Stratigraphy is a fundamental component of floodplain heterogeneity and hydraulic conductivity and connectivity of alluvial aquifers, which affect hydrologic processes such as groundwater flow and hyporheic exchange. Watershed-scale hydrological models commonly simplify the sedimentology and stratigraphy of floodplains, neglecting natural floodplain heterogeneity and anisotropy. This study, conducted in the upper reach of the East River in the East River Basin, Colorado, USA, combines point-, meander-, and floodplain-scale data to determine key features of alluvial aquifers important for estimating hydrologic processes. We compare stratigraphy of two meanders with disparate geometries to explore floodplain heterogeneity and connectivity controls on flow and transport. Meander shape, orientation, and internal stratigraphy affected residence time estimates of laterally exchanged hyporheic water. Although the two meanders share a sediment source, vegetation, and climate, their divergent river migration histories resulted in contrasting meander hydrofacies. In turn, the extent and orientation of these elements controlled the effective hydraulic conductivity and, ultimately, estimates of groundwater transport and hyporheic residence times. Additionally, the meanders’ orientation relative to the valley gradient impacted the hydraulic gradient across the meanders—a key control of groundwater velocity. Lastly, we combine our field data with remotely sensed data and introduce a potential approach to estimate key hydrostratigraphic packages across floodplains. Prospective applications include contaminant transport studies, hyporheic models, and watershed models. © 2019 John Wiley & Sons, Ltd.

Glanders, caused by Burkholderia (B.) mallei is a notifiable zoonotic disease in equidae. For international trade and movement of equids, certificates of negative serological test results for antibodies against B. mallei are required. To date, the complement fixation test (CFT) is the mandatory test to issue these health certificates. The CFT is difficult to standardize and, due to its poor specificity, often leads to false-positive reactions resulting in trade restrictions with considerable financial consequences. In the present study, the new ID Screen Glanders Double Antigen Multispecies ELISA (GLANDA- ELISA) (IDvet, Grabels, France) was evaluated using 400 negative and 370 glanders positive field samples of equidae. The GLANDA-ELISA was significantly more specific (99.8%) than the CFT (97.0%). Considering the comparable sensitivities of CFT (96.5%) and ELISA (98.1%), this new GLANDA-ELISA test appears a suitable confirmatory test and a realistic alternative for serological testing of horses for trade or movement.

Current transcriptome-wide analyses have identified a growing number of regulatory RNA with expression that is characterized in a cell-type-specific manner. Herein, we describe RNA metabolic labeling with improved cell-specificity utilizing the in vivo expression of an optimized uracil phosphoribosyltransferase (UPRT) enzyme. We demonstrate improved selectivity for metabolic incorporation of a modified nucleobase (5-vinyuracil) into nascent RNA, using a battery of tests. The selective incorporation of vinyl-U residues was demonstrated in 3xUPRT LM2 cells through validation with dot blot, qPCR, LC-MS/MS and microscopy analysis. We also report using this approach in a metastatic human breast cancer mouse model for profiling cell-specific nascent RNA.

Tissues and organs are composed of many diverse cell types, making cell-specific gene expression profiling a major challenge. Herein we report that endogenous enzymes, unique to a cell of interest, can be utilized to enable cell-specific metabolic labeling of RNA. We demonstrate that appropriately designed "caged" nucleosides can be rendered active by serving as a substrate for cancer-cell specific enzymes to enable RNA metabolic labeling, only in cancer cells. We envision that the ease and high stringency of our approach will enable expression analysis of tumor cells in complex environments.

Profiling RNA expression in a cell-specific manner continues to be a grand challenge in biochemical research. Bioorthogonal nucleosides can be utilized to track RNA expression; however, these methods currently have limitations due to background and incorporation of analogs into undesired cells. Herein, we design and demonstrate that uracil phosphoribosyltransferase can be engineered to match 5-vinyluracil for cell-specific metabolic labeling of RNA with exceptional specificity and stringency.

