Interval-integration underlies amplitude modulation band-suppression selectivity in the anuran midbrain

We examined the mechanisms that underlie band-suppression amplitude modulation selectivity in the auditory midbrain of anurans. Band-suppression neurons respond well to low (5–10 Hz) and high (>70 Hz) rates of sinusoidal amplitude modulation, but poorly, if at all, to intermediate rates. The effectiveness of slow rates of sinusoidal amplitude modulation is due to the long duration of individual pulses; short-duration pulses (<10 ms) failed to elicit spikes when presented at 5–10 pulses s^–1. Each unit responded only after a threshold number of pulses (median=3, range=2–5) were delivered at an optimal rate. The salient stimulus feature was the number of consecutive interpulse intervals that were within a cell-specific tolerance. This interval-integrating process could be reset by a single long interval, even if preceded by a suprathreshold number of intervals. These findings indicate that band-suppression units are a subset of interval-integrating neurons. Band-suppression neurons differed from band-pass interval-integrating cells in having lower interval-number thresholds and broader interval tolerance. We suggest that these properties increase the probability of a postsynaptic spike, given a particular temporal pattern of afferent action potentials in response to long-duration pulses, i.e., predispose them to respond to slow rates of amplitude modulation. Modeling evidence is provided that supports this conclusion.Abbreviations AM amplitude modulation - PRR pulse repetition rate - SAM sinusoidal amplitude modulation     

Walking and running at resonance

Humans and other animals can temporarily store mechanical energy in elastic oscillations, f(el), of body parts and in pendulum oscillations, f(p) = const sq.rt (g/L), of legs, length L, or other appendages, and thereby reduce the energy consumption of locomotion. However, energy saving only occurs if these oscillations are tuned to the leg propagation frequency f. It has long been known that f is tuned to the pendulum frequency of the free-swinging leg of walkers. During running the leg frequency increases to some new value f = f(r). We propose that in order to maintain resonance the animal, mass M, actively increases its leg pendulum frequency to the new value f(p,r) =const sq.rt (a(y)/L)=f(r), by giving its hips a vertical acceleration a(y)= F(y)/M. The pendulum frequency is increased if the impact force F(y) of the stance foot is larger than Mg, explaining the observation by Alexander and Bennet-Clark (1976) that F(v) becomes larger than Mg when animals start to run. Our model predictions of the running velocity U(r) as function of L, F(v), are in agreement with measurements of these quantities (Farley et al. 1993). The leg's longitudinal elastic oscillation frequency scales as f(el) = const sq.rt (k/M). Experiments by Ferris et al., (1998) show that runners adjust their leg's stiffness, k, when running on surfaces of different elasticity so that the total stiffness k remains constant. Our analysis of their data suggests that the longitudinal oscillations of the stance leg are indeed kept in tune with the running frequency. Therefore we conclude that humans, and by extension all animals, maintain resonance during running. Our model also predicts the Froude number of walking-running transitions, Fr = U(2)/gL approximately 0.5 in good agreement with measurements.     

THE COMPLEX EVOLUTIONARY HISTORY OF SEEING RED: MOLECULAR PHYLOGENY AND THE EVOLUTION OF AN ADAPTIVE VISUAL SYSTEM IN DEEP‐SEA DRAGONFISHES (STOMIIFORMES: STOMIIDAE)

The vast majority of deep‐sea fishes have retinas composed of only rod cells sensitive to only shortwave blue light, approximately 480–490 nm. A group of deep‐sea dragonfishes, the loosejaws (family Stomiidae), possesses far‐red emitting photophores and rhodopsins sensitive to long‐wave emissions greater than 650 nm. In this study, the rhodopsin diversity within the Stomiidae is surveyed based on an analysis of rod opsin‐coding sequences from representatives of 23 of the 28 genera. Using phylogenetic inference, fossil‐calibrated estimates of divergence times, and a comparative approach scanning the stomiid phylogeny for shared genotypes and substitution histories, we explore the evolution and timing of spectral tuning in the family. Our results challenge both the monophyly of the family Stomiidae and the loosejaws. Despite paraphyly of the loosejaws, we infer for the first time that far‐red visual systems have a single evolutionary origin within the family and that this shift in phenotype occurred at approximately 15.4 Ma. In addition, we found strong evidence that at approximately 11.2 Ma the most recent common ancestor of two dragonfish genera reverted to a primitive shortwave visual system during its evolution from a far‐red sensitive dragonfish. According to branch‐site tests for adaptive evolution, we hypothesize that positive selection may be driving spectral tuning in the Stomiidae. These results indicate that the evolutionary history of visual systems in deep‐sea species is complex and a more thorough understanding of this system requires an integrative comparative approach.     

