Extensive horizontal gene transfer in cheese-associated bacteria.

Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that HGT is prevalent in cheese rind microbiomes, and that identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities

A Genomic Point Mutation in the Extracellular Domain of the Thyrotropin Receptor in Patients with Graves’ Ophthalmopathy

Orbital and pretibial fibroblasts are targets of autoimmune attack in Graves' ophthalmopathy (GO) and pretibial dermopathy (PTD). The fibroblast autoantigen involved in these peripheral manifestations of Graves' disease and the reason for the association of GO and PTD with hyperthyroidism are unknown. RNA encoding the full-length extracellular domain of the TSH receptor has been demonstrated in orbital and dermal fibroblasts from patients with GO and normal subjects, suggesting a possible antigenic link between fibroblasts and thyrocytes. RNA was isolated from cultured orbital, pretibial, and abdominal fibroblasts obtained from patients with severe GO (n = 22) and normal subjects (n = 5). RNA was reverse transcribed, and the resulting cDNA was amplified by the polymerase chain reaction, using primers spanning overlapping regions of the entire extracellular domain of the TSH receptor. Nucleotide sequence analysis showed an A for C substitution in the first position of codon 52 in 2 of the patients, both of whom had GO, PTD, and acropachy. Genomic DNA isolated from the 2 affected patients, and not from an additional 12 normal subjects, revealed the codon 52 mutation by direct sequencing and AciI restriction enzyme digestions. In conclusion, we have demonstrated the presence of a genomic point mutation, leading to a threonine for proline amino acid shift in the predicted peptide, in the extracellular domain of the TSH receptor in two patients with severe GO, PTD, acropachy, and high thyroid-stimulating immunoglobulin levels. RNA encoding this mutant product was demonstrated in the fibroblasts of these patients. We suggest that the TSH receptor may be an important fibroblast autoantigen in GO and PTD, and that this mutant form of the receptor may have unique immunogenic properties

Sagnac interferometry based on ultra-slow polaritons in cold atomic vapors

The advantages of light and matter-wave Sagnac interferometers -- large area on one hand and high rotational sensitivity per unit area on the other -- can be combined utilizing ultra-slow light in cold atomic gases. While a group-velocity reduction alone does not affect the Sagnac phase shift, the associated momentum transfer from light to atoms generates a coherent matter-wave component which gives rise to a substantially enhanced rotational signal. It is shown that matter-wave sensitivity in a large-area interferometer can be achieved if an optically dense vapor at sub-recoil temperatures is used. Already a noticeable enhancement of the Sagnac phase shift is possible however with much less cooling requirements.Comment: 4 pages, 3 figure

Dominant ferromagnetism in the spin-1/2 half-twist ladder 334 compounds, Ba3Cu3In4O12 and Ba3Cu3Sc4O12

The magnetic properties of polycrystalline samples of Ba3Cu3In4O12 (In-334) and Ba3Cu3Sc4O12 (Sc-334) are reported. Both 334 phases have a structure derived from perovskite, with CuO4 squares interconnected to form half-twist ladders along the c-axis. The Cu-O-Cu angles, ~ 90o, and the positive Weiss temperatures indicate the presence of significant ferromagnetic (FM) interactions along the Cu ladders. At low temperatures, T < 20 K, sharp transitions in the magnetic susceptibility and heat capacity measurements indicate three-dimensional (3D) antiferromagnetic (AFM) ordering at TN. TN is suppressed on application of a field and a complex magnetic phase diagram with three distinct magnetic regimes below the upper critical field can be inferred from our measurements. The magnetic interactions are discussed in relation to a modified spin-1/2 FM-AFM model and the 334 half-twist ladder is compared to other 2-rung ladder spin-1/2 systems.Comment: 20 pages, 7 figure

Storing and processing optical information with ultra-slow light in Bose-Einstein condensates

We theoretically explore coherent information transfer between ultra-slow light pulses and Bose-Einstein condensates (BECs) and find that storing light pulses in BECs, by switching off the coupling field, allows the coherent condensate dynamics to process optical information. We develop a formalism, applicable in both the weak and strong probe regimes, to analyze such experiments and establish several new results. Investigating examples relevant to Rb-87 experimental parameters we see a variety of novel two-component BEC dynamics occur during the storage, including interference fringes, gentle breathing excitations, and two-component solitons. We find the dynamics when the levels |F=1, M_F=-1> and |F=2, M_F=+1> are well suited to designing controlled processing of the information. By switching the coupling field back on, the processed information is rewritten onto probe pulses which then propagate out as slow light pulses. We calculate the fidelity of information transfer between the atomic and light fields upon the switch-on and subsequent output. The fidelity is affected both by absorption of small length scale features and absorption of regions of the pulse stored near the condensate edge. In the strong probe case, we find that when the oscillator strengths for the two transitions are equal the fidelity is not strongly sensitive to the probe strength, while when they are unequal the fidelity is worse for stronger probes. Applications to distant communication between BECs, squeezed light generation and quantum information are anticipated.Comment: 19 pages, 12 figures, submitted to Phys. Rev.

Probing Decoherence with Electromagnetically Induced Transparency in Superconductive Quantum Circuits

Superconductive quantum circuits (SQCs) comprise quantized energy levels that may be coupled via microwave electromagnetic fields. Described in this way, one may draw a close analogy to atoms with internal (electronic) levels coupled by laser light fields. In this Letter, we present a superconductive analog to electromagnetically induced transparency (S-EIT) that utilizes SQC designs of present day experimental consideration. We discuss how S-EIT can be used to establish macroscopic coherence in such systems and, thereby, utilized as a sensitive probe of decoherence.Comment: 5 pages, 3 figure