Clear cell renal cell carcinoma (CC-RCC) is a devastating disease with limited therapeutic options available for advanced stages. The objective of this study was to investigate HMG-CoA reductase inhibitors, also known as statins, as potential therapeutics for CC-RCC. Importantly, treatment with statins was found to be synthetically lethal with the loss of the von Hippel-Lindau (VHL) tumor suppressor gene, which occurs in 90% of CC-RCC driving the disease. This effect has been confirmed in three different CC-RCC cell lines with three different lipophilic statins. Inhibition of mevalonate synthesis by statins causes a profound cytostatic effect at nanomolar concentrations and becomes cytotoxic at low micromolar concentrations in VHL-deficient CC-RCC. The synthetic lethal effect can be fully rescued by both mevalonate and geranylgeranylpyrophosphate, but not by squalene, indicating that the effect is due to disruption of small GTPase isoprenylation and not the inhibition of cholesterol synthesis. Inhibition of Rho and Rho kinase (ROCK) signaling contributes to the synthetic lethality effect, and overactivation of hypoxia-inducible factor signaling resulting from VHL loss is required. Finally, statin treatment is able to inhibit both tumor initiation and progression of subcutaneous 786-OT1-based CC-RCC tumors in mice. Thus, statins represent potential therapeutics for the treatment of VHL-deficient CC-RCC. Mol Cancer Ther; 17(8); 1781-92. ©2018 AACR.

Chronic HIV infection may exacerbate atherosclerotic vascular disease, which at advanced stages presents as necrotic plaques rich in crystalline cholesterol. Such lesions can catastrophically rupture precipitating myocardial infarct and stroke, now important causes of mortality in those living with HIV. However, in this population little is known about plaque structure relative to crystalline content and its chemical composition. Here, we first interrogated plaque crystal structure and composition in atherosclerotic SIV-infected macaques using non-linear optical microscopy. By stimulated Raman scattering and second harmonic generation approaches both amorphous and crystalline plaque lipid was detected and the crystal spectral profile indicated a cholesterol ester (CE) dominated composition. Versus controls, SIV+ samples had a greater number of cholesterol crystals (CCs), with the difference, in part, accounted for by crystals of a smaller length. Given the ester finding, we profiled HIV+ plaques and also observed a CE crystalline spectral signature. We further profiled plaques from Ldlr-/- mice fed a high fat diet, and likewise, found CE-dominate crystals. Finally, macrophage exposure to CCs or AcLDL induced auto-fluorescent puncta that co-stained with the LC3B autophagy sensor. In aggregate, we show that atheromatous plaques from mice, macaques and humans, display necrotic cores dominated by esterified CCs, and that plaque macrophages may induce autophagic vesicle formation upon encountering CCs. These findings help inform our knowledge of plaque core lipid evolution and how the process may incite systemic inflammation.

Glanders is a zoonotic contagious disease of equids caused by Burkholderia (B.) mallei. Serodiagnosis of the disease is challenging because of false-positive and false-negative test results. The accuracy of the complement fixation test (CFT) which is prescribed for international trade by the World Organisation for Animal Health (OIE), five ELISAs and a Western blot (WB) were compared for serodiagnosis of glanders using sera from 3,000 glanders-free and 254 glanderous equids. Four ELISA tests are based on recombinant antigens (TssA, TssB, BimA and Hcp1), the IDVet ELISA is based on a semi-purified fraction of B. mallei and WB makes use of a purified LPS-containing B. mallei-antigen. Sensitivity and specificity of tests were estimated using cut-off values recommended by the test developers. The WB and all ELISAs, except BimA, were significantly more specific than the CFT. ELISAs based on TssA, TssB, and BimA antigens had significantly lower sensitivity compared to CFT while the sensitivities of the Hcp1-ELISA, the IDVet-ELISA and the WB did not differ significantly from that of the CFT. Given their comparable sensitivities and specificities, the CFT (98.0%, 96.4%), the WB (96.8%, 99.4%), the Hcp1-ELISA (95.3%, 99.6%) and the IDVet-ELISA (92.5%, 99.5%) should be further developed to meet OIE requirements.