The precipitation of poly-L-glutamic acid. II. beta-Precipitation.

Infrared and X-ray diffraction studies have established that in the β-precipitation region of poly-L -glutamic acid the chains are in the β-conformation. Therefore, a major molecular conformational change has taken place upon precipitation. It is shown that the size of the α-helical aggregates remains constant with time in the β-region. Strong evidence can be offered to indicate that the transformation involves a transitory random-coil intermediate. Reasons are advanced, in view of the stability of the β-form, as to why two distinct precipitation regions exist.     

A deoxyribonucleic acid ligase from nuclei of rat liver. Purification and properties.

A DNA ligase has been extensively purified from nuclei of rat livers. The ligase seals single strand nicks in DNA with any of the four usual bases on either the 3 or 5 sides. It requires ATP and a divalent cation (Mg-2plus or Mn-2plus) for activity. At low Mg-2plus concentrations the activity is greatly stimulated by a variety of monovalent cations. Relatively small excesses of either monovalent or divalent cation above the amounts which give maximal activity lead to inhibition of activity. Poly(G) and poly(I) inhibit ligase activity; several other polyribonucleotides are not inhibitory. Low concentrations of inorganic pyrophosphate are inhibitory. The molecular weight of the ligase is estimated from gel filtration to be about 10 times 10-4.     

Follistatin Protein Enhances Satellite Cell Counts in Reinnervated Muscle

Background Muscle recovery following peripheral nerve repair is sup-optimal. Follistatin (FST), a potent muscle stimulant, enhances muscle size and satellite cell counts following reinnervation when administered as recombinant FST DNA via viral vectors. Local administration of recombinant FST protein, if effective, would be more clinically translatable but has yet to be investigated following muscle reinnervation. Objective  The aim of this study is to assess the effect of direct delivery of recombinant FST protein on muscle recovery following muscle reinnervation. Materials and Methods  In total, 72 Sprague-Dawley rats underwent temporary (3 or 6 months) denervation or sham denervation. After reinnervation, rats received FST protein (isoform FS-288) or sham treatment via a subcutaneous osmotic pump delivery system. Outcome measures included muscle force, muscle histomorphology, and FST protein quantification. Results  Follistatin treatment resulted in smaller muscles after 3 months denervation ( p  = 0.019) and reduced force after 3 months sham denervation ( p  < 0.001). Conversely, after 6 months of denervation, FST treatment trended toward increased force output ( p  = 0.066). Follistatin increased satellite cell counts after denervation ( p  < 0.001) but reduced satellite cell counts after sham denervation ( p  = 0.037). Conclusion  Follistatin had mixed effects on muscle weight and force. Direct FST protein delivery enhanced satellite cell counts following reinnervation. The positive effect on the satellite cell population is intriguing and warrants further investigation.     

Distributional change and conservation on the Andean flank: a palaeoecological perspective

Aim To review the insights that palaeoecology can offer on the threat posed to Andean communities by global climate change. Location The geographical focus is the eastern flank of the tropical Andes, with particular reference to Peru. Method The article presents a synthetic review of the problem. Results Species‐rich communities of the eastern Andean flank are threatened both by development and climate change. If, as predicted, the cloudbase and frost line lifts 600 m elevation this century, there will be a substantial loss of cloud forest habitat. Palaeoecology provides insights on the location and nature of past ecotones, the continuity of niche availability, and estimates for rates and modes of migration. With further warming and drying of lower montane regions, upslope migration of species will be individualistic: a new equilibrium with the altered climate is unlikely to be attained. The zone of agriculture will move upslope faster than the migrating trees and so landscape conversion will negate the ability of some species to respond to the new conditions. Conservation of the lower reaches of modern cloud forest is advocated as a means to limit this foreseeable extinction event. Main Conclusions Climate change will induce changes in plant and animal communities. Human disturbance will invade climatically marginal agricultural lands at the pace of climate change. Rapid migratory response such as that witnessed at the onset of the Holocene may not be evident as climates warm, because Holocene climatic stability has reduced outlying upslope populations that may have served as expansion nuclei. Conservation must aim to maintain plant and animal niches, rather than particular communities of species.     

Alleviation of Both Water and Nutrient Limitations is Necessary to Accelerate Ecological Restoration of Waste Rock Tips

Hard rock quarries are commonly located close to national parks and special areas of conservation and are generally regarded as visually intrusive. Consequently, restoration strategies that effectively accelerate natural plant regeneration processes are required. Slate waste tips present extreme conditions for plant establishment with multiple potential limiting factors (e.g., lack of organic matter, nutrients, and poor water retention). In this study, we investigated ecological strategies to accelerate natural regeneration at the largest slate quarry in Europe. A field experiment was conducted to assess ecosystem restoration using a contrasting set of native woody species. Treatments included amendments of waste tips with: polyacrylamide gel to increase water‐holding capacity; mineral fertilizer to increase nutrient supply; and two treatments that increased both (organic waste or boulder clay addition). Ecosystem recovery was evaluated through above‐ and below‐ground productivity (plant and microbial, respectively) and soil analyses. Neither increasing nutrient supply (with mineral fertilizer) nor water‐holding capacity (with polyacrylamide gel) was sufficient, alone, to improve plant establishment. However, both boulder clay and organic waste amendment significantly enhanced plant growth. There was a marked positive interaction in the effects on tree growth of the amendment with organic waste and boulder clay. Large interactions occurred between tree species and substrate amendments. The growth of N₂‐fixing species was strongly favored over non‐fixers where there was no addition of material increasing soil nitrogen supply, whereas the growth advantage of pioneer species over non‐pioneers was greatest with fertilizer, organic waste, or clay additions. Organic waste addition had the greatest positive impact on soil processes.     

