James Harnly

• PhD
• research leader at United States Department of Agriculture

One-class modeling is a supervised multivariate botanical identification method based on principal component analysis (PCA) that constructs a model based only on the characteristics of the reference samples and uses the Q statistic as a combined metric. Test samples are judged to be similar (authentic) if their combined metric falls within the mode...

Glucosinolates (GLSs) are a well-studied sulfur-containing compound found in Brassicaceae plants that play critical roles in plant resistance and human health. Correctly identifying and reliably quantifying the total and individual GLS content is of great importance. An improved method as an alternative to the ISO 9167-1 (ISO) method is developed i...

Background: Botanical reference materials (BRMs) generally account for the species, cultivar, and year and location of harvest that result in variability in the chemical composition that may lead to statistically significant differences using chemometric methods. Objective: To Compare the chemical composition of 5 species of Actaea root BRMs, 4...

Database and Documentation can be downloaded at https://www.ars.usda.gov/northeast-area/beltsville-md-bhnrc/beltsville-human-nutrition-research-center/methods-and-application-of-food-composition-laboratory/mafcl-site-pages/ingid-thesaurus/ Citation: Ahuja, JK, Li, Y, Pehrsson, PR, Harnly, J. USDA IngID Thesaurus: an application dataset for systema...

Age is a major risk factor for age-related macular degeneration (AMD), and age has a role in the disease phenotypes of heritable macular dystrophies. The proteomes of C57Bl6/J mouse choroids at 2 ages were analyzed to identify biochemical processes affected by aging. Proteins of interest were identified as those contributing most to the variance in...

Background Authentication methods are necessary to guarantee the integrity of botanical supplements and their ingredients. In 2012, AOAC International published “Guidelines for Validation of Botanical Identification Methods” however these guidelines proved rather cumbersome. Objective Develop a simpler method for validatation based on one-class mo...

Dietary fiber has long been known to be an essential component of a healthy diet, and recent investigations into the gut microbiome-health paradigm have identified fiber as a prime determinant in this interaction. Further, fiber is now known to impact the gut microbiome in a structure-specific manner, conferring differential bioactivities to these...

Mass spectrometry (MS)-based techniques have been extensively applied in food and agricultural research. This review aims to address the advances and applications of MS-based analytical strategies in nontargeted and targeted analysis and summarizes the recent publications of MS-based techniques, including flow injection MS fingerprinting, chromatog...

Gluten-free bean pastas utilizing bean composite flour (bean flour, tapioca starch, and xanthan gum) from three bean varieties and the controlled durum wheat pasta were analyzed by ultrahigh performance liquid chromatography high-resolution accurate-mass multistage mass spectrometry (UHPLC-HRAM-MSn) with electrospray ionization (ESI). The secondary...

Background Branched-chain fatty acids (BCFAs) are rumen-derived fatty acids comprising ∼2% of bovine-milk fatty acids. BCFAs possess anti-inflammatory properties and enriching the BCFA content of bovine milk may provide human health benefits. Objective We determined whether forage content impacts the BCFA content of milk from Holstein cows and ide...

The increased utilization of metrology resources and expanded application of its’ approaches in the development of internationally agreed upon measurements can lay the basis for regulatory harmonization, support reproducible research, and advance scientific understanding, especially of dietary supplements and herbal medicines. Yet, metrology is oft...

FoodData Central (FDC) is the center of the US Department of Agriculture (USDA)-based food composition information web. It is an integrated data system that presently provides-in one place-five distinct types of data containing information on food and nutrient profiles. Each data type has a unique purpose. Two of the data types-Foundation Foods (FF...

Machine learning and classical statistics were used to unravel the complex data set generated by the analysis of 77 fatty acids in milk from 76 cows fed 3 forages. Multivariate analysis of variance – principal components analysis (mANOVA-PCA) was used to deconvolute the data and determine the variance contributed by the main experimental factors: f...

A Correction to this paper has been published: https://doi.org/10.1007/s00216-021-03594-z

Objectives Branched chain fatty acids (BCFA) are rumen-derived fatty acids comprising about 2% of bovine milk fatty acids. BCFA possess anti-inflammatory properties and enriching the BCFA content of bovine milk may provide human health benefits of milk consumption. In this work, we determined whether high vs low forage diets impact the BCFA content...

Objectives A dynamic US food supply and need for assessment of diet on health demands transparent, easily accessible information on foods and food components and related data on production and variability for researchers, health and nutrition policymakers and professionals, and food manufacturers. USDA is to develop an integrated food data system t...

