REVIEWS REVIEWS REVIEWS Disturbance and the rising tide: the

low-island ecosystem

Viral population estimation using pyrosequencing

The diversity of virus populations within single infected hosts presents a major difficulty for the natural immune response as well as for vaccine design and antiviral drug therapy. Recently developed pyrophosphate based sequencing technologies (pyrosequencing) can be used for quantifying this diversity by ultra-deep sequencing of virus samples. We present computational methods for the analysis of such sequence data and apply these techniques to pyrosequencing data obtained from HIV populations within patients harboring drug resistant virus strains. Our main result is the estimation of the population structure of the sample from the pyrosequencing reads. This inference is based on a statistical approach to error correction, followed by a combinatorial algorithm for constructing a minimal set of haplotypes that explain the data. Using this set of explaining haplotypes, we apply a statistical model to infer the frequencies of the haplotypes in the population via an EM algorithm. We demonstrate that pyrosequencing reads allow for effective population reconstruction by extensive simulations and by comparison to 165 sequences obtained directly from clonal sequencing of four independent, diverse HIV populations. Thus, pyrosequencing can be used for cost-effective estimation of the structure of virus populations, promising new insights into viral evolutionary dynamics and disease control strategies.Comment: 23 pages, 13 figure

Single Cell Profiling of Circulating Tumor Cells: Transcriptional Heterogeneity and Diversity from Breast Cancer Cell Lines

BACKGROUND: To improve cancer therapy, it is critical to target metastasizing cells. Circulating tumor cells (CTCs) are rare cells found in the blood of patients with solid tumors and may play a key role in cancer dissemination. Uncovering CTC phenotypes offers a potential avenue to inform treatment. However, CTC transcriptional profiling is limited by leukocyte contamination; an approach to surmount this problem is single cell analysis. Here we demonstrate feasibility of performing high dimensional single CTC profiling, providing early insight into CTC heterogeneity and allowing comparisons to breast cancer cell lines widely used for drug discovery. METHODOLOGY/PRINCIPAL FINDINGS: We purified CTCs using the MagSweeper, an immunomagnetic enrichment device that isolates live tumor cells from unfractionated blood. CTCs that met stringent criteria for further analysis were obtained from 70% (14/20) of primary and 70% (21/30) of metastatic breast cancer patients; none were captured from patients with non-epithelial cancer (n = 20) or healthy subjects (n = 25). Microfluidic-based single cell transcriptional profiling of 87 cancer-associated and reference genes showed heterogeneity among individual CTCs, separating them into two major subgroups, based on 31 highly expressed genes. In contrast, single cells from seven breast cancer cell lines were tightly clustered together by sample ID and ER status. CTC profiles were distinct from those of cancer cell lines, questioning the suitability of such lines for drug discovery efforts for late stage cancer therapy. CONCLUSIONS/SIGNIFICANCE: For the first time, we directly measured high dimensional gene expression in individual CTCs without the common practice of pooling such cells. Elevated transcript levels of genes associated with metastasis NPTN, S100A4, S100A9, and with epithelial mesenchymal transition: VIM, TGFß1, ZEB2, FOXC1, CXCR4, were striking compared to cell lines. Our findings demonstrate that profiling CTCs on a cell-by-cell basis is possible and may facilitate the application of 'liquid biopsies' to better model drug discovery

Killer whales and marine mammal trends in the North Pacific : a re-examination of evidence for sequential megafauna collapse and the prey-switching hypothesis

This paper is not subject to U.S. copyright. The definitive version was published in Marine Mammal Science 23 (2007): 766–802, doi:10.1111/j.1748-7692.2006.00093.x.Springer et al. (2003) contend that sequential declines occurred in North Pacific populations of harbor and fur seals, Steller sea lions, and sea otters. They hypothesize that these were due to increased predation by killer whales, when industrial whaling's removal of large whales as a supposed primary food source precipitated a prey switch. Using a regional approach, we reexamined whale catch data, killer whale predation observations, and the current biomass and trends of potential prey, and found little support for the prey-switching hypothesis. Large whale biomass in the Bering Sea did not decline as much as suggested by Springer et al., and much of the reduction occurred 50–100 yr ago, well before the declines of pinnipeds and sea otters began; thus, the need to switch prey starting in the 1970s is doubtful. With the sole exception that the sea otter decline followed the decline of pinnipeds, the reported declines were not in fact sequential. Given this, it is unlikely that a sequential megafaunal collapse from whales to sea otters occurred. The spatial and temporal patterns of pinniped and sea otter population trends are more complex than Springer et al. suggest, and are often inconsistent with their hypothesis. Populations remained stable or increased in many areas, despite extensive historical whaling and high killer whale abundance. Furthermore, observed killer whale predation has largely involved pinnipeds and small cetaceans; there is little evidence that large whales were ever a major prey item in high latitudes. Small cetaceans (ignored by Springer et al.) were likely abundant throughout the period. Overall, we suggest that the Springer et al. hypothesis represents a misleading and simplistic view of events and trophic relationships within this complex marine ecosystem

