Optimal Control of Transitions between Nonequilibrium Steady States

Biological systems fundamentally exist out of equilibrium in order to preserve organized structures and processes. Many changing cellular conditions can be represented as transitions between nonequilibrium steady states, and organisms have an interest in optimizing such transitions. Using the Hatano-Sasa Y-value, we extend a recently developed geometrical framework for determining optimal protocols so that it can be applied to systems driven from nonequilibrium steady states. We calculate and numerically verify optimal protocols for a colloidal particle dragged through solution by a translating optical trap with two controllable parameters. We offer experimental predictions, specifically that optimal protocols are significantly less costly than naive ones. Optimal protocols similar to these may ultimately point to design principles for biological energy transduction systems and guide the design of artificial molecular machines.     

The refractive significance of the nictitating membrane of the bird eye

Summary Previous authors have suggested that in certain aquatic birds a transparent nictitating membrane of high refractive index could compensate for the refractive loss of the cornea in water. Measurements of refractive indices, refractive state and curvature carried out on a number of aquatic birds indicate that the nictitating membrane does not have a refractive function; the refractive indices of the cornea and nictitating membrane are very similar (approximately 1.37), the nictitating membrane does not alter the refractive state of the eye, and its curvature, when it is in place in front of the globe, is virtually the same as that of the cornea.This research was supported by grants from the National Research Council of Canada and the Canadian National Sportsmen's Fund. The assistance of Mote Marine Laboratory, The Mount Desert Island Biological Laboratory, the Niska Wildlife Foundation and the Felicadades Wildlife Foundation is gratefully acknowledged. The herring gulls and black guillemots were provided by Dr. W.B. Kinter. In addition, the authors are grateful for the assistance provided by Drs. J.L. Lincer and D. Peakall and Mr. R. Orleib.     

Ebola hemorrhagic fever: Properties of the pathogen and development of vaccines and chemotherapeutic agents

Molecular Biology - Ebola hemorrhagic fever (EHF) epidemic currently ongoing in West Africa is not the first among numerous epidemics in the continent. Yet it seems to be the worst EHF epidemic...     

Optical function and mitochondrial metabolic properties in damage and recovery of bovine lens after in vitro carbonyl cyanide m-chlorophenylhydrazone treatment

In order to elucidate the correlation between lens optical function and metabolic function, in vitro bovine lens optical quality and mitochondrial integrity was measured following treatment with carbonyl cyanide m-chlorophenylhydrazone (the mitochondrial depolarizing agent, CCCP). The results indicate that in vitro exposure to CCCP resulted in concentration and time-dependent loss of sharp focus. The concentrations tested included 65.0, 32.5, 16.25 and 8.125 microm CCCP. Lenses treated with two lower concentrations show recovery from damage at the 24-h scan point. In lenses treated with 65 microM CCCP, mitochondria in lens epithelial and superficial cortical fibre cells appeared short and swollen. The results of this study indicate that lens optical function and mitochondrial integrity are closely correlated.     

Nucleotide sequence of the FNR-regulated fumarase gene (fumB) of Escherichia coli K-12

The nucleotide sequence of a 3,162-base-pair (bp) segment of DNA containing the FNR-regulated fumB gene, which encodes the anaerobic class I fumarase (FUMB) of Escherichia coli, was determined. The structural gene was found to comprise 1,641 bp, 547 codons (excluding the initiation and termination codons), and the gene product had a predicted Mr of 59,956. The amino acid sequence of FUMB contained the same number of residues as did that of the aerobic class I fumarase (FUMA), and there were identical amino acids at all but 56 positions (89.8% identity). There was no significant similarity between the class I fumarases and the class II enzyme (FUMC) except in one region containing the following consensus: Gly-Ser-Xxx-Ile-Met-Xxx-Xxx-Lys-Xxx-Asn. Some of the 56 amino acid substitutions must be responsible for the functional preferences of the enzymes for malate dehydration (FUMB) and fumarate hydration (FUMA). Significant similarities between the cysteine-containing sequence of the class I fumarases (FUMA and FUMB) and the mammalian aconitases were detected, and this finding further supports the view that these enzymes are all members of a family of iron-containing hydrolyases. The nucleotide sequence of a 1,142-bp distal sequence of an unidentified gene (genF) located upstream of fumB was also defined and found to encode a product that is homologous to the product of another unidentified gene (genA), located downstream of the neighboring aspartase gene (aspA).     

