History and Epistemology of Models: Meteorology (1946–1963) as a Case Study

An early example is von Neumann's and Charney's Princeton Meteorological Project in the period 1946–53 which ended with daily numerical prediction in less than 2 hours. After this stage, the questions of long-range forecasting and general circulation of the atmosphere became of greater importance. The late 1950s saw the emergence of an alternative: were atmospheric models used mainly for prediction or understanding? This controversial debate in particular occurred during an important colloquium in Tokyo in 1960 which gathered together J. Charney, E. Lorenz, A. Eliassen, and B. Saltzman, among others, and witnessed discussions on statistical methods for predictions and/or maximum simplification of dynamic equations. This phase ended in 1963 with Lorenzs seminal paper on “Deterministic non periodic flows.” (Received February 11, 2000)     

A proteasomal ATPase subunit recognizes the polyubiquitin degradation signal

The 26S proteasome is the chief site of regulatory protein turnover in eukaryotic cells. It comprises one 20S catalytic complex (composed of four stacked rings of seven members) and two axially positioned 19S regulatory complexes (each containing about 18 subunits) that control substrate access to the catalytic chamber. In most cases, targeting to the 26S proteasome depends on tagging of the substrate with a specific type of polyubiquitin chain. Recognition of this signal is followed by substrate unfolding and translocation, which are presumably catalysed by one or more of six distinct AAA ATPases located in the base-a ring-like 19S subdomain that abuts the axial pore of the 20S complex and exhibits chaperone activity in vitro. Despite the importance of polyubiquitin chain recognition in proteasome function, the site of this signal's interaction with the 19S complex has not been identified previously. Here we use crosslinking to a reactive polyubiquitin chain to show that a specific ATPase subunit, S6' (also known as Rpt5), contacts the bound chain. The interaction of this signal with 26S proteasomes is modulated by ATP hydrolysis. Our results suggest that productive recognition of the proteolytic signal, as well as proteasome assembly and substrate unfolding, are ATP-dependent events.     

Crystal structure of a catalytic intermediate of the maltose transporter

The maltose uptake system of Escherichia coli is a well-characterized member of the ATP-binding cassette transporter superfamily. Here we present the 2.8-A crystal structure of the intact maltose transporter in complex with the maltose-binding protein, maltose and ATP. This structure, stabilized by a mutation that prevents ATP hydrolysis, captures the ATP-binding cassette dimer in a closed, ATP-bound conformation. Maltose is occluded within a solvent-filled cavity at the interface of the two transmembrane subunits, about halfway into the lipid bilayer. The binding protein docks onto the entrance of the cavity in an open conformation and serves as a cap to ensure unidirectional translocation of the sugar molecule. These results provide direct evidence for a concerted mechanism of transport in which solute is transferred from the binding protein to the transmembrane subunits when the cassette dimer closes to hydrolyse ATP.     

Occurrence and habitat use of passage neotropical migrants in the Sonoran Desert

Little is known about stopover habitat use by neotropical migratory birds in the deserts of North America. We determined distribution, abundance, and habitat associations of neotropical migrants during spring migration in the Sonoran Desert of southwestern Arizona along large washes that supported xeroriparian scrub vegetation. We detected 91 bird species during surveys, 50 (52%) of which were passage neotropical migrants. Although xeroriparian scrub covered less than 55% of the area surveyed, 97% of all detections of passage migrants were from this vegetation type. By calculating habitat breadth for each species, we classified 87% of passage migrants as xeroriparian specialists. Richness of passage migrants was strongly associated with the presence of overstory (> 2.5 m) mesquite and paloverde. The highest species richness of breeding neotropical migrants was associated with width of the xeroriparian corridor. Habitat characteristics we have shown to be important to neotropical migrants can be preserved and managed by protecting xeroriparian areas, particularly those supporting mature (> 2.5 m) paloverde, mesquite, desert willow, and catclaw acacia trees. Additionally, xeroriparian scrub within the creosote-bursage vegetation type may be particularly important to passage neotropical migrants.     

cAMP initiates early phase neuron-like morphology changes and late phase neural differentiation in mesenchymal stem cells

The intracellular second messenger cAMP is frequently used in induction media to induce mesenchymal stem cells (MSCs) into neural lineage cells. To date, an understanding of the role cAMP exerts on MSCs and whether cAMP can induce MSCs into functional neurons is still lacking. We found cAMP initiated neuron-like morphology changes early and neural differentiation much later. The early phase changes in morphology were due to cell shrinkage, which subsequently rendered some cells apoptotic. While the morphology changes occurred prior to the expression of neural markers, it is not required for neural marker expression and the two processes are differentially regulated downstream of cAMP-activated protein kinase A. cAMP enabled MSCs to gain neural marker expressions with neuronal function, such as, calcium rise in response to neuronal activators, dopamine, glutamate, and potassium chloride. However, only some of the cells induced by cAMP responded to the three neuronal activators and further lack the neuronal morphology, suggesting that although cAMP is able to direct MSCs towards neural differentiation, they do not achieve terminal differentiation.     

Embracing the Complexity: Surfacing Problem Situations with Multiple Actors of the Pineapple Value Chain in Uganda

The complexity of local situations in which agricultural value chains are enacted requires a systemic understanding when seeking to improve interlinked livelihoods. Studying the fresh pineapple value chain in Uganda offers an illustrative example. Individually negotiated and context-specific actor relationships, along with their connected activities can be revealed by conceptualizing the chain as a purposeful human activity system. We followed a systems learning approach to elicit value chain actors’ perspectives on factors influencing their activities while surfacing relevant problem situations, resolutions and constraints. Participatory methods, including cognitive mapping, were used to spark dialogue during meetings with only farmers, traders and brokers and also with mixed groups. The results present the multiple natural, technical and social factors identified by value chain actors leading to losses and benefits to their income. System driving and shaping influences included infrastructure, seasonality, perishability and weather conditions. Process-oriented analysis of multi-stakeholder discussions revealed feedback cycles related to fragmentation of the chain. This resulted from and contributed to problematic communication, price fluctuations and challenges in actor relations. For example, actors proposed uniform pricing and debated the implications. Although the systemic perspective brought forward actors’ awareness of potential benefits of improved collaboration and recognition of interdependent activities, it also exposed barriers. Participatory systems learning helped to capture actors’ room of maneuver, and can support processes towards actor-driven change.     

Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid

Salmonella enterica serovars often have a broad host range, and some cause both gastrointestinal and systemic disease. But the serovars Paratyphi A and Typhi are restricted to humans and cause only systemic disease. It has been estimated that Typhi arose in the last few thousand years. The sequence and microarray analysis of the Paratyphi A genome indicates that it is similar to the Typhi genome but suggests that it has a more recent evolutionary origin. Both genomes have independently accumulated many pseudogenes among their approximately 4,400 protein coding sequences: 173 in Paratyphi A and approximately 210 in Typhi. The recent convergence of these two similar genomes on a similar phenotype is subtly reflected in their genotypes: only 30 genes are degraded in both serovars. Nevertheless, these 30 genes include three known to be important in gastroenteritis, which does not occur in these serovars, and four for Salmonella-translocated effectors, which are normally secreted into host cells to subvert host functions. Loss of function also occurs by mutation in different genes in the same pathway (e.g., in chemotaxis and in the production of fimbriae).