Primer selection impacts specific population abundances but not community dynamics in a monthly time-series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton.

Primers targeting the 16S small subunit ribosomal RNA marker gene, used to characterize bacterial and archaeal communities, have recently been re-evaluated for marine planktonic habitats. To investigate whether primer selection affects the ecological interpretation of bacterioplankton populations and community dynamics, amplicon sequencing with four primer sets targeting several hypervariable regions of the 16S rRNA gene was conducted on both mock communities constructed from cloned 16S rRNA genes and a time-series of DNA samples from the temperate coastal Santa Barbara Channel. Ecological interpretations of community structure (delineation of depth and seasonality, correlations with environmental factors) were similar across primer sets, while population dynamics varied. We observed substantial differences in relative abundances of taxa known to be poorly resolved by some primer sets, such as Thaumarchaeota and SAR11, and unexpected taxa including Roseobacter clades. Though the magnitude of relative abundances of common OTUs differed between primer sets, the relative abundances of the OTUs were nonetheless strongly correlated. We do not endorse one primer set but rather enumerate strengths and weaknesses to facilitate selection appropriate to a system or experimental goal. While 16S rRNA gene primer bias suggests caution in assessing quantitative population dynamics, community dynamics appear robust across studies using different primers

Limits on the Peculiar Velocities of Two Distant Clusters Using the Kinematic Sunyaev-Zel'dovich Effect

We report millimeter-wavelength observations of the Sunyaev-Zel'dovich (S-Z) effect in two distant galaxy clusters. A relativistically correct analysis of the S-Z data is combined with the results of X-ray observations to determine the radial peculiar velocities v_r of the clusters. We observed Abell 2163 (z=.201) in three mm-wavelength bands centered at 2.1, 1.4, and 1.1 mm. We report a significant detection of the thermal component of the S-Z effect seen as both a decrement in the brightness of the CMB at 2.1 mm, and as an increment at 1.1 mm. Including uncertainties due to the calibration of the instrument, distribution and temperature of the IC gas, and astrophysical confusion, a simultaneous fit to the data in all three bands gives v_r=+490 +1370/-880 km/s at 68% confidence. We observed Abell 1689 (z=.181) in the 2.1 and 1.4 mm bands. Including the same detailed accounting of uncertainty, a simultaneous fit to the data in both bands gives v_r=+170 +815/-630 km/s. The limits on the peculiar velocities of A2163 and A1689 correspond to deviations from the uniform Hubble flow of <= 2-3%.Comment: 21 pages, 13 postscript figures, LaTeX(aaspptwo.sty), ApJ(in press

Using mlearning in the education of radiation science students

Radiation science is a highly visual field that is constantly evolving due to technological advances. Technology has significantly improved almost all aspects of the field over the past 10-15 years. These advances in technology have also played a significant role in the education of radiation science students didactically and clinically. The enormous increase in the capabilities of information technology provides the opportunity for educators to dramatically change their way of teaching.1 mLearning or mobile learning involves the use of mobile devices (i.e. personal digital assistants, smart phones, iPhones, iTouch, iPad, laptops and tablets) to enhance teaching and learning. The most significant advantage of mLearning is the mobility of the technology which allows for unlimited, immediate and continuous access to course materials. The goal of this initial research is to discuss the implementation of mobile learning, specifically through the use of the Apple iTouch, into the education of radiation science students

Toward a sustainable and resilient future

This chapter focuses on the implications of changing climate extremes for development, and considers how disaster risk management and climate change adaptation together can contribute to a sustainable and resilient future. Changes in the frequency, timing, magnitude, and characteristics of extreme events pose challenges to the goals of reducing disaster risk and vulnerability, both in the present and in the future. Enhancing the capacity of social-ecological systems to cope with, adapt to, and shape change is central to building sustainable and resilient development pathways in the face of climate change. The concept for social-ecological systems recognizes the interdependence of social and ecological factors in the generation and management of risk, as well as in the pursuit of sustainable development. Despite 20 years on the policy agenda, sustainable development remains contested and elusive. However, within the context of climate change, it is becoming increasingly clear that the sustainability of humans on the Earth is closely linked to resilient social-ecological systems, which is influenced by social institutions, human agency, and human capabilities

The Sunyaev-Zel'dovich Infrared Experiment: A Millimeter-wave Receiver for Cluster Cosmology

