Microheated substrates for patterning cells and controlling development

Here, we seek to control cellular development by devising a means through which cells can be subjected to a microheated environment in standard culture conditions. Numerous techniques have been devised for controlling cellular function and development via manipulation of surface environmental cues at the micro- and nanoscale. It is well understood that temperature plays a significant role in the rate of cellular activities, migratory behavior (thermotaxis), and in some cases, protein expression. Yet, the effects and possible utilization of micrometer-scale temperature fields in cell cultures have not been explored. Toward this end, two types of thermally isolated microheated substrates were designed and fabricated, one with standard backside etching beneath a dielectric film and another with a combination of surface and bulk micromachining and backside etching. The substrates were characterized with infrared microscopy, finite element modeling, scanning electron microscopy, stylus profilometry, and electrothermal calibrations. Neuron culture studies were conducted on these substrates to 1) examine the feasibility of using a microheated environment to achieve patterned cell growth and 2) selectively accelerate neural development on regions less than 100$mu m$wide. Results show that attached neurons, grown on microheated regions set at 37$~^circ C$, extended processes substantially faster than those incubated at 25$~^circ C$on the same substrate. Further, unattached neurons were positioned precisely along the length of the heater filament (operating at 45$~^circ C$) using free convection currents. These preliminary findings indicate that microheated substrates may be used to direct cellular development spatially in a practical manner.$hfillhbox[1414]

Linking activity and function to ecosystem dynamics in a coastal bacterioplankton community

For bacterial communities containing hundreds to thousands of distinct populations, connecting functional processes and environmental dynamics at high taxonomic resolution has remained challenging. Here we use the expression of ribosomal proteins (%RP) as a proxy for in situ activity of 200 taxa within 20 metatranscriptomic samples in a coastal ocean time series encompassing both seasonal variability and diel dynamics. %RP patterns grouped the taxa into seven activity clusters with distinct profiles in functional gene expression and correlations with environmental gradients. Clusters 1-3 had their highest potential activity in the winter and fall, and included some of the most active taxa, while Clusters 4-7 had their highest potential activity in the spring and summer. Cluster 1 taxa were characterized by gene expression for motility and complex carbohydrate degradation (dominated by Gammaproteobacteria and Bacteroidetes), and Cluster 2 taxa by transcription of genes for amino acid and aromatic compound metabolism and aerobic anoxygenic phototrophy (Roseobacter). Other activity clusters were enriched in transcripts for proteorhodopsin and methylotrophy (Cluster 4; SAR11 and methylotrophs), photosynthesis and attachment (Clusters 5 and 7; Synechococcus, picoeukaryotes, Verucomicrobia, and Planctomycetes), and sulfur oxidation (Cluster 7; Gammaproteobacteria). The seasonal patterns in activity were overlain, and sometimes obscured, by large differences in %RP over shorter day-night timescales. Seventy-eight taxa, many of them heterotrophs, had a higher %RP activity index during the day than night, indicating a strong diel activity rhythm at this coastal site. Emerging from these taxonomically-and time-resolved estimates of in situ microbial activity are predictions of specific ecological groupings of microbial taxa in a dynamic coastal environment

A panoramic mid-infrared survey of two distant clusters

We present panoramic Spitzer MIPS 24 μm observations, covering ~9 × 9 Mpc2 (25' × 25') fields around two massive clusters, Cl 0024+16 and MS 0451-03, at z = 0.39 and z = 0.55, respectively, reaching a 5 σ flux limit of ~200 μJy. Our observations cover a very wide range of environments within these clusters, from high-density regions around the cores out to the turnaround radius. Cross-correlating the mid-infrared catalogs with deep optical and near-infrared imaging of these fields, we investigate the optical/near-infrared colors of the mid-infrared sources. We find excesses of mid-infrared sources with the optical/near-infrared colors expected of cluster members in the two clusters and test this selection using spectroscopically confirmed 24 μm members. The much more significant excess is associated with Cl 0024+16, whereas MS 0451-03 has comparatively few mid-infrared sources. The mid-infrared galaxy population in Cl 0024+16 appears to be associated with dusty star-forming galaxies (typically redder than the general cluster population by up to AV ~ 1-2 mag) rather than emission from dusty tori around active galactic nuclei in early-type hosts. We compare the star formation rates derived from the total infrared (8-1000 μm) luminosities for the mid-infrared sources in Cl 0024+16 with those estimated from a published Hα survey, finding rates 5 times those found from Hα, indicating significant obscured activity in the cluster population. Compared to previous mid-infrared surveys of clusters from z ~ 0-0.5, we find evidence for strong evolution of the level of dust-obscured star formation in dense environments to z = 0.5, analogous to the rise in the fraction of optically selected star-forming galaxies seen in clusters and the field out to similar redshifts. However, there are clearly significant cluster-to-cluster variations in the populations of mid-infrared sources, probably reflecting differences in the intracluster media and recent dynamical evolution of these systems

Bacterial dimethylsulfoniopropionate degradation genes in the oligotrophic North Pacific subtropical gyre