First Observation of Υ(1S)→γππ\Upsilon(1S)\to \gamma\pi\pi

We report on a study of exclusive radiative decays of the Upsilon(1S) resonance collected with the CLEO-II detector operating at CESR. We present the first observation of the radiative decays Upsilon(1S)->gamma pi+pi- and Upsilon(1S)->gamma pi0pi0. For the dipion mass regime m(pipi)>1.0 GeV, we obtain Br(Upsilon(1S)->gamma pi+pi-=(6.3+/-1.2+/-1.3) x 10^(-5), and Br(Upsilon(1S)->gamma pi0pi0=(1.7+/-0.6+/-0.3) x 10^(-5). The observed gamma pipi events are consistent with the hypothesis Upsilon(1S)->gamma f2(1270).Comment: 9 pages, postscript file also available through http://w4.lns.cornell.edu/public/CLN

Flavor-Specific Inclusive B Decays to Charm

We have measured the branching fractions for B -> D_bar X, B -> D X, and B -> D_bar X \ell^+ \nu, where ``B'' is an average over B^0 and B^+, ``D'' is a sum over D^0 and D^+, and``D_bar'' is a sum over D^0_bar and D^-. From these results and some previously measured branching fractions, we obtain Br(b -> c c_bar s) = (21.9 $\pm$ 3.7)%, Br(b -> s g) K^- \pi^+) = (3.69 $\pm$ 0.20)%. Implications for the ``B semileptonic decay problem'' (measured branching fraction being below theoretical expectations) are discussed. The increase in the value of Br(b -> c c_bar s) due to $B -> D X$ eliminates 40% of the discrepancy.Comment: 12 page postscript file, postscript file also available through http://w4.lns.cornell.edu/public/CLN

Observation of Two Narrow States Decaying into Ξc+γ\Xi_{c}^{+}\gamma and Ξc0γ\Xi_{c}^{0}\gamma

We report the first observation of two narrow charmed strange baryons decaying to $\Xi_c^+\gamma$ and $\Xi_c^0\gamma$, respectively, using data from the CLEO II detector at CESR. We interpret the observed signals as the $\Xi_c^{+\prime}(c{su})$ and $\Xi_c^{0\prime}(c{sd})$, the symmetric partners of the well-established antisymmetric $\Xi_c^+(c[su])$ and $\Xi_c^0(c[sd])$. The mass differences $M(\Xi_c^{+\prime})-M(\Xi_c^+)$ and $M(\Xi_c^{0\prime})-M(\Xi_c^0)$ are measured to be $107.8\pm 1.7\pm 2.5$ and $107.0\pm 1.4\pm 2.5 MeV/c^2$, respectively.Comment: 11 pages, postscript file also available through http://w4.lns.cornell.edu/public/CLN

Further Search for the Two-Photon Production of the Glueball Candidate fJ(2220)f_{J}(2220)

The CLEOII detector at the Cornell e+ e- storage ring CESR has been used to search for the two-photon production of the $f_J(2220)$ decaying into pi+ pi-. No evidence for a signal is found in data corresponding to an integrated luminosity of 4.77/fb and a 95% CL upper limit on $\Gamma_{two-photon} * BR{pi+ pi-}$ of 2.5 eV is set. If this result is combined with the BES Collaboration's measurement of $f_J(2220) -> pi+ pi-$ in radiative $J/\psi$ decay, a 95% CL lower limit on the stickiness of the $f_J(2220)$ of 73 is obtained. If the recent CLEO result for \Gamma_{two-photon} * BR{\K_S K_S} is combined with the present result, the stickiness of the $f_J(2220)$ is found to be larger than 102 at the 95% CL. These results for the stickiness (the ratio of the probabilities for two-gluon coupling and two-photon coupling) provide further support for a substantial neutral parton content in the $f_J(2220)$.Comment: 8 pages, postscript file also available through http://w4.lns.cornell.edu/public/CLN