rate, respectively. We further explored the reactions of congenitally blind users during their first interaction with a more complex virtual environment than in the previous tasks–walking down a virtual street, recognizing different features of houses and trees, navigating to cross-walks, etc. Users reacted enthusiastically and reported feeling immersed within the environment. They highlighted the potential usefulness of such environments for understanding what visual scenes are supposed to look like and their potential for complex training and suggested many future environments they wished to experience.