Internship Projects

Principle Investigator: Sharma Shashi /, Marc Allard

Location: CFSAN Wiley Building, 5001 Campus Drive, College Park, MD (In-person)

Objective:

Responsible for assisting laboratory operations and perform examinations and experiments under the supervision of tenured laboratory staff.
The intern is expected to shadow all the laboratory processes, document their observations, and conduct an in-depth analysis of the results.

1. Prepare media, reagents etc. and ensures proper use of all protocols for specimen handling including pre-analytical, analytical and post-analytical processes.
2. Assures the accuracy and precision of all experiments performed by adhering to the laboratory’s Quality Control Standard Operating Procedures.
3. Performs routine equipment maintenance and function checks.

Interns will have an opportunity to learn NGS sequence data, gain hands-on experience in sample preparation, honing skills in DNA technology,
and mastering advanced laboratory techniques. This exposure enhances their ability to analyze and evaluate results, fostering a comprehensive understanding of the entire process. Additionally, interns develop a practical foundation in data analysis, crucial for navigating the intricacies
of NGS technology. This multifaceted experience equips interns with a well-rounded skill set, preparing them for diverse roles in genomics and
molecular biology”. 

Scope of Training:

The participant will receive hands-on training in the following tasks:

1. Collection, processing, and sequencing of whole genome, microbiomes and metagenomes of food and related environmental sample of interest
to FDA stakeholders.

2. Analysis of NGS sequence data from food ecology samples using available bioinformatic software and instrumentation and other customized
pipelines as well as evaluation and development of emerging analytical solutions.

3. Shotgun metagenomic analysis, including taxonomic and functional annotation using programs as needed.

4. Microbiome profiling using 16S rRNA gene amplicons, including sample preparation, sequencing and data analysis using an in-house and
Friend or Foe program provided bioinformatic pipeline.

5. The integration of custom pipelines into CFSAN HPC modules.

6. Evaluation of results from the perspective of forensic DNA typing virulence prediction to include review of controls, replicate sampling,
reproducibility, and confidence statements.

7. Report generation. Review of reports for clarity and consistency.

8. Analysis approaches of whole genome and microbiome deep sequencing, to include mixture ratios, species identification, quantitative
and qualitative variation over time, sampling, and confidence statements using Penn State E. coli Reference Center isolates.

9. Laboratory QC from the perspective of common forensic DNA typing practices.

Project Needs and Duration:

• Must have taken courses in Biology, microbiology, or related discipline.
• Demonstrate basic math and counting skills.
• Demonstrates interpersonal communication skills, both written and verbal
• Should be able to prioritize responsibilities and recognize when it’s appropriate to multitask or focus on one particular project at a time.
• Willing to take initiative.

This internship may have physical demands including, but not limited to, lifting, bending, pushing, pulling and/or extended walking and standing.
This role may also require usage of Personal Protective Equipment (PPE) and following institutional microbiological safety guidelines. Intern
past experience in these skills is helpful but not required.

The estimated duration of the internship project is one year. Time requirements include 8-10 h/week during the school year and 30 h/week during break sessions.

Description:

DARPA Friend or Foe program has developed biosurveillance technologies that detect bacterial pathogens quickly determining whether an unknown bacterium is harmless or virulent by directly identifying pathogenic behavior, avoiding conventional strategies that rely on known biomarkers. Current biosurveillance strategies based on biochemical markers fall short in identifying potentially harmful bacteria since they do not work on undiscovered bacterial strains. These new DARPA funded tools characterize bacteria by identifying pathogenic behavior itself with microfluidics and microscopic video capture. The high-throughput platforms from Harvard Medical School (HMS) and Texas A&M University (TAMU) screen millions of unfamiliar strains of bacteria at once to reveal their phenotypes to determine pathogenicity.  CFSAN Microbiology will be receiving two new instruments and will be working to evaluate these systems further, to assess whether they have added value for food safety applications.  FDA’s vast frozen collections of past outbreak pathogens will be used to train these systems for future predictions of pathogenicity.

One compelling expected research outcome based on the research strategies for using integrated microfluidic instrumentation to assess the pathogenicity of microorganisms is the development of a reliable and rapid method for pathogenicity screening. The iSentry integrated microfluidic instrumentation developed at Texas A&M University has the potential to provide a more accurate and high-throughput method for pathogenicity assessment compared to traditional methods. This could result in a significant reduction in the time and cost required for pathogenicity screening, as well as an increase in the accuracy of the results.

The use of iSentry integrated microfluidic devices for the assessment of pathogenicity in microorganisms has the potential to have a significant regulatory science impact. Specifically, the use of simplified microfluidic devices can provide a more rapid and accurate assessment of the pathogenicity of microorganisms, which can help in the development of more effective and targeted regulatory strategies. One potential impact of using such devices for pathogenicity assessment is the ability to rapidly detect and identify emerging pathogens. The device can allow for the high-throughput screening of microorganisms, which can help to identify new and emerging pathogens that may pose a threat to public health. This can enable regulatory agencies to quickly develop and implement strategies to prevent the spread of these pathogens, such as quarantine measures or the development of new preventive strategies.

Another potential impact for pathogenicity assessment is the ability to reduce the reliance on animal testing in regulatory studies. Traditional methods of pathogenicity assessment often involve the use of animals, which can be expensive and time-consuming. Microfluidic devices offer an alternative method for pathogenicity assessment that does not require the use of animals, which can help to reduce the cost and time required for regulatory studies.  Overall, the use of iSentry integrated microfluidic for the assessment of pathogenicity in microorganisms, as well as the Mother Machine have the potential to revolutionize the field of regulatory science. By providing a more rapid and accurate assessment of pathogenicity, microfluidic devices can help regulatory agencies to develop more effective strategies for protecting public health and can reduce the reliance on animal testing in regulatory studies.

