Potential Mentors for 2020 - 2021

A

Jairaj Acharya

Laboratory of Cell and Developmental Signaling

Research Goals/Purpose:

Our group studies sphingolipid/phospholipid signaling using Drosophila and mouse as model organisms. We use a combination of genetic, biochemical and cell biological approaches to evaluate the role of genes of sphingolipid metabolism/signaling in physiologcial and pathological conditions

Training Plan:

The student will be trained in all basic methodologies required in our studies. The student will work under the supervision of a post-doctoral fellow. The student will have the opportunity to pursue small