One in three people in the world suffers from some form of malnutrition. A possible solution to malnutrition is dietary diversity, especially diversifying plant food consumption. However, there has not been a suitable method to guide the acquisition of balanced nutrients from diverse plant sources. Here, we report a tool for categorizing raw plant...

A strategy was developed for the identification of saponins in Alliums using ultra-high performance liquid chromatography high-resolution accurate-mass/multi-stage mass spectrometry (UHPLC-HRAM/MSⁿ). The identification process was facilitated by a systematic classification of 152 previously reported sapogenins (saponin aglycones) in Allium based on...

Ginkgo biloba extract (GbE) is a dietary supplement derived from an ethanolic extract of Ginkgo biloba leaves. Unfinished bulk GbE is used to make finished products that are sold as dietary supplements. The variable, complex composition of GbE makes it difficult to obtain consistent toxicological assessments of potential risk. The National Toxicolo...

Objectives To determine the impact of garlic on the metabolic profile of urine. Methods On the first day 17 fasting subjects were fed a breakfast of bread and butter. Urines were collected before and 3 hours after the meal. On a second day, the same 17 fasting subjects were fed a meal of bread, butter, and garlic. Urines were again collected befor...

Two wheat genetic lines (responsive and non-responsive to elevated CO2) grown under ambient and free-air CO2 enrichment (FACE) conditions were compared using fuzzy chromatography mass spectrometry (FCMS) metabolite fingerprinting. A more comprehensive survey of the changes in their chemical composition was made on selected samples using ultra-high-...

Maca (Lepidium meyenii, synonym L. peruvianum) was analyzed using a systematic approach employing principal component analysis of flow injection mass spectrometry fingerprints (no chromatographic separation) to guide the selection of samples for metabolite profiling and DNA next generation sequencing. Samples consisted of 39 commercial maca supplem...

Adulteration remains an issue in the dietary supplement industry, including botanical supplements. While it is common to employ a targeted analysis to detect known adulterants, this is difficult when little is known about the sample set. With this study, untargeted metabolomics using liquid chromatography coupled to ultraviolet-visible spectroscopy...

In the present study, the effect of particle size (PS) on phenolic acid content and proximate composition (moisture, ash, protein, total fat, crude fiber and total carbohydrates) of whole-wheat flour (WWF) was determined. Five different particle size fractions <1.18 to>0.43, <0.43 to>0.30, <0.30 to>0.15, < 0.15 to>0.08 mm, and < 0.08 mm (ASTM recom...

Ester and amide derivatives of hydroxycinnamic acids are found in black cohosh (Actaea racemosa) and other Actaea plants. These two compound groups were evaluated for authentication of black cohosh dietary supplements. The hydroxycinnamic acid esters (HCAE) were profiled by ultra-performance liquid chromatography-photodiode array detection (UPLC-PD...

A non-targeted method for classifying authentic and adulterated skim and nonfat dry milk powders (MP) by solution-state, high-field ¹H NMR spectroscopy and conformity index analysis has been developed. Authentic MP samples from the global market and synthetically-adulterated MP samples involving eight adulterants were used in a pre-validation study...

Lettuce (Lactuca sativa L.) is one of the most consumed vegetables in the world and different management practice can result in considerable variability of the secondary metabolites. Flow injection mass spectrometry (FIMS) combined with analysis of variance–principle component analysis (ANOVA–PCA) was used to study differences in the secondary meta...

Objective: To describe the history, key features, recent enhancements, and common applications of the Dietary Supplement Label Database (DSLD). Background and history: Although many Americans use dietary supplements, databases of dietary supplements sold in the United States have not been widely available. The DSLD, an easily accessible public-u...

Botanical dietary supplements are complex mixtures that can be highly variable in composition and quality, making safety evaluation difficult. A key challenge is determining how diverse products in the marketplace relate to chemically and toxicologically characterized reference samples (i.e., how similar must a product be in order to be well-repres...

1H-NMR spectra for 66 commercial powdered milk samples were analyzed by PCA, SIMCA, and pooled, crossed ANOVA. It was found that the sample type (skim milk powder or non-fat dry milk), the supplier, the production site, the processing temperature (high, medium, or low temperature), and the day of analysis provided statistically significant sources...

The coffee berry borer continues to pose a formidable challenge to coffee growers worldwide. Because of the cryptic life habit of the insect inside coffee berries, effective pest management strategies have been difficult to develop. A sesquiterpene, (E,E)-α-farnesene, produced by infested coffee berries has been identified as a potential repellent...

