Adding backbone to protein folding: why proteins are polypeptides

It is argued that the chemical nature of the polypeptide backbone is the central determinant of the three-dimensional structures of proteins. The requirement that buried polar groups form intramolecular hydrogen bonds limits the fold of the backbone to the well known units of secondary structure while the amino acid sequence chooses among the set of conformations available to the backbone. ‘Sidechain-only’ models, based for example on hydrophobicity patterns, fail to account for the properties of the backbone and thus will have difficulty capturing essential features of a folding pathway. This is evident from the incorrect predictions they make for the conformations of the limiting cases of all-hydrophobic or all-polar sequences

Predicted Abundances of Carbon Compounds in Volcanic Gases on Io

We use chemical equilibrium calculations to model the speciation of carbon in volcanic gases on Io. The calculations cover wide temperature (500-2000 K), pressure (10^-8 to 10^+2 bars), and composition ranges (bulk O/S atomic ratios \~0 to 3), which overlap the nominal conditions at Pele (1760 K, 0.01 bar, O/S ~ 1.5). Bulk C/S atomic ratios ranging from 10^-6 to 10^-1 in volcanic gases are used with a nominal value of 10^-3 based upon upper limits from Voyager for carbon in the Loki plume on Io. Carbon monoxide and CO2 are the two major carbon gases under all conditions studied. Carbonyl sulfide and CS2 are orders of magnitude less abundant. Consideration of different loss processes (photolysis, condensation, kinetic reactions in the plume) indicates that photolysis is probably the major loss process for all gases. Both CO and CO2 should be observable in volcanic plumes and in Io's atmosphere at abundances of several hundred parts per million by volume for a bulk C/S ratio of 10^-3.Comment: 21 pages, 4 figures, 4 tables; accepted by Astrophysical Journa

Agrin isoforms and their role in synaptogenesis

Agrin is thought to mediate the motor neuron-induced aggregation of synaptic proteins on the surface of muscle fibers at neuromuscular junctions. Recent experiments provide direct evidence in support of this hypothesis, reveal the nature of agrin immunoreactivity at sites other than neuromuscular junctions, and have resulted in findings that are consistent with the possibility that agrin plays a role in synaptogenesis throughout the nervous system

Modus Vivendi Beyond the Social Contract: Peace, Justice, and Survival in Realist Political Theory

This essay examines the promise of the notion of modus vivendi for realist political theory. I interpret recent theories of modus vivendi as affirming the priority of peace over justice, and explore several ways of making sense of this idea. I proceed to identify two key problems for modus vivendi theory, so conceived. Normatively speaking, it remains unclear how this approach can sustain a realist critique of Rawlsian theorizing about justice while avoiding a Hobbesian endorsement of absolutism. And conceptually, the theory remains wedded to a key feature of social contract theory: political order is conceived as based on agreement. This construes the horizontal tensions among individual or group agents in society as prior to the vertical, authoritative relations between authorities and their subjects. Political authority thereby appears from the start as a solution to societal conflict, rather than a problem in itself. I argue that this way of framing the issue abstracts from political experience. Instead I attempt to rethink the notion of modus vivendi from within the lived experience of political conflict, as oriented not primarily toward peace, but political survival. With this shift of perspective, the idea of modus vivendi shows us, pace Bernard Williams, that the “first political question” is not how to achieve order and stability, but rather: what can I live with

Zener double exchange from local valence fluctuations in magnetite

Magnetite (Fe$_{3}$O$_{4}$) is a mixed valent system where electronic conductivity occurs on the B-site (octahedral) iron sublattice of the spinel structure. Below $T_{V}=122$ K, a metal-insulator transition occurs which is argued to arise from the charge ordering of 2+ and 3+ iron valences on the B-sites (Verwey transition). Inelastic neutron scattering measurements show that optical spin waves propagating on the B-site sublattice ($\sim$80 meV) are shifted upwards in energy above $T_{V}$ due to the occurrence of B-B ferromagnetic double exchange in the mixed valent metallic phase. The double exchange interaction affects only spin waves of $\Delta_{5}$ symmetry, not all modes, indicating that valence fluctuations are slow and the double exchange is constrained by electron correlations above $T_{V}$.Comment: 4 pages, 5 figure

Relation among concentrations of incorporated Mn atoms, ionized Mn acceptors, and holes in p-(Ga,Mn)As epilayers

The amount of ionized Mn acceptors in various p-type Mn-doped GaAs epilayers has been evaluated by electrochemical capacitance-voltage measurements, and has been compared systematically with concentrations of incorporated Mn atoms and holes for wide range of Mn concentration (10^17 ~ 10^21 cm^-3). Quantitative assessment of anomalous Hall effect at room temperature is also carried out for the first time.Comment: 8 pages, 4 figures, tabl

Effectiveness of fecal-derived microbiota transfer using orally administered capsules for recurrent Clostridium difficile infection

BACKGROUND: Clostridium difficile infection (CDI), a complication of antibiotic-induced injury to the gut microbiome, is a prevalent and dangerous cause of infectious diarrhea. Antimicrobial therapy for CDI is typically effective for acute symptoms, but up to one third of patients later experience recurrent CDI. Fecal-derived microbiota transplantation (FMT) can ameliorate the underlying dysbiosis and is highly effective for recurrent CDI. Traditional methods of FMT are limited by patient discomfort, risk and inefficient procedures. Many individuals with recurrent CDI have extensive comorbidities and advanced age. Widespread use of FMT requires strategies that are non-invasive, scalable and applicable across healthcare settings. METHODS: A method to facilitate microbiota transfer was developed. Fecal samples were collected and screened for potential pathogens. Bacteria were purified, concentrated, cryopreserved and formulated into multi-layered capsules. Capsules were administered to patients with recurrent CDI, who were then monitored for 90 days. RESULTS: Thirteen women and six men with recurrent CDI were provided with microbiota transfer with orally administered capsules. The procedure was well tolerated. Thirteen individuals responded to a single course. Four patients were cured after a second course. There were 2 failures. The cumulative clinical cure rate of 89% is similar to the rates achieved with reported fecal-derived transplantation procedures. CONCLUSIONS: Recurrent CDI represents a profound dysbiosis and a debilitating chronic disease. Stable cure can be achieved by restoring the gut microbiome with an effective, well-tolerated oral capsule treatment. This strategy of microbiota transfer can be widely applied and is particularly appropriate for frail patients

Fast Non-Adiabatic Two Qubit Gates for the Kane Quantum Computer

In this paper we apply the canonical decomposition of two qubit unitaries to find pulse schemes to control the proposed Kane quantum computer. We explicitly find pulse sequences for the CNOT, swap, square root of swap and controlled Z rotations. We analyze the speed and fidelity of these gates, both of which compare favorably to existing schemes. The pulse sequences presented in this paper are theoretically faster, higher fidelity, and simpler than existing schemes. Any two qubit gate may be easily found and implemented using similar pulse sequences. Numerical simulation is used to verify the accuracy of each pulse scheme