Relationship between a 47-kDa cytoplasmic membrane polypeptide and nitrate transport in Anacystis nidulans

The polypeptide composition of cytoplasmic membranes of the cyanobacterium Anacystis nidulans changes in response to variations in the nitrogen source available to the cells, differing specifically in the amount of a polypeptide of 47-kDa molecular mass. Synthesis of the polypeptide and expression of nitrate transport activity are repressed by ammonium. Transfer of ammonium-grown cells to a medium containing nitrate as the sole nitrogen source results in parallel development of the 47-kDa polypeptide and nitrate transport activity of the cells. These results suggest the involvement of the 47-kDa cytoplasmic membrane polypeptide in nitrate transport by A. nidulans.     

Optical characteristics of the eye of the flounder

Summary The winter flounder,Pseudopleuronectes americanus, is mildly hyperopic. However, chromatic aberration exists in significant amounts and therefore the eye may be emmetropic (zero refractive error) in natural conditions when light is restricted to shorter wavelengths. Large accommodative lens motion was observed along the direction of the pupil axis. This direction is rare among the teleosts and is the result of the unusual split origin of the retractor lentis muscle. While the lens is spherical, as in other teleosts, the retina is not uniformly distant from the lens. Rather, a vertical asymmetry exists such that dorsal and ventral portions of the retina are further from the lens than the central retina. In view of the existing large accommodative ability, this distortion of the globe is not likely to have an optical function but is probably due to the shape of the cartilagenous scleral cup supporting the eye in its extraorbital location. Further, the lens is overcorrected for spherical aberration so that rays passing through the periphery of the lens are focused further away. The value of a lens of this type is unclear.     

Diversity of the understory vascular vegetation in 40 year-old and old-growth forest stands on Vancouver Island,British Columbia

Abstract. We studied plant diversity of the understory vascular vegetation in 40 yr-old plantations (immature stands) and old-growth forest stands on southwestern Vancouver Island, British Columbia, Canada. Site-specific comparisons using several indices of species diversity were made between: (1) immature stands segregated according to the canopy cover and dominant canopy tree species; and (2) immature and old-growth stands. There were no significant differences (P < 0.05) among immature stands in species richness (S) and the Shannon-Wiener index (H′), in relation to the canopy cover or in S, H′ and evenness (E) in relation to the dominant canopy tree species. Using the same indices, the plant diversity varied with edaphic conditions (represented by five site associations) and time (represented by two developmental stages). At both stand- and site levels, plant diversity increased with increasing soil moisture, from slightly dry to moist sites, and with increasing plant-available soil nitrogen in both immature and old-growth stands; and the plant diversity of immature stands across the sites studied was considerably lower than in old-growth stands, regardless of site association. The indices of plant diversity, floristic similarity indices, and species turnover rates indicated that the immature stands had their plant diversity at a minimum, but a drastic loss of diversity expected in the stem exclusion stage had not materialized. We attributed decline in plant diversity to the absence of old-growth structural features in immature stands. Several measures to foster the stand-level diversity were proposed.     

Optical measurement of mechanical forces inside short DNA loops

Knowledge of the mechanical properties of double-stranded DNA (dsDNA) is essential to understand the role of dsDNA looping in gene regulation and the mechanochemistry of molecular machines that operate on dsDNA. Here, we use a newly developed tool, force sensors with optical readout, to measure the forces inside short, strained loops composed of both dsDNA and single-stranded DNA. By varying the length of the loops and their proportion of dsDNA, it was possible to vary their internal forces from 1 pN to >20 pN. Surprisingly, internal loop forces changed erratically as the amount of dsDNA was increased for a given loop length, with the effect most notable in the smallest loop (57 nucleotides). Monte Carlo simulations based on the helical wormlike chain model accurately predict internal forces when more than half of the loop is dsDNA but fail otherwise. Mismatches engineered into the double-stranded regions increased flexibility, suggesting that Watson-Crick basepaired dsDNA can withstand high compressive forces without recourse to multibase melts. Fluorescence correlation spectroscopy further excluded transient melting (microsecond to millisecond duration) as a mechanism for relief of compressive forces in the tested dsDNAs. DNA loops with integrated force sensors may allow the comprehensive mapping of the elasticity of short dsDNAs as a function of both sequence and salt.     

1.15 A crystal structure of the X. tropicalis Spred1 EVH1 domain suggests a fourth distinct peptide-binding mechanism within the EVH1 family

The recently described Spred protein family has been implicated in the modulation of receptor tyrosine kinase signalling. We report the crystal structure of the Enabled/vasodilator-stimulated phosphoprotein homology-1 (EVH1) domain from Xenopus tropicalis Spred1, solved to 1.15 A resolution. This structure confirms that the Spred EVH1 adopts the pleckstrin-homology fold, with a similar secondary structure to Enabled. A translation of one of the peptide-binding groove beta-strands narrows this groove, whilst one end of the groove shows structural flexibility. We propose that Spred1 will bind peptides that are less proline-rich than other EVH1 domains, with conformational changes indicating an induced fit.