Isolation and Characterization of Bacteria That Degrade Phosphonates in Marine Dissolved Organic Matter

Semi-labile dissolved organic matter (DOM) accumulates in surface waters of the oligotrophic ocean gyres and turns over on seasonal to annual timescales. This reservoir of DOM represents an important source of carbon, energy, and nutrients to marine microbial communities but the identity of the microorganisms and the biochemical pathways underlying the cycling of DOM remain largely uncharacterized. In this study we describe bacteria isolated from the North Pacific Subtropical Gyre (NPSG) near Hawaii that are able to degrade phosphonates associated with high molecular weight dissolved organic matter (HMWDOM), which represents a large fraction of semi-labile DOM. We amended dilution-to-extinction cultures with HMWDOM collected from NPSG surface waters and with purified HMWDOM enriched with polysaccharides bearing alkylphosphonate esters. The HMWDOM-amended cultures were enriched in Roseobacter isolates closely related to Sulfitobacter and close relatives of hydrocarbon-degrading bacteria of the Oceanospirillaceae family, many of which encoded phosphonate degradation pathways. Sulfitobacter cultures encoding C-P lyase were able to catabolize methylphosphonate and 2-hydroxyethylphosphonate, as well as the esters of these phosphonates found in native HMWDOM polysaccharides to acquire phosphorus while producing methane and ethylene, respectively. Conversely, growth of these isolates on HMWDOM polysaccharides as carbon source did not support robust increases in cell yields, suggesting that the constituent carbohydrates in HMWDOM were not readily available to these individual isolates. We postulate that the complete remineralization of HMWDOM polysaccharides requires more complex microbial inter-species interactions. The degradation of phosphonate esters and other common substitutions in marine polysaccharides may be key steps in the turnover of marine DOM.Gordon and Betty Moore Foundation (Award GBMF3298)Simons Foundation (Grant 329108

The Biogeography of Putative Microbial Antibiotic Production

Understanding patterns in the distribution and abundance of functional traits across a landscape is of fundamental importance to ecology. Mapping these distributions is particularly challenging for species-rich groups with sparse trait measurement coverage, such as flowering plants, insects, and microorganisms. Here, we use likelihood-based character reconstruction to infer and analyze the spatial distribution of unmeasured traits. We apply this framework to a microbial dataset comprised of 11,732 ketosynthase alpha gene sequences extracted from 144 soil samples from three continents to document the spatial distribution of putative microbial polyketide antibiotic production. Antibiotic production is a key competitive strategy for soil microbial survival and performance. Additionally, novel antibiotic discovery is highly relevant to human health, making natural antibiotic production by soil microorganisms a major target for bioprospecting. Our comparison of trait-based biogeographical patterns to patterns based on taxonomy and phylogeny is relevant to our basic understanding of microbial biogeography as well as the pressing need for new antibiotics

Distinct dissolved organic matter sources induce rapid transcriptional responses in coexisting populations of Prochlorococcus, Pelagibacter and the OM60 clade

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Environmental Microbiology 16 (2014): 2815-2830, doi:10.1111/1462-2920.12254.A considerable fraction of the Earth's organic carbon exists in dissolved form in seawater. To investigate the roles of planktonic marine microbes in the biogeochemical cycling of this dissolved organic matter (DOM), we performed controlled seawater incubation experiments and followed the responses of an oligotrophic surface water microbial assemblage to perturbations with DOM derived from an axenic culture of Prochlorococcus, or high-molecular weight DOM concentrated from nearby surface waters. The rapid transcriptional responses of both Prochlorococcus and Pelagibacter populations suggested the utilization of organic nitrogen compounds common to both DOM treatments. Along with these responses, both populations demonstrated decreases in gene transcripts associated with nitrogen stress, including those involved in ammonium acquisition. In contrast, responses from low abundance organisms of the NOR5/OM60 gammaproteobacteria were observed later in the experiment, and included elevated levels of gene transcripts associated with polysaccharide uptake and oxidation. In total, these results suggest that numerically dominant oligotrophic microbes rapidly acquire nitrogen from commonly available organic sources, and also point to an important role for carbohydrates found within the DOM pool for sustaining the less abundant microorganisms in these oligotrophic systems.This work was supported by a National Science Foundation Science and Technology Center Award EF0424599 (E.F.D and D.M.K.), grants to D.M.K., D.J.R and E.F.D from the Gordon and Betty Moore Foundation, a gift from the Agouron Institute (to E.F.D.) and a fellowship (202180) to A.K.S. from the Canadian Institutes of Health Research (CIHR)

Neutral Gas Distribution and Kinematics of the Nearly Face-on Spiral Galaxy NGC 1232

We have analyzed high velocity resolution HI synthesis observations of the nearly face-on Sc galaxy NGC 1232. The neutral gas distribution extends well beyond the optical extent of the galaxy. As expected, local peaks in the HI column density are associated with the spiral arms. Further, the HI column density drops precipitously near the center of the galaxy. Closed contours in the velocity field suggest either that the system is warped, or that the rotation curve declines. The velocity dispersion is approximately constant throughout the system, with a median value of 9.9 +/- 1.8 km/s. When corrected for rotational broadening, there is no indication of a radial trend in the neutral gas velocity dispersion in this galaxy.Comment: 14 pages of text, 10 pages of figures. Accepted to the A

