San Diego State University

About: San Diego State University is a education organization based out in San Diego, California, United States. It is known for research contribution in the topics: Population & Poison control. The organization has 12418 authors who have published 27950 publications receiving 1192375 citations. The organization is also known as: SDSU & San Diego State College.

Predictive vegetation mapping: geographic modelling of biospatial patterns in relation to environmental gradients:

Abstract: Predictive vegetation mapping can be defined as predicting the geographic distribution of the vegetation composition across a landscape from mapped environmental variables. Comput erized predictive vegetation mapping is made possible by the availability of digital maps of topography and other environmental variables such as soils, geology and climate variables, and geographic information system software for manipulating these data. Especially important to predictive vegetation mapping are interpolated climatic variables related to physiological tolerances, and topographic variables, derived from digital elevation grids, related to site energy and moisture balance. Predictive vegetation mapping is founded in ecological niche theory and gradient analysis, and driven by the need to map vegetation patterns over large areas for resource conservation planning, and to predict the effects of environmental change on vegetation distributions. Predictive vegetation mapping has advanced over the past two decades espe...

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

Abstract: Microbial communities carry out the majority of the biochemical activity on the planet, and they play integral roles in processes including metabolism and immune homeostasis in the human microbiome. Shotgun sequencing of such communities' metagenomes provides information complementary to organismal abundances from taxonomic markers, but the resulting data typically comprise short reads from hundreds of different organisms and are at best challenging to assemble comparably to single-organism genomes. Here, we describe an alternative approach to infer the functional and metabolic potential of a microbial community metagenome. We determined the gene families and pathways present or absent within a community, as well as their relative abundances, directly from short sequence reads. We validated this methodology using a collection of synthetic metagenomes, recovering the presence and abundance both of large pathways and of small functional modules with high accuracy. We subsequently applied this method, HUMAnN, to the microbial communities of 649 metagenomes drawn from seven primary body sites on 102 individuals as part of the Human Microbiome Project (HMP). This provided a means to compare functional diversity and organismal ecology in the human microbiome, and we determined a core of 24 ubiquitously present modules. Core pathways were often implemented by different enzyme families within different body sites, and 168 functional modules and 196 metabolic pathways varied in metagenomic abundance specifically to one or more niches within the microbiome. These included glycosaminoglycan degradation in the gut, as well as phosphate and amino acid transport linked to host phenotype (vaginal pH) in the posterior fornix. An implementation of our methodology is available at http://huttenhower.sph.harvard.edu/humann. This provides a means to accurately and efficiently characterize microbial metabolic pathways and functional modules directly from high-throughput sequencing reads, enabling the determination of community roles in the HMP cohort and in future metagenomic studies.

Catalytic Decomposition of Hydrogen Peroxide on Iron Oxide: Kinetics, Mechanism, and Implications

Abstract: This research describes the heterogeneous catalytic reactions of H2O2 with granular size goethite (α-FeOOH) particles in aqueous solution under various experimental conditions. This is an important reaction for the environment since both H2O2 and iron oxides are common constituents of natural and atmospheric waters. Furthermore, iron oxides function as catalysts in chemical oxidation processes used for treatment of contaminated waters with H2O2. The results of this study demonstrated that the decomposition rate of H2O2 over goethite surface can be described by the second-order kinetic expression −d[H2O2]/dt = k[FeOOH][H2O2], where k = 0.031 M-1 s-1, at pH 7 in the absence of any inorganic or organic chemical species. The apparent reaction rate was dominated by the intrinsic reaction rates on the oxide surfaces rather than the mass transfer rate of H2O2 to the surface. The activation energy of the reaction of H2O2 with the iron oxide surface was determined to be 32.8 kJ/M. The reaction mechanism for the de...

The marine viromes of four oceanic regions

Abstract: Viruses are the most common biological entities in the marine environment. There has not been a global survey of these viruses, and consequently, it is not known what types of viruses are in Earth's oceans or how they are distributed. Metagenomic analyses of 184 viral assemblages collected over a decade and representing 68 sites in four major oceanic regions showed that most of the viral sequences were not similar to those in the current databases. There was a distinct “marine-ness” quality to the viral assemblages. Global diversity was very high, presumably several hundred thousand of species, and regional richness varied on a North-South latitudinal gradient. The marine regions had different assemblages of viruses. Cyanophages and a newly discovered clade of single-stranded DNA phages dominated the Sargasso Sea sample, whereas prophage-like sequences were most common in the Arctic. However most viral species were found to be widespread. With a majority of shared species between oceanic regions, most of the differences between viral assemblages seemed to be explained by variation in the occurrence of the most common viral species and not by exclusion of different viral genomes. These results support the idea that viruses are widely dispersed and that local environmental conditions enrich for certain viral types through selective pressure.