The crystal structure of a high affinity RNA stem-loop complexed with the bacteriophage MS2 capsid: further challenges in the modeling of ligand-RNA interactions

We have determined the structure to 2.8 A of an RNA aptamer (F5), containing 2'-deoxy-2-aminopurine (2AP) at the -10 position, complexed with MS2 coat protein by soaking the RNA into precrystallised MS2 capsids. The -10 position of the RNA is an important determinant of binding affinity for coat protein. Adenine at this position in other RNA stem-loops makes three hydrogen bonds to protein functional groups. Substituting 2AP for the -10 adenine in the F5 aptamer yields an RNA with the highest yet reported affinity for coat protein. The refined X-ray structure shows that the 2AP base makes an additional hydrogen bond to the protein compared to adenine that is presumably the principal origin of the increased affinity. There are also slight changes in phosphate backbone positions compared to unmodified F5 that probably also contribute to affinity. Such phosphate movements are common in structures of RNAs bound to the MS2 T = 3 protein shell and highlight problems for de novo design of RNA binding ligands.     

Simulation of diffusion time of small molecules in protein crystals

A simple model for evaluation of diffusion times of small molecule into protein crystals has been developed, which takes into account the physical and chemical properties both of protein crystal and the diffusing molecules. The model also includes consideration of binding and the binding affinity of a ligand to the protein. The model has been validated by simulation of experimental set-ups of several examples found in the literature. These experiments cover a wide range of situations: from small to relatively large diffusing molecules, crystals having low, medium, or high protein density, and different size. The reproduced experiments include ligand exchange in protein crystals by soaking techniques. Despite the simplifying assumptions of the model, theoretical and experimental data are in agreement with available data, with experimental diffusion times ranging from a few seconds to several hours. The method has been used successfully for planning intermediate cryotrapping experiments in maltodextrin phosphorylase crystals.     

Insulin-like growth factors: Putative muscle-derived trophic agents that promote motoneuron survival

Treatment of chick embryos in ovo with IGF-I during the period of normal, developmentally regulated neuronal death (embryonic days 5–10) resulted in a dose-dependent rescue of a significant number of lumbar motoneurons from degeneration and death. IGF-II and two variants of IGF-I with reduced affinity for IGF binding proteins, des(1-3) IGF-I and long R³ IGF-I, also elicited enhanced survival of motoneurons equal to that seen in IGF-I-treated embryos. IGF-I did not enhance mitogenic activity in motoneuronal populations when applied to embryos during the period of normal neuronal proliferation (E2-5). Treatment of embryos with IGF-I also reduced two types of injury-induced neuronal death. Following either deafferentation or axotomy, treatment of embryos with IGF-I rescued approximately 75% and 50%, respectively, of the motoneurons that die in control embryos as a result of these procedures. Consistent with the survival-promoting activity on motoneurons in ovo, IGF-I, -II, and des(1-3) IGF-I elevated choline acetyltransferase activity in embryonic rat spinal cord cultures, with des (1-3) IGF-I demonstrating 2.5 times greater potency than did IGF-I. A single addition of IGF-I at culture initiation resulted in the maintenance of 80% of the initial ChAT activity for up to 5 days, during which time ChAT activity in untreated control cultures fell to 9%. In summary, these results demonstrate clear motoneuronal trophic activity for the IGFs. These findings, together with previous reports that IGFs are synthesized in muscle and may participate in motoneuron axonal regeneration and sprouting, indicate that these growth factors may have an important role in motoneuron development, maintenance, and recovery from injury. © 1993 John Wiley & Sons, Inc.     

Massage and stretching reduce spinal reflex excitability without affecting twitch contractile properties

Both stretching and massage can increase range of motion. Whereas the stretching-induced increases in ROM have been attributed to changes in neural and muscle responses, there is no literature investigating the ROM mechanisms underlying the interaction of stretch and massage. The objective of this paper was to evaluate changes in neural and evoked muscle responses with two types of massage and static stretching. With this repeated measures design, 30 s of plantar flexors musculotendinous junction (MTJ) and tapotement (TAP) massage were implemented either with or without 1 min of concurrent stretching as well as a control condition. Measures included the soleus maximum H-reflex/M-wave (H/M) ratio, as well as electromechanical delay (EMD), and evoked contractile properties of the triceps surae. With the exception of EMD, massage and stretch did not significantly alter triceps surae evoked contractile properties. Massage with and without stretching decreased the soleus H/M ratio. Both TAP conditions provided greater H/M ratio depression than MTJ massage while the addition of stretch provided the greatest inhibition. Both massage types when combined with stretching increased the duration of the EMD. In conclusion, MTJ and TAP massage as well as stretching decreased spinal reflex excitability, with TAP providing the strongest suppression. While static stretching prolongs EMD, massage did not affect contractile properties.     

