A simple method to isolate fluorescence spectra from small dissolved organic matter datasets

Dissolved organic matter (DOM) is a complex pool of compounds with a key role in the global carbon cycle. To understand its role in natural and engineered systems, efficient approaches are necessary for tracking DOM quality and quantity. Fluorescence spectroscopy combined with parallel factor analysis (PARAFAC) is very widely used to identify and quantify different fractions of DOM as proxies of DOM source, concentration and biogeochemical processing. A major limitation of the PARAFAC approach is the requirement for a large data set containing many variable samples in which the fractions vary independently. This severely curtails the possibilities to study fluorescence composition and behavior in small or unique datasets. Herein, we present a simple and inexpensive experimental procedure that makes it possible to mathematically decompose a small dataset containing only highly-correlated fluorescent fractions. The approach, which uses widely-available commercial extraction sorbents and previously established protocols to expand the original dataset and inject the missing chemical variability, can be widely implemented at low cost. A demonstration of the procedure shows how a robust six-component PARAFAC model can be extracted from even a river-water dataset with only five bulk samples. Widespread adoption of the procedure for analyzing small fluorescence datasets is needed to confirm the suspected ubiquity of certain DOM fluorescence fractions and to create a shared inventory of ubiquitous components. Such an inventory could greatly simplify and improve the use of fluorescence as a tool to investigate biogeochemical processing of DOM in diverse water sources

Temperature-dependent mechanisms of DOM removal by biological activated carbon filters

Seasonal variability in the removal of dissolved organic matter (DOM) by drinking water biological activated carbon (BAC) filters is often attributed to temperature changes. However, it can be rather difficult to directly relate temperature to treatment efficiency at full scale due to seasonal variations in other influential parameters like DOM concentration and character, and microbial activity. Furthermore, processes in BAC filters include adsorption, desorption and biodegradation within biofilms while each respond differently to temperature. This study aimed to decouple these processes by studying the removal of various DOM fractions from coagulated and settled drinking water when in contact with aged (>3 years) BAC filter material at different water temperatures. DOM removal was measured as changes in dissolved organic carbon (DOC), ultraviolet absorbance at 254 nm (UV254) and fluorescence. Under the particular experimental conditions there was little evidence of biological removal; instead, removal of DOM fractions emitting at longer wavelengths ("humic-like", >430 nm) was consistent with chemisorption, removal of DOM emitting at intermediate wavelengths ("humic-like", 390-420 nm) was consistent with physisorption, and multiple mechanisms were indicated for "protein-like" (<380 nm) DOM. Non-biological mechanisms of DOM removal by aged BAC filters are often assumed to be unimportant; however, these results suggest they are important for some DOM fractions, especially during periods of reduced microbial activity

Liver Is Able to Activate Naïve CD8+ T Cells with Dysfunctional Anti-Viral Activity in the Murine System

The liver possesses distinct tolerogenic properties because of continuous exposure to bacterial constituents and nonpathogenic food antigen. The central immune mediators required for the generation of effective immune responses in the liver environment have not been fully elucidated. In this report, we demonstrate that the liver can indeed support effector CD8+ T cells during adenovirus infection when the T cells are primed in secondary lymphoid tissues. In contrast, when viral antigen is delivered predominantly to the liver via intravenous (IV) adenovirus infection, intrahepatic CD8+ T cells are significantly impaired in their ability to produce inflammatory cytokines and lyse target cells. Additionally, intrahepatic CD8+ T cells generated during IV adenovirus infection express elevated levels of PD-1. Notably, lower doses of adenovirus infection do not rescue the impaired effector function of intrahepatic CD8+ T cell responses. Instead, intrahepatic antigen recognition limits the generation of potent anti-viral responses at both priming and effector stages of the CD8+ T cell response and accounts for the dysfunctional CD8+ T cell response observed during IV adenovirus infection. These results also implicate that manipulation of antigen delivery will facilitate the design of improved vaccination strategies to persistent viral infection

staRdom: Versatile Software for Analyzing Spectroscopic Data of Dissolved Organic Matter in R

