Molecular epidemiologic investigations of Mycoplasma gallisepticum conjunctivitis in songbirds by random amplified polymorphic DNA analyses.

An ongoing outbreak of conjunctivitis in free-ranging house finches (Carpodacus mexicanus) began in 1994 in the eastern United States. Bacterial organisms identified as Mycoplasma gallisepticum (MG) were isolated from lesions of infected birds. MG was also isolated from a blue jay (Cyanocitta cristata) that contracted conjunctivitis after being housed in a cage previously occupied by house finches with conjunctivitis, and from free-ranging American goldfinches (Carduelis tristis) in North Carolina in 1996. To investigate the molecular epidemiology of this outbreak, we produced DNA fingerprints of MG isolates by random amplification of polymorphic DNA (RAPD). We compared MG isolates from songbirds examined from 1994 through 1996 in 11 states, representing three host species, with vaccine and reference strains and with contemporary MG isolates from commercial poultry. All MG isolates from songbirds had RAPD banding patterns identical to each other but different from other strains and isolates tested. These results indicate that the outbreak of MG in songbirds is caused by the same strain, which suggests a single source; the outbreak is not caused by the vaccine or reference strains analyzed; and MG infection has not been shared between songbirds and commercial poultry

Expression profiling of snoRNAs in normal hematopoiesis and AML

Key Points A subset of snoRNAs is expressed in a developmental- and lineage-specific manner during human hematopoiesis. Neither host gene expression nor alternative splicing accounted for the observed differential expression of snoRNAs in a subset of AML.</jats:p

Prevention and management of type 2 diabetes: dietary components and nutritional strategies

In the past couple of decades, evidence from prospective observational studies and clinical trials has converged to support the importance of individual nutrients, foods, and dietary patterns in the prevention and management of type 2 diabetes. The quality of dietary fats and carbohydrates consumed is more crucial than is the quantity of these macronutrients. Diets rich in wholegrains, fruits, vegetables, legumes, and nuts; moderate in alcohol consumption; and lower in refined grains, red or processed meats, and sugar-sweetened beverages have been shown to reduce the risk of diabetes and improve glycaemic control and blood lipids in patients with diabetes. With an emphasis on overall diet quality, several dietary patterns such as Mediterranean, low glycaemic index, moderately low carbohydrate, and vegetarian diets can be tailored to personal and cultural food preferences and appropriate calorie needs for weight control and diabetes prevention and management. Although much progress has been made in development and implementation of evidence-based nutrition recommendations in developed countries, concerted worldwide efforts and policies are warranted to alleviate regional disparities

Factors Associated with the Diversification of the Gut Microbial Communities within Chimpanzees from Gombe National Park.

The gastrointestinal tract harbors large and diverse populations of bacteria that vary among individuals and within individuals over time. Numerous internal and external factors can influence the contents of these microbial communities, including diet, geography, physiology, and the extent of contact among hosts. To investigate the contributions of such factors to the variation and changes in gut microbial communities, we analyzed the distal gut microbiota of individual chimpanzees from two communities in Gombe National Park, Tanzania. These samples, which were derived from 35 chimpanzees, many of whom have been monitored for multiple years, provide an unusually comprehensive longitudinal depth for individuals of known genetic relationships. Although the composition of the great-ape microbiota has been shown to codiversify with host species, indicating that host genetics and phylogeny have played a major role in its differentiation over evolutionary timescales, the geneaological relationships of individual chimpanzees did not coincide with the similarity in their gut microbial communities. However, the inhabitants from adjacent chimpanzee communities could be distinguished based on the contents of their gut microbiota. Despite the broad similarity of community members, as would be expected from shared diet or interactions, long-term immigrants to a community often harbored the most distinctive gut microbiota, suggesting that individuals retain hallmarks of their previous gut microbial communities for extended periods. This pattern was reinforced in several chimpanzees sampled over long temporal scales, in which the major constituents of the gut microbiota were maintained for nearly a decade

Regulation of surface architecture by symbiotic bacteria mediates host colonization

Microbes occupy countless ecological niches in nature. Sometimes these environments may be on or within another organism, as is the case in both microbial infections and symbiosis of mammals. Unlike pathogens that establish opportunistic infections, hundreds of human commensal bacterial species establish a lifelong cohabitation with their hosts. Although many virulence factors of infectious bacteria have been described, the molecular mechanisms used during beneficial host–symbiont colonization remain almost entirely unknown. The novel identification of multiple surface polysaccharides in the important human symbiont Bacteroides fragilis raised the critical question of how these molecules contribute to commensalism. To understand the function of the bacterial capsule during symbiotic colonization of mammals, we generated B. fragilis strains deleted in the global regulator of polysaccharide expression and isolated mutants with defects in capsule expression. Surprisingly, attempts to completely eliminate capsule production are not tolerated by the microorganism, which displays growth deficits and subsequent reversion to express capsular polysaccharides. We identify an alternative pathway by which B. fragilis is able to reestablish capsule production and modulate expression of surface structures. Most importantly, mutants expressing single, defined surface polysaccharides are defective for intestinal colonization compared with bacteria expressing a complete polysaccharide repertoire. Restoring the expression of multiple capsular polysaccharides rescues the inability of mutants to compete for commensalism. These findings suggest a model whereby display of multiple capsular polysaccharides provides essential functions for bacterial colonization during host–symbiont mutualism