A systematic comparison was made of the detected metabolite profiles for two plant materials (black beans and soybeans) and a dietary supplement (black cohosh) extracted using sequential (hexane, ethyl acetate, and 50% aqueous methanol) and direct extraction with three solvent systems (80% aqueous methanol, methanol/chloroform/water (2.5:1:1, v/v/v...

Glucosinolates are a group of important cancer chemo-preventive sulfur-containing compounds in cruciferous vegetables. To estimate their dietary intake, there is a great need to develop a valid glucosinolate database. The aim of this study was to investigate the key challenges in developing such database. First, three commonly used enzyme deactivat...

Preparation of commercial supplements from botanical ingredients results in a change in the chemical composition that is easily followed with flow injection mass spectrometry. Spectral fingerprints (counts vs ion with no chromatographic separation) were acquired by flow injection mass spectrometry (FIMS) for aerial parts of 16 Echinacea purpurea bo...

Liquid Chromatography and mass spectrometry methods, especially ultra‐high performance liquid chromatography coupled with high resolution accurate mass‐mass spectrometry (UHPLC‐HRAM‐MS), have become the best methods for flavonoid identification and quantification. However, processing acquired UHPLC‐HRAM‐MS data for flavonoid analysis is very challe...

Due to the complexity and variation of the chemical constituents in authentic black cohosh (Actaea racemosa) and its potential adulterant species, an accurate and feasible method for black cohosh authentication is not easy. A high-resolution accurate mass (HRAM) LC-MS fingerprinting method combined with chemometric approach was employed to discover...

Commercial success of whole wheat products has warranted development of new analytical approaches for differentiating whole grain products from conventional food products made from refined grains. Here, we have analyzed three different wheat fractions namely bran, germ, and refined flour of two wheat varieties. In addition, a whole wheat sample con...

A comprehensive characterization of C-glycosyl flavones in wheat germ has been conducted using multi-stage high resolution mass spectrometry (HRMS(n) ) in combination with a mass defect filtering (MDF) technique. MDF performed the initial search of raw data with defined C-glycosyl flavone mass windows and mass defect windows to generate the noise-r...

Assessment of total vitamin D intake from foods and dietary supplements (DSs) may be incomplete if 25-hydroxyvitamin D [25(OH)D] intake is not included. However, 25(OH)D data for such intake assessments are lacking, no food or DS reference materials (RMs) are available, and comparison of laboratory performance has been needed. The primary goal of t...

Thermal processes such as cooking have a large influence on flavonoids in foods, which further impact the accuracy of developing food flavonoid database and the estimation of their dietary intake. The objective of this study was to determine how common cooking methods alter complex flavonoids in broccoli, and to compare the effects of different coo...

Food Composition and Methods Development Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture, Building‐161, BARC‐East, 10300 Baltimore Avenue, Beltsville, Maryland 20705, United States Flavonoids are well‐known for their health benefits and can be found in nearly every plant. There a...

According to the 2007–10 NHANES, 7.5% of the US population reports botanical dietary supplement (DS) use. The DSID provides analytically‐derived estimates of the ingredient contents of DS. Commonly consumed and frequently studied, green tea (GT) DS were chosen as the first botanical DS for the DSID botanical initiative. The most abundant GT constit...

Conceptually, identification, or authentication, of a botanical material is simple. You collect authentic materials, make a series of analytical measurements, build a model, set statistical limits, and then determine whether the unknown test material fits the model. The challenges to implementing such a method are 1) collecting authentic materials...

Background: Consumption of cocoa-derived polyphenols has been associated with several health benefits; however, their effects on the intestinal microbiome and related features of host intestinal health are not adequately understood. Objective: The objective of this study was to determine the effects of eating flavanol-enriched cocoa powder on th...

Accurate measurements of the secondary metabolites in natural products and plant foods are critical for establishing relations between diet and health. There are as many as 50,000 secondary metabolites that may influence human health. Their structural and chemical diversity presents a challenge to analytical chemistry. With respect to flavonoids, p...

A fuzzy chromatography mass spectrometric (FCMS) fingerprinting method combined with chemometric analysis was established to differentiate between breads made from whole wheat (WW) flour and refined wheat (RW) flour. The chemical compositions of the bread samples were profiled using ultrahigh-performance liquid chromatography with high-resolution a...

Flow injection mass spectrometry and proton nuclear magnetic resonance spectrometry, two metabolic fingerprinting methods, and DNA sequencing were used to identify and authenticate Actaea species. Initially, samples of Actaea racemosa from a single source were distinguished from other Actaea species based on principal component analysis and soft in...