The SAMI Galaxy Survey: Shocks and Outflows in a normal star-forming galaxy

We demonstrate the feasibility and potential of using large integral field spectroscopic surveys to investigate the prevalence of galactic-scale outflows in the local Universe. Using integral field data from SAMI and the Wide Field Spectrograph, we study the nature of an isolated disk galaxy, SDSS J090005.05+000446.7 (z = 0.05386). In the integral field datasets, the galaxy presents skewed line profiles changing with position in the galaxy. The skewed line profiles are caused by different kinematic components overlapping in the line-of-sight direction. We perform spectral decomposition to separate the line profiles in each spatial pixel as combinations of (1) a narrow kinematic component consistent with HII regions, (2) a broad kinematic component consistent with shock excitation, and (3) an intermediate component consistent with shock excitation and photoionisation mixing. The three kinematic components have distinctly different velocity fields, velocity dispersions, line ratios, and electron densities. We model the line ratios, velocity dispersions, and electron densities with our MAPPINGS IV shock and photoionisation models, and we reach remarkable agreement between the data and the models. The models demonstrate that the different emission line properties are caused by major galactic outflows that introduce shock excitation in addition to photoionisation by star-forming activities. Interstellar shocks embedded in the outflows shock-excite and compress the gas, causing the elevated line ratios, velocity dispersions, and electron densities observed in the broad kinematic component. We argue from energy considerations that, with the lack of a powerful active galactic nucleus, the outflows are likely to be driven by starburst activities. Our results set a benchmark of the type of analysis that can be achieved by the SAMI Galaxy Survey on large numbers of galaxies.Comment: 17 pages, 15 figures. Accepted to MNRAS. References update

Characterization of BRD4 during mammalian post-meiotic sperm development

During spermiogenesis, the post-meiotic phase of mammalian spermatogenesis, transcription is progressively repressed as nuclei of haploid spermatids are compacted through a dramatic chromatin reorganization involving hyper-acetylation and replacement of most histones with protamines. Although BRDT functions in transcription and histone removal in spermatids, it is unknown whether other BET family proteins play a role. Immunofluorescence of spermatogenic cells revealed BRD4 in a ring around the nuclei of spermatids containing hyper-acetylated histones. The ring lies directly adjacent to the acroplaxome, the cytoskeletal base of the acrosome, previously linked to chromatin reorganization. The BRD4 ring does not form in acrosomal mutant mice. ChIP sequencing in spermatids revealed enrichment of BRD4 and acetylated histones at the promoters of active genes. BRD4 and BRDT show distinct and synergistic binding patterns, with a pronounced enrichment of BRD4 at spermatogenesis-specific genes. Direct association of BRD4 with acetylated H4 decreases in late spermatids as acetylated histones are removed from the condensing nucleus in a wave following the progressing acrosome. These data provide evidence for a prominent transcriptional role of BRD4 and suggest a possible removal mechanism for chromatin components from the genome via the progressing acrosome as transcription is repressed in response to chromatin condensation during spermiogenesis

Sustainable drainage systems: Helping people live with water

Sustainable drainage systems or ‘Suds’ are increasingly accepted as an effective means of ‘making space for water’, adapting to possible climate change and helping communities become more flood and drought resilient. This study explores potential shifts in perception and attitude through Suds installation, development and habituation. Attitudes and awareness in communities in the USA and UK, where Suds have been in place for some time, were compared and contrasted, examining any evolution of beliefs and practices and wider community resilience. The principal finding was that there existed a lack of understanding about the existence and function of Suds. The paper concludes that consultation regarding solutions during Suds planning and installation, and ongoing dialogue afterwards, could usefully be explored as a means to improve local awareness of and satisfaction with Suds and promote greater understanding of their function. This may in turn encourage behaviour change to improve longer-term functionality of Suds and increase community resilience to flooding and drought

GNOSIS: The first instrument to use fiber bragg gratings for OH suppression

The near-infrared is an important part of the spectrum in astronomy, especially in cosmology because the light from objects in the early universe is redshifted to these wavelengths. However, deep near-infrared observations are extremely difficult to makeThe GNOSIS team acknowledges funding by ARC LIEF grant LE100100164. C.Q.T. gratefully acknowledges support by the National Science Foundation Graduate Research Fellowship under grant No. DGE-1035963

International meta-analysis of PTSD genome-wide association studies identifies sex- and ancestry-specific genetic risk loci.

The risk of posttraumatic stress disorder (PTSD) following trauma is heritable, but robust common variants have yet to be identified. In a multi-ethnic cohort including over 30,000 PTSD cases and 170,000 controls we conduct a genome-wide association study of PTSD. We demonstrate SNP-based heritability estimates of 5-20%, varying by sex. Three genome-wide significant loci are identified, 2 in European and 1 in African-ancestry analyses. Analyses stratified by sex implicate 3 additional loci in men. Along with other novel genes and non-coding RNAs, a Parkinson's disease gene involved in dopamine regulation, PARK2, is associated with PTSD. Finally, we demonstrate that polygenic risk for PTSD is significantly predictive of re-experiencing symptoms in the Million Veteran Program dataset, although specific loci did not replicate. These results demonstrate the role of genetic variation in the biology of risk for PTSD and highlight the necessity of conducting sex-stratified analyses and expanding GWAS beyond European ancestry populations

Specialty Care Use in US Patients with Chronic Diseases

Despite efforts to eliminate health disparities, racial, ethnic, and geographic groups continue lag behind their counterparts in health outcomes in the United States. The purpose of this study is to determine variation in specialty care utilization by chronic disease status. Data were extracted from the Commonwealth Fund 2006 Health Care Quality Survey (n = 2475). A stratified minority sample design was employed to ensure a representative sample. Logistic regression was used in analyses to predict specialty care utilization in the sample. Poor perceived health, minority status, and lack of insurance was associated with reduced specialty care use and chronic disease diagnosis