Input-Output Relations in Optical Cavities: a Simple Point of View

In this work we present a very simple approach to input-output relations in optical cavities, limiting ourselves to one- and two-photon states of the field. After field quantization, we derive the non-unitary transformation between {\em Inside} and {\em Outside} annihilation and creation operators. Then we express the most general two-photon state generated by {\em Inside} creation operators, through base states generated by {\em Outside} creation operators. After renormalization of coefficients of inside two-photon state, we calculate the outside photon-number probability distribution in a general case. Finally we treat with some detail the single mode and symmetrical cavity case.Comment: 34 pages, 5 figures jpg, LaTe

Quantum Communication with Phantom Photons

We show that quantum information may be transferred between atoms in different locations by using ``phantom photons'': the atoms are coupled through electromagnetic fields, but the corresponding field modes do not have to be fully populated. In the case where atoms are placed inside optical cavities, errors in quantum information processing due to photon absorption inside the cavity are diminished in this way. This effect persists up to intercavity distances of about a meter for the current levels of cavity losses, and may be useful for distributed quantum computing.Comment: 6 pages RevTex, 4 eps figures included. Revised calculation with more details about mode structure calculation and the introduction of losse

Coherent coupling of two quantum dots embedded in an Aharonov-Bohm ring

We define two laterally gated small quantum dots (~ 15 electrons) in an Aharonov-Bohm geometry in which the coupling between the two dots can be broadly changed. For weakly coupled quantum dots we find Aharonov-Bohm oscillations. In an intermediate coupling regime we concentrate on the molecular states of the double dot and extract the magnetic field dependence of the coherent coupling.Comment: 6 pages, 4 figure

Full capacitance-matrix effects in driven Josephson-junction arrays

We study the dynamic response to external currents of periodic arrays of Josephson junctions, in a resistively capacitively shunted junction (RCSJ) model, including full capacitance-matrix effects}. We define and study three different models of the capacitance matrix $C_{\vec{r},\vec{r}'}$: Model A includes only mutual capacitances; Model B includes mutual and self capacitances, leading to exponential screening of the electrostatic fields; Model C includes a dense matrix $C_{\vec{r},\vec{r}'}$ that is constructed approximately from superposition of an exact analytic solution for the capacitance between two disks of finite radius and thickness. In the latter case the electrostatic fields decay algebraically. For comparison, we have also evaluated the full capacitance matrix using the MIT fastcap algorithm, good for small lattices, as well as a corresponding continuum effective-medium analytic evaluation of a finite voltage disk inside a zero-potential plane. In all cases the effective $C_{\vec{r},\vec{r}'}$ decays algebraically with distance, with different powers. We have then calculated current voltage characteristics for DC+AC currents for all models. We find that there are novel giant capacitive fractional steps in the I-V's for Models B and C, strongly dependent on the amount of screening involved. We find that these fractional steps are quantized in units inversely proportional to the lattice sizes and depend on the properties of $C_{\vec{r},\vec{r}'}$. We also show that the capacitive steps are not related to vortex oscillations but to localized screened phase-locking of a few rows in the lattice. The possible experimental relevance of these results is also discussed.Comment: 12 pages 18 Postscript figures, REVTEX style. Paper to appear in July 1, Vol. 58, Phys. Rev. B 1998 All PS figures include

Accumulation of driver and passenger mutations during tumor progression

Major efforts to sequence cancer genomes are now occurring throughout the world. Though the emerging data from these studies are illuminating, their reconciliation with epidemiologic and clinical observations poses a major challenge. In the current study, we provide a novel mathematical model that begins to address this challenge. We model tumors as a discrete time branching process that starts with a single driver mutation and proceeds as each new driver mutation leads to a slightly increased rate of clonal expansion. Using the model, we observe tremendous variation in the rate of tumor development - providing an understanding of the heterogeneity in tumor sizes and development times that have been observed by epidemiologists and clinicians. Furthermore, the model provides a simple formula for the number of driver mutations as a function of the total number of mutations in the tumor. Finally, when applied to recent experimental data, the model allows us to calculate, for the first time, the actual selective advantage provided by typical somatic mutations in human tumors in situ. This selective advantage is surprisingly small, 0.005 +- 0.0005, and has major implications for experimental cancer research