Horizontally acquired glycosyltransferase operons drive salmonellae lipopolysaccharide diversity.

The immunodominant lipopolysaccharide is a key antigenic factor for Gram-negative pathogens such as salmonellae where it plays key roles in host adaptation, virulence, immune evasion, and persistence. Variation in the lipopolysaccharide is also the major differentiating factor that is used to classify Salmonella into over 2600 serovars as part of the Kaufmann-White scheme. While lipopolysaccharide diversity is generally associated with sequence variation in the lipopolysaccharide biosynthesis operon, extraneous genetic factors such as those encoded by the glucosyltransferase (gtr) operons provide further structural heterogeneity by adding additional sugars onto the O-antigen component of the lipopolysaccharide. Here we identify and examine the O-antigen modifying glucosyltransferase genes from the genomes of Salmonella enterica and Salmonella bongori serovars. We show that Salmonella generally carries between 1 and 4 gtr operons that we have classified into 10 families on the basis of gtrC sequence with apparent O-antigen modification detected for five of these families. The gtr operons localize to bacteriophage-associated genomic regions and exhibit a dynamic evolutionary history driven by recombination and gene shuffling events leading to new gene combinations. Furthermore, evidence of Dam- and OxyR-dependent phase variation of gtr gene expression was identified within eight gtr families. Thus, as O-antigen modification generates significant intra- and inter-strain phenotypic diversity, gtr-mediated modification is fundamental in assessing Salmonella strain variability. This will inform appropriate vaccine and diagnostic approaches, in addition to contributing to our understanding of host-pathogen interactions

GLORIA - A globally representative hyperspectral in situ dataset for optical sensing of water quality

The development of algorithms for remote sensing of water quality (RSWQ) requires a large amount of in situ data to account for the bio-geo-optical diversity of inland and coastal waters. The GLObal Reflectance community dataset for Imaging and optical sensing of Aquatic environments (GLORIA) includes 7,572 curated hyperspectral remote sensing reflectance measurements at 1 nm intervals within the 350 to 900 nm wavelength range. In addition, at least one co-located water quality measurement of chlorophyll a, total suspended solids, absorption by dissolved substances, and Secchi depth, is provided. The data were contributed by researchers affiliated with 59 institutions worldwide and come from 450 different water bodies, making GLORIA the de-facto state of knowledge of in situ coastal and inland aquatic optical diversity. Each measurement is documented with comprehensive methodological details, allowing users to evaluate fitness-for-purpose, and providing a reference for practitioners planning similar measurements. We provide open and free access to this dataset with the goal of enabling scientific and technological advancement towards operational regional and global RSWQ monitoring

IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes.

GWAS have identified >200 risk loci for Inflammatory Bowel Disease (IBD). The majority of disease associations are known to be driven by regulatory variants. To identify the putative causative genes that are perturbed by these variants, we generate a large transcriptome data set (nine disease-relevant cell types) and identify 23,650 cis-eQTL. We show that these are determined by ∼9720 regulatory modules, of which ∼3000 operate in multiple tissues and ∼970 on multiple genes. We identify regulatory modules that drive the disease association for 63 of the 200 risk loci, and show that these are enriched in multigenic modules. Based on these analyses, we resequence 45 of the corresponding 100 candidate genes in 6600 Crohn disease (CD) cases and 5500 controls, and show with burden tests that they include likely causative genes. Our analyses indicate that ≥10-fold larger sample sizes will be required to demonstrate the causality of individual genes using this approach

A safe-at-home benzoin condensation from imitation almond extract

COVID-19 remote learning forced instructors to scramble for meaningful organic laboratory experiences safe enough to perform at home. While resources are available for laboratory experiments at home, organic synthesis suffers from issues involving safety, availabilities of reagents, difficulties measuring reagents, and difficulties analyzing products. We report a new take on the classic benzoin condensation using safe and commonly available reagents, capable of being setup with commonly available kitchen materials, and displaying visible and distinctive product. This experiment is aimed at reinforcing concepts of carbonyl chemistry in the undergraduate organic chemistry laboratory

Mapping harmful algae blooms (HABs) in the Great Lakes using MODIS and MERIS satellite data

Harmful Algal Blooms (HABs) in the Great Lakes are becoming increasingly problematic as these events are happening more often, in more areas, and lasting longer. Satellite remote sensing can be effectively used to map and monitor HAB events in the Great Lakes to help resource managers and decision makers address the problem. A satellite based HAB mapping algorithm has been developed and tested in the Western basin of Lake Erie where severe HAB events have regularly occurred. The algorithm has been developed from in situ spectral reflectance measurements and coincident concentration samples and has been applied to both MODIS and MERIS satellite imagery. The algorithm also utilizes ancillary data to help differentiate harmful from non- harmful algal blooms that can occur simultaneously. Also examined is the utility of hyperspectral (HICO) satellite imagery from the Space Station for mapping HABs and a comparison to ship based hyperspectral radiometric measurements was made. Extent and duration were derived for a time series of satellite images during the 2011 summer HAB event in Lake Erie. Also presented is a comparison of Cyanobacteria shipborne in situ spectral profiles and measured concentrations collected during the Lake Erie summer field season

New Insights into the Controls and Mechanisms of Plankton Productivity Along the US West Coast

During the lifetime of the National Science Foundation\u27s Coastal Ocean Processes program, four experiments were conducted on the US West Coast in the northern California Current System. Although each project had a unique scientific focus, all four addressed the mechanisms causing eastern boundary current systems in general, and the California Current System in particular, to be biologically rich, from phytoplankton to apex predators. Taken together, findings from these projects provide new insights into the canonical view that upwelling systems are simple wind-driven conveyor belts, bringing cold, nutrient-rich waters to the well-lit surface ocean where biological organisms flourish. We highlight new insights and advances gained from these programs, including recognition that (a) elements other than nitrogen, particularly iron, may limit the base of the food chain, and (b) the source of these nutrients is not solely a result of wind-driven Ekman transport. The importance of retentive features has clearly emerged, whether these are associated with topography, bathymetry, or more transient features such as river plumes. These new insights into the drivers and fate of this high biological productivity should greatly improve current and future generations of ecosystem models and provide a better understanding of the unique physical-biological coupling that makes the California Current System so rich

A satellite algorithm for river plume mapping within the Great Lakes basin

A robust river sediment plume algorithm that utilizes color satellite data has been developed for the Great Lakes. The algorithm, which utilizes any ocean color satellite that has a blue, red, green and NIR band such as MODIS and the recently launched NASA NPP VIIRS satellite sensor, first generates a Total Suspended Sediment Index (TSSIGL) that is used to map the extent of the plume. The TSSIGL represents the total suspended solids (TSS) which includes both the organic and inorganic constituents of the plume. The Normalized Difference Vegetative Difference (NDVI) is calculated to generate a representation of the organic dominated concentration at the water surface. The highest TSSIGL values indicate heavy suspended sediment concentration (SSC or total suspended mineral). By comparing the TSSIGL output to the NDVI result, the composition of the plume can be ascertained (sediment dominated versus organic material). The relative concentration of the plume is obtained by examination of the index values. Given the area of the plume and its relative concentration, along with bathymetry, an estimate of the sediment load within the plume can be made. This new approach to mapping plumes in the Great Lakes is applicable to plumes in river mouths, embayment areas, and hydrodynamically complex basins such as Western Lake Erie