Dimethylsulfoniopropionate (DMSP) is an organic sulfur compound that is rapidly metabolized by marine bacteria either by cleavage to dimethylsulfide (DMS) or demethylation to 3-methiolpropionate. The abundance and diversity of genes encoding bacterial DMS production (dddP) and demethylation (dmdA) were measured in the North Pacific subtropical gyre (NPSG) between May 2008 and February 2009 at Station ALOHA (22°45=N, 158°00=W) at two depths: 25mand the deep chlorophyll maximum (DCM;~100 m). The highest abundance of dmdA genes was in May 2008 at 25 m, with~16.5% of cells harboring a gene in one of the eight subclades surveyed, while the highest abundance of dddP genes was in July 2008 at 25 m, with~2% of cells harboring a gene. The dmdA gene pool was consistently dominated by homologs from SAR11 subclades, which was supported by findings in metagenomic data sets derived from Station ALOHA. Expression of the SAR11 dmdA genes was low, with typical transcript:gene ratios between 1:350 and 1:1,400. The abundance of DMSP genes was statistically different between 25mand the DCM and correlated with a number of environmental variables, including primary production, photosynthetically active radiation, particulate DMSP, and DMS concentrations. At 25 m, dddP abundance was positively correlated with pigments that are diagnostic of diatoms; at the DCM, dmdA abundance was positively correlated with temperature. Based on gene abundance, we hypothesize that SAR11 bacterioplankton dominate DMSP cycling in the oligotrophic NPSG, with lesser but consistent involvement of other members of the bacterioplankton community

Coastal ocean metagenomes and curated metagenome-assembled genomes from Marsh Landing, Sapelo Island (Georgia, USA)

Microbes play a dominant role in the biogeochemistry of coastal waters, which receive organic matter from diverse sources. We present metagenomes and 45 metagenome-assembled genomes (MAGs) from Sapelo Island, Georgia, to further understand coastal microbial populations. Notably, four MAGs are archaea, with two Thaumarchaeota and two marine group II Euryarchaeota

Microbially-mediated transformations of estuarine dissolved organic matter

Microbially-mediated transformations of dissolved organic matter (DOM) in a marsh-dominated estuarine system were investigated at the molecular level using ultrahigh resolution mass spectrometry. In addition to observing spatial and temporal variability in DOM sources in the estuary, multiple incubations with endogenous microorganisms identified the influence of DOM composition on biodegradation. A clear microbial preference for degradation of compounds associated with marine DOM relative to those of terrestrial origin was observed, resulting in an overall shift of the remaining DOM toward a stronger terrigenous signature. During short, 1-day long incubations of samples rich in marine DOM, the molecular formulae that were enriched had slightly smaller mass (20-30 Da) and number of carbon atoms compared to the molecular formulae that were depleted. Over longer time scales (70 days), the mean differences in molecular mass between formulae that were depleted and enriched were substantially larger (~270 Da). The differences in elemental composition over daily time scales were consistent with transformations in functional groups; over longer time scales, the differences in elemental composition may be related to progressive transformations of functional groups of intermediate products and/or other reactions. Our results infused new data toward the understanding of DOM processing by bacterioplankton in estuarine systems

Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community

Aquatic environments contain large communities of microorganisms whose synergistic interactions mediate the cycling of major and trace nutrients, including vitamins. B-vitamins are essential coenzymes that many organisms cannot synthesize. Thus, their exchange among de novo synthesizers and auxotrophs is expected to play an important role in the microbial consortia and explain some of the temporal and spatial changes observed in diversity. In this study, we analyzed metatranscriptomes of a natural marine microbial community, diel sampled quarterly over one year to try to identify the potential major B-vitamin synthesizers and consumers. Transcriptomic data showed that the best-represented taxa dominated the expression of synthesis genes for some B-vitamins but lacked transcripts for others. For instance, Rhodobacterales dominated the expression of vitamin-B12 synthesis, but not of vitamin-B7, whose synthesis transcripts were mainly represented by Flavobacteria. In contrast, bacterial groups that constituted less than 4% of the community (e.g., Verrucomicrobia) accounted for most of the vitamin-B1 synthesis transcripts. Furthermore, ambient vitamin-B1 concentrations were higher in samples collected during the day, and were positively correlated with chlorophyll-a concentrations. Our analysis supports the hypothesis that the mosaic of metabolic interdependencies through B-vitamin synthesis and exchange are key processes that contribute to shaping microbial communities in nature

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

X-ray Survey Results on Active Galaxy Physics and Evolution

This "pedagogical" review describes the key Chandra and XMM-Newton extragalactic surveys to date and details some of their implications for AGN physics and evolution. We additionally highlight two topics of current widespread interest: (1) X-ray constraints on the AGN content of luminous submillimeter galaxies, and (2) the demography and physics of high-redshift (z > 4) AGN as revealed by X-ray observations. Finally, we discuss prospects for future X-ray surveys with Chandra, XMM-Newton, and upcoming missions.Comment: 26 pages, in Physics of Active Galactic Nuclei at All Scales, eds. Alloin D., Johnson R., Lira P. (Springer-Verlag, Berlin), version with all figures at http://www.astro.psu.edu/users/niel/papers/papers.htm

Preface paper to the Semi-Arid Land-Surface-Atmosphere (SALSA) Program special issue

The Semi-Arid Land-Surface-Atmosphere Program (SALSA) is a multi-agency, multi-national research effort that seeks to evaluate the consequences of natural and human-induced environmental change in semi-arid regions. The ultimate goal of SALSA is to advance scientific understanding of the semi-arid portion of the hydrosphere–biosphere interface in order to provide reliable information for environmental decision making. SALSA approaches this goal through a program of long-term, integrated observations, process research, modeling, assessment, and information management that is sustained by cooperation among scientists and information users. In this preface to the SALSA special issue, general program background information and the critical nature of semi-arid regions is presented. A brief description of the Upper San Pedro River Basin, the initial location for focused SALSA research follows. Several overarching research objectives under which much of the interdisciplinary research contained in the special issue was undertaken are discussed. Principal methods, primary research sites and data collection used by numerous investigators during 1997–1999 are then presented. Scientists from about 20 US, five European (four French and one Dutch), and three Mexican agencies and institutions have collaborated closely to make the research leading to this special issue a reality. The SALSA Program has served as a model of interagency cooperation by breaking new ground in the approach to large scale interdisciplinary science with relatively limited resources