Functional profiling of the Saccharomyces cerevisiae genome

Determining the effect of gene deletion is a fundamental approach to understanding gene function. Conventional genetic screens exhibit biases, and genes contributing to a phenotype are often missed. We systematically constructed a nearly complete collection of gene-deletion mutants (96% of annotated open reading frames, or ORFs) of the yeast Saccharomyces cerevisiae. DNA sequences dubbed 'molecular bar codes' uniquely identify each strain, enabling their growth to be analysed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays. We show that previously known and new genes are necessary for optimal growth under six well-studied conditions: high salt, sorbitol, galactose, pH 8, minimal medium and nystatin treatment. Less than 7% of genes that exhibit a significant increase in messenger RNA expression are also required for optimal growth in four of the tested conditions. Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics.     

T-cell priming by dendritic cells in lymph nodes occurs in three distinct phases

Primary T-cell responses in lymph nodes (LNs) require contact-dependent information exchange between T cells and dendritic cells (DCs). Because lymphocytes continually enter and leave normal LNs, the resident lymphocyte pool is composed of non-synchronized cells with different dwell times that display heterogeneous behaviour in mouse LNs in vitro. Here we employ two-photon microscopy in vivo to study antigen-presenting DCs and naive T cells whose dwell time in LNs was synchronized. During the first 8 h after entering from the blood, T cells underwent multiple short encounters with DCs, progressively decreased their motility, and upregulated activation markers. During the subsequent 12 h T cells formed long-lasting stable conjugates with DCs and began to secrete interleukin-2 and interferon-gamma. On the second day, coinciding with the onset of proliferation, T cells resumed their rapid migration and short DC contacts. Thus, T-cell priming by DCs occurs in three successive stages: transient serial encounters during the first activation phase are followed by a second phase of stable contacts culminating in cytokine production, which makes a transition into a third phase of high motility and rapid proliferation.     

Power requirement of the geodynamo from ohmic losses in numerical and laboratory dynamos

In the Earth's fluid outer core, a dynamo process converts thermal and gravitational energy into magnetic energy. The power needed to sustain the geomagnetic field is set by the ohmic losses (dissipation due to electrical resistance). Recent estimates of ohmic losses cover a wide range, from 0.1 to 3.5 TW, or roughly 0.3-10% of the Earth's surface heat flow. The energy requirement of the dynamo puts constraints on the thermal budget and evolution of the core through Earth's history. Here we use a set of numerical dynamo models to derive scaling relations between the core's characteristic dissipation time and the core's magnetic and hydrodynamic Reynolds numbers--dimensionless numbers that measure the ratio of advective transport to magnetic and viscous diffusion, respectively. The ohmic dissipation of the Karlsruhe dynamo experiment supports a simple dependence on the magnetic Reynolds number alone, indicating that flow turbulence in the experiment and in the Earth's core has little influence on its characteristic dissipation time. We use these results to predict moderate ohmic dissipation in the range of 0.2-0.5 TW, which removes the need for strong radioactive heating in the core and allows the age of the solid inner core to exceed 2.5 billion years.     

No cold dust within the supernova remnant Cassiopeia A

A large amount (about three solar masses) of cold (18 K) dust in the prototypical type II supernova remnant Cassiopeia A was recently reported. It was concluded that dust production in type II supernovae can explain how the large quantities (approximately 10(8) solar masses) of dust observed in the most distant quasars could have been produced within only 700 million years after the Big Bang. Foreground clouds of interstellar material, however, complicate the interpretation of the earlier submillimetre observations of Cas A. Here we report far-infrared and molecular line observations that demonstrate that most of the detected submillimetre emission originates from interstellar dust in a molecular cloud complex located in the line of sight between the Earth and Cas A, and is therefore not associated with the remnant. The argument that type II supernovae produce copious amounts of dust is not supported by the case of Cas A, which previously appeared to provide the best evidence for this possibility.     