Rapid detection would speed up current methods requiring bacterial culture, isolation and sequencing or PCR to determine the presence of genes associated with pathogenicity. Currently both STEC E. coli and Listeria monocytogenes are slow and difficult to determine pathogenicity, virulence varies widely and so each outbreak is assessed on a case-by-case basis. While genomic tools are assisting predictions of virulence and pathogenicity, based on the presence of know genes these methods are slow. Up front environmental surveillance may also support the food production industry and farmers in assessing risks in their environments and proactively preventing contamination from occurring.  

Principle Investigator: Almeria, Maria (Sonia)

Location: CFSAN MOD-1, 8301 Muirkirk Road, Laurel, MD (In-person)

Objective:

1) Learn concentration techniques based on flotation in dense solutions for detection of C. cayetanensis oocysts in soil.
1.1 Sample preparation step and seeding with C. cayetanensis oocysts.
1.2 Concentration and washing to remove the parasite’s oocysts from soil
1.3 DNA extraction methods
1.4 TaqMan qPCR assay with internal amplification control to detect the parasite in the extracted samples.

2) Apply approaches to optimize recovery and detection of oocysts from soil and compare to methods of detection directly from soil without concentration.
2.1 Evaluation of different methods for detection of the parasite in soil.
2.2 Analysis of detection limits in each one of the methods.
2.3 Sample size adjustments.
2.4 Removal of matrix-associated PCR inhibitors.

3) Apply the approached in 1) and 2) to soil artificially contaminated with oocysts using the GEN1000 CONVIRON growth chambers or under controlled environmental conditions.

Project Needs and Duration:

The student should have general Microbiology knowledge and, if possible, some Molecular Biology experience. The estimated duration of the internship project is one year. Time requirements include 8-10 h/week during the school year and 30 h/week during break sessions.

Description:

Cyclospora cayetanensis causes a diarrheal illness called cyclosporiasis. Outbreaks of cyclosporiasis have historically affected thousands of persons in the U.S and often occur in multi-state fashion. The outbreaks in the U.S. have been frequently linked to fresh produce. However, there are significant gaps in our knowledge of the epidemiology of C. cayetanensis, and still to date there is not a clear understanding of the relative importance of the sources and routes of transmission of C. cayetanensis infection. The potential of contaminated soil as a source of infection needs to be considered. Cyclospora oocysts are highly resistant in the environment (soil and/or water) and to chemical disinfectants, and to date there is not a clear understanding of the relative importance of the sources and routes of transmission of C. cayetanensis infection. Contact with soil has been found to be a risk factor for C. cayetanensis infection in endemic areas, such as in Peru, Guatemala, and Venezuela, as well as in an outbreak in the U.S. Furthermore, C. cayetanensis has been recently found in soil collected from under the water drippers from vegetable plots in Italy and in soil from commercial berry farms in Mexico. These data suggest that contact with soil may be an important mode of transmission and could play a role in the contamination of foods. Our group recently developed a fast and sensitive method for the detection of C. cayetanensis in soil. This method will be used in the present project for detection of the parasite in soil artificially contaminated with oocysts using the GEN1000 CONVIRON growth chambers, under controlled environmental conditions. The main objective is to determine the effects that the environmental factors (type of soil, temperature, water, humidity, and photoperiod) have in C. cayetanensis detection, and possibly survival/sporulation, in soil and herbs artificially contaminated with the parasite, and to evaluate the seasonality trends. These data will allow FDA to better understand ways of C. cayetanensis transmission and to establish control measures to disrupt the cycle of transmission. This project will also help in filling gaps in risk assessment of C. cayetanensis in soil, which to date has not been performed.

Principle Investigator: Chen, Yi

Location: CFSAN Wiley Building, 5001 Campus Drive, College Park, MD (In-person)

Objective:

Evaluation of commercially available chromogenic agars for the isolation of Cronobacter from powdered infant formula and environmental samples.

Evaluation and update of the qPCR assay protocol in the FDA Bacteriological Analytical Manual (BAM), including master mix, primer and probe sequences.

Evaluation of rapid identification assays for Cronobacter.

Project Needs and Duration:

Course work and preferably lab course work in microbiology. Prior work experience in a microbiology lab preferred. The estimated duration of the internship project is one year. Time requirements include 8-10 h/week during the school year and 30 h/week during break sessions.

Description:

Cronobacter is a rare cause of invasive diseases, including bacteremia, meningitis, and necrotizing enterocolitis. Infants younger than 2 months old are at highest risk. The organism is able to survive in low moisture foods, such as powdered infant formula (PIF), for long periods. In late 2021 and early 2022, a series of Cronobacter spp. illnesses among infants in the U.S. was associated with PIF. FDA inspection of the suspected facility revealed the presence of Cronobacter spp. within the production environment, leading to a voluntary recall. This recall and the temporary shutdown of the facility were a major contributing factor to the infant formula shortage across the U.S. in 2022. This incident highlights the critical need for FDA to enhance the testing of Cronobacter in PIF and its production environment, as well as other samples related to Cronobacter infection investigations. The FDA Bacteriological Analytical Manual (BAM) contains FDA’s preferred laboratory procedures for the detection of Cronobacter in PIF. However, this chapter was last updated more than 10 years ago. Since that update, new enrichment broths, chromogenic agars, qPCR master mixes and rapid identification assays have been developed or updated, some of which might perform better than those in the BAM. In addition, ISO published its Cronobacter standard in 2017 and prescribes a sample size smaller than that in the BAM. Furthermore, Cronobacter has gone through some nomenclature changes since 2012, and thus, the specificity of the BAM screening and identification methods needs to be evaluated. Finally, the testing of Cronobacter is expanding to matrices other than powdered infant formula, such as environmental swabs, nursery water and baby cereal. The current enrichment scheme in the BAM may not be optimal for recovering Cronobacter from these matrices. Therefore, a major update of the BAM is needed for improved testing of Cronobacter and any changes should be subsequently validated.

Principle Investigator: Cinar, Hediye

Location: CFSAN MOD-1, 8301 Muirkirk Road, Laurel, MD (In-person)

Objective:

1. Assist in the establishment and maintenance of the organ-on-a-chip system.
2. Perform/assist experiments designed to evaluate system parameters for propagation of the apicomplexan parasites.
3. Contribute to data analysis using currently available statistical analysis tools.
4. Contribute to communication of the research findings by involving in preparations on posters, and manuscripts.

