Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models.

Knowing the catalytic turnover numbers of enzymes is essential for understanding the growth rate, proteome composition, and physiology of organisms, but experimental data on enzyme turnover numbers is sparse and noisy. Here, we demonstrate that machine learning can successfully predict catalytic turnover numbers in Escherichia coli based on integrated data on enzyme biochemistry, protein structure, and network context. We identify a diverse set of features that are consistently predictive for both in vivo and in vitro enzyme turnover rates, revealing novel protein structural correlates of catalytic turnover. We use our predictions to parameterize two mechanistic genome-scale modelling frameworks for proteome-limited metabolism, leading to significantly higher accuracy in the prediction of quantitative proteome data than previous approaches. The presented machine learning models thus provide a valuable tool for understanding metabolism and the proteome at the genome scale, and elucidate structural, biochemical, and network properties that underlie enzyme kinetics

High Harmonic Generation in SF6_{6}: Raman-excited Vibrational Quantum Beats

In a recent experiment (N. Wagner et al., PNAS v103, p13279) on SF$_{6}$, a high-harmonic generating laser pulse is preceded by a pump pulse which stimulates Raman-active modes in the molecule. Varying the time delay between the two pulses modulates high harmonic intensity, with frequencies equal to the vibration frequencies of the Raman-active modes. We propose an explanation of this modulation as a quantum interference between competing pathways that occur via adjacent vibrational states of the molecule. The Raman and high harmonic processes act as beamsplitters, producing vibrational quantum beats among the Raman-active vibrational modes that are excited by the first pulse. We introduce a rigorous treatment of the electron-ion recombination process and the effect of the ionic Coulomb field in the electron propagation outside the molecule, improving over the widely-used three-step model.Comment: submitted to PR

Symmetric Autocompensating Quantum Key Distribution

We present quantum key distribution schemes which are autocompensating (require no alignment) and symmetric (Alice and Bob receive photons from a central source) for both polarization and time-bin qubits. The primary benefit of the symmetric configuration is that both Alice and Bob may have passive setups (neither Alice nor Bob is required to make active changes for each run of the protocol). We show that both the polarization and the time-bin schemes may be implemented with existing technology. The new schemes are related to previously described schemes by the concept of advanced waves.Comment: 4 pages, 2 figur

Community Detection as an Inference Problem

We express community detection as an inference problem of determining the most likely arrangement of communities. We then apply belief propagation and mean-field theory to this problem, and show that this leads to fast, accurate algorithms for community detection.Comment: 4 pages, 2 figure

Exploratory shopping: attention affects in-store exploration and unplanned purchasing

A fundamental function of retailing is to bring products into the view of shoppers, because viewing products can activate forgotten or new needs. Retailers thus employ various strategies to entice shoppers to explore the product assortment and store environment, in the hopes of stimulating unplanned purchasing. Here we investigate consumers’ breadth of attention as a mechanism of such in-store exploration and hence of unplanned purchasing. Specifically, attentional breadth is the focus that is directed to a wider or more limited area in processing visual scenes. In a series of lab and field experiments we show that shoppers’ attentional breadth activates an exploratory mindset that stimulates visual and physical exploration of shopping environments, ultimately affecting their product choices and unplanned purchasing. We also show that more impulsive buyers are more susceptible to these effects. These results complement and constrain prior theorizing on mindset theory, attention, store exploration, and unplanned purchasing, all of which are of practical importance to both retailers and consumers

Quantum dynamics of the avian compass

The ability of migratory birds to orient relative to the Earth's magnetic field is believed to involve a coherent superposition of two spin states of a radical electron pair. However, the mechanism by which this coherence can be maintained in the face of strong interactions with the cellular environment has remained unclear. This Letter addresses the problem of decoherence between two electron spins due to hyperfine interaction with a bath of spin 1/2 nuclei. Dynamics of the radical pair density matrix are derived and shown to yield a simple mechanism for sensing magnetic field orientation. Rates of dephasing and decoherence are calculated ab initio and found to yield millisecond coherence times, consistent with behavioral experiments

