Enabling user-inclusive innovation in African Agriculture

Ignitia has developed a disruptive technology that allows smallholder farmers in West Africa to access accurate weather predictions. Engaging with local partners and initiating reliable impact measurements were key factors to gain trust and scale-up the business

Substrate discrimination in RNase P RNA-mediated cleavage: importance of the structural environment of the RNase P cleavage site

Like the translational elongation factor EF-Tu, RNase P interacts with a large number of substrates where RNase P with its RNA subunit generates tRNAs with matured 5′ termini by cleaving tRNA precursors immediately 5′ of the residue at +1, i.e. at the position that corresponds to the first residue in tRNA. Most tRNAs carry a G(+1)C(+72) base pair at the end of the aminoacyl acceptor-stem whereas in tRNA(Gln) G(+1)C(+72) is replaced with U(+1)A(+72). Here, we investigated RNase P RNA-mediated cleavage as a function of having G(+1)C(+72) versus U(+1)A(+72) in various substrate backgrounds, two full-size tRNA precursors (pre-tRNA(Gln) and pre-tRNA(Tyr)Su3) and a model RNA hairpin substrate (pATSer). Our data showed that replacement of G(+1)C(+72) with U(+1)A(+72) influenced ground state binding, cleavage efficiency under multiple and single turnover conditions in a substrate-dependent manner. Interestingly, we observed differences both in ground state binding and rate of cleavage comparing two full-size tRNA precursors, pre-tRNA(Gln) and pre-tRNA(Tyr)Su3. These findings provide evidence for substrate discrimination in RNase P RNA-mediated cleavage both at the level of binding, as previously observed for EF-Tu, as well as at the catalytic step. In our experiments where we used model substrate derivatives further indicated the importance of the +1/+72 base pair in substrate discrimination by RNase P RNA. Finally, we provide evidence that the structural architecture influences Mg(2+) binding, most likely in its vicinity

Longitudinal spin fluctuations in bcc and liquid Fe at high temperature and pressure calculated with a supercell approach

Investigation of magnetic materials at realistic conditions with first-principles methods is a challenging task due to the interplay of vibrational and magnetic degrees of freedom. The most difficult contribution to include in simulations is represented by the longitudinal magnetic degrees of freedom (LSF) due to their inherent many-body nature; nonetheless, schemes that enable to take into account this effect on a semiclassical level have been proposed and employed in the investigation of magnetic systems. However, assessment of the effect of vibrations on LSF is lacking in the literature. For this reason, in this work we develop a supercell approach within the framework of constrained density functional theory to calculate self-consistently the size of local-environment-dependent magnetic moments in the paramagnetic, high-temperature state in presence of lattice vibrations and for liquid Fe in different conditions. First, we consider the case of bcc Fe at the Curie temperature and ambient pressure. Then, we perform a similar analysis on bcc Fe at Earth's inner core conditions, and we find that LSF stabilize non-zero moments which affect atomic forces and electronic density of states of the system. Finally, we employ the present scheme on liquid Fe at the melting point at ambient pressure, and at Earth's outer core conditions ($p \approx 200$ GPa, $T \approx 6000$ K). In both cases, we obtain local magnetic moments of sizes comparable to the solid-state counterparts.Comment: 12 pages, 12 figure

Towards a Holistic Controller: Reinforcement Learning for Data Center Control

The increased use of cloud and other large scale datacenter IT services and the associated power usage has put the spotlight on more energy-efficient datacenter management. In this paper, a simple model was developed to represent the heat rejection system and energy usage in a small DC setup. The model was then controlled by a reinforcement learning agent that handles both the load balancing of the IT workload, as well as cooling system setpoints.The main contribution is the holistic approach to datacenter control where both facility metrics, IT hardware metric and cloud service logs are used as inputs. The application of reinforcement learning in the proposed holistic setup is feasible and achieves results that outperform standard algorithms. The paper presents both the simplified DC model and the reinforcement learning agent in detail and discusses how this work can be extended towards a richer datacenter model