High-resolution intra- and interbasinal correlation of the Danian-Selandian transition (Early Paleocene): The Bjala section (Bulgaria) and the Selandian GSSP at Zumaia (Spain)

The Danian-Selandian (D-S) boundary has been identified for the first time in the Black Sea coast at Bjala (Bulgaria) based on a new integrated bio-, magneto- and cyclostratigraphic study. Several correlation criteria as established for the basal Selandian GSSP from Zumaia (Basque Basin) are evaluated. Noteworthy, is the almost complete lack of calcareous nannoplankton species Braarudosphaera bigelowi in the Bulgarian sections, a sharp decrease of which was indicated as suitable criteria for defining the D-S boundary as it occurred both at Zumaia and in the classical locations of the North Sea basin. Conversely, the second evolutionary radiation of the calcareous nannofossil genus Fasciculithus together with the occurrence of Fasciculithus tympaniformis that define the NP4/NP5 zonal boundary seem to be reliable criteria to approximate the D-S boundary. In detail, however, the best approach is to integrate biostratigraphic data within a magnetostratigraphic and/or cyclostratigraphic framework. Refinements on the placement of chron C27n at Zumaia and robust bed-by-bed correlation between several Basque sections and Bjala indicates that the D-S boundary is located 30 precession cycles (~ 630 ky) above C27n. In addition to the precession-related marl-limestone couplets and 100-ky eccentricity bundles recognized in the studied sections, expression of the stable 405-ky long eccentricity allows direct tuning to the astronomical solutions. A correlation of the land-based sections with previously tuned data from ODP Site1262 from the Southern Atlantic is challenged. Our choice is consistent with original tuning at Zumaia but shifts one 100-ky cycle older previous tuning from Site 1262 along the interval above C27n. Under the preferred tuning scheme the D-S boundary can be given an age of 61.641 ±0.040 Ma on the La04 orbital solution.     

Evolutionary dynamics of Rh2 opsins in birds demonstrate an episode of accelerated evolution in the New World warblers (Setophaga)

Low rates of sequence evolution associated with purifying selection can be interrupted by episodic changes in selective regimes. Visual pigments are a unique system in which we can investigate the functional consequences of genetic changes, therefore connecting genotype to phenotype in the context of natural and sexual selection pressures. We study the RH2 and RH1 visual pigments (opsins) across 22 bird species belonging to two ecologically convergent clades, the New World warblers (Parulidae) and Old World warblers (Phylloscopidae) and evaluate rates of evolution in these clades along with data from 21 additional species. We demonstrate generally slow evolution of these opsins: both Rh1 and Rh2 are highly conserved across Old World and New World warblers. However, Rh2 underwent a burst of evolution within the New World genus Setophaga, where it accumulated substitutions at 6 amino acid sites across the species we studied. Evolutionary analyses revealed a significant increase in d_N/d_S in Setophaga, implying relatively strong selective pressures to overcome long‐standing purifying selection. We studied the effects of each substitution on spectral tuning and found they do not cause large spectral shifts. Thus, substitutions may reflect other aspects of opsin function, such as those affecting photosensitivity and/or dark–light adaptation. Although it is unclear what these alterations mean for colour perception, we suggest that rapid evolution is linked to sexual selection, given the exceptional plumage colour diversification in Setophaga.     

Pyranopterin Coordination Controls Molybdenum Electrochemistry in Escherichia coli Nitrate Reductase

