Conservative N cycling despite high atmospheric deposition in early successional African tropical lowland forests

Plant and Soil - Many applied disciplines have recognized problems related to the practice of data analysis within their own communities. Some of them have even declared the existence of a...     

Insightful problem solving in an Asian elephant

The "aha" moment or the sudden arrival of the solution to a problem is a common human experience. Spontaneous problem solving without evident trial and error behavior in humans and other animals has been referred to as insight. Surprisingly, elephants, thought to be highly intelligent, have failed to exhibit insightful problem solving in previous cognitive studies. We tested whether three Asian elephants (Elephas maximus) would use sticks or other objects to obtain food items placed out-of-reach and overhead. Without prior trial and error behavior, a 7-year-old male Asian elephant showed spontaneous problem solving by moving a large plastic cube, on which he then stood, to acquire the food. In further testing he showed behavioral flexibility, using this technique to reach other items and retrieving the cube from various locations to use as a tool to acquire food. In the cube's absence, he generalized this tool utilization technique to other objects and, when given smaller objects, stacked them in an attempt to reach the food. The elephant's overall behavior was consistent with the definition of insightful problem solving. Previous failures to demonstrate this ability in elephants may have resulted not from a lack of cognitive ability but from the presentation of tasks requiring trunk-held sticks as potential tools, thereby interfering with the trunk's use as a sensory organ to locate the targeted food.     

Availability of a pediatric trauma center in a disaster surge decreases triage time of the pediatric surge population: a population kinetics model

Background

The concept of disaster surge has arisen in recent years to describe the phenomenon of severely increased demands on healthcare systems resulting from catastrophic mass casualty events (MCEs) such as natural disasters and terrorist attacks. The major challenge in dealing with a disaster surge is the efficient triage and utilization of the healthcare resources appropriate to the magnitude and character of the affected population in terms of its demographics and the types of injuries that have been sustained.

Results

In this paper a deterministic population kinetics model is used to predict the effect of the availability of a pediatric trauma center (PTC) upon the response to an arbitrary disaster surge as a function of the rates of pediatric patients' admission to adult and pediatric centers and the corresponding discharge rates of these centers. We find that adding a hypothetical pediatric trauma center to the response documented in an historical example (the Israeli Defense Forces field hospital that responded to the Haiti earthquake of 2010) would have allowed for a significant increase in the overall rate of admission of the pediatric surge cohort. This would have reduced the time to treatment in this example by approximately half. The time needed to completely treat all children affected by the disaster would have decreased by slightly more than a third, with the caveat that the PTC would have to have been approximately as fast as the adult center in discharging its patients. Lastly, if disaster death rates from other events reported in the literature are included in the model, availability of a PTC would result in a relative mortality risk reduction of 37%.

Conclusions

Our model provides a mathematical justification for aggressive inclusion of PTCs in planning for disasters by public health agencies.     

Phosphoinositide 3-kinase signaling in the cellular response to oxidative stress

Oxidative stress is linked to the pathogenesis and pathobiochemistry of various diseases, including cancer, diabetes and cardiovascular disorders. The non-specific damaging effect of reactive oxygen species (ROS) generated during oxidative stress is involved in the development of diseases, as well as the activation of specific signaling cascades in cells exposed to the higher oxidant load. A cellular signaling cascade that is activated by several types of reactive oxygen species is the phosphoinositide 3'-kinase (PI 3-kinase)/protein kinase B (PKB) pathway, which regulates cellular survival and fuel metabolism, thus establishing a link between oxidative stress and signaling in neoplastic, metabolic or degenerative diseases. Several links of PI 3-kinase/PKB signaling to ROS are discussed in this review, with particular focus on the molecular mechanisms involved in the regulation of PI 3-kinase signaling by oxidative stress and important players such as (i) the glutathione and glutaredoxin system, (ii) the thioredoxin system and (iii) Ser/Thr- and Tyr phosphatases.     

A method of mapping protein sumoylation sites by mass spectrometry using a modified small ubiquitin-like modifier 1 (SUMO-1) and a computational program

Post-translational modification by small ubiquitin-like modifier 1 (SUMO-1) is a highly conserved process from yeast to humans and plays important regulatory roles in many cellular processes. Sumoylation occurs at certain internal lysine residues of target proteins via an isopeptide bond linkage. Unlike ubiquitin whose carboxyl-terminal sequence is RGG, the tripeptide at the carboxyl terminus of SUMO is TGG. The presence of the arginine residue at the carboxyl terminus of ubiquitin allows tryptic digestion of ubiquitin conjugates to yield a signature peptide containing a diglycine remnant attached to the target lysine residue and rapid identification of the ubiquitination site by mass spectrometry. The absence of lysine or arginine residues in the carboxyl terminus of mammalian SUMO makes it difficult to apply this approach to mapping sumoylation sites. We performed Arg scanning mutagenesis by systematically substituting amino acid residues surrounding the diglycine motif and found that a SUMO variant terminated with RGG can be conjugated efficiently to its target protein under normal sumoylation conditions. We developed a Programmed Data Acquisition (PDA) mass spectrometric approach to map target sumoylation sites using this SUMO variant. A web-based computational program designed for efficient identification of the modified peptides is described.     

