Distinct ubiquitin binding modes exhibited by SH3 domains: Molecular determinants and functional implications

SH3 domains constitute a new type of ubiquitin-binding domains. We previously showed that the third SH3 domain (SH3-C) of CD2AP binds ubiquitin in an alternative orientation. We have determined the structure of the complex between first CD2AP SH3 domain and ubiquitin and performed a structural and mutational analysis to decipher the determinants of the SH3-C binding mode to ubiquitin. We found that the Phe-to-Tyr mutation in CD2AP and in the homologous CIN85 SH3-C domain does not abrogate ubiquitin binding, in contrast to previous hypothesis and our findings for the first two CD2AP SH3 domains. The similar alternative binding mode of the SH3-C domains of these related adaptor proteins is characterised by a higher affinity to C-terminal extended ubiquitin molecules. We conclude that CD2AP/CIN85 SH3-C domain interaction with ubiquitin constitutes a new ubiquitin-binding mode involved in a different cellular function and thus changes the previously established mechanism of EGF-dependent CD2AP/CIN85 mono-ubiquitination. © 2013 Ortega Roldan et al

Screening for snow/snowmelt in SNPP VIIRS aerosol optical depth algorithm

The Visible Infrared Imaging Radiometer Suite (VIIRS) on board the Suomi National Polar-orbiting Partnership (S-NPP) spacecraft provides validated daily global aerosol optical depth (AOD) retrievals; however, a close examination of the VIIRS aerosol product identified residual snow and snowmelt contamination, resulting generally in an overestimation of AOD. The contamination was particularly evident over Northern Hemisphere high-latitude regions during the spring thaw. To improve the product performance, we introduced a new empirical snow and snowmelt screening scheme that combines a normalized difference snow index (NDSI)- and brightness temperature (BT)-based snow test, a snow adjacency test and a spatial homogeneity test (a.k.a. spatial filter). Testing of retrievals for 18 May 2014 indicated that, compared to the previous, visible reflectance anomaly (VRA)-based snow test, the new NDSI- and BT-based snow test screened out an additional 3.44&thinsp;% of VIIRS AOD retrievals, most of which were over high latitudes experiencing snowmelt. The new snow adjacency test and the homogeneity test degraded another 5.57&thinsp;% and 0.26&thinsp;%, respectively, otherwise good-quality AOD retrievals. For the VIIRS–AERONET (Aerosol Robotic Network) matchups over Northern Hemisphere high-latitude regions during 3 years of spring (2013–2015), the new scheme also effectively screened out a significant number of the matchups that had anomalously high positive biases attributable to snow and snowmelt contamination. The new snow and snowmelt screening scheme was transferred to the Interface Data Processing Segment (IDPS) VIIRS aerosol algorithm on 22 June 2015. Subsequently no significant snow and snowmelt contamination was found during spring 2016. The scheme is also implemented in the new Enterprise VIIRS aerosol algorithm in the National Oceanic and Atmospheric Administration (NOAA) Enterprise Processing System (EPS) that became operational in 2017.</p

Computational and Biological Analogies for Understanding Fine-Tuned Parameters in Physics

In this philosophical paper, we explore computational and biological analogies to address the fine-tuning problem in cosmology. We first clarify what it means for physical constants or initial conditions to be fine-tuned. We review important distinctions such as the dimensionless and dimensional physical constants, and the classification of constants proposed by Levy-Leblond. Then we explore how two great analogies, computational and biological, can give new insights into our problem. This paper includes a preliminary study to examine the two analogies. Importantly, analogies are both useful and fundamental cognitive tools, but can also be misused or misinterpreted. The idea that our universe might be modelled as a computational entity is analysed, and we discuss the distinction between physical laws and initial conditions using algorithmic information theory. Smolin introduced the theory of "Cosmological Natural Selection" with a biological analogy in mind. We examine an extension of this analogy involving intelligent life. We discuss if and how this extension could be legitimated. Keywords: origin of the universe, fine-tuning, physical constants, initial conditions, computational universe, biological universe, role of intelligent life, cosmological natural selection, cosmological artificial selection, artificial cosmogenesis.Comment: 25 pages, Foundations of Science, in pres

Reversal of age-related learning deficiency by the vertebrate PACAP and IGF-1 in a novel invertebrate model of aging: the pond snail (Lymnaea Stagnalis)

With the increase of life span, nonpathological age-related memory decline is affecting an increasing number of people. However, there is evidence that age-associated memory impairment only suspends, rather than irreversibly extinguishes, the intrinsic capacity of the aging nervous system for plasticity (1). Here, using a molluscan model system, we show that the age-related decline in memory performance can be reversed by administration of the pituitary adenylate cyclase activating polypeptide (PACAP). Our earlier findings showed that a homolog of the vertebrate PACAP38 and its receptors exist in the pond snail (Lymnaea stagnalis) brain (2), and it is both necessary and instructive for memory formation after reward conditioning in young animals (3). Here we show that exogenous PACAP38 boosts memory formation in aged Lymnaea, where endogenous PACAP38 levels are low in the brain. Treatment with insulin-like growth factor-1, which in vertebrates was shown to transactivate PACAP type I (PAC1) receptors (4) also boosts memory formation in aged pond snails. Due to the evolutionarily conserved nature of these polypeptides and their established role in memory and synaptic plasticity, there is a very high probability that they could also act as “memory rejuvenating” agents in humans

Solid State Physics

Contains reports on three research projects

NA49 results on hadron production: indications of the onset of deconfinement ?

The NA49 experiment at the CERN SPS measured the energy and system size dependence of particle production in A+A collisions. A change of the energy dependence of several hadron production properties at low SPS energies is observed which suggests a scenario requiring the onset of deconfinement.Comment: XXXV International Symposium on Multiparticle Dynamics 200