Project Needs and Duration:

a. The student intern should have had at least some General Microbiology courses with labs.

b. The student should have some familiarity in using computer programs other than MS office.

c. Students should be able to work in the laboratory using different kinds of experimental procedures, including cell biology and molecular biology methodologies.

The estimated duration of the internship project is one year. Time requirements include 8-10 h/week during the school year and 30 h/week during break sessions.

Description:

Cyclospora cayetanensis, a microscopic intestinal parasite, causes food-borne and water-borne infections in endemic and epidemic fashion worldwide. In the US, food-borne outbreaks of C. cayetanensis have been an ongoing public health problem since mid-1990s. Current scientific knowledge suggest that this parasite is human specific, causes an intestinal disease called cyclosporiasis. Previous studies were unable to show propagation of C. cayetanensis in in vivo or in vitro systems. Also, due to the lack of animal models, the only source for oocysts for the research program to propagate C. cayetanensis in vitro, would be the oocysts obtained from patient stool samples. Scarcity of these samples renders such research impossible. To overcome this hurdle, we propose to use other related apicomplexan organisms such as Cryptosporidium spp., Toxoplasma gondii, and/or Eimeria spp., that could serve as a model for evaluating the gut-on-a-chip model, prior to testing C. cayetanensis. Cryptosporidium oocysts are the only commercially available oocysts, making these organisms amenable for starting this research projects. The organ-on-a-chip technology emulates the complexity of human gut structurally and physiologically in vitro, providing a viable research platform for challenging scientific problems such as in vitro propagation of C. cayetanensis.

Principle Investigator: Durigan, Mauricio

Location: CFSAN MOD-1, 8301 Muirkirk Road, Laurel, MD (In-person)

Objective:

• Perform detection methods like qPCR, conventional PCR, and digital PCR on the DNA extracted from environmental samples.
• Perform the Dead-end ultrafiltration on different water sources to compare the recovery on different matrices.
• Perform sample purification with state-of-the-art methodologies such as immune magnetic beads and/or DNA purification methodologies.
• Contribute to data analysis using currently available bioinformatics tools.
• Contribute to communication of the research findings by involving in preparations on posters, and manuscripts.

Project Needs and Duration:

• The student intern should have had at least some General Microbiology courses with labs.
• The student should have some familiarity in using computer programs other than MS office
• The student should have an interest to learn about PCR, qPCR and dPCR
• The student should be able to work in the laboratory using different kinds of sample processing, DNA preparation, spiking of samples, and microscopy.

The estimated duration of the internship project is one year. Time requirements include 8-10 h/week during the school year and 30 h/week during break sessions.

Description:

Cyclospora cayetanensis is a protozoan parasite that causes a foodborne diarrheal illness called cyclosporiasis which is linked to the consumption of contaminated fresh produce including leafy greens, snow peas, and berries. Since 2013 there has been an increase in the number of domestically acquired laboratory-confirmed cases of cyclosporiasis. The potential use of contaminated water for agricultural purposes poses a significant public health issue to millions of people worldwide and a method for detection of C. cayetanensis in agricultural water was recently validated and published in the FDA’s BAM Chapter 19c. There is a need to evaluate the performance of this method in different water sources such as well water, produce wash water, wastewater, and surface water, among others. There is also a need to develop and apply new generation of molecular markers for detection and for genotyping in environmental samples. This study will provide FDA with tools to accumulate scientific data about the different water matrices and their impact in the transmission of C. cayetanensis.

Principle Investigator: Gopinath, Gopal

Location: CFSAN MOD-1, 8301 Muirkirk Road, Laurel, MD and CFSAN Wiley Building, 5001 Campus Drive, College Park, MD (In-Person)

Objective:

Prepare DNA from our Cronobacter strain collection to test primers.

2. Sequence strains that are new to GenomeTrakr database.
3. Use sequences to select diversity of Cronobacter strains spanning top 3 species in one group and others in another group.
4. Compare genomes and datasets from different methods generated as part of this project to identify specific targets.
5. Design primers for conventional PCRs and qPCRs and test them in the laboratory for efficiency.
6. Work with mentor to learn bioinformatic methods to compare genomes for designing AmpliSeq panel for Cronobacter typing and speciation goals.

Project Needs and Duration:

1. Course work in microbiology. molecular biology
2. Any experience in microbiology laboratory and general molecular biology techniques
3. Any experience om sequencing will be a plus
4. Familiarity with Python for doing bioinformatic analysis.

The estimated duration of the internship project is one year. Time requirements include 8-10 h/week during the school year and 30 h/week during break sessions.

Description:

In 2022, a major crisis connected with the presence and identification of Cronobacter species in powdered infant formula (PIF), associated manufacturing sites and in patients highlighted the food- safety impacts of this organism. Some gaps in the Bacteriological Analysis Methods (BAM) used by FDA analysts were accentuated during the Agency’s response to the crisis. Based on that experience, the Agency had recommended improvements in the decade-old laboratory methodologies used for testing and identification of Cronobacter sakazakii in PIF and manufacturing plants. Also, Cronobacter strains at the level of species have become ‘reportable’ necessitating a validated protocol to speciate this genus consisting of 7 species. Three of the seven species are known to cause neonatal infections and illnesses in adults with compromised immune systems.

Accordingly, continuing the efforts to enhance culture and qPCR methods is a priority. Cronobacter species are opportunistic pathogens capable of adapting and surviving in dried foods like PIF and on inert surfaces present in food production facilities due to their xerotolerance (i.e., desiccation resistance).

The microbiological and molecular methods used for routine surveillance require important updates. New strategies using genomics for molecular fingerprinting of isolates from PIF and environmental samples are needed at this time. An improved set of targets for qPCR informed by genomic analysis will increase sensitivity and specificity for unambiguous detection.

