TULIPs: tunable, light-controlled interacting protein tags for cell biology

Naturally photoswitchable proteins offer a means of directly manipulating the formation of protein complexes that drive a diversity of cellular processes. We developed tunable light-inducible dimerization tags (TULIPs) based on a synthetic interaction between the LOV2 domain of Avena sativa phototropin 1 (AsLOV2) and an engineered PDZ domain (ePDZ). TULIPs can recruit proteins to diverse structures in living yeast and mammalian cells, either globally or with precise spatial control using a steerable laser. The equilibrium binding and kinetic parameters of the interaction are tunable by mutation, making TULIPs readily adaptable to signaling pathways with varying sensitivities and response times. We demonstrate the utility of TULIPs by conferring light sensitivity to functionally distinct components of the yeast mating pathway and by directing the site of cell polarization.     

Effect of skeletal muscle myosin light chain 2 on the Ca2+-sensitive interaction of myosin and heavy meromyosin with regulated actin

A low-speed centrifugation assay has been used to examine the binding of myosin filaments to F-action and to regulated actin in the presence of MgATP. While the cross-linking of F-actin by myosin was Ca2+ insensitive, much less regulated actin was cross-linked by myosin in the absence of Ca2+ than in its presence. Removal of the 19000-dalton, phosphorylatable light chain from myosin resulted in the loss of this Ca2+ sensitivity. Readdition of this light chain partially restored the Ca2+-sensitive cross-linking of regulated actin by myosin. Urea gel electrophoresis has been used to distinguish that fraction of heavy meromyosin which contains intact phosphorylatable light chain from that which contains a 17000-dalton fragment of this light chain. In the absence of Ca2+, heavy meromyosin which contained digested light chain bound to regulated actin in MgATP about 10-fold more tightly than did heavy meromyosin which contained intact light chain. The regulated actin-activated ATPases of heavy meromyosin also showed that cleavage of this light chain causes a substantial increase in the affinity of heavy meromyosin for regulated actin in the absence of Ca2+. Thus, the binding of both myosin and heavy meromyosin to regulated actin is Ca2+ sensitive, and this sensitivity is dependent on the phosphorylatable light chain.     

Density-dependent shift from facilitation to competition in a dwarf <Emphasis Type="Italic">Avicennia germinans</Emphasis> forest

The global effort to rehabilitate and restore destroyed mangrove forests is unable to keep up with the high mangrove deforestation rates, which exceed the average pace of global deforestation. Although facilitation theory presents new possibilities for the restoration of heavily degraded mangrove sites, knowledge of tree–tree interactions in stressed mangrove forest ecosystems is too limited to utilize facilitation appropriately. The aim was to determine the mode of local interaction among stressed mangrove trees by investigating the effect of clustering on tree size and crown morphology under contrasting stand densities. The study was conducted in a dwarf Avicennia germinans forest in Northern Brazil, in which tree growth is limited by infrequent inundation and high pore-water salinity. Autoregressive regression, Voronoi tessellation and spatial point pattern statistics were used to address the spatial processes underlying tree interaction. Under low stand density (1.2 trees m^?2) dwarf trees which grew in clustered cohorts of A. germinans had a less stunted crown morphology revealing the dominance of a positive neighborhood influence among plants. In contrast, dwarf trees in the denser forest stand (2.7 trees m^?2) were interacting competitively as indicated by the more negative effect of neighbors on crown morphology and size. The shift from facilitative to competitive interactions is an important feature of mangrove forest regeneration under harsh environmental conditions. If mangrove trees are unable to regenerate naturally on severely degraded sites, intraspecific facilitation could be used to assist regeneration by planting seedlings in clusters and not evenly spaced.     

Hyperglycemia and aberrant <Emphasis Type="Italic">O-GlcNAc</Emphasis>ylation: contributions to tumor progression

A number of cancer types have shown an increased prevalence and a higher mortality rate in patients with hyperglycemic associated pathologies. Although the correlation between diabetes and cancer incidence has been increasingly reported, the underlying molecular mechanisms beyond this association are not yet fully understood. Recent studies have suggested that high glucose levels support tumor progression through multiple mechanisms that are hallmarks of cancer, including cell proliferation, resistance to apoptosis, increased cell migration and invasiveness, epigenetic regulation (hyperglycemic memory), resistance to chemotherapy and altered metabolism. Most of the above occur because hyperglycemia through hexosamine biosynthetic pathway leads to aberrant O-GlcNAcylation of many intracellular proteins that are involved in those mechanisms. Deregulated O-GlcNAcylation is emerging as a general feature of cancer. Despite strong evidence suggesting that aberrant O-GlcNAcylation is or may be involved in the acquisition of all cancer hallmarks, it remains out of the list of the next generation of emerging hallmarks. Here, we discuss some of the current understanding on how hyperglycemia affects cancer cell biology and how aberrant O-GlcNAcylation stands in this context.     

