No abstract

Gold nanoparticles functionalized with water-soluble zwitterionic ligands form kinetically stable complexes with hydrophobic drugs and dyes. These drugs and dyes are efficiently released into cells, as demonstrated through fluorescence microscopy and cytotoxicity assays. Significantly, there is little or no cellular uptake of particle, making these low toxicity particles promising for delivery applications.

Untargeted metabolomics provides a comprehensive platform to identify metabolites whose levels are altered between two or more populations. By using liquid chromatography quadrupole time-of-flight mass spectrometry (LC-Q-ToF-MS), hundreds to thousands of peaks with a unique m/z and retention time are routinely detected from most biological samples in an untargeted profiling experiment. Each peak, termed a metabolomic feature, can be characterized on the basis of its accurate mass, retention time, and tandem mass spectral fragmentation pattern. Here a 7-step protocol is suggested for such a characterization by using the METLIN metabolite database. The protocol starts from untargeted metabolomic LC-Q-ToF-MS data that has been analyzed with the bioinformatic program XCMS, and describes a strategy for selecting interesting features as well as performing subsequent targeted tandem mass spectrometry. The 7 steps described will require 2-4 hours to complete per feature, depending on the compound.

Large-scale metabolite annotation is a challenge in liquid chromatogram-mass spectrometry (LC-MS)-based untargeted metabolomics. Here, we develop a metabolic reaction network (MRN)-based recursive algorithm (MetDNA) that expands metabolite annotations without the need for a comprehensive standard spectral library. MetDNA is based on the rationale that seed metabolites and their reaction-paired neighbors tend to share structural similarities resulting in similar MS2 spectra. MetDNA characterizes initial seed metabolites using a small library of MS2 spectra, and utilizes their experimental MS2 spectra as surrogate spectra to annotate their reaction-paired neighbor metabolites, which subsequently serve as the basis for recursive analysis. Using different LC-MS platforms, data acquisition methods, and biological samples, we showcase the utility and versatility of MetDNA and demonstrate that about 2000 metabolites can cumulatively be annotated from one experiment. Our results demonstrate that MetDNA substantially expands metabolite annotation, enabling quantitative assessment of metabolic pathways and facilitating integrative multi-omics analysis.

Rapid and sensitive detection of pathogens is a key requirement for both environmental and clinical settings. We report here a colorimetric enzyme-nanoparticle conjugate system for detection of microbial contamination. In this approach cationic gold nanoparticles (NP) featuring quaternary amine head-groups are electrostatically bound to an enzyme (β-galactosidase, β-Gal), inhibiting enzyme activity. Analyte bacteria bind to the NP, releasing the β -Gal, restoring activity, and providing an enzyme-amplified colorimetric read-out of the binding event. Using this strategy we have been able to quantify bacteria at 1×102 bacteria/mL in solution and at 1×104 bacteria/mL in a field-friendly test strip format.

Although the objective of any ‘omic science is broad measurement of its constituents, such coverage has been challenging in metabolomics because the metabolome is comprised of a chemically diverse set of small molecules with variable physical properties. While extensive studies have been performed to identify metabolite isolation and separation methods, these strategies introduce bias toward lipophilic or water-soluble metabolites depending on whether reversed-phase (RP) or hydrophilic interaction liquid chromatography (HILIC) is used respectively. Here we extend our consideration of metabolome isolation and separation procedures to integrate RPLC/MS and HILIC/MS profiling. An aminopropyl-based HILIC/MS method was optimized on the basis of mobile-phase additives and pH, followed by evaluation of reproducibility. When applied to the untargeted study of perturbed bacterial metabolomes, the HILIC method enabled the accurate assessment of key, dysregulated metabolites in central carbon pathways (e.g., amino acids, organic acids, phosphorylated sugars, energy currency metabolites), which could not be retained by RPLC. To demonstrate the value of the integrative approach, bacterial cells, human plasma, and cancer cells were analyzed by combined RPLC/HILIC separation coupled to ESI positive/negative MS detection. The combined approach resulted in the observation of metabolites associated with lipid and central carbon metabolism from a single biological extract, using 80 % organic solvent (ACN:MeOH:H2O 2:2:1). It enabled the detection of more than 30,000 features from each sample type, with the highest number of uniquely detected features by RPLC in ESI positive mode and by HILIC in ESI negative mode. Therefore, we conclude that when time and sample are limited, the maximum amount of biological information related to lipid and central carbon metabolism can be acquired by combining RPLC ESI positive and HILIC ESI negative mode analysis.

Small (6-10 nm) functionalized gold nanoparticles (AuNPs) featuring different, well-defined surface charges were used to probe the uptake and distribution of nanomaterials in terrestrial plants, including rice, radish, pumpkin, and perennial ryegrass. Exposure of the AuNPs to plant seedlings under hydroponic conditions for a 5-day period was investigated. Results from these studies indicate that AuNP uptake and distribution depend on both nanoparticle surface charge and plant species. The experiments show that positively charged AuNPs are most readily taken up by plant roots, while negatively charged AuNPs are most efficiently translocated into plant shoots (including stems and leaves) from the roots. Radish and ryegrass roots generally accumulated higher amounts of the AuNPs (14-900 ng/mg) than rice and pumpkin roots (7-59 ng/mg). Each of the AuNPs used in this study were found to accumulate to statistically significant extents in rice shoots (1.1-2.9 ng/mg), while none of the AuNPs accumulated in the shoots of radishes and pumpkins.

Supramolecular chemistry provides a versatile tool for the organization of molecular systems into functional structures and the actuation of these assemblies for applications through the reversible association between complementary components. Application of this methodology in living systems represents a significant challenge due to the chemical complexity of cellular environments and lack of selectivity of conventional supramolecular interactions. Herein, we present a host-guest system featuring diaminohexane-terminated gold nanoparticles (AuNP-NH2) and complementary cucurbit[7]uril (CB[7]). In this system, threading of CB[7] on the particle surface reduces the cytotoxicity of AuNP-NH2 through sequestration of the particle in endosomes. Intracellular triggering of the therapeutic effect of AuNP-NH2 was then achieved via the administration of 1-adamantylamine (ADA), removing CB[7] from the nanoparticle surface and triggering the endosomal release and concomitant in situ cytotoxicity of AuNP-NH2. This supramolecular strategy for intracellular activation provides a new tool for potential therapeutic applications.