Selected Past Projects

This list includes selected past projects that were funded by CDRF and are listed alphabetically by researcher.  Publications resulting from these projects are provided where applicable.

Adaska, John

Prevalence of Mycobacterium Avium Subspecies Paratuberculosis in Waste Milk Delivered to Five California Ranches

Isolation of Mycobacterium avium subsp. paratuberculosis from waste milk delivered to California calf ranches

Low rate of detectable in utero transmission of Mycobacterium avium subspecies paratuberculosis in a dairy herd with a low prevalence of Johne’s disease.

Dairy Food Safety and Security Professional Training Program Fellowship


Baer, Dave

Effect of Whey Protein on Body Weight, Body Fat, and Health Indices

Whey Protein but Not Soy Protein Supplementation Alters Body Weight and Composition in Free-Living Overweight and Obese Adults


Barile, Daniela

Effectiveness of Bovine Milk Oligosaccharides in Modifying Gastrointestinal Function in Healthy Individuals

Bovine Milk as a Source of Functional Oligosaccharides for Improving Human Health

Quantitative Analysis of Gangliosides in Bovine Milk and Colostrum Based
Dairy Products by Ultrahigh Performance Liquid Chromatography-Tandem Mass Spectrometry


Carpenter, Tim

A Model of Intra-Herd Transmission of FMD and its Transmission in California Dairies

A Predictive Model of the Spread and Control of FMD in CA, Using Data from the 2001 FMD Epidemic in Argentina

Simulation Modeling of Foot & Mouth Disease Spread and Control

A dynamic, optimal disease control model for foot-and-mouth disease: I. Model description

A dynamic, optimal disease control model for foot-and-mouth-disease: II. Model results and policy implications

Model could aid emergency response planning for foot-and-mouth disease outbreaks

Epidemic and economic impacts of delayed detection of foot-and-mouth disease: a case study of a simulated outbreak in California

Simulation modeling as an exotic livestock disease disaster planning tool

A simulation model of intraherd transmission of foot and mouth disease with reference to disease spread before and after clinical diagnosis

Emergency vaccination to control foot-and mouth disease: Implications of its inclusion as a U.S. policy option

Potential impact of introduction of foot-and mouth disease from wild pigs into commercial livestock premises in California


Crossley, Beate

Rapid High-throughput Milk Assay Adaptable to Foot and Mouth Disease and Other Pathogens


Cullor, Jim

Dairy Food Safety Laboratory

Differential levels of mRNA transcripts encoding immunologic mediators in mammary secretions from dairy cows with subclinical environmental Streptococci infections.

Biological markers of neonatal performance: the relationship of insulin-like growth factors-I, zinc and copper to poor neonatal growth. 

Quantitative Microbial Risk Assessment for Staphylococcus
aureus and Staphylococcus Enterotoxin A in Raw Milk

Toxoplasma in animals, food, and humans: An old parasite of new concern. 

Diagnostic Testing and Management Schemes for the Control of Johne’s Agent in Milk


DePeters, Ed

Effect of Diet on Nutrient Excretion and Air Emissions of VOC Methane, and Ammonia by Dry and Lactating Cows

Volatile organic compound emissions from dairy cows and their waste as measured by proton-transfer-reaction mass spectrometry


Drake, MaryAnne 

Establishing Uniqueness of Dairy proteins Against Competitive Soy Protein Products

Sensory properties of whey and soy proteins. 

Sensory properties of meal replacement bars and beverages made from whey or soy proteins.

Consumer perception of whey and soy protein in meal replacement products.

Comparison of lexicons for descriptive analysis of whey and soy proteins in New Zealand and the United States

Methods to Increase the Shelf Life of Whole Milk Powder

Effect of nitrogen flushing and storage temperature on flavor and shelf-life of whole milk powder

Flavor variability and flavor stability of US-produced whole milk powder

The Flavor and Flavor Stability of Skim and Whole Milk Powders

Mineral Analysis in California Milk Powder


Everett, David

Cal Poly Industry Outreach Program


Gardner, Ian

Certification of California Cattle Herds as Free of Johne’s Disease Using Bayesian Methods

Hierarchical Bayesian model for prevalence inferences and determination of a country’s status for an animal pathogen.

Determining the  infection status of a herd..

Sample size calculations for surveys  to substantiate freedom of populations from infectious agents.


German, Bruce

Milk Glycolipids: Capturing the Value of a Novel Class of Complex Molecular Conjugates

Method for the identification of lipid classes based on referenced Kendrick mass analysis

Rapid profiling of bovine and human milk gangliosides by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry.

Microbes and health Sackler colloquium: Human milk glycobiome and its impact on the infant gastrointestinal microbiota.

Saturated fats: A perspective from lactation and milk composition

Lactosomes: Structural and compositional classification of unique nanometer-sized protein lipid particles of human milk.