Differential engagement of modules 1 and 4 of vascular cell adhesion molecule-1 (CD106) by integrins alpha4beta1 (CD49d/29) and alphaMbeta2 (CD11b/18) of eosinophils

We have studied adhesion of eosinophils to various forms of vascular cell adhesion molecule 1 (VCAM-1, CD106), an integrin counter-receptor implicated in eosinophil recruitment to the airway in asthma. Full-length 7d-VCAM-1, with seven immunoglobulin-like modules, contains integrin-binding sites in modules 1 and 4. The alternatively spliced six-module protein, 6d-VCAM-1, lacks module 4. In static assays, unactivated purified human blood eosinophils adhered similarly to recombinant soluble human 6d-VCAM-1 and 7d-VCAM-1 coated onto polystyrene microtiter wells. Further experiments, however, revealed differences in recognition of modules 1 and 4. Antibody blocking indicated that eosinophil adhesion to 6d-VCAM-1 or a VCAM-1 construct containing only modules 1-3, 1-3VCAM-1, is mediated by alpha4beta1 (CD49d/29), whereas adhesion to a construct containing modules 4-7, 4-7VCAM-1, is mediated by bothalpha4beta1 andalphaMbeta2 (CD11b/18). Inhibitors of phosphoinositide 3-kinase, which block adhesion of eosinophils mediated by alphaMbeta2, blocked adhesion to 4-7VCAM-1 but had no effect on adhesion to 6d-VCAM-1. Consistent with the antibody and pharmacological blocking experiments, eosinophilic leukemic cell lines lacking alphaMbeta2 did not adhere to 4-7VCAM-1 but did adhere to 6d-VCAM-1 or 1-3VCAM-1. Activation of eosinophils by interleukin (IL)-5 enhanced static adhesion to 6d-VCAM-1, 7d-VCAM-1, or 4-7VCAM-1; IL-5-enhanced adhesion to all 3 constructs was blocked by anti-alphaMbeta2. Adhesion of unstimulated eosinophils to 7d-VCAM-1 under flow conditions was inhibited by anti-alpha4 or anti-alphaM. IL-5 treatment decreased eosinophil adhesion to 7d-VCAM-1 under flow, and anti-alphaM had the paradoxical effect of increasing adhesion. These results demonstrate that alphaMbeta2 modulatesalpha4beta1-mediated eosinophil adhesion to VCAM-1 under both static and flow conditions.     

Conformational transitions in RNA single uridine and adenosine bulge structures: a molecular dynamics free energy simulation study

Extra unmatched nucleotides (single base bulges) are common structural motifs in folded RNA molecules and can participate in RNA-ligand binding and RNA tertiary structure formation. Often these processes are associated with conformational transitions in the bulge region such as flipping out of the bulge base from an intrahelical stacked toward a looped out state. Knowledge of the flexibility of bulge structures and energetics of conformational transitions is an important prerequisite to better understand the function of this RNA motif. Molecular dynamics simulations were performed on single uridine and adenosine bulge nucleotides at the center of eight basepair RNA molecules and indicated larger flexibility of the bulge bases compared to basepaired regions. The umbrella sampling method was applied to study the bulge base looping out process and accompanying conformational and free energy changes. Looping out toward the major groove resulted in partial disruption of adjacent basepairs and was found to be less favorable compared to looping out toward the minor groove. For both uridine and adenosine bulges, a positive free energy change for full looping out was obtained which was approximately 1.5 kcal mol-1 higher in the case of the adenosine compared to the uridine bulge system. The simulations also indicated stable partially looped out states with the bulge bases located in the RNA minor groove and forming base triples with 5'-neighboring basepairs. In the case of the uridine bulge this state was more stable than the intrahelical stacked bulge structure. Induced looping out toward the minor groove involved crossing of an energy barrier of approximately 3.5 kcal mol-1 before reaching the base triple state. A continuum solvent analysis of intermediate bulge states indicated that electrostatic interactions stabilize looped out and base triple states, whereas van der Waals interactions and nonpolar contributions favor the stacked bulge conformation.