Age Estimation of Burbot Using Pectoral Fin Rays, Branchiostegal Rays and Otoliths

Throughout much of its native distribution, burbot (Lota lota) is a species of conservation concern.  Understanding dynamic rate functions is critical for the effective management of sensitive burbot populations, which necessitates accurate and precise age estimates.  Managing sensitive burbot populations requires an accurate and precise non-lethal alternative.  In an effort to identify a non-lethal ageing structure, we compared the precision of age estimates obtained from otoliths, pectoral fin rays, dorsal fin rays and branchiostegal rays from 208 burbot collected from the Green River drainage, Wyoming.  Additionally, we compared the accuracy of age estimates from pectoral fin rays, dorsal fin rays and branchiostegal rays to those of otoliths.  Dorsal fin rays were immediately deemed a poor ageing structure and removed from further analysis.  Age-bias plots of consensus ages derived from branchiostegal rays and pectoral fin rays were appreciably different from those obtained from otoliths.  Exact agreement between readers and reader confidence was highest for otoliths and lowest for branchiostegal rays.  Age-bias plots indicated that age estimates obtained from branchiostegal rays and pectoral fin rays were substantially different from age estimates obtained from otoliths.  Our results indicate that otoliths provide the most precise age estimates for burbot

Multiple origins of green blood in New Guinea lizards

© 2018 The Authors. Several species of lizards from the megadiverse island of New Guinea have evolved green blood. An unusually high concentration of the green bile pigment biliverdin in the circulatory system of these lizards makes the blood, muscles, bones, tongue, and mucosal tissues bright green in color, eclipsing the crimson color from their red blood cells. This is a remarkable physiological feature because bile pigments are toxic physiological waste products of red blood cell catabolism and, when chronically elevated, cause jaundice in humans and all other vertebrates. Although these lizards offer a promising system to examine the evolution of extraordinary physiological characteristics, little is known about the phylogenetic relationships of green-blooded lizards or the evolutionary origins of green blood. We present the first extensive phylogeny for green-blooded lizards and closely related Australasian lizards using thousands of genomic regions to examine the evolutionary history of this unusual trait. Maximum likelihood ancestral character state reconstruction supports four independent origins of green blood. Our results lay the phylogenetic foundation necessary to determine the role, if any, of natural selection in shaping this enigmatic physiological trait as well as understanding the genetic, proteomic, and biochemical basis for the lack of jaundice in those species that have independently evolved green blood

DIET OF JUVENILE BURBOT AND INSIGHT INTO GAPE LIMITATION

Throughout much of their distribution, Burbot (Lota lota ) populations are declining or have been extirpated.  Burbot in the Kootenai River, Idaho represent one such imperiled population.  In an effort to restore Burbot in the Kootenai River, managers have turned to conservation aquaculture.  However, no appreciable increase in natural recruitment has been observed in the system.  The lack of natural recruitment is believed to be partly due to a deficiency of high-quality prey.  As a result, we sought to i) describe the diet of juvenile Burbot, ii) evaluate the influence of Burbot mouth gape on diet and iii) estimate prey availability at release locations.  Burbot were stocked into two earthen ponds at the Boundary Creek Wildlife Management Area (BCWMA) and sampled weekly to evaluate diet.  Zooplankton were sampled weekly from each pond and from release locations of hatchery-reared Burbot (i.e., Kootenai River, Goat River, Boundary Creek, Deep Creek) to quantify prey availability.  Over the course of the study (~3 months), Burbot primarily fed on Cyclopoida.  Burbot never appeared to be gape limited and exhibited little variability in the size of zooplankton ingested.  Zooplankton densities at stocking locations were relatively low in comparison to BCWMA ponds.  Low zooplankton densities at release sites indicate that alternative management actions may need to be considered to enhance Burbot recruitment in the Kootenai River drainage