Cleavage mediated by the P15 domain of bacterial RNase P RNA

Independently folded domains in RNAs frequently adopt identical tertiary structures regardless of whether they are in isolation or are part of larger RNA molecules. This is exemplified by the P15 domain in the RNA subunit (RPR) of the universally conserved endoribonuclease P, which is involved in the processing of tRNA precursors. One of its domains, encompassing the P15 loop, binds to the 3′-end of tRNA precursors resulting in the formation of the RCCA–RNase P RNA interaction (interacting residues underlined) in the bacterial RPR–substrate complex. The function of this interaction was hypothesized to anchor the substrate, expose the cleavage site and result in re-coordination of Mg2+ at the cleavage site. Here we show that small model-RNA molecules (~30 nt) carrying the P15-loop mediated cleavage at the canonical RNase P cleavage site with significantly reduced rates compared to cleavage with full-size RPR. These data provide further experimental evidence for our model that the P15 domain contributes to both substrate binding and catalysis. Our data raises intriguing evolutionary possibilities for ‘RNA-mediated’ cleavage of RNA

Regulation of Boundary Cap Neural Crest Stem Cell Differentiation After Transplantation

Success of cell replacement therapies for neurological disorders will depend largely on the optimization of strategies to enhance viability and control the developmental fate of stem cells after transplantation. Once transplanted, stem/progenitor cells display a tendency to maintain an undifferentiated phenotype or differentiate into inappropriate cell types. Gain and loss of function experiments have revealed key transcription factors which drive differentiation of immature stem/progenitor cells toward more mature stages and eventually to full differentiation. An attractive course of action to promote survival and direct the differentiation of transplanted stem cells to a specific cell type would therefore be to force expression of regulatory differentiation molecules in already transplanted stem cells, using inducible gene expression systems which can be controlled from the outside. Here, we explore this hypothesis by employing a tetracycline gene regulating system (Tet-On) to drive the differentiation of boundary cap neural crest stem cells (bNCSCs) toward a sensory neuron fate after transplantation. We induced the expression of the key transcription factor Runx1 in Sox10-expressing bNCSCs. Forced expression of Runx1 strongly increased transplant survival in the enriched neurotrophic environment of the dorsal root ganglion cavity, and was sufficient to guide differentiation of bNCSCs toward a nonpeptidergic nociceptive sensory neuron phenotype both in vitro and in vivo after transplantation. These findings suggest that exogenous activation of transcription factors expression after transplantation in stem/progenitor cell grafts can be a constructive approach to control their survival as well as their differentiation to the desired type of cell and that the Tet-system is a useful tool to achieve this

Minor changes largely restore catalytic activity of archaeal RNase P RNA from Methanothermobacter thermoautotrophicus

The increased protein proportion of archaeal and eukaryal ribonuclease (RNase) P holoenzymes parallels a vast decrease in the catalytic activity of their RNA subunits (P RNAs) alone. We show that a few mutations toward the bacterial P RNA consensus substantially activate the catalytic (C-) domain of archaeal P RNA from Methanothermobacter, in the absence and presence of the bacterial RNase P protein. Large increases in ribozyme activity required the cooperative effect of at least two structural alterations. The P1 helix of P RNA from Methanothermobacter was found to be extended, which increases ribozyme activity (ca 200-fold) and stabilizes the tertiary structure. Activity increases of mutated archaeal C-domain variants were more pronounced in the context of chimeric P RNAs carrying the bacterial specificity (S-) domain of Escherichia coli instead of the archaeal S-domain. This could be explained by the loss of the archaeal S-domain's capacity to support tight and productive substrate binding in the absence of protein cofactors. Our results demonstrate that the catalytic capacity of archaeal P RNAs is close to that of their bacterial counterparts, but is masked by minor changes in the C-domain and, particularly, by poor function of the archaeal S-domain in the absence of archaeal protein cofactors