Flying over water: how “On bird species diversity” influenced aquatic ecology

Habitat complexity has long been known to influence animal community structure by increasing the number of available habitats. Fifty years have passed since MacArthur brothers published the seminal paper “On bird species diversity”, which revolutionized studies of habitat structure. This paper first evidenced and quantified the relationship between species diversity (birds) and habitat structural complexity (the number of stratified layers of landscape vegetation). In this article, we aim to pay homage to R. H. MacArthur’s contribution and to briefly analyze the citation history and influence of “On bird species diversity”, focusing primarily on aquatic studies. We searched for all papers that cited “On bird species diversity” on Thomson Reuters (ISI—Web of Knowledge) and analyzed them for temporal citation trends. In addition, considering only aquatic papers, we explored whether and how habitat complexity was measured, as well as the ecological organization level, attributes of organisms, taxonomic groups and study design (observational or experimental). “On bird species diversity” citations increased over time, but this paper was less cited by limnologists compared to terrestrial and marine scientists. The majority of investigations in aquatic ecosystems quantified habitat complexity, but few used mathematical modeling. The high number of citations, which continues to increase, shows the great influence of “On bird species diversity” on ecological studies and typifies it as a classic in the ecological literature. However, the low citation frequency found in papers devoted to freshwater ecosystems indicates that limnologists in general neglect this original contribution in studies of habitat complexity.     

Frequency of the 735G → A mutation of the 5′-splice donor site of intron 14 of the dihydropyrimidine dehydrogenase gene (<Emphasis Type="Italic">DPYD</Emphasis>) in residents of novosibirsk region (Russia) as revealed with fluorescent oligonucleotides

A simple method was developed for end-point fluorescence detection of the 735G → A mutation of the 5′-splice donor site of intron 14 of the dihidropyrimidine dehydrogenase gene (DPYD). The method was based on allele-specific PCR with duplex Scorpion primers. The genotyping results obtained by the fluorescent end-point PCR technique completely coincided with the results obtained by allele-specific PCR with amplicon detection in agarose gel. Genotyping was performed in 291 DNA samples from residents of Novosibirsk region (Russia), and two heterozygotes (0.69%) were detected.     

Overexpression of Spry1 in chondrocytes causes attenuated FGFR ubiquitination and sustained ERK activation resulting in chondrodysplasia

The FGF signaling pathway plays essential roles in endochondral ossification by regulating osteoblast proliferation and differentiation, chondrocyte proliferation, hypertrophy, and apoptosis. FGF signaling is controlled by the complementary action of both positive and negative regulators of the signal transduction pathway. The Spry proteins are crucial regulators of receptor tyrosine kinase-mediated MAPK signaling activity. Sprys are expressed in close proximity to FGF signaling centers and regulate FGFR-ERK-mediated organogenesis. During endochondral ossification, Spry genes are expressed in prehypertrophic and hypertrophic chondrocytes. Using a conditional transgenic approach in chondrocytes in vivo, the forced expression of Spry1 resulted in neonatal lethality with accompanying skeletal abnormalities resembling thanatophoric dysplasia II, including increased apoptosis and decreased chondrocyte proliferation in the presumptive reserve and proliferating zones. In vitro chondrocyte cultures recapitulated the inhibitory effect of Spry1 on chondrocyte proliferation. In addition, overexpression of Spry1 resulted in sustained ERK activation and increased expression of p21 and STAT1. Immunoprecipitation experiments revealed that Spry1 expression in chondrocyte cultures resulted in decreased FGFR2 ubiquitination and increased FGFR2 stability. These results suggest that constitutive expression of Spry1 in chondrocytes results in attenuated FGFR2 degradation, sustained ERK activation, and up-regulation of p21Cip and STAT1 causing dysregulated chondrocyte proliferation and terminal differentiation.     

Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm

We present a general-purpose model for biomolecular simulations at the molecular level that incorporates stochasticity, spatial dependence, and volume exclusion, using diffusing and reacting particles with physical dimensions. To validate the model, we first established the formal relationship between the microscopic model parameters (timestep, move length, and reaction probabilities) and the macroscopic coefficients for diffusion and reaction rate. We then compared simulation results with Smoluchowski theory for diffusion-limited irreversible reactions and the best available approximation for diffusion-influenced reversible reactions. To simulate the volumetric effects of a crowded intracellular environment, we created a virtual cytoplasm composed of a heterogeneous population of particles diffusing at rates appropriate to their size. The particle-size distribution was estimated from the relative abundance, mass, and stoichiometries of protein complexes using an experimentally derived proteome catalog from Escherichia coli K12. Simulated diffusion constants exhibited anomalous behavior as a function of time and crowding. Although significant, the volumetric impact of crowding on diffusion cannot fully account for retarded protein mobility in vivo, suggesting that other biophysical factors are at play. The simulated effect of crowding on barnase-barstar dimerization, an experimentally characterized example of a bimolecular association reaction, reveals a biphasic time course, indicating that crowding exerts different effects over different timescales. These observations illustrate that quantitative realism in biosimulation will depend to some extent on mesoscale phenomena that are not currently well understood.     

Experiments with small-size dynamic loads in the S-300 high-power pulsed generator

Results are presented from experimental studies of promising output units for high-current pulsed generators within the framework of the program on inertial confinement fusion research with the use of fast Z-pinches. The experiments were carried out on the S-300 facility (4 MA, 70 ns, 0.15 Ω). Specifically, sharpening systems similar to plasma flow switches but operating in a nanosecond range were investigated. Switching rates to a load as high as 2.5 MA per 2.5 ns, stable switching of a 750-kA current to a low-size Z-pinch, and the radiative temperature of the load cavity wall of up to 50 eV were achieved.     

Cardiac Rhythm Variability: Approaches to Mechanisms

Physiological mechanisms of cardiac rhythm variability (CRV) are reviewed. The results of original experiments are discussed together with the history of the problem and data available from the literature. Special emphasis is placed on the spectral analysis of cardiac rhythm. Various mechanisms of the generation of periodic and aperiodic components of CRV are considered. Although the variability of cardiac rhythm has been studied for many years in many laboratories worldwide, fine mechanisms of CRV remain obscure. However, a number of specific features of CRV are presently widely recognized. Periodic CRV components isolated from short-term records in patients at rest are represented by high-frequency, low-frequency, and very low-frequency oscillations. Fourier-transform spectral analysis of cardiac rhythm is the most appropriate method of the detection of these oscillations. High-frequency components are associated with respiration and represent the effects of the parasympathetic nervous system on myocardium. Low-frequency components are due to the activity of the postganglionic sympathetic fibers and represent the processes of cardiac rhythm modulation by the sympathetic nervous system. Genesis of very low-frequency oscillations is still uncertain. Most probably, these oscillations are associated with the effects of suprasegmental (primarily, hypothalamic) centers of autonomic regulation. Aperiodic CRV components represent random events associated with the reflex regulation of the heart rate by external or internal factors. Because aperiodic components significantly modify the results of the CRV analysis, the effects of these factors should be eliminated. It is concluded that because many problems associated with cardiac rhythm variability remain to be solved, extensive research in this direction should be continued.