Draft Genome Sequence of Mycobacterium arupense Strain GUC1.

We report the draft genome sequence of Mycobacterium arupense strain GUC1 from a sputum sample of a patient with bronchiectasis. This is the first draft genome sequence of Mycobacterium arupense, a rapidly growing nonchromogenic mycobacteria

Draft Genome Sequence of Mycobacterium elephantis Strain Lipa.

We report the draft genome sequence of Mycobacterium elephantis strain Lipa from a sputum sample of a patient with pulmonary disease. This is the first draft genome sequence of M. elephantis, a rapidly growing mycobacterium

Draft Genome Sequence of Mycobacterium obuense Strain UC1, Isolated from Patient Sputum.

We report the draft genome sequence of Mycobacterium obuense strain UC1 from a patient sputum sample. This is the first draft genome sequence of Mycobacterium obuense, a rapidly growing scotochromogenic mycobacterium

Differentiation enhances Zika virus infection of neuronal brain cells.

Zika virus (ZIKV) is an emerging, mosquito-borne pathogen associated with a widespread 2015-2016 epidemic in the Western Hemisphere and a proven cause of microcephaly and other fetal brain defects in infants born to infected mothers. ZIKV infections have been also linked to other neurological illnesses in infected adults and children, including Guillain-Barré syndrome (GBS), acute flaccid paralysis (AFP) and meningoencephalitis, but the viral pathophysiology behind those conditions remains poorly understood. Here we investigated ZIKV infectivity in neuroblastoma SH-SY5Y cells, both undifferentiated and following differentiation with retinoic acid. We found that multiple ZIKV strains, representing both the prototype African and contemporary Asian epidemic lineages, were able to replicate in SH-SY5Y cells. Differentiation with resultant expression of mature neuron markers increased infectivity in these cells, and the extent of infectivity correlated with degree of differentiation. New viral particles in infected cells were visualized by electron microscopy and found to be primarily situated inside vesicles; overt damage to the Golgi apparatus was also observed. Enhanced ZIKV infectivity in a neural cell line following differentiation may contribute to viral neuropathogenesis in the developing or mature central nervous system

Phonitons as a sound-based analogue of cavity quantum electrodynamics

A quantum mechanical superposition of a long-lived, localized phonon and a matter excitation is described. We identify a realization in strained silicon: a low-lying donor transition (P or Li) driven solely by acoustic phonons at wavelengths where high-Q phonon cavities can be built. This phonon-matter resonance is shown to enter the strongly coupled regime where the "vacuum" Rabi frequency exceeds the spontaneous phonon emission into non-cavity modes, phonon leakage from the cavity, and phonon anharmonicity and scattering. We introduce a micropillar distributed Bragg reflector Si/Ge cavity, where Q=10^5-10^6 and mode volumes V<=25*lambda^3 are reachable. These results indicate that single or many-body devices based on these systems are experimentally realizable.Comment: Published PRL version. Note that the previous arXiv version has more commentary, figures, etc. Also see http://research.tahan.com

Grazing‐angle characterization of photosynthetic oxygen evolution protein monolayers

Variable‐period x‐ray standing wave (XSW) spectroscopy has been shown to be a practical probe for studying metalloproteins. The photosynthetic oxygen evolving complex (OEC) is a transmembrane multipolypeptide complex that catalyzes the oxidation of water to dioxygen. The OEC contains Mn, Ca, and Cl and is potentially amenable to study by XSW. In this feasibility study, preliminary results on OEC samples deposited on Au mirrors are discussed. First XSW measurements from the SSRL grazing‐incidence setup are presented. © 1996 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/70867/2/RSINAK-67-9-3364-5.pd

Convexity criteria and uniqueness of absolutely minimizing functions

We show that absolutely minimizing functions relative to a convex Hamiltonian $H:\mathbb{R}^n \to \mathbb{R}$ are uniquely determined by their boundary values under minimal assumptions on $H.$ Along the way, we extend the known equivalences between comparison with cones, convexity criteria, and absolutely minimizing properties, to this generality. These results perfect a long development in the uniqueness/existence theory of the archetypal problem of the calculus of variations in $L^\infty.$Comment: 34 page

Valley Splitting Theory of SiGe/Si/SiGe Quantum Wells

We present an effective mass theory for SiGe/Si/SiGe quantum wells, with an emphasis on calculating the valley splitting. The theory introduces a valley coupling parameter, $v_v$, which encapsulates the physics of the quantum well interface. The new effective mass parameter is computed by means of a tight binding theory. The resulting formalism provides rather simple analytical results for several geometries of interest, including a finite square well, a quantum well in an electric field, and a modulation doped two-dimensional electron gas. Of particular importance is the problem of a quantum well in a magnetic field, grown on a miscut substrate. The latter may pose a numerical challenge for atomistic techniques like tight-binding, because of its two-dimensional nature. In the effective mass theory, however, the results are straightforward and analytical. We compare our effective mass results with those of the tight binding theory, obtaining excellent agreement.Comment: 13 pages, 7 figures. Version submitted to PR

An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies

BACKGROUND: The use of environmental DNA for species detection via metabarcoding is growing rapidly. We present a co-designed lab workflow and bioinformatic pipeline to mitigate the 2 most important risks of environmental DNA use: sample contamination and taxonomic misassignment. These risks arise from the need for polymerase chain reaction (PCR) amplification to detect the trace amounts of DNA combined with the necessity of using short target regions due to DNA degradation. FINDINGS: Our high-throughput workflow minimizes these risks via a 4-step strategy: (i) technical replication with 2 PCR replicates and 2 extraction replicates; (ii) using multi-markers (12S,16S,CytB); (iii) a "twin-tagging," 2-step PCR protocol; and (iv) use of the probabilistic taxonomic assignment method PROTAX, which can account for incomplete reference databases. Because annotation errors in the reference sequences can result in taxonomic misassignment, we supply a protocol for curating sequence datasets. For some taxonomic groups and some markers, curation resulted in >50% of sequences being deleted from public reference databases, owing to (i) limited overlap between our target amplicon and reference sequences, (ii) mislabelling of reference sequences, and (iii) redundancy. Finally, we provide a bioinformatic pipeline to process amplicons and conduct PROTAX assignment and tested it on an invertebrate-derived DNA dataset from 1,532 leeches from Sabah, Malaysia. Twin-tagging allowed us to detect and exclude sequences with non-matching tags. The smallest DNA fragment (16S) amplified most frequently for all samples but was less powerful for discriminating at species rank. Using a stringent and lax acceptance criterion we found 162 (stringent) and 190 (lax) vertebrate detections of 95 (stringent) and 109 (lax) leech samples. CONCLUSIONS: Our metabarcoding workflow should help research groups increase the robustness of their results and therefore facilitate wider use of environmental and invertebrate-derived DNA, which is turning into a valuable source of ecological and conservation information on tetrapods