University of Zurich

About: University of Zurich is a education organization based out in Zurich, Switzerland. It is known for research contribution in the topics: Population & Medicine. The organization has 50842 authors who have published 124042 publications receiving 5304521 citations. The organization is also known as: UZH & Uni Zurich.

Deciphering the evolution and metabolism of an anammox bacterium from a community genome

Abstract: Ten years ago a fortuitous discovery led to the identification of oceanic bacteria capable of anaerobic ammonium oxidation (anammox). It was soon recognized that the anammox reaction has great ecological significance, as it is responsible for removing up to 50% of fixed nitrogen from the oceans. The genome of the anammox bacterium Kuenenia stuttgartiensis has now been sequenced in a remarkable feat of what is called environmental genomics. Anammox bacteria grow very slowly and are not available in pure culture. For genome analysis an inoculum of wastewater sludge was grown in a bioreactor for one year, clocking up 10–15 generations. The DNA of the whole microbial community was sequenced and the genome of this one anammox bacterium was deduced from the results. With the genome sequence known, it will be possible to gain insight into the metabolism and evolution of these important bacteria. The genome of Kuenenia stuttgartiensis has been sequenced to learn more about anaerobic ammonium oxidation. Anaerobic ammonium oxidation (anammox) has become a main focus in oceanography and wastewater treatment1,2. It is also the nitrogen cycle's major remaining biochemical enigma. Among its features, the occurrence of hydrazine as a free intermediate of catabolism3,4, the biosynthesis of ladderane lipids5,6 and the role of cytoplasm differentiation7 are unique in biology. Here we use environmental genomics8,9—the reconstruction of genomic data directly from the environment—to assemble the genome of the uncultured anammox bacterium Kuenenia stuttgartiensis10 from a complex bioreactor community. The genome data illuminate the evolutionary history of the Planctomycetes and allow us to expose the genetic blueprint of the organism's special properties. Most significantly, we identified candidate genes responsible for ladderane biosynthesis and biological hydrazine metabolism, and discovered unexpected metabolic versatility.

Unsupervised learning of digit recognition using spike-timing-dependent plasticity.

Abstract: In order to understand how the mammalian neocortex is performing computations, two things are necessary; we need to have a good understanding of the available neuronal processing units and mechanisms, and we need to gain a better understanding of how those mechanisms are combined to build functioning systems. Therefore, in recent years there is an increasing interest in how spiking neural networks (SNN) can be used to perform complex computations or solve pattern recognition tasks. However, it remains a challenging task to design SNNs which use biologically plausible mechanisms (especially for learning new patterns), since most of such SNN architectures rely on training in a rate-based network and subsequent conversion to a SNN. We present a SNN for digit recognition which is based on mechanisms with increased biological plausibility, i.e. conductance-based instead of current-based synapses, spike-timing-dependent plasticity with time-dependent weight change, lateral inhibition, and an adaptive spiking threshold. Unlike most other systems, we do not use a teaching signal and do not present any class labels to the network. Using this unsupervised learning scheme, our architecture achieves 95% accuracy on the MNIST benchmark, which is better than previous SNN implementations without supervision. The fact that we used no domain-specific knowledge points toward the general applicability of our network design. Also, the performance of our network scales well with the number of neurons used and shows similar performance for four different learning rules, indicating robustness of the full combination of mechanisms, which suggests applicability in heterogeneous biological neural networks.

Molecular definitions of autophagy and related processes

Abstract: Over the past two decades, the molecular machinery that underlies autophagic responses has been characterized with ever increasing precision in multiple model organisms. Moreover, it has become clear that autophagy and autophagy-related processes have profound implications for human pathophysiology. However, considerable confusion persists about the use of appropriate terms to indicate specific types of autophagy and some components of the autophagy machinery, which may have detrimental effects on the expansion of the field. Driven by the overt recognition of such a potential obstacle, a panel of leading experts in the field attempts here to define several autophagy-related terms based on specific biochemical features. The ultimate objective of this collaborative exchange is to formulate recommendations that facilitate the dissemination of knowledge within and outside the field of autophagy research.

Bulgeless dwarf galaxies and dark matter cores from supernova-driven outflows

Abstract: For almost two decades the properties of ‘dwarf’ galaxies have challenged the cold dark matter (CDM) model of galaxy formation^1. Most observed dwarf galaxies consist of a rotating stellar disk^2 embedded in a massive dark-matter halo with a near-constant-density core^3. Models based on the dominance of CDM, however, invariably form galaxies with dense spheroidal stellar bulges and steep central dark-matter profiles^(4,5,6,) because low-angular-momentum baryons and dark matter sink to the centres of galaxies through accretion and repeated mergers^7. Processes that decrease the central density of CDM halos^8 have been identified, but have not yet reconciled theory with observations of present-day dwarfs. This failure is potentially catastrophic for the CDM model, possibly requiring a different dark-matter particle candidate^9. Here we report hydrodynamical simulations (in a framework^(10) assuming the presence of CDM and a cosmological constant) in which the inhomogeneous interstellar medium is resolved. Strong outflows from supernovae remove low-angular-momentum gas, which inhibits the formation of bulges and decreases the dark-matter density to less than half of what it would otherwise be within the central kiloparsec. The analogues of dwarf galaxies—bulgeless and with shallow central dark-matter profiles—arise naturally in these simulations.