Reconstituted lipoprotein: A versatile class of biologically-inspired nanostructures.

Feeding the world today and tomorrow: The importance of food science and technology

Dietary lipids from an evolutionary perspective: sources, structures and functions.

Use of attenuated total reflectance Fourier transform infrared spectroscopy to study lactosylceramide and GD3 DMPC bilayers

Multiple precursor ion scanning of gangliosides and sulfatides with a reverse-phase microfluidic chip and quadrupole time-of-flight mass spectrometry

The Functional Deconstruction of Milk Oligosaccharides

The complete genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome

Permeate from cheese whey ultrafiltration is a source of milk oligosaccharides.

Glycoprofiling Bifidobacterial consumption of galacto-oligosaccharides by mass spectrometry reveals strain-specific, preferential consumption of glycans

Glycoprotein expression in human milk during lactation

Consumption of human milk oligosaccharides by gut-related microbes

The development of an annotated library of neutral human milk oligosaccharides

Neutral and acidic oligosaccharides in Holstein-Friesian colostrum during the first 3 days of lactation measured by high performance liquid chromatography on a microfluidic chip and time-of-flight mass spectrometry.

Evolutionary glycomics: Characterization of milk oligosaccharides in primates

An infant-associated bacterial commensal utilizes breast milk sialyloligosaccharides

Oligosaccharide binding proteins from Bifidobacterium longum subsp. infantis reveal a preference for host glycans

The influence of milk oligosaccharides on microbiota of infants: Opportunities for formulas

Transcriptome profiling of bovine milk oligosaccharide metabolism genes using RNA-sequencing.

Nano-LC-MS/MS of glycopeptides produced by nonspecific proteolysis enables rapid and extensive site-specific glycosylation determination

Site-specific protein glycosylation analysis with glycan isomer differentiation

Bacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways cell host microbe

Polymorphisms in genes in the SREBP1 signalling pathway and SCD are associated with milk fatty acid composition in Holstein cattle

Bifidobacteria isolated from infants and cultured on human milk oligosaccharides affect intestinal epithelial function.

Glycosylation of human milk lactoferrin exhibits dynamic changes during early lactationenhancing its role in pathogenic bacteria-host interactions

Natural variability in bovine milk oligosaccharides from Danish Jersey and Holstein-Friesian breeds

Comparison of the human and bovine milk N-glycome via high-performance microfluidic chip liquid chromatography and tandem mass spectrometry

The Milk Genome: Discovering the Molecular Basis of Milk’s Health Value

Implications of genomics for food and nutrition

Milk: a model for nutrition in the 21st century

Understanding milk’s bioactive components: a goal for the genomics toolbox

Bioguided processing: a paradigm change in food production

Saturated fats: what dietary intake?

Milk beyond essential nutrients: the metabolic food

Genetic dietetics: nutrigenomics and the future of dietetics practice

Nanoliquid chromatography‑mass spectrometry of oligosaccharides employing graphitized carbon chromatography on microchip with a high‑accuracy mass analyzer

Composition, applications, fractionation, technological and nutritional significance of milk fat globule membrane material

Composition, structure, and absorption of milk lipids: a source of energy, fat‑soluble nutrients and bioactive molecules

In vitro fermentation of breast milk oligosaccharides by Bifidobacterium infantis and Lactobacillus gasseri

A strategy for annotating the human milk glycome.

International milk genomics consortium trends food science & technology

Methods for the quantitation of human milk oligosaccharides in bacterial fermentation by mass spectrometry

Comparative review of diets for the metabolic syndrome: implications for nonalcoholic fatty liver disease.

Glycoprofiling of Bifidobacterial consumption of human milk oligosaccharides demonstrates strain specific, preferential consumption of small chain glycans secreted in early human lactation

In vitro fermentability of human milk oligosaccharides by several strains of bifidobacteria

Building the bridges to bioinformatics in nutrition research

Analysis and quantitation of fructooligosaccharides using  matrix-assisted laser desorption/Ionization Fourier transform ion cyclotron resonance mass spectrometry

Gene regulatory networks in lactation: identification of global principles using bioinformatics

Daily variations in oligosaccharides of human milk determined by microfluidic chips and mass spectrometry

Human milk oligosaccharides: evolution, structures and bioselectivity as substrates for intestinal bacteria

Size-dependent lipid content in human milk fat globules

Milk fat globule structure and function: nanoscience comes to milk production Trends in Food Science & Technology

The bovine lactation genome: insights into the evolution of mammalian milk

The genome sequence of Taurine cattle: A window to ruminant biology and evolution

A reappraisal of the impact of dairy foods and milk fat on cardiovascular disease risk

Lessons from the bovine genome: implications for human nutrition and research.

Permeate from cheese whey ultrafiltration is a source of milk oligosaccharides

Food in an evolutionary context: insights from mother’s milk

Predicting the Important Enzymes in Human Breast Milk Digestion


 Hammock, Bruce

Comprehensive Profiling of Vitamin D Metabolism

Metabolic profiling of major vitamin D metabolites using Diels-Alder derivatization and ultra-performance liquid chromatography-tandem mass spectrometry

Vitamin D intake needed to maintain target serum 25-hydroxyvitamin D concentrations in participants with low sun exposure and dark skin pigmentation is substantially higher than current recommendations

Vitamin D enhances corneal epithelial barrier function

Enhancement of vitamin D metabolites in the eye following vitamin D3 supplementation and UV-B irradiation


Harter, Thomas

Impact on Waste Management in Chronic Exposure of Dairy Cattle to Well Water Nitrate

Dairy Nutrient Management and Groundwater Quality

Evaluation of a simple, inexpensive dialysis sampler for small diameter monitoring wells

Characterizing sources of nitrate leaching from an irrigated dairy farm in Merced County, California

Shallow groundwater quality on dairy farms with irrigated forage crops


Karakas, Sidika

Effect of Whey Protein on Weight Loss, Glucose and Lipid Metabolism in Obese Subjects with Insulin Resistance, Polycystic Ovary Syndrome, and Type 2 Diabetes

Glucose-lowering effect of whey protein depends upon clinical characteristics of patients with type 2 diabetes

Relation of nutrients and hormones in polycystic ovary syndrome

Effects of Whey Protein on Weight Loss in Individuals with Metabolic Syndrome

Whey protein supplementation does not alter plasma branched-chained amino acid profiles but results in unique metabolomics patterns in obese women enrolled in an 8-week weight loss trial

Kebreab, Ermias

Developing Better Prediction Equations for Enteric Methane Emissions by U.S. Dairy Cattle

Environmental Impact of California Dairy Industry over 50 Years

Feed Formulation Variability and Environmental Impact Analysis

Korf, Ian

Milk, Health, and Genetics


Krochta, John

Applications and Bioactive Compound Incorporation for Protein Films and Coatings

Whey protein solution coating for fat-update reduction in deep fried chicken breast strips.

Storage stability of ascorbic acid incorporated in edible whey protein films.  

Whey protein-okra polysaccharide fraction blend edible films: tensile properties, water vapor permeability and oxygen permeability. 

Whey protein-polysaccharide blended edible film formation and barrier, tensile thermal and transparency properties. 

Grease penetration and browning resistance of pulpboard and paperboard coated with whey protein. 

Starch-methylcellulose-whey protein film properties. 

Triggering mechanisms for oxygen-scavenging function of ascorbic acid-incorporated whey protein isolate films.  

Barrier and tensile properties of whey protein-candelilla wax film/sheet. 


Lebrilla, Carlito

Milk Glycopeptides: A New Class of Bioactive Ingredients from Milk

The Glycoproteomics of Bovine and Human Milk

Enhanced Detection and Identification of Glycopeptides in Negative Ion Mode Mass Spectrometry

Comparison of the human and bovine milk N-glycome via high-performance microfluidic chip liquid chromatography and tandem mass spectrometry

Site-specific protein glycosylation analysis with glycan isomer differentiation

Simultaneous and Extensive Site-specific N- and O-Glycosylation Analysis in Protein Mixtures

Coupling Flash LC with MS for enrichment and isolation of milk oligosaccharides for functional studie

Site Determination of Protein Glycosylation Based on Digestion with Immobilized Nonspecific Proteases and Fourier Transform Ion
Cyclotron Resonance Mass Spectrometry

Analytical Performance of Immobilized Pronase for Glycopeptide Footprinting and Implications for Surpassing Reductionist Glycoproteomics

A Strategy for Annotating the Human Milk Glycome

Annotation and Structural Analysis of Sialylated Human Milk Oligosaccharides

Methods for the quantitation of human milk oligosaccharides in bacterial fermentation by mass spectrometry

Structural Determination and Daily Variations of Porcine Milk Oligosaccharides

Analysis and role of oligosaccharides in milk

Rapid Profiling of Bovine and Human Milk Gangliosides by Matrix-Assisted Laser Desorption/Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

Bovine Milk Glycome

Mass spectrometric methods for analysis of oligosaccharides in human milk


Lemay, Danielle

Translating the Science of Milk Genomics

SPLASH! Milk Science Update

Milk, Health, and Genetics


Maga, Elizabeth

Analysis of Microbial Biodiversity of Commercial Dairy Cattle Milk and Feces

Housing Type Affects the Fecal Microbiome of Commercial California Dairy Cattle

Microbial Diversity of Manure Streams and Bulk Milk


Marco, Maria

Does Milk Matter? The Importance of Milk

Attenuation of Colitis by Lactobacillus casei BL23 Is Dependent on the Dairy Delivery Matrix

Lactobacillus casei Low-Temperature, Dairy-Associated Proteome
Promotes Persistence in the Mammalian Digestive Tract

Short communication: Effect of milk and milk containing Lactobacillus casei on the intestinal microbiota of mice

Rapid Methods for Microbial Detection and Quality Assessment of Milk

The Core and Seasonal Microbiota of Raw Bovine Milk in Tanker Trucks and the Impact of Transfer to a Milk Processing Facility

Microbial Source Tracking & Endospores in Milk

Lactobacillus and Milk Interactions to Improve Epithelial Barrier Function


Medrano, Juan

Genomic Approach to Optimize the Content of Beneficial Oligosaccharides in the Cow Milk Supply

Transcriptome Profiling of Bovine Milk Oligosaccharide Metabolism Genes Using RNA-Sequencing

Primer on genes encoding enzymes in sialic acid metabolism in mammals

Valuation of milk composition and genotype in cheddar cheese production using an optimization model of cheese and whey production

Genomic Understanding of Milk Lipids; A Blueprint for Exploiting Milk’s Natural Variability

SNP discovery in the bovine milk transcriptome using RNA-Seq technology

The bovine lactation genome: insights into the evolution of mammalian milk

Fine mapping and association analysis of a quantitative trait locus for milk production traits on Bos taurus autosome 4.

Differential expression of bovine beta-lactoglobulin A and B promoter variants in transiently transfected HC11 cells

Transcriptional profiling of bovine milk using RNA sequencing

Polymorphisms in genes in the SREBP1 signalling pathway and SCD are associated with milk fatty acid composition in Holstein cattle


Meyer, Deanne

Facilitate Producer Management of Environmental Program

Analysis of Microbial Biodiversity of Commercial Dairy Cattle Milk and Feces

Development of an eLearning Decision Support Tree

Microbial Diversity of Manure Streams and Bulk Milk


Mills, David

Development of Engineered Probiotics for the Reduction of Pathogens

Isolation and characterization of lactic acid bacteria that selectively grow on the unique set of oligosaccharides found in milk

Genetic manipulation of Lactococcus lactis using targeted group II introns: generation of stable insertions without selection

Multicopy integration of heterologous genes using the lactococcal group II intron targeted to bacterial insertion sequences

Kinetics of Lactococcus lactis growth and metabolite formation under aerobic and anaerobic conditions at the presence or absence of hemin

Optimization of fed batch production of the model recombinant protein GFP in Lactococcus lactis

Development of chemically-defined media supporting high-cell density growth of lactococci, enterococci, and streptococci

Incorporation of nisI-mediated nisin immunity improves vector-based nisin-controlled gene expression in lactic acid bacteria

Dual inducible expression of recombinant GFP and targeted antisense RNA in Lactococcus lactis

A dynamic, genome-scale flux model of Lactococcus lactis to increase specific recombinant protein expression

Endo-β-N-acetylglucosaminidases from Infant Gut-associated Bifidobacteria Release Complex N-glycans from Human Milk Glycoproteins

Variation in Consumption of Human Milk Oligosaccharides by Infant Gut-Associated Strains of Bifidobacterium breve

A versatile and scalable strategy for glycoprofiling bifidobacterial consumption of human milk oligosaccharides


Raybould, Helen

Effects of Milk Components on Gastrointestinal Signaling Pathways

Host Effects Derived from Milk-Dependent Production of Soluble Signals from Bifidobacteria


Revzin, Alexander

Rapid Sensing for Bovine Interferon Gamma

An electrochemical aptasensor for detection of bovine interferon gamma 


Rossow, Heidi

Feed industry fellowship with a focus on dairy feeding systems


Thurmond, Mark

Development of Methods in Diagnostic Epidemiology: Surveillance Models to Enhance Biodefense and Biosecurity Against FMD

Epidemiology of Bovine Protozoal Abortion (BPA) a.k.a. Neospora Caninum: Determinants of Infection and Abortion on Affected Dairies


Tong, Phil

Impact of Dairy Protein Ingredients Options on Frozen Dairy Desserts

Composition of Milk for Cheese Manufacturing Plants


Van Loan, Marta

Milk & Yogurt vs. Calcium and Vitamin D Supplements for Bone Health in Postmenopausal Women

Is bone equally responsive to calcium and vitamin D intake from food vs. supplements? Use of (41)calcium tracer kinetic model

Cardiovascular and Immune Benefits to Elders From Increased Dairy Consumption


Whithaus, Carl

Translating the Science of Milk Genomics

SPLASH! Milk Science Update


Zivkovic, Angela

Effects of Dairy Fat on Postprandial Inflammation

The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types