How much heat can we grow in our cities? Modelling UK urban biofuel production potential

Biofuel provides a globally significant opportunity to reduce fossil fuel dependence; however, its sustainability can only be meaningfully explored for individual cases. It depends on multiple considerations including: life cycle greenhouse gas emissions, air quality impacts, food versus fuel trade‐offs, biodiversity impacts of land use change and socio‐economic impacts of energy transitions. One solution that may address many of these issues is local production of biofuel on non‐agricultural land. Urban areas drive global change, for example, they are responsible for 70% of global energy use, but are largely ignored in their resource production potential; however, underused urban greenspaces could be utilized for biofuel production near the point of consumption. This could avoid food versus fuel land conflicts in agricultural land and long‐distance transport costs, provide ecosystem service benefits to urban dwellers and increase the sustainability and resilience of cities and towns. Here, we use a Geographic Information System to identify urban greenspaces suitable for biofuel production, using exclusion criteria, in 10 UK cities. We then model production potential of three different biofuels: Miscanthus grass, short rotation coppice (SRC) willow and SRC poplar, within the greenspaces identified and extrapolate up to a UK‐scale. We demonstrate that approximately 10% of urban greenspace (3% of built‐up land) is potentially suitable for biofuel production. We estimate the potential of this to meet energy demand through heat generation, electricity and combined heat and power (CHP) operations. Our findings show that, if fully utilized, urban biofuel production could meet nearly a fifth of demand for biomass in CHP systems in the United Kingdom's climate compatible energy scenarios by 2030, with potentially similar implications for other comparable countries and regions.     

What shapes the range edge of a dominant African savanna tree,Colophospermum mopane? A demographic approach

Climate is widely assumed to be the primary process that limits the distribution ranges of plants. Yet, savannas have vegetation not at equilibrium with climate, instead its structure and function are shaped by interactions between fire, herbivory, climate, and vegetation. I use the rich literature of a dominant African savanna woody plant, Colophospermum mopane, to demonstrate that climate and disturbance interact with each demographic stage to shape this species range limits. This synthesis highlights that climate‐based predictions for the range of C. mopane inadequately represents the processes that shape its distribution. Instead, seed bank depletion and rainfall limitation create a demographic bottleneck at the early seedling stage. The legacy of top‐kill from disturbance changes tree stand architecture causing a critical limitation in seed supply. Exposure to top‐kill at all demographic stages causes a vigorous resprouting response and shifts tree architecture from that of 1–2 stemmed tall trees to that of a short multi‐stemmed shrub. The shorter, multi‐stemmed shrubs are below the height threshold (4 m) at which they can produce seeds, resulting in shrub‐dominated landscapes that are effectively sterile. This effect is likely most pronounced at the range edge where top‐kill‐inducing disturbances increase in frequency. The proposed mechanistic, demographic‐based understanding of C. mopane''s range limits highlights the complexity of processes that interact to shape its range edges. This insight serves as a conceptual model for understanding the determinants of range limits of other dominant woody savannas species living in disturbance limited ecosystems.     

Diel patterns of predation and fledging at nests of four species of grassland songbirds

Although it is common for nestlings to exhibit a strong bias for fledging in the morning, the mechanisms underlying this behavior are not well understood. Avoiding predation risk has been proposed as a likely mechanism by a number of researchers. We used video surveillance records from studies of grassland birds nesting in North Dakota, Minnesota, and Wisconsin to determine the diel pattern of nest predation and fledging patterns of four ground‐nesting obligate grassland passerines (Grasshopper Sparrow (Ammodramus savannarum), Savannah Sparrow (Passerculus sandwichensis), Bobolink (Dolichonyx oryzivorus), and Eastern Meadowlark (Sturnella magna)). We used the nest predation pattern as a surrogate for predation activity to test whether nestlings minimized predation risk by avoiding fledging when predation activity was high and preferentially fledging when predation risk was low. Predation activity was significantly lower starting 3 hr before sunrise and ending 3 hr after sunrise, followed by a transition to a period of significantly higher activity lasting for 4 hr, before declining to an average activity level for the rest of the diel period. There was little evidence that the four grassland bird species avoided fledging during the high‐risk period and Savannah Sparrow fledged at higher rates during that period. All four species had hours during the low‐risk period where they fledged at higher rates, but only Grasshopper Sparrow fledged preferentially during that period. Bobolink and Eastern Meadowlark had multiple hours with high fledging rates throughout the daytime period, resulting in no relationship between probability of fledging and predation risk. Given the species variability in fledging pattern seen in our study, it is unlikely that there is a universal response to any driver that affects time of fledging. Further study is needed to understand the complex interplay between species ecology and drivers such as physiology, energetics, and predation in affecting grassland bird fledging behavior.     

Synthesis of homoagmatine and GC–MS analysis of tissue homoagmatine and agmatine: evidence that homoagmatine but not agmatine is a metabolite of pharmacological L-homoarginine in the anesthetized rat

Amino Acids - Low L-homoarginine (hArg) concentrations in human blood and urine are associated with renal and cardiovascular morbidity and mortality, yet the underlying mechanisms and the...