Sequence dependence of isothermal DNA amplification via EXPAR

Isothermal nucleic acid amplification is becoming increasingly important for molecular diagnostics. Therefore, new computational tools are needed to facilitate assay design. In the isothermal EXPonential Amplification Reaction (EXPAR), template sequences with similar thermodynamic characteristics perform very differently. To understand what causes this variability, we characterized the performance of 384 template sequences, and used this data to develop two computational methods to predict EXPAR template performance based on sequence: a position weight matrix approach with support vector machine classifier, and RELIEF attribute evaluation with Naïve Bayes classification. The methods identified well and poorly performing EXPAR templates with 67–70% sensitivity and 77–80% specificity. We combined these methods into a computational tool that can accelerate new assay design by ruling out likely poor performers. Furthermore, our data suggest that variability in template performance is linked to specific sequence motifs. Cytidine, a pyrimidine base, is over-represented in certain positions of well-performing templates. Guanosine and adenosine, both purine bases, are over-represented in similar regions of poorly performing templates, frequently as GA or AG dimers. Since polymerases have a higher affinity for purine oligonucleotides, polymerase binding to GA-rich regions of a single-stranded DNA template may promote non-specific amplification in EXPAR and other nucleic acid amplification reactions

Protein-metabolite association studies identify novel proteomic determinants of metabolite levels in human plasma

Although many novel gene-metabolite and gene-protein associations have been identified using high-throughput biochemical profiling, systematic studies that leverage human genetics to illuminate causal relationships between circulating proteins and metabolites are lacking. Here, we performed protein-metabolite association studies in 3,626 plasma samples from three human cohorts. We detected 171,800 significant protein-metabolite pairwise correlations between 1,265 proteins and 365 metabolites, including established relationships in metabolic and signaling pathways such as the protein thyroxine-binding globulin and the metabolite thyroxine, as well as thousands of new findings. In Mendelian randomization (MR) analyses, we identified putative causal protein-to-metabolite associations. We experimentally validated top MR associations in proof-of-concept plasma metabolomics studies in three murine knockout strains of key protein regulators. These analyses identified previously unrecognized associations between bioactive proteins and metabolites in human plasma. We provide publicly available data to be leveraged for studies in human metabolism and disease

Restoring Angiotensin Type 2 Receptor Function Reverses PFOS-Induced Vascular Hyper-Reactivity and Hypertension in Pregnancy

Perfluorooctane sulfonic acid (PFOS) exposure during pregnancy induces hypertension with decreased vasodilatory angiotensin type-2 receptor (AT2R) expression and impaired vascular reactivity and fetal weights. We hypothesized that AT2R activation restores the AT1R/AT2R balance and reverses gestational hypertension by improving vascular mechanisms. Pregnant Sprague-Dawley rats were exposed to PFOS through drinking water (50 μg/mL) from gestation day (GD) 4–20. Controls received drinking water with no detectable PFOS. Control and PFOS-exposed rats were treated with AT2R agonist Compound 21 (C21; 0.3 mg/kg/day, SC) from GD 15–20. In PFOS dams, blood pressure was higher, blood flow in the uterine artery was reduced, and C21 reversed these to control levels. C21 mitigated the heightened contraction response to Ang II and enhanced endothelium-dependent vasorelaxation in uterine arteries of PFOS dams. The observed vascular effects of C21 were correlated with reduced AT1R levels and increased AT2R and eNOS protein levels. C21 also increased plasma bradykinin production in PFOS dams and attenuated the fetoplacental growth restriction. These data suggest that C21 improves the PFOS-induced maternal vascular dysfunction and blood flow to the fetoplacental unit, providing preclinical evidence to support that AT2R activation may be an important target for preventing or treating PFOS-induced adverse maternal and fetal outcomes

Molecular Water Lilies: Orienting Single Molecules in a Polymer Film by Solvent Vapor Annealing

The microscopic orientation and position of photoactive molecules is crucial to the operation of optoelectronic devices such as OLEDs and solar cells. Here, we introduce a shape-persistent macrocyclic molecule as an excellent fluorescent probe to simply measure (i) its orientation by rotating the excitation polarization and recording the strength of modulation in photoluminescence (PL) and (ii) its position in a film by analyzing the overall PL brightness at the molecular level. The unique shape, the absorption and the fluorescence properties of this probe yield information on molecular orientation and position. We control orientation and positioning of the probe in a polymer film by solvent vapor annealing (SVA). During the SVA process the molecules accumulate at the polymer/air interface, where they adopt a flat orientation, much like water lilies on the surface of a pond. The results are potentially significant for OLED fabrication and single-molecule spectroscopy (SMS) in general

Reconciling material cultures in archaeology with genetic data: The nomenclature of clusters emerging from archaeogenomic analysis

Abstract Genome-wide ancient DNA analysis of skeletons retrieved from archaeological excavations has provided a powerful new tool for the investigation of past populations and migrations. An important objective for the coming years is to properly integrate ancient genomics into archaeological research. This article aims to contribute to developing a better understanding and cooperation between the two disciplines and beyond. It focuses on the question of how best to name clusters encountered when analysing the genetic makeup of past human populations. Recent studies have frequently borrowed archaeological cultural designations to name these genetic groups, while neglecting the historically problematic nature of the concept of cultures in archaeology. After reviewing current practices in naming genetic clusters, we introduce three possible nomenclature systems (‘numeric system’, ‘mixed system (a)’, ‘geographic-temporal system’) along with their advantages and challenges