The ongoing project that started in Oct 2023 will develop specific qPCR methods for speciation and targeted genome panel – AmpliSeq- that would help in source tracking and subtyping of the contaminants in PIF and environmental samples.

Principle Investigator: Holt, Leighna

Location: CFSAN University Station, 4300 River Road, College Park, MD (Hybrid of Remote/ In-person)

Objective:

• Develop experience and understanding of OFAS data systems (CERES, FARM, STARI, etc.) to leverage the information across these systems to collect a holistic record of the scientific information and data on food additives and food contacts.
• Develop knowledge of various toxicology testing protocols (genetic toxicology, subchronic and chronic) to accurately capture the data and endpoints reported in toxicological study reports. This requires developing familiarity with FDA guidance and OECD test guidelines.
• Perform specialized investigative research and provide scientific guidance and advice on subjects related to legacy data harvesting, data management, and operation of OFAS data systems.
• Evaluate the new CERES Toxicology Data Entry Tool by suggesting changes to the user interface, analyzing the current state of the tool, and identifying areas for future development.

Project Needs and Duration:

• Awareness of basic principles of toxicology and toxicology tests (genetic toxicology, subchronic and chronic)
• Ability to work independently
• Experience with performing searches of databases
• Attention to detail

The estimated duration of the internship project is one year. Time requirements include 8-10 h/week during the school year and 30 h/week during break sessions.

Description:

The intern will assist with the collection of toxicology data from OFAS legacy records for incorporation into the Chemical Evaluation and Risk Estimation System (CERES). Updated and detailed toxicology information in CERES is used by OFAS scientists to support their scientific evaluations of food additives and packaging materials through read across, filling data gaps, and computational toxicology analyses. Utilizing legacy data in this manner is in line with the 3Rs (Replacement, Reduction, and Refinement) as it reduces the need for additional testing potentially involving animal studies.

Principle Investigator: Khuda, Sefat

Location: CFSAN MOD-1, 8301 Muirkirk Road, Laurel, MD (In-person)

Objective:

• Assist in the establishment of the experimental model for combined exposures.
• Assist in assessment of cell epithelial barrier integrity
• Assist in assessment of biomarkers (expression of tight junction and mucin genes) of epithelial integrity at the RNA and protein levels
• Assist in the analysis of the secreted immune biomarkers
• Assist in the analysis of the experimental samples for dietary supplement/probiotics in response to treatments

Project Needs and Duration:

• Basic laboratory calculations such as dilutions, normality, molarity, and preparing various reagents, pipetting techniques
• Skill to utilize laboratory equipment, computer programing to perform assays and manage records
• Lab experience in the area of general biochemistry, immunology, cellular and molecular biology, food chemistry/science

The estimated duration of the internship project is one year. Time requirements include 8-10 h/week during the school year and 30 h/week during break sessions.

Description:

The gut epithelium allows efficient passage of selective nutrients into the body and restricts the entry of harmful molecules and foreign antigens. Compromised tight junctions between gut epithelial cells contribute to the pathology of obesity, inflammatory bowel disease, autoimmune disease, allergic disease, colon cancer, as well as other diseases. Dietary components such as live microbial ingredients, polyphenols, lipids, and proteins can restore inflammation-induced intestinal barrier dysfunctions including tight junction integrity in in vitro models. Intact intestinal barrier is necessary for expecting the beneficial effect of live microbial food ingredients without aberrant immune responses. Conversely, some emulsifiers among food ingredients (also called surfactants or detergents) have already been shown to increase gut permeability by modulating tight junctions between epithelial cells. Thus, substances that normally are kept inside the gut lumen may pass through the epithelial barrier, thereby enhancing, rather than restricting, the absorption of those substances including live microbial ingredients. Since food ingredients interact with, and exert such effects on, the epithelial barrier, this makes intestinal epithelial cell models suitable to investigate the biological effect of commonly used ingredients. We have recently established an intestinal epithelial cell (Caco-2)-based bioassay (CARTS #: IF01685) to study the effect of emulsifiers on intestinal barrier functions and exposure to food allergens. We propose to investigate the complex effect of dietary components on the intestinal barrier using our previously established in vitro model, and in a co-culture model (Caco-2 with human intestinal goblet [HT29-MTX] cell line). This study can provide scientifically important information for the public understanding on the biological effect of overall components following consumption of complex food matrices.

Principle Investigator: , Li, Miao / An, Nan, / Fairman, Kiara

Location: CFSAN University Station, 4300 River Road, College Park, MD (Hybrid of Remote/ In-person)

Objective:

• Establish a database for skin permeability of chemicals. This would include gathering skin permeability data from published literature, curation of the data obtained and organization of these data into one repository. (Dr. Kiara Fairman will mentor the intern for database establishment, and Dr. Nan An will be responsible training the intern on data curation)
   
• Establish a repository of models for skin permeability prediction. Review current models and develop a repository with model equations in R. (Drs. Nan An and Miao Li will be responsible for the intern’s training)
   
• Identify Artificial Intelligence/Machine Learning (AI/ML) and/or mechanistically based models to predict skin permeability. Apply appropriate AI/ML algorithms and/or mechanistically based models for skin permeability data, and compare the predictions with current models. (Drs. Miao Li and Kiara Fairman will serve as mentors to the intern to establish AI/ML and/or mechanistically based models)

Project Needs and Duration:

• A strong background conducting literature searches form various databases and extracting, analyzing and integrating data into tabular and narrative summaries.
• Knowledge of at least one scripting language (e.g. Python, R, and Julia).
• Basic knowledge of statistics and computational modeling.
• Demonstrated written and oral communications skills.

Time requirements include 8-10 h/week during the school year and 30 h/week during break sessions.

