Mapping genomic regulation of kidney disease and traits through high-resolution and interpretable eQTLs

Expression quantitative trait locus (eQTL) studies illuminate genomic variants that regulate specific genes and contribute to fine-mapped loci discovered via genome-wide association studies (GWAS). Efforts to maximize their accuracy are ongoing. Using 240 glomerular (GLOM) and 311 tubulointerstitial (TUBE) micro-dissected samples from human kidney biopsies, we discovered 5371 GLOM and 9787 TUBE genes with at least one variant significantly associated with expression (eGene) by incorporating kidney single-nucleus open chromatin data and transcription start site distance as an integrative prior for Bayesian statistical fine-mapping. The use of an integrative prior resulted in higher resolution eQTLs illustrated by (1) smaller numbers of variants in credible sets with greater confidence, (2) increased enrichment of partitioned heritability for GWAS of two kidney traits, (3) an increased number of variants colocalized with the GWAS loci, and (4) enrichment of computationally predicted functional regulatory variants. A subset of variants and genes were validated experimentally in vitro and using a Drosophila nephrocyte model. More broadly, this study demonstrates that tissue-specific eQTL maps informed by single-nucleus open chromatin data have enhanced utility for diverse downstream analyses

Surface-based constraints on target selection and distractor rejection: Evidence from preview search

In preview search when an observer ignores an early appearing set of distractors, there can subsequently be impeded detection of new targets that share the colour of this preview. This “negative carry-over effect” has been attributed to an active inhibitory process targeted against the old items and inadvertently their features. Here we extend negative carry-over effects to the case of stereoscopically defined surfaces of coplanar elements without common features. In Experiment 1 observers previewed distractors in one surface (1000 ms), before being presented with the target and new distractors divided over the old and a new surface either above or below the old one. Participants were slower and less efficient to detect targets in the old surface. In Experiment 2 in both the first and second display the items were divided over two planes in the proportion 66/33% such that no new planes appeared following the preview, and there was no majority of items in any one plane in the final combined display. The results showed that participants were slower to detect the target when it occurred in the old majority surface. Experiment 3 held constant the 2D properties of the stimuli while varying the presence of binocular depth cues. The carry-over effect only occurred in the presence of binocular depth cues, ruling out any account of the results in terms of 2-D cues. The results suggest well formed surfaces in addition to simple features may be targets for inhibition in search

Isolation of sophorose during sophorolipid production and studies of its stability in aqueous alkali: epimerisation of sophorose to 2-O-β-d-glucopyranosyl-d-mannose

NMR and anion exchange chromatography analysis of the waste streams generated during the commercial production of sophorolipids by the yeast Candida bombicola identified the presence of small but significant quantities (1% w/v) of free sophorose. Sophorose, a valuable disaccharide, was isolated from the aqueous wastes using a simple extraction procedure and was purified by chromatography on a carbon celite column providing easy access to large quantities of the disaccharide. Experiments were undertaken to identify the origin of sophorose and it is likely that acetylated sophorose derivatives were produced by an enzyme catalysed hydrolysis of the glucosyl-lipid bond of sophorolipids; the acetylated sophorose derivatives then undergo hydrolysis to release the parent disaccharide. Treatment of sophorose with aqueous alkali at elevated temperatures (0.1M NaOH at 50 °C) resulted in C2-epimerisation of the terminal reducing sugar and its conversion to the corresponding 2-O-β-d-glucopyranosyl-d-mannose which was isolated and characterised. In aqueous alkaline solution β-(1,2)-linked glycosidic bonds do not undergo either hydrolysis or peeling reactions

Mucosal T-cell responses to chronic viral infections: Implications for vaccine design

Mucosal surfaces that line the respiratory, gastrointestinal and genitourinary tracts are the major interfaces between the immune system and the environment. Their unique immunological landscape is characterized by the necessity of balancing tolerance to commensal microorganisms and other innocuous exposures against protection from pathogenic threats such as viruses. Numerous pathogenic viruses, including herpesviruses and retroviruses, exploit this environment to establish chronic infection. Effector and regulatory T-cell populations, including effector and resident memory T cells, play instrumental roles in mediating the transition from acute to chronic infection, where a degree of viral replication is tolerated to minimize immunopathology. Persistent antigen exposure during chronic viral infection leads to the evolution and divergence of these responses. In this review, we discuss advances in the understanding of mucosal T-cell immunity during chronic viral infections and how features of T-cell responses develop in different chronic viral infections of the mucosa. We consider how insights into T-cell immunity at mucosal surfaces could inform vaccine strategies: not only to protect hosts from chronic viral infections but also to exploit viruses that can persist within mucosal surfaces as vaccine vectors