The roles of dissolved organic matter (DOM) in microbial processes and nutrient cycles depend on its composition, which requires detailed measurements and analyses. We introduce a package for R, called staRdom (“spectroscopic analysis of DOM in R”), to analyze DOM spectroscopic data (absorbance and fluorescence), which is key to deliver fast insight into DOM composition of many samples. staRdom provides functions that standardize data preparation and analysis of spectroscopic data and are inspired by practical work. The user can perform blank subtraction, dilution correction, Raman normalization, scatter removal and interpolation, and fluorescence normalization. The software performs parallel factor analysis (PARAFAC) of excitation–emission matrices (EEMs), including peak picking of EEMs, and calculates fluorescence indices, absorbance indices, and absorbance slope indices from EEMs and absorbance spectra. A comparison between PARAFAC solutions by staRdom in R compared with drEEM in MATLAB showed nearly identical solutions for most datasets, although different convergence criteria are needed to obtain similar results and interpolation of missing data is important when working with staRdom. In conclusion, staRdom offers the opportunity for standardized multivariate decomposition of spectroscopic data without requiring software licensing fees and presuming only basic R knowledge

Quantifying the impact of solid-phase extraction on chromophoric dissolved organic matter composition

Advancing our understanding of the behaviour of dissolved organic matter (DOM) in aquatic environments necessitates efforts to combine complementary analytical data sets. However, some analytical measurements require sample pre-treatment, while others are carried out on bulk water samples, and it remains unclear if the resulting data sets can be compared. Here, we investigated the impact of solid-phase extraction with PPL resins on DOM optical properties. In samples from contrasting Arctic fjords, extraction efficiencies based on optical properties varied spectrally with averages between 31 \ub1 13% at 411 nm and 40 \ub1 12% at 363 nm for chromophoric DOM. Similarly, the extraction efficiency for specific fluorescence components varied between 37 \ub1 16% and 58 \ub1 18%. Solid-phase extraction also decreased S275–295, fluorescence index, and the freshness index, but increased S350–400, and apparent fluorescence quantum yields, indicating that the extraction process was qualitatively selective. Six fluorescence components identified independently in bulk water samples and extracted DOM using parallel factor analysis exhibited different behaviours. Three had identical spectral properties before and after extraction, although their extraction efficiencies varied with water mass characteristics and DOM composition, whereas three other components appeared to change after extraction. With the exception of one fluorescence component, the dynamics of optical properties in bulk water samples were not accurately reflected by DOM extracts. These results indicate that solid-phase extraction imparts a qualitative selectivity that leads to the homogenization of DOM extracts relative to their original samples. Efforts to integrate chemical information from different analytical methods should prioritize comparisons of measurements obtained on the same samples

DOM Molecular Weight Fractionation and Fluorescence Quantum Yield Assessment Using a Coupled In-Line SEC Optical Property System

Size exclusion chromatography (SEC) in combination with optical measurements has become a popular form of analysis to characterize dissolved organic matter (DOM) as a function of molecular size. Here, SEC coupled with in-line absorbance scans and fluorescence emission scans was utilized to derive apparent fluorescence quantum yield (φf) as a function of molecular weight (MW) for DOM. Individual instrument-specific SEC-fluorescence detector correction factors were developed by comparison of an SEC-based excitation emission matrix (EEM) to an EEM generated by a calibrated benchtop fluorometer. The method was then applied to several sample sets to demonstrate how to measure the φf of unknown DOM samples and to observe changes to φf following a processing mechanism (ozonation). The φf of riverine water samples and DOM fulvic acid isolates from Suwannee River and Pony Lake increased from < 0.5% to a maximum of 2.5-3% across the medium- to low-MW range. Following ozonation of PLFA, φf increased most notably in the large-MW fractions (elution volumes < 40 mL). Overall, this method provides a means by which highly fluorescent size fractions of DOM can be identified for more detailed analyses of chemical composition and its changes through different processing mechanisms