Brassicales contain a myrosinase enzyme that hydrolyzes glucosinolates to form toxic isothiocyanates (ITC), as a defense against bacteria, fungi, insects and herbivores including man. Low levels of ITC trigger a host defense system in mammals that protects them against chronic diseases. Because humans typically cook their brassica vegetables, destr...

A fuzzy chromatography mass spectrometric (FCMS) fingerprinting method combined with chemometric analysis has been established for rapid discrimination of whole-grain flour (WF) from refined wheat flour (RF). Bran, germ, endosperm, and WF from three local cultivars or purchased from a grocery store were studied. The state of refinement (whole vs. r...

The Dietary Supplement Ingredient Database (DSID) provides analytically-derived estimates of the ingredient content in dietary supplements (DS). DSID 3.0 now includes 4 categories of DS: adult, children's and non-prescription prenatal multivitamin/mineral products (MVM), and omega-3 fatty acid DS. Green tea was chosen for analysis in the pilot stud...

A comprehensive analysis of wheat lipids from milling fractions of bran, germ, and endosperm was performed using ultra high-performance liquid chromatography high-resolution accurate-mass multi-stage mass spectrometry (UHPLC-HRAM-MSn) with electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) in both positive and negativ...

Numerous observational and intervention-based human studies support the notion of a beneficial role for dietary flavonoids in human health. Despite these studies, it is not yet possible to make dietary recommendations with regard to the types and amounts of flavonoids to be consumed. The inherent diversity of flavonoid structure, chemistry, and nat...

To determine the effects of eating cocoa‐derived flavanols on the composition of the gut microbiota, associated metabolic profiles, and related features of host intestinal health, pigs were fed with 0, 2.5, 10, or 20 grams of flavanol‐enriched cocoa powder/day for 27 days. Analysis of phase II metabolites of cocoa‐derived flavanols demonstrated tha...

Flow injection mass spectrometry (FIMS) was used to provide chemical fingerprints of black cohosh (Actaea racemosa L.) in a manner of minutes by omitting the separation step. This method has proven to be a powerful tool for botanical authentication and in this study it was used to distinguish between three Actaea species prior to a more detailed ch...

The Dietary Supplement Ingredient Database (DSID) is a federally funded, publicly accessible dietary supplement database that currently contains analytically derived information on micronutrients in selected adult and children's multivitamin and mineral (MVM) supplements. Other constituents in dietary supplement products such as botanicals are also...

A new computational tool is proposed here for tentatively identifying major (UV quantifiable) flavone/flavonol glycoside peaks of high performance liquid chromatogram (HPLC)-diode array detection (DAD)-tandem mass spectrometry (MS/MS) profiles based on a MATLAB-based script implementing an in-house algorithm. The HPLC-DAD-MS/MS profiles of red onio...

ABSTRACT Oligomeric proanthocyanidins were successfully identified by UHPLC-PDA-HRMSn in a selection of plant derived materials (jujube fruit, Fuji apple, fruit pericarps of litchi and mangosteen, dark chocolate, and grape seed and cranberry extracts). The identifies of around 247 proanthocyanidins were theoretically predicted by computing high acc...

Forty-one samples of skim milk powder (SMP) and nonfat dry milk (NFDM) from 8 suppliers, 13 production sites, and 3 processing temperatures were analyzed by NIR diffuse reflectance spectrometry over a period of 3 days. NIR reflectance spectra (1700-2500 nm) were converted to pseudoabsorbance and examined using (a) analysis of variance-principal com...

An UHPLC-PDA-ESI/HRMSn profiling method was used to identify the glucosinolates and flavonoids of Rorippa indica (Cruciferae), a wild vegetable and Chinese herb used to treat cough, diarrhea and rheumatoid arthritis. Thirty three glucosinolates, more than 40 flavonol glycosides, and more than 20 other phenolic and common organic compounds were iden...

Chromatographic profiles of skim milk powder (SMP) and mixtures of SMP with soy (SPI), pea (PPI), brown rice (BRP), and hydrolyzed wheat protein (HWPI) isolates were obtained by ultra-high performance liquid chromatography (UHPLC) with 215 nm detection. Two data analysis approaches were compared for their utility to classifying samples as authentic...

Caffeine in energy products is currently a focus of concern. However, not all energy products are caffeinated. Objective : To profile dietary ingredients (DI) in DS sold as energy products. Methods : We used the Dietary Supplement Label Database (DSLD) to identify DS with “energy” in the product name and compile their composition. We categorized th...

According to 2007‐2010 NHANES, 7.5% of the US population reports taking botanical dietary supplements (DS). One of the botanical ingredients in DS most commonly consumed and studied for its health benefits is green tea. Green tea consumption is associated with decreased risk for mortality, cardiovascular disease and cancer. However, DS labels and l...