Trace element concentrations in feathers from three seabird species breeding in the Timor Sea

Mobile marine predators, such as seabirds, are frequently used as broad samplers of contaminants that are widespread in the marine environment. The Timor Sea off remote Western Australia is a poorly studied, yet rapidly expanding area of offshore development. To provide much needed data on contamination in this region, we quantified trace element concentrations in breast feathers of three seabird species breeding on Bedout Island. While adult Masked Boobies Sula dactylatra exhibited some of the highest concentrations, values for all species were below toxicology thresholds for seabirds and were comparable to those reported in other closely related species. The low concentrations detected in the birds provide a valuable baseline and suggest that the local marine environment around Bedout is in relatively good condition. However, careful monitoring is warranted in light increasing anthropogenic activity in this region.© 2019 Published by Elsevier Ltd. The attached file is the final authors' accepted manuscript version

Defining cellular complexity in human autosomal dominant polycystic kidney disease by multimodal single cell analysis

Autosomal dominant polycystic kidney disease (ADPKD) is the leading genetic cause of end stage renal disease characterized by progressive expansion of kidney cysts. To better understand the cell types and states driving ADPKD progression, we analyze eight ADPKD and five healthy human kidney samples, generating single cell multiomic atlas consisting of ~100,000 single nucleus transcriptomes and ~50,000 single nucleus epigenomes. Activation of proinflammatory, profibrotic signaling pathways are driven by proximal tubular cells with a failed repair transcriptomic signature, proinflammatory fibroblasts and collecting duct cells. We identify GPRC5A as a marker for cyst-lining collecting duct cells that exhibits increased transcription factor binding motif availability for NF-κB, TEAD, CREB and retinoic acid receptors. We identify and validate a distal enhancer regulating GPRC5A expression containing these motifs. This single cell multiomic analysis of human ADPKD reveals previously unrecognized cellular heterogeneity and provides a foundation to develop better diagnostic and therapeutic approaches

Tubular CPT1A deletion minimally affects aging and chronic kidney injury

Kidney tubules use fatty acid oxidation (FAO) to support their high energetic requirements. Carnitine palmitoyltransferase 1A (CPT1A) is the rate-limiting enzyme for FAO, and it is necessary to transport long-chain fatty acids into mitochondria. To define the role of tubular CPT1A in aging and injury, we generated mice with tubule-specific deletion of Cpt1a (Cpt1aCKO mice), and the mice were either aged for 2 years or injured by aristolochic acid or unilateral ureteral obstruction. Surprisingly, Cpt1aCKO mice had no significant differences in kidney function or fibrosis compared with wild-type mice after aging or chronic injury. Primary tubule cells from aged Cpt1aCKO mice had a modest decrease in palmitate oxidation but retained the ability to metabolize long-chain fatty acids. Very-long-chain fatty acids, exclusively oxidized by peroxisomes, were reduced in kidneys lacking tubular CPT1A, consistent with increased peroxisomal activity. Single-nuclear RNA-Seq showed significantly increased expression of peroxisomal FAO enzymes in proximal tubules of mice lacking tubular CPT1A. These data suggest that peroxisomal FAO may compensate in the absence of CPT1A, and future genetic studies are needed to confirm the role of peroxisomal β-oxidation when mitochondrial FAO is impaired

A protocol for precise comparisons of small vessel disease lesions between ex vivo magnetic resonance imaging and histopathology

pp. 310-32La neuroimagen y los estudios clínicos han definido la enfermedad cerebral de los vasos pequeños humanos, pero la fisiopatología sigue siendo relativamente poco comprendida. Para desarrollar terapias eficaces y estrategias preventivas, debemos comprender mejor la heterogeneidad y el desarrollo de la enfermedad de los vasos pequeños a nivel celular.S