Standard and Non-Standard Plasma Neutrino Emission Revisited

On the basis of Braaten and Segel's representation of the electromagnetic dispersion relations in a QED plasma we check the numerical accuracy of several published analytic approximations to the plasma neutrino emission rates. As we find none of them satisfactory we derive a new analytic approximation which is accurate to within 4\%\ where the plasma process dominates. The correct emission rates in the parameter regime relevant for the red giant branch in globular clusters are larger by about $10-20$\% than those of previous stellar evolution calculations. Therefore, the core mass of red giants at the He flash is larger by about 0.005\M_\odot or 1\% than previously thought. Our bounds on neutrino magnetic dipole moments remain virtually unchanged.Comment: LaTeX, 16 pages, 12 figures on request from authors, MPI-Ph/93-6

Impurity-enhanced Aharonov-Bohm effect in neutral quantum-ring magnetoexcitons

We study the role of impurity scattering on the photoluminescence (PL) emission of polarized magnetoexcitons. We consider systems where both the electron and hole are confined on a ring structure (quantum rings) as well as on a type-II quantum dot. Despite their neutral character, excitons exhibit strong modulation of energy and oscillator strength in the presence of magnetic fields. Scattering impurities enhance the PL intensity on otherwise "dark" magnetic field windows and non-zero PL emission appears for a wide magnetic field range even at zero temperature. For higher temperatures, impurity-induced anticrossings on the excitonic spectrum lead to unexpected peaks and valleys on the PL intensity as function of magnetic field. Such behavior is absent on ideal systems and can account for prominent features in recent experimental results.Comment: 7 pages, 7 figures, RevTe

Reversible Conductive Inkjet Printing of Healable and Recyclable Electrodes on Cardboard and Paper

Conductive inkjet printing with metal nanoparticles is irreversible because the particles are sintered into a continuous metal film. The resulting structures are difficult to remove or repair and prone to cracking. Here, a hybrid ink is used to obviate the sintering step and print interconnected particle networks that become highly conductive immediately after drying. It is shown that reversible conductive printing is possible on low-cost cardboard samples after applying standard paper industry coats that are adapted in terms of surface energy and porosity. The conductivity of the printed films approaches that of sintered standard inks on the same substrate, but the mobility of the hybrid particle film makes them less sensitive to cracks during bending and folding of the substrate. Damages that occur can be partially repaired by wetting the film such that particle mobility is increased and particles move to bridge insulating gaps in the film. It is demonstrated that the conductive material can be recovered from the cardboard at the end of its life time and be redispersed to recycle the particles and reuse them in conductive inks

Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners

<p>Abstract</p> <p>Background</p> <p>Enzymes in the radical SAM (rSAM) domain family serve in a wide variety of biological processes, including RNA modification, enzyme activation, bacteriocin core peptide maturation, and cofactor biosynthesis. Evolutionary pressures and relationships to other cellular constituents impose recognizable grammars on each class of rSAM-containing system, shaping patterns in results obtained through various comparative genomics analyses.</p> <p>Results</p> <p>An uncharacterized gene cluster found in many Actinobacteria and sporadically in Firmicutes, Chloroflexi, Deltaproteobacteria, and one Archaeal plasmid contains a PqqE-like rSAM protein family that includes Rv0693 from <it>Mycobacterium tuberculosis</it>. Members occur clustered with a strikingly well-conserved small polypeptide we designate "mycofactocin," similar in size to bacteriocins and PqqA, precursor of pyrroloquinoline quinone (PQQ). Partial Phylogenetic Profiling (PPP) based on the distribution of these markers identifies the mycofactocin cluster, but also a second tier of high-scoring proteins. This tier, strikingly, is filled with up to thirty-one members per genome from three variant subfamilies that occur, one each, in three unrelated classes of nicotinoproteins. The pattern suggests these variant enzymes require not only NAD(P), but also the novel gene cluster. Further study was conducted using SIMBAL, a PPP-like tool, to search these nicotinoproteins for subsequences best correlated across multiple genomes to the presence of mycofactocin. For both the short chain dehydrogenase/reductase (SDR) and iron-containing dehydrogenase families, aligning SIMBAL's top-scoring sequences to homologous solved crystal structures shows signals centered over NAD(P)-binding sites rather than over substrate-binding or active site residues. Previous studies on some of these proteins have revealed a non-exchangeable NAD cofactor, such that enzymatic activity <it>in vitro </it>requires an artificial electron acceptor such as N,N-dimethyl-4-nitrosoaniline (NDMA) for the enzyme to cycle.</p> <p>Conclusions</p> <p>Taken together, these findings suggest that the mycofactocin precursor is modified by the Rv0693 family rSAM protein and other enzymes in its cluster. It becomes an electron carrier molecule that serves <it>in vivo </it>as NDMA and other artificial electron acceptors do <it>in vitro</it>. Subclasses from three different nicotinoprotein families show "only-if" relationships to mycofactocin because they require its presence. This framework suggests a segregated redox pool in which mycofactocin mediates communication among enzymes with non-exchangeable cofactors.</p