Description:

 Understanding dermal absorption is important for risk assessment of cosmetic ingredients. Skin permeability is a key parameter to predict the absorption and disposition of chemicals through skin into systemic circulation. A reliable prediction of skin permeability of chemicals can support the development of a physiologically based pharmacokinetic (PBPK) model after dermal exposure; which would predict an internal dose to facilitate a toxicological risk assessment. Predictive modeling of transdermal absorption started in the early 1940s. With advancements in computational modeling, different types of algorithms and models, such as Potts-Guy model, Cleek-Bunge model, Wang-Kasting-Nitsche model, etc., were reported. Compilation of a well-curated database that includes permeability data for chemicals of interest to cosmetics risk assessment would be beneficial for both research and regulatory use to create reliable predictive models for skin permeation. The Modernization of Cosmetics Regulation Act of 2022 (MoCRA) indicates the sense from Congress that animal testing should not be used for the purposes of cosmetic safety assessment (with the exception of appropriate allowances). In addition, given that animal testing is being banned in a number of jurisdictions and cosmetics are marketed internationally, it is critical that validated alternative methods are developed. Therefore, reliable and robust skin permeability data will be needed to predict the toxicity from exposure to cosmetics. A database of skin permeation data and a repository of skin permeability predictive models would support dermal exposure assessment of cosmetic ingredients and potential impurities in cosmetic products.

Principle Investigator: McMahon, Carrie

Location: CFSAN University Station, 4300 River Road, College Park, MD (Hybrid of Remote/ In-person)

Objective:

• Design and/or refine existing systematic search strategy.
• Perform searches of publicly available news and science literature.
• Update internal “plant biotechnology pipeline monitoring” database with new entries.
• Analyze data and summarize conclusions drawn from internal database.
• (Time-permitting) support work on plant biotech monitoring component of WILEE.
• Present findings to Plant Biotechnology Program staff.

Project Needs and Duration:

The applicant should have a background in biology, preferably plant science, molecular and/or cellular biology, or genetics, with an interest in
agricultural biotechnology. Familiarity with searching scientific literature databases such as PubMed and strong analytical and written communication
skills also needed.

The estimated duration of the internship project is one year. Time requirements include 8-10 h/week during the school year and 30 h/week during break sessions.

Description:

What? This project is a horizon scanning activity that involves monitoring publicly available news and scientific literature for information about the use of biotechnology (e.g., genetic engineering, genome editing) to add new traits (e.g., increased nutrients, disease resistance, tolerance to changing climate conditions) to plants used as food. Information gathered about plants being developed with biotechnology – commonly referred to as “GMOs” – will be used to update an internal database and to enable subsequent analysis. The information may also be used in the development of the plant biotech monitoring component of CFSAN’s Warp Intelligent Learning Engine (WILEE).

How? The intern will refine/design and conduct a systematic search of reports in the news and scientific literature on products of plant biotechnology with the potential for commercialization. The intern will work with a mentor on OFAS’s Plant Biotechnology Team to analyze the results of their review and to summarize the findings. In addition, the intern will update OFAS’s internal monitoring database using their results and, time-permitting, will support work on the development of an automated approach to the plant biotech monitoring component of WILEE.

Why? Plant genetic engineering and genome editing are rapidly advancing, making it possible for a growing number of plant biotechnology developers to bring food crops with innovative new traits to the market. The Plant Biotechnology Team in FDA’s Office of Food Additive Safety works with developers to ensure that food from new plant varieties developed with biotechnology – commonly referred to as “GMOs” – are safe and lawful. To be successful in their mission to protect public health while supporting scientific innovation, it is important that members of this team are knowledgeable about developments in the use of plant biotechnology in the food supply. OFAS’s internal “plant biotechnology pipeline monitoring” database was last updated in May of 2022, by a former JIFSAN Intern, and is therefore out-of-date. An updated database and its analysis will help OFAS and the agency understand new trends, identify emerging developers, and track global developments in food and agricultural biotechnology.

Principle Investigator: Panda, Rakhi

Location: CFSAN Wiley Building, 5001 Campus Drive, College Park, MD (In-Person)

Objective:

• Selection of hydrolyzed calibrants that is suitable for quantitating gluten in fermented or hydrolyzed foods.
• Preparation of model gluten-incurred yeast and bacteria-fermented food products such as cheese, sourdough breads, sorghum beers and alcoholic ciders.
• Analysis of gluten-incurred fermented food samples using the multiplex-competitive ELISA with gluten-incurred yogurt as a calibrant, and evaluation of the precision and accuracy of the quantitation.
• Compare the analytical results obtained from the multiplex-competitive ELISA with other commercial competitive ELISAs for fermented/hydrolyzed gluten analysis.

Project Needs and Duration:

Basic pipetting skill, skills of weighing and measuring accurately, knowledge of food product preparation. Courses in Analytical Chemistry and Basic Food Science would also be helpful.

The estimated duration of the internship project is one year. Time requirements include 8-10 h/week during the school year and 30 h/week during break sessions.

Description:

Celiac disease (CD) affects approximately 1% of the world’s population and is triggered by the interaction of gluten (from wheat, rye, and barley and possibly oat) with the intestinal mucosa of sensitive individuals. Currently there is no treatment available for CD, and the only option to avoid a serious reaction is to follow a lifelong gluten-free diet. Reliable and accurate quantitation of gluten in foods and ingredients is paramount to meet this goal as well as to comply with the gluten-free regulations enacted by the regulatory bodies throughout the world. Accurate quantitation of gluten in fermented or hydrolyzed foods is challenging due to the lack of appropriate calibrants and variable proteolysis. As a step forward in this direction, a multiplex-competitive ELISA was developed that recognizes the protein/peptide profile differences among the different types of fermented and hydrolyzed foods such as wheat beers, barley beers, sourdough breads, soy-based sauces, barley malts, sprouted grains and hydrolyzed wheat proteins. Recently, it was possible to accurately quantitate gluten in certain fermented dairy products (yogurt, kefir, and buttermilk) by using gluten-incurred yogurt as a calibrant with the multiplex-competitive ELISA. This project will utilize several different hydrolyzed calibrants, including the recently developed gluten-incurred yogurt calibrant, with the multiplex-competitive ELISA to accurately quantitate the gluten content in several fermented and hydrolyzed food products. The intern will be involved in the selection of calibrants, preparation of gluten incurred model fermented or hydrolyzed food products, analysis of the products by the multiplex-competitive ELISA and assist with the validation process of the method once a calibrant is selected.