Control of spontaneous and damage-induced mutagenesis by SUMO and ubiquitin conjugation

Protein modification by ubiquitin is emerging as a signal for various biological processes in eukaryotes, including regulated proteolysis, but also for non-degradative functions such as protein localization, DNA repair and regulation of chromatin structure. A small ubiquitin-related modifier (SUMO) uses a similar conjugation system that sometimes counteracts the effects of ubiquitination. Ubiquitin and SUMO compete for modification of proliferating cell nuclear antigen (PCNA), an essential processivity factor for DNA replication and repair. Whereas multi-ubiquitination is mediated by components of the RAD6 pathway and promotes error-free repair, SUMO modification is associated with replication. Here we show that RAD6-mediated mono-ubiquitination of PCNA activates translesion DNA synthesis by the damage-tolerant polymerases eta and zeta in yeast. Moreover, polymerase zeta is differentially affected by mono-ubiquitin and SUMO modification of PCNA. Whereas ubiquitination is required for damage-induced mutagenesis, both SUMO and mono-ubiquitin contribute to spontaneous mutagenesis in the absence of DNA damage. Our findings assign a function to SUMO during S phase and demonstrate how ubiquitin and SUMO, by regulating the accuracy of replication and repair, contribute to overall genomic stability.     

Orientierende netzhautnahe pH-Messung im Glaskörper des Kaninchens bei intravenöser Glukose-infusion

Summary After i.v. infusion of glucose a decrease of pH to 6,85±0,12 measured in the vitreous body of the rabbit eye near the retina can be recorded.     

Allometric degree distributions facilitate food-web stability

In natural ecosystems, species are linked by feeding interactions that determine energy fluxes and create complex food webs. The stability of these food webs enables many species to coexist and to form diverse ecosystems. Recent theory finds predator-prey body-mass ratios to be critically important for food-web stability. However, the mechanisms responsible for this stability are unclear. Here we use a bioenergetic consumer-resource model to explore how and why only particular predator-prey body-mass ratios promote stability in tri-trophic (three-species) food chains. We find that this 'persistence domain' of ratios is constrained by bottom-up energy availability when predators are much smaller than their prey and by enrichment-driven dynamics when predators are much larger. We also find that 97% of the tri-trophic food chains across five natural food webs exhibit body-mass ratios within the predicted persistence domain. Further analyses of randomly rewired food webs show that body mass and allometric degree distributions in natural food webs mediate this consistency. The allometric degree distributions hold that the diversity of species' predators and prey decreases and increases, respectively, with increasing species' body masses. Our results demonstrate how simple relationships between species' body masses and feeding interactions may promote the stability of complex food webs.     

8-oxo-guanine bypass by human DNA polymerases in the presence of auxiliary proteins

Specialized DNA polymerases (DNA pols) are required for lesion bypass in human cells. Auxiliary factors have an important, but so far poorly understood, role. Here we analyse the effects of human proliferating cell nuclear antigen (PCNA) and replication protein A (RP-A) on six different human DNA pols--belonging to the B, Y and X classes--during in vitro bypass of different lesions. The mutagenic lesion 8-oxo-guanine (8-oxo-G) has high miscoding potential. A major and specific effect was found for 8-oxo-G bypass with DNA pols lambda and eta. PCNA and RP-A allowed correct incorporation of dCTP opposite a 8-oxo-G template 1,200-fold more efficiently than the incorrect dATP by DNA pol lambda, and 68-fold by DNA pol eta, respectively. Experiments with DNA-pol-lambda-null cell extracts suggested an important role for DNA pol lambda. On the other hand, DNA pol iota, together with DNA pols alpha, delta and beta, showed a much lower correct bypass efficiency. Our findings show the existence of an accurate mechanism to reduce the deleterious consequences of oxidative damage and, in addition, point to an important role for PCNA and RP-A in determining a functional hierarchy among different DNA pols in lesion bypass.