Measurements of the Sunyaev-Zel'dovich (S-Z) effect towards distant clusters of galaxies can be used to determine the Hubble constant and the radial component of cluster peculiar velocities. Determination of the cluster peculiar velocity requires the separation of the two components of the S-Z effect, which are due to the thermal and bulk velocities of the intracluster plasma. The two components can be separated practically only at millimeter (mm) wavelengths. Measurements of the S-Z effect at mm wavelengths are subject to minimal astrophysical confusion and, therefore, provide an important test of results obtained at longer wavelengths. We describe the instrument used to make the first significant detections of the S-Z effect at millimeter wavelengths. This instrument employs new filter, detector, and readout technologies to produce sensitive measurements of differential sky brightness stable on long time scales. These advances allow drift scan observations which achieve high sensitivity while minimizing common sources of systematic error.Comment: 19 pages, 15 postscript figures, LaTeX(aaspptwo.sty), ApJ(in press

Shape-based peak identification for ChIP-Seq

We present a new algorithm for the identification of bound regions from ChIP-seq experiments. Our method for identifying statistically significant peaks from read coverage is inspired by the notion of persistence in topological data analysis and provides a non-parametric approach that is robust to noise in experiments. Specifically, our method reduces the peak calling problem to the study of tree-based statistics derived from the data. We demonstrate the accuracy of our method on existing datasets, and we show that it can discover previously missed regions and can more clearly discriminate between multiple binding events. The software T-PIC (Tree shape Peak Identification for ChIP-Seq) is available at http://math.berkeley.edu/~vhower/tpic.htmlComment: 12 pages, 6 figure

A new approach to construct pathway connected networks and its application in dose responsive gene expression profiles of rat liver regulated by 2,4DNT

<p>Abstract</p> <p>Background</p> <p>Military and industrial activities have lead to reported release of 2,4-dinitrotoluene (2,4DNT) into soil, groundwater or surface water. It has been reported that 2,4DNT can induce toxic effects on humans and other organisms. However the mechanism of 2,4DNT induced toxicity is still unclear. Although a series of methods for gene network construction have been developed, few instances of applying such technology to generate pathway connected networks have been reported.</p> <p>Results</p> <p>Microarray analyses were conducted using liver tissue of rats collected 24h after exposure to a single oral gavage with one of five concentrations of 2,4DNT. We observed a strong dose response of differentially expressed genes after 2,4DNT treatment. The most affected pathways included: long term depression, breast cancer regulation by stathmin1, WNT Signaling; and PI3K signaling pathways. In addition, we propose a new approach to construct pathway connected networks regulated by 2,4DNT. We also observed clear dose response pathway networks regulated by 2,4DNT.</p> <p>Conclusions</p> <p>We developed a new method for constructing pathway connected networks. This new method was successfully applied to microarray data from liver tissue of 2,4DNT exposed animals and resulted in the identification of unique dose responsive biomarkers in regards to affected pathways.</p

Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh

Microbial metabolism is the engine that drives global biogeochemical cycles, yet many key transformations are carried out by microbial consortia over short spatiotemporal scales that elude detection by traditional analytical approaches. We investigate syntrophic sulfur cycling in the ‘pink berry’ consortia of the Sippewissett Salt Marsh through an integrative study at the microbial scale. The pink berries are macroscopic, photosynthetic microbial aggregates composed primarily of two closely associated species: sulfide-oxidizing purple sulfur bacteria (PB-PSB1) and sulfate-reducing bacteria (PB-SRB1). Using metagenomic sequencing and 34S-enriched sulfate stable isotope probing coupled with nanoSIMS, we demonstrate interspecies transfer of reduced sulfur metabolites from PB-SRB1 to PB-PSB1. The pink berries catalyse net sulfide oxidation and maintain internal sulfide concentrations of 0–500 μm. Sulfide within the berries, captured on silver wires and analysed using secondary ion mass spectrometer, increased in abundance towards the berry interior, while δ34S-sulfide decreased from 6‰ to −31‰ from the exterior to interior of the berry. These values correspond to sulfate–sulfide isotopic fractionations (15–53‰) consistent with either sulfate reduction or a mixture of reductive and oxidative metabolisms. Together this combined metagenomic and high-resolution isotopic analysis demonstrates active sulfur cycling at the microscale within well-structured macroscopic consortia consisting of sulfide-oxidizing anoxygenic phototrophs and sulfate-reducing bacteria