The polyphenol content of cocoa is high and consumption is associated with benefits to human health. To determine the metabolites of cocoa derived flavanols after consumption, five months old conventional crossbred pigs were fed 5, 10, and 20 g of flavanol‐enriched cocoa powder per day for 26 days. The total flavanol content in the cocoa powder was...

Standard Reference Material 3280 Multivitamin/ Multielement Tablets was issued by the National Institute of Standards and Technology in 2009, and has certified and reference mass fraction values for 13 vitamins, 26 elements, and two carotenoids. Elements were measured using two or more analytical methods at NIST with additional data contributed by...

The AOAC INTERNATIONAL guidelines for validation of botanical identification methods were applied to the detection of Asian Ginseng [Panax ginseng (PG)] as an adulterant for American Ginseng [P. quinquefolius (PQ)] using spectral fingerprints obtained by flow injection mass spectrometry (FIMS). Samples of 100% PQ and 100% PG were physically mixed t...

Brassica vegetables are known to contain relatively high concentrations of bioactive compounds associated with human health. A comprehensive profiling of polyphenols from five Brassica species microgreens was conducted using ultra high-performance liquid chromatography photo diode array high-resolution multi-stage mass spectrometry (UHPLC-PDA-ESI/H...

A multinational collaborative team led by the US Pharmacopeial Convention is currently investigating the potential of NIR spectroscopy for nontargeted detection of adulterants in skim and nonfat dry milk powder. The development of a compendial method is challenged by the range of authentic or nonadulterated milk powders available worldwide. This pa...

Macular degenerations, inherited and age related, are important causes of vision loss. Human genetic studies have suggested perturbation of the complement system is important in the pathogenesis of age-related macular degeneration. The mechanisms underlying the involvement of the complement system are not understood, although complement and inflamm...

Non-targeted detection of botanical adulterants is conceptually simple. Analyze authentic materials, build a model, establish acceptable statistical limits, and then determine if the unknown material lies within those limits. But, the devil is in the details. The definition for “authentic” should be as tight as possible, otherwise the variance of t...

The hepatoprotective potential of ethanolic extract of Cardiospermum halicacabum (ECH) was evaluated in Wistar rats having liver injury induced by CCl4. The free radical scavenging activity of ECH was evaluated by ABTS and DPPH assay. Phenolic compounds like luteolin 7-o-glucoronide, apigenin 7-o-glucoronide and chrysoerisol 7-o-glucoronide were id...

A balance of experts and international representation were integral to the ERP in ensuring that methods are accepted worldwide and meet regulatory testing requirements. Panel members were thoroughly vetted by the AOAC Official Methods Board. Based on this discussion, the ERP decided to review methods whether they provided equivalent results or not....

The fingerprints of 18 commercially available Ginkgo biloba supplements, 12 samples of raw G. biloba leaves, and three G. biloba standard reference materials from the National Institute of Standards and Technology were acquired directly (no chromatography) by UV spectrometry and after separation using HPLC with a diode array detector. The fingerpri...

Animal studies have demonstrated that iron may be related to carcinogenesis, and human studies found that heme iron can increase the formation of N-nitroso compounds, which are known carcinogens. One of the postulated mechanisms linking red meat intake to cancer risk involves iron. Epidemiologic studies attempt to investigate the association betwee...

Chamomile (Matricaria chamomilla L.), tarragon (Artemisia dracunculus L.) and Mexican arnica (Heterotheca inuoides) are common compositae spices and herbs found in the US market. They contain flavonoids and hydroxycinnamates that are potentially beneficial to human health. A standardized LC-PDA-ESI/MS profiling method was used to identify 51 flavon...

A general method was developed for the systematic quantitation of flavanols, proanthocyanidins, isoflavones, flavanones, dihydrochalcones, stilbenes, and hydroxybenzoic acid derivatives (mainly hydrolyzable tannins) based on UV band II absorbance arising from the benzoyl structure. The compound structures and the wavelength maximum were well correl...

Television shows featuring crime scene investigators have been keeping viewers intrigued for years. But the Agricultural Research Service’s intriguing “food composition investigators” are just as innovative at deciphering truth from fiction relating to ingredients of plant-based foods and dietary supplements. The researchers are at the ARS Food Com...

Panax quinquefolius L ( P. quinquefolius L) samples grown in the United States and China were analyzed with high performance liquid chromatography-mass spectrometry (HPLC-MS). Prior to classification, the two-way data sets were subjected to pretreatment including baseline correction and retention time (RT) alignment. Principal component analysis (P...