Size-dependent predator–prey relationships between perch and their fish prey

Size-dependent interactions between piscivorous perch Perca fluviatilis (age ≥1 year) and their fish prey age 0 year perch, pikeperch Sander lucioperca and roach Rutilus rutilus in the biomanipulated Bautzen Reservoir indicated that the highest ratio of prey total length ( L _T) to predator L _T was 59%. Perch L _T and prey fish L _T were positively and linearly related. Perch L _T was strongly related with both gape width and gape height. Within the range 80–110 mm L _T, the gape height of perch exceeded gape width, while beginning at 120 mm L _T the gape width exceeded gape height. The minimum, maximum and mean prey L _T and prey body depths of all three prey species increased with increasing predator size, but the increases in mean sizes of perch and pikeperch as prey were less than that of roach. The low limit of the 'predation window' observed in this study coupled with results of previous studies on perch in the Bautzen Reservoir indicated that perch had a major impact on the population dynamics of both perch and pikeperch.     

Synthesis of derivatives of the novel cyclophilin-binding immunosuppressant sanglifehrin A with reduced numbers of polar functions.

The syntheses and the biological activities of 53-deoxo sanglifehrin A (2) and 61-deoxy octahydrosanglifehrin A (3) are described. Compound 2 shows intracellular cyclophilin (CyP)-binding and immunosuppressive activity in the mixed-lymphocyte reaction (MLR) similar to that of sanglifehrin A (1). Compound 3 is much less active in the MLR despite unchanged intracellular CyP-binding. This indicates that the 53-keto group is not necessary for immunosuppressive activity, while the 61 hydroxy group is required.     

Sustainable agriculture: how to sustain a production system in a changing environment

During the past 10-15 years, sustainable agriculture has progressed from a focus primarily on a low-input, organic farming approach with a major emphasis on small fruit or vegetable production farms, often described as Low Input Sustainable Agriculture, to the current situation where sustainability is an important part of mainstream animal and plant production units. The US Department of Agriculture programmes cover a broad range of activities, including conserving the natural resource base, enhancing environmental quality, and sustaining productivity of the nation's farms. The use of Geographic Information Systems technology to direct application of fertilisers, pesticides, and herbicides is one example of a rapidly emerging technology that can reduce use of external inputs, protect the agricultural environment, and improve economic returns. This Geographic Information Systems technology also is being used to localise animal pest and disease problems, assist in regulatory or control measures, and identify high risk areas that might need different management systems or should be avoided as sites for animal production. Use of intensive grazing systems also has increased markedly over the past 5-6 years. These systems will allow longer grazing seasons in southern parts of the USA, provide more efficient use of the forages being produced and reduce labour costs in the typical dairy operation. Major animal and plant production agriculture-oriented programmes at the US Department of Agriculture focus on integrated production systems, use of Integrated Pest Management techniques, and development of alternative methods to manage pests and diseases that reduce or avoid the use of drugs and chemicals. The US Department of Agriculture has a programme for sustainable agriculture, the Sustainable Agriculture Research and Education programme, which emphasises alternative approaches for animal and plant production systems.     

Viral RNA and evolved mutational robustness.

Many properties of organisms show great robustness against mutations. Whether this robustness is an evolved property or intrinsic to genetic systems is by and large unknown. An evolutionary origin of robustness would require a rethinking of key concepts in the field of molecular evolution, such as gene-specific neutral mutation rates, or the context-independence of deleterious mutations. We provide evidence that mutational robustness of the genome of RNA viruses to mutational changes in secondary structure has evolved. J. Exp. Zool. ( Mol. Dev. Evol.) 285:119-127, 1999.     

A comparison of neural computations underlying stereo vision and sound localization.

Stereo vision and sound localization are behaviors that help organisms to orient in space. Stereo vision provides information about the distance of an object. In sound localization mainly directional signals are analyzed. Two specific cues, binocular disparities underlying stereo vision, and the interaural time difference, suited to represent azimuth in sound localization, have many computational problems in common, although they are generated in two different modalities. The extraction of both cues requires a comparison of signals that arise from two independent sensors, called two-sensor comparison here. This two-sensor comparison is achieved by algorithms similar to summation, half-wave rectification and multiplication. Since the underlying neurons are band-pass filters, the two-sensor comparison results in ambiguities. These are removed in a hierarchical way in several computational steps, involving squaring, inhibition and across-frequency integration.