Effects of grazing on grassland soil carbon: a global review

Soils of grasslands represent a large potential reservoir for storing CO₂, but this potential likely depends on how grasslands are managed for large mammal grazing. Previous studies found both strong positive and negative grazing effects on soil organic carbon (SOC) but explanations for this variation are poorly developed. Expanding on previous reviews, we performed a multifactorial meta‐analysis of grazer effects on SOC density on 47 independent experimental contrasts from 17 studies. We explicitly tested hypotheses that grazer effects would shift from negative to positive with decreasing precipitation, increasing fineness of soil texture, transition from dominant grass species with C₃ to C₄ photosynthesis, and decreasing grazing intensity, after controlling for study duration and sampling depth. The six variables of soil texture, precipitation, grass type, grazing intensity, study duration, and sampling depth explained 85% of a large variation (±150 g m^?2 yr^?1) in grazing effects, and the best model included significant interactions between precipitation and soil texture (P = 0.002), grass type, and grazing intensity (P = 0.012), and study duration and soil sampling depth (P = 0.020). Specifically, an increase in mean annual precipitation of 600 mm resulted in a 24% decrease in grazer effect size on finer textured soils, while on sandy soils the same increase in precipitation produced a 22% increase in grazer effect on SOC. Increasing grazing intensity increased SOC by 6–7% on C₄‐dominated and C₄–C₃ mixed grasslands, but decreased SOC by an average 18% in C₃‐dominated grasslands. We discovered these patterns despite a lack of studies in natural, wildlife‐dominated ecosystems, and tropical grasslands. Our results, which suggest a future focus on why C₃ vs. C₄‐dominated grasslands differ so strongly in their response of SOC to grazing, show that grazer effects on SOC are highly context‐specific and imply that grazers in different regions might be managed differently to help mitigate greenhouse gas emissions.     

Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions

Ancient DNA (aDNA) research has long depended on the power of PCR to amplify trace amounts of surviving genetic material from preserved specimens. While PCR permits specific loci to be targeted and amplified, in many ways it can be intrinsically unsuited to damaged and degraded aDNA templates. PCR amplification of aDNA can produce highly-skewed distributions with significant contributions from miscoding lesion damage and non-authentic sequence artefacts. As traditional PCR-based approaches have been unable to fully resolve the molecular nature of aDNA damage over many years, we have developed a novel single primer extension (SPEX)-based approach to generate more accurate sequence information. SPEX targets selected template strands at defined loci and can generate a quantifiable redundancy of coverage; providing new insights into the molecular nature of aDNA damage and fragmentation. SPEX sequence data reveals inherent limitations in both traditional and metagenomic PCR-based approaches to aDNA, which can make current damage analyses and correct genotyping of ancient specimens problematic. In contrast to previous aDNA studies, SPEX provides strong quantitative evidence that C > U-type base modifications are the sole cause of authentic endogenous damage-derived miscoding lesions. This new approach could allow ancient specimens to be genotyped with unprecedented accuracy.     

Development of a 16S rRNA gene-based prototype microarray for the detection of selected actinomycetes genera

Actinomycetes are known for their secondary metabolites, which have been successfully used as drugs in human and veterinary medicines. However, information on the distribution of this group of Gram-positive bacteria in diverse ecosystems and a comprehension of their activities in ecosystem processes are still scarce. We have developed a 16S rRNA-based taxonomic microarray that targets key actinomycetes at the genus level. In total, 113 actinomycete 16S rRNA probes, corresponding to 55 of the 202 described genera, were designed. The microarray accuracy was evaluated by comparing signal intensities with probe/target-weighted mismatch values and the Gibbs energy of the probe/target duplex formation by hybridizing 17 non-actinomycete and 29 actinomycete strains/clones with the probe set. The validation proved that the probe set was specific, with only 1.3% of false results. The incomplete coverage of actinomycetes by a genus-specific probe was caused by the limited number of 16S rRNA gene sequences in databases or insufficient 16S rRNA gene polymorphism. The microarray enabled discrimination between actinomycete communities from three forest soil samples collected at one site. Cloning and sequencing of 16S rRNA genes from one of the soil samples confirmed the microarray results. We propose that this newly constructed microarray will be a valuable tool for genus-level comparisons of actinomycete communities in various ecological conditions.