A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes

Clustered regularly interspaced short palindromic repeats (CRISPRs) are a family of DNA direct repeats found in many prokaryotic genomes. Repeats of 21–37 bp typically show weak dyad symmetry and are separated by regularly sized, nonrepetitive spacer sequences. Four CRISPR-associated (Cas) protein families, designated Cas1 to Cas4, are strictly associated with CRISPR elements and always occur near a repeat cluster. Some spacers originate from mobile genetic elements and are thought to confer “immunity” against the elements that harbor these sequences. In the present study, we have systematically investigated uncharacterized proteins encoded in the vicinity of these CRISPRs and found many additional protein families that are strictly associated with CRISPR loci across multiple prokaryotic species. Multiple sequence alignments and hidden Markov models have been built for 45 Cas protein families. These models identify family members with high sensitivity and selectivity and classify key regulators of development, DevR and DevS, in Myxococcus xanthus as Cas proteins. These identifications show that CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a repeat cluster or filling the region between two repeat clusters. Distinctive subsets of the collection of Cas proteins recur in phylogenetically distant species and correlate with characteristic repeat periodicity. The analyses presented here support initial proposals of mobility of these units, along with the likelihood that loci of different subtypes interact with one another as well as with host cell defensive, replicative, and regulatory systems. It is evident from this analysis that CRISPR/cas loci are larger, more complex, and more heterogeneous than previously appreciated

Accurate Profiling of Microbial Communities from Massively Parallel Sequencing using Convex Optimization

We describe the Microbial Community Reconstruction ({\bf MCR}) Problem, which is fundamental for microbiome analysis. In this problem, the goal is to reconstruct the identity and frequency of species comprising a microbial community, using short sequence reads from Massively Parallel Sequencing (MPS) data obtained for specified genomic regions. We formulate the problem mathematically as a convex optimization problem and provide sufficient conditions for identifiability, namely the ability to reconstruct species identity and frequency correctly when the data size (number of reads) grows to infinity. We discuss different metrics for assessing the quality of the reconstructed solution, including a novel phylogenetically-aware metric based on the Mahalanobis distance, and give upper-bounds on the reconstruction error for a finite number of reads under different metrics. We propose a scalable divide-and-conquer algorithm for the problem using convex optimization, which enables us to handle large problems (with $\sim10^6$ species). We show using numerical simulations that for realistic scenarios, where the microbial communities are sparse, our algorithm gives solutions with high accuracy, both in terms of obtaining accurate frequency, and in terms of species phylogenetic resolution.Comment: To appear in SPIRE 1

Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901

We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a “minimal” model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously

Particle dynamics in sheared granular matter

The particle dynamics and shear forces of granular matter in a Couette geometry are determined experimentally. The normalized tangential velocity $V(y)$ declines strongly with distance $y$ from the moving wall, independent of the shear rate and of the shear dynamics. Local RMS velocity fluctuations $\delta V(y)$ scale with the local velocity gradient to the power $0.4 \pm 0.05$. These results agree with a locally Newtonian, continuum model, where the granular medium is assumed to behave as a liquid with a local temperature $\delta V(y)^2$ and density dependent viscosity

Spherical collapse of supermassive stars: neutrino emission and gamma-ray bursts

We present the results of numerical simulations of the spherically symmetric gravitational collapse of supermassive stars (SMS). The collapse is studied using a general relativistic hydrodynamics code. The coupled system of Einstein and fluid equations is solved employing observer time coordinates, by foliating the spacetime by means of outgoing null hypersurfaces. The code contains an equation of state which includes effects due to radiation, electrons and baryons, and detailed microphysics to account for electron-positron pairs. In addition energy losses by thermal neutrino emission are included. We are able to follow the collapse of SMS from the onset of instability up to the point of black hole formation. Several SMS with masses in the range $5\times 10^5 M_{\odot}- 10^9 M_{\odot}$ are simulated. In all models an apparent horizon forms initially, enclosing the innermost 25% of the stellar mass. From the computed neutrino luminosities, estimates of the energy deposition by $\nu\bar{\nu}$-annihilation are obtained. Only a small fraction of this energy is deposited near the surface of the star, where, as proposed recently by Fuller & Shi (1998), it could cause the ultrarelativistic flow believed to be responsible for $\gamma$-ray bursts. Our simulations show that for collapsing SMS with masses larger than $5\times 10^5 M_{\odot}$ the energy deposition is at least two orders of magnitude too small to explain the energetics of observed long-duration bursts at cosmological redshifts. In addition, in the absence of rotational effects the energy is deposited in a region containing most of the stellar mass. Therefore relativistic ejection of matter is impossible.Comment: 13 pages, 11 figures, submitted to A&

Splenectomy for Splenic Abscess

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/140209/1/sur.2012.073.pd