Principle Investigator: Pava-Ripoll, Monica

Location: CFSAN Wiley Building, 5001 Campus Drive, College Park, MD (In-Person)

Objective:

• Extract genomic DNA from a variety of food products and insect specimens.
• Perform genomic library preparation and/or target enrichment protocols.
• Analyze sequencing data.

Project Needs and Duration:

•       Intern will gain skills with genetics, genomics, laboratory experience with micropipettes, reagent preparation, etc.

The estimated duration of the internship project is one year. Time requirements include 8-10 h/week during the school year and 30 h/week during break sessions.

Description:

Food products can be adulterated with insects. Insect fragments in food are currently detected by removing them from the food matrix and then quantifying and taxonomically identifying them via microscopic analysis. For regulatory purposes, both identification and quantification are pertinent because they offer details about the degree and source of insect adulteration (field pests versus storage pests, for instance). Nevertheless, taxonomical identification of the insect fragments through microscopy takes a long time and requires a high level of expertise from the analysts. It also doesn't always yield resolution down to the species level.

The study of metagenomics makes it possible to create new methods for more accurately identifying eukaryotes, like insects, in food samples. Because eucaryotic species have multiple copies of their mitochondrial DNA, metagenomics becomes extremely sensitive when paired with mitochondrial sequencing.

This project uses shotgun metagenomics to develop and validate a new method for detection and identification of insect fragments in food products. Once validated, this method will be applied in labs to identify more insects found in food and stop food that contains avoidable insect contamination from getting to consumers.

Principle Investigator: Sahu, Surasri Nandan

Location: CFSAN MOD-1, 8301 Muirkirk Road, Laurel, MD (In-person)

Objective:

1. Assist in the establishment and maintenance of the organ-on-a-chip system.
2. Perform/assist experiments designed to evaluate system parameters for propagation of the apicomplexan parasites.
3. Contribute to data analysis using currently available statistical analysis tools.
4. Contribute to communication of the research findings by involving in preparations on posters, and manuscripts.
5. Evaluate the growth/survival possibility of microscopic parasites, such as Cryptosporidium and Toxoplasma in biopsy-derived organoids in-vitro and/or organ-on-chip system.
6. Help to develop a detection method of testing parasites using different molecular biological methods including dPCR, genome sequencing.
7. Help to develop imaging methods to be used in this project.

Project Needs and Duration:

a. The student intern should have had at least some General Microbiology courses with labs.

b. The student should have some familiarity in using computer programs other than MS office.

c. Students should be able to work in the laboratory using different kinds of experimental procedures, including cell biology and molecular biology methodologies.

Description:

Cyclospora cayetanensis, a microscopic intestinal parasite, causes food-borne and water-borne infections in endemic and epidemic fashion worldwide. In the US, food-borne outbreaks of C. cayetanensis have been an ongoing public health problem since mid-1990s. Current scientific knowledge suggest that this parasite is human specific, causes an intestinal disease called cyclosporiasis. Previous studies were unable to show propagation of C. cayetanensis in in vivo or in vitro systems. Also, due to the lack of animal models, the only source for oocysts for the research program to propagate C. cayetanensis in vitro, would be the oocysts obtained from patient stool samples. Scarcity of these samples renders such research impossible. To overcome this hurdle, we propose to use other related apicomplexan organisms such as Cryptosporidium spp., Toxoplasma gondii, and/or Eimeria spp., that could serve as a model for evaluating the gut-on-a-chip model, prior to testing C. cayetanensis. Cryptosporidium oocysts are the only commercially available oocysts, making these organisms amenable for starting this research projects. The organ-on-a-chip technology emulates the complexity of human gut structurally and physiologically in vitro, providing a viable research platform for challenging scientific problems such as in vitro propagation of C. cayetanensis.

Principle Investigator: Pawar, Rahul

Location: CFSAN Wiley Building, 5001 Campus Drive, College Park, MD (In-Person)

Objective:

1. Prepare analytical standards.
2. Maintain inventory of chemical standards.
3. Learn daily operations of an analytical laboratory including planning experiments, assisting in sample preparation and instrumental analysis.
4. Analysis of LC-MS data including statistical approaches and the preparation of scientific reports.

Project Needs and Duration:

1.  Good academic standing.

2.  Strong work ethic, inquisitive, pro-active, comfortable in a laboratory environment.

3.  Coursework in general and organic chemistry.

4.  Interest in chemistry.

5. Prior laboratory experience.

6.  Basic computer skills, including Excel.

The estimated duration of the internship project is one year. Time requirements include 8-10 h/week during the school year and 30 h/week during
break sessions.

Description:

Hemp products, including foods and products marketed as dietary supplements, have proliferated in the US marketplace since the passage of the 2018 Farm Bill. Interest in these products and their composition has grown rapidly in tandem with the market. Recently, products containing rare natural, cannabinoid-derived synthetic, and synthetic ‘unnatural’ cannabinoids have emerged as a growing market sector. To answer outstanding questions within FDA regarding hemp products, robust, accurate, and efficient methods for the analysis of cannabinoids in foods and products marketed as dietary supplements are needed.

This project will evaluate the use of a validated, targeted liquid chromatography-tandem mass spectrometry (LC-MS) method to determine cannabinoid content in approximately 200 market samples. All samples will be analyzed for 17 cannabinoids, including a quantitative determination of total cannabidiol, total Δ9-tetrahydrocannabinol, and Δ8 tetrahydrocannabinol. Targeted data will be compared to a non-targeted high-resolution mass spectrometry method developed to recognize cannabinoids and structurally related compounds using molecular networking. Combined, these results provide the Agency with a real-time, data-driven approach to characterize products in the current cannabis-derived product marketplace and are available as a data source to complement existing safety monitoring capabilities, inform risk assessment, and guide future policy development.