We test the hypothesis that pyranopterin (PPT) coordination plays a critical role in defining molybdenum active site redox chemistry and reactivity in the mononuclear molybdoenzymes. The molybdenum atom of Escherichia coli nitrate reductase A (NarGHI) is coordinated by two PPT-dithiolene chelates that are defined as proximal and distal based on their proximity to a [4Fe-4S] cluster known as FS0. We examined variants of two sets of residues involved in PPT coordination: (i) those interacting directly or indirectly with the pyran oxygen of the bicyclic distal PPT (NarG-Ser⁷¹⁹, NarG-His¹¹⁶³, and NarG-His¹¹⁸⁴); and (ii) those involved in bridging the two PPTs and stabilizing the oxidation state of the proximal PPT (NarG-His¹⁰⁹² and NarG-His¹⁰⁹⁸). A S719A variant has essentially no effect on the overall Mo(VI/IV) reduction potential, whereas the H1163A and H1184A variants elicit large effects (ΔE_m values of −88 and −36 mV, respectively). Ala variants of His¹⁰⁹² and His¹⁰⁹⁸ also elicit large ΔE_m values of −143 and −101 mV, respectively. An Arg variant of His¹⁰⁹² elicits a small ΔE_m of +18 mV on the Mo(VI/IV) reduction potential. There is a linear correlation between the molybdenum E_m value and both enzyme activity and the ability to support anaerobic respiratory growth on nitrate. These data support a non-innocent role for the PPT moieties in controlling active site metal redox chemistry and catalysis.     

Plasmid‐free T7‐based Escherichia coli expression systems

In order to release host cells from plasmid‐mediated increases in metabolic load and high gene dosages, we developed a plasmid‐free, T7‐based E. coli expression system in which the target gene is site‐specifically integrated into the genome of the host. With this system, plasmid‐loss, a source of instability for conventional expression systems, was eliminated. At the same time, system leakiness, a challenging problem with recombinant systems, was minimized. The efficiency of the T7 RNA polymerase compensates for low gene dosage and provides high rates of recombinant gene expression without fatal consequences to host metabolism. Relative to conventional pET systems, this system permits improved process stability and increases the host cell's capacity for recombinant gene expression, resulting in higher product yields. The stability of the plasmid‐free system was proven in chemostat cultivation for 40 generations in a non‐induced and for 10 generations in a fully induced state. For this reason plasmid‐free systems benefit the development of continuous production processes with E. coli. However, time and effort of the more complex cloning procedure have to be considered in relation to the advantages of plasmid‐free systems in upstream‐processing. Biotechnol. Bioeng. 2010. 105: 786–794. © 2009 Wiley Periodicals, Inc.     

Hair Cells – Beyond the Transducer

Overview This review considers the “tween twixt and twain” of hair cell physiology, specifically the signaling elements and membrane conductances which underpin forward and reverse transduction at the input stage of hair cell function and neurotransmitter release at the output stage. Other sections of this review series outline the advances which have been made in understanding the molecular physiology of mechanoelectrical transduction and outer hair cell electromotility. Here we outline the contributions of a considerable array of ion channels and receptor signaling pathways that define the biophysical status of the sensory hair cells, contributing to hair cell development and subsequently defining the operational condition of the hair cells across the broad dynamic range of physiological function.     

tRNA residues that have coevolved with their anticodon to ensure uniform and accurate codon recognition

The structure, phylogeny and in vivo function of the base pair formed between nucleotides 32 and 38 of the tRNA anticodon loop are reviewed. The A32-U38 pair, which is highly conserved in tRNA2(Ala) and sometimes observed in tRNA2(Pro), was recently found to decrease the affinity of tRNAs to the ribosomal A site relative to other 32-38 combinations. This suggests that the role of 32-38 pair is to tune the tRNA affinity in the A site to a uniform value. New experiments presented here show that the U32C mutation in tRNA1(Gly) increases its affinity to the cognate codon and to codons with third position mismatches in the A site. This suggests that one reason for uniform tRNA binding to evolve was to avoid incorrect codon recognition.     

Investigating the mechanisms of photosynthetic proteins using continuum electrostatics

Computational methods based on continuum electrostatics are widely used in theoretical biochemistry to analyze the function of proteins. Continuum electrostatic methods in combination with quantum chemical and molecular mechanical methods can help to analyze even very complex biochemical systems. In this article, applications of these methods to proteins involved in photosynthesis are reviewed. After giving a short introduction to the basic concepts of the continuum electrostatic model based on the Poisson-Boltzmann equation, we describe the application of this approach to the docking of electron transfer proteins, to the comparison of isofunctional proteins, to the tuning of absorption spectra, to the analysis of the coupling of electron and proton transfer, to the analysis of the effect of membrane potentials on the energetics of membrane proteins, and to the kinetics of charge transfer reactions. Simulations as those reviewed in this article help to analyze molecular mechanisms on the basis of the structure of the protein, guide new experiments, and provide a better and deeper understanding of protein functions.