Principle Investigator: Zhang, Kai

Location: CFSAN Wiley Building, 5001 Campus Drive, College Park, MD (In-Person)

Objective:

• Characterize homogeneity using laser diffraction particle size analysis and real-time image analysis in representative (e.g., cereal grains) and challenging matrix groups (e.g., spices).

• Perform matrix extension of Compendial Method C-003 to priority commodities for regulatory analysis (e.g., dried fruits, DDGs, tree nuts, confectionary/candy, coffee, tortillas, and spices).

• Perform analyte extension to evaluate the co-occurrence of deoxynivalenol metabolites (e.g., nivalenol, 3- acetyl-deoxynivalenol, 15-acetyl-deoxynivalenol, and deoxynivalenol 3-glucoside).

Project Needs and Duration:

• Dedication to food safety

• Interests in food analysis

• Basic understanding of analytical chemistry

The estimated duration of the internship project is one year. Time requirements include 8-10 h/week during the school year and 30 h/week during break sessions.

Description:

 Aligned with the ongoing evaluation of automation, we aim to expand the use of an automated sample preparation platform and incorporate particle
size analysis to improve mycotoxin testing in new and challenging matrices. Laborious sample preparation and insufficient characterization of sample homogeneity are well-known challenges but often excluded from LC-MS based multi-mycotoxin analysis due to the lack of methodologies. The goal
of this study is to develop an automated sample preparation workflow using robotic tools, to streamline sample preparation for mycotoxin testing. This study will also evaluate the integration of a rotary sample divider and a laser diffraction particle size analyzer to characterize sample homogeneity in representative and challenging commodities such as cereal grains, peanut butter, dried fruits, confectionary/candy, coffee, tortillas, dried distillers
grains (DDGs), tree nuts, and spices. For new matrix groups, a matrix extension of Compendial Method C-003 will be performed following the FDA
Foods Program Guidelines for the Validation of Chemical Methods. Commodities outside of the standard performance range for C-003 will be
catalogued and considered for advanced development. In addition to sample and matrix considerations, monitoring the co-occurrence of
deoxynivalenol and its metabolites has been an important but underexplored topic. To assess occurrence, the current study will also evaluate the extension of C-003 to deoxynivalenol metabolites in cereal grain commodities. Combined, the study will generate scientific data to evaluate the
suitability of automated sample preparation, the incorporation of particle size analysis to characterize sample homogeneity, and extension of
Compendial Method C-003 to build capacity and support growth of the mycotoxin program.

Principle Investigator: Naum, Marianna

Location: CFSAN Wiley Building, 5001 Campus Drive, College Park, MD Hybrid of Remote/In-Person))

Objective:

Our primary role is to help manage communications by sometimes actively pushing information to the media, and others taking steps to draw as little
attention to an issue as possible. Therefore, retrospectively assessing how successful we are at achieving the desired outcome can greatly impact
future communications strategic decisions. The applicant will be responsible for monitoring news stories and subsequent social media impact on
CFSAN related issues, evaluating whether the content reflects the developed messaging, assessing whether the story portrayed the agency in a
positive, neutral, or negative way, and providing insight on how communications might be improved to better achieve the chosen objective. Further,
the applicant will monitor social media sites, such as Twitter, Facebook and Linkedin, to determine the role they played in propagating the relevant
news stories.

Project Needs and Duration:

The applicant could be a communications or journalism major with an interest in food safety. Applicants with a science background who are interested
in communications and have a good grasp of the English language and are able to communicate in written form will also be considered.

The estimated duration of the internship project is one year. Time requirements include 8-10 h/week during the school year and 30 h/week during break sessions.

Description:

Members of the CFSAN Strategic Communications and Public Engagement Staff (CPES) in collaboration with CFSAN program office staff spend much
of their time developing and clearing materials to communicate the Center’s policies and actions with various stakeholders. The media serve as a
conduit for the FDA to communicate to consumers, industry, Congress, state, local and international governments, and other stakeholders. Therefore,
it is supremely important that our communications be effective.  Presently, with the help of our current student intern we are able to monitor and
capture news articles in a weekly media report and we can evaluate the effectiveness of our efforts. Investing time to retrospectively evaluate the
success of our communications strategies helps us better understand for which issues/topics we are communicating clearly and reaching the target
audience. This helps inform decisions about future communications strategy and policy ventures, helping CPES and program office staff work smarter
not harder on the development and clearance of communications material.

 In the past year the information our current JIFSAN intern researched helped inform our communications strategy on healthy, PFAS, cosmetics
issues, food additive announcements, warning letter initiatives and safety alerts.

Principle Investigator: Friedlander, Adam

Location: CFSAN Wiley Building, 5001 Campus Drive, College Park, MD (100% Remote)

Objective:

The intern will:

• Review the FDA’s Low- or No-Cost Tech-Enabled Traceability Challenge submissions.
• Help create episodes in a video series highlighting key topic areas from previous Challenge submissions.
• Coordinate video deliverables with episode participants and draft scripts for the final episodes.
• Review an internal FDA tracing system.
• Reproduce traceback investigations to test the tracing system’s ability to improve current manual traceback methods.

Project Needs and Duration:

Applicants for this project should have sound skills in data analysis. Applicants for this project

should also have excellent oral and written communications skills and organizational skills.

The estimated duration of the internship project is one year. Time requirements include 8-10 h/week during the school year and 30 h/week during break sessions.

Description:

This multidisciplinary project will support the Office of Coordinated Outbreak Response and Evaluation (CORE) in advancing tech-enabled food traceability initiatives. The intern will research various supply chain technologies and data standards utilized by the food industry and help coordinate a five-part video series centered around low-cost technologies and data interoperability efforts, all to support domestic and international foodborne outbreak investigation improvements. In addition, this intern will serve as a business end-user and help test out the internal FDA Product Tracing System (PTS), which is still under development and will eventually be used to collect and analyze the food industry’s traceability data under the newly published Food Traceability Rule. Professional development experiences from this internship include project management, information technology, web application development (business user), public health, food science, regulatory affairs, and communications.

Principle Investigator: Girmay, Berhane

Location: CFSAN University Station, 4300 River Road, College Park, MD (Hybrid of Remote/ In-person)

Objective:

The intern will research and learn the FARM Data Quality utility and apply this knowledge:

• Identify mismatched data, curate, and apply corrections to the appropriate folder structure and roadmap.
• Document the methodology used in the curation process and generate periodic reports summarizing corrections made using the Food Applications and Regulatory Management system (FARM) reporting tools.
• Identify limitations of FARM utility tools and assist in providing requirements for the enhancement of FARM utility tools.
• The intern will also learn the regulatory processes used by OFAS, ODSP, and ONFL by interacting with the technical staff, regulatory and scientific reviewers while performing and supporting the data curation tasks.

Project Needs and Duration:

Computer science, information technology, or data science related courses that enable the intern to understand databases and information technology applications. The intern will interact with regulatory scientists and contractors to learn and contribute new ideas or methods for the enhancement of the system utility for performing data quality measures. The estimated duration of the internship project is one year. Time requirements include 8-10 h/week during the school year and 30 h/week during break sessions.

Description:

This is an opportunity to learn about an end-to-end regulatory information management system known as the Food Applications and Regulatory
Management system (FARM) which houses scientific and regulatory data. The project will help assist with the accurate classification and ready access of documents for use in safety reviews by scientific reviewers in CFSAN. The project includes performing quality control using the system data correction
utility, developing enhancements to the utility tool, documenting methodology, and learning how to generate summary reports. The Offices of Food
Additive Safety (OFAS), Dietary Supplement Programs (ODSP), and Office of Nutrition and Food Labeling (ONFL) in FDA's Center for Food Safety
and Applied Nutrition (CFSAN) utilize the FARM system as an official regulatory document repository because it captures scientific, regulatory, and
administrative information about submissions pertaining to the food additives, food packaging materials, dietary supplements, and health claims. In
addition, the system is a repository of correspondence from congress, industry, and citizens as well as Freedom of Information (FOI) requests and
responses. The system has gone through several upgrades, and CFSAN continues to improve and enhance system capabilities for use by the Office
of Color and Cosmetics (OCAC) for tracking correspondence and inquiries. FARM system is also enhancing its capabilities to optimize regulatory data management by integrating with other FDA interfacing systems that are used by regulatory review scientists in performing their duties to meet FDA
statutory deadlines.

Principle Investigator: Kwegyir-Afful, Ernest

Location: CFSAN University Station, 4300 River Road, College Park, MD (Remote)

Objective:

The intern will research and learn the FARM Data Quality utility and apply this knowledge:

• Use the Warp Intelligent Learning Engine’s knowledge discovery interface to label signal data
• Use data cleaning and merging tool to match name similarities for chemicals, products and pathogens.
• Extract toxicity data for chemicals from ChemTunes

Project Needs and Duration:

• A background in Biological Science or Chemistry is required to for the intern to be successful in this project.

The estimated duration of the internship project is one year. Time requirements include 8-10 h/week during the school year and 30 h/week during break sessions.

Description:

The Warp Intelligent Learning Engine (WILEE) is a Division of Science and Technology initiated project to develop a data product that will provide
the Office of Food Additive Safety with an advanced data driven risked based decision-making tool. This tool will leverage AI technologies to
integrate and process a large variety of data sources, generating reports with quick insights that will significantly improve our time-to-results in
predicting and analyzing market and regulatory trends that directly affect products under the Office's regulatory purview.  At completion, WILEE
will have multiple modules that enhances the Office’s capacity for postmarket surveillance and signal detection. ​

The intern will generate a large corpus of training data that can be viewed and further refined using expert opinion from CFSAN scientists.  These refined training set(s) will be used to train WILEE’s other machine learning predictive algorithms. The project will include using an application that provides easy access to the generated training data and the ability to correctly tag the record, either affirming the prediction made by the machine learning algorithm or indicating that machine learning algorithm needs modification. The intern will also use another user interface developed to help correct misspelled names and merge common items into a single item. The results of this data preparation step will help extract toxicity data for identified substance which WILEE will use in it’s risk ranking process for identified signals.  

Principle Investigator: Petro, Elizabeth

Location: CFSAN University Station, 4300 River Road, College Park, MD (Hybrid of Remote/ In-person)

Objective:

• The intern will review inquiries, identify frequently-asked questions (FAQs), draft responses to these FAQs (in collaboration with FDA colleagues with cosmetics expertise, both scientific and regulatory), and respond to inquiries that are not addressed in the FAQs.
•  Consolidated FAQs will be posted proactively to our FDA web page, to provide better customer service to both consumers and the regulated industry alike.
• The new knowledge that the intern would acquire would be knowledge about how cosmetics are regulated, including the regulatory process for making cosmetics safe, including additional insight on the process of developing guidance documents, promulgating proposed rules, finalizing proposed rules into final rules, and enforcing final rules.  What the intern learns about the regulatory process would be applicable to governmental oversight of food safety.

Project Needs and Duration:

The ideal intern will have strong communication skills and a science/public health background such that the individual will be able to recognize
patterns, handle competing priorities, and be very curious and ask many questions.

Time requirements include 8-10 h/week during the school year and 30 h/week during break sessions.

Description:

The Modernization of Cosmetics Regulation Act of 2022 (MoCRA) is the most significant expansion of FDA’s authority to regulate cosmetics since the Federal Food, Drug, and Cosmetic (FD&C) Act was passed in 1938. This new law will help ensure the safety of cosmetic products many consumers use daily.  With the passage of this new law, we have received an influx of questions from consumers and the regulated industry alike to our FDA Questions About MoCRA email address.  These questions have provided insights into areas of the law that need further clarification and eventual guidance, as well as letting us know some of industry’s concerns regarding implementation of many of the provisions. In addition to providing customer service to these inquirers, these inquiries provide valuable data, which, when analyzed, will allow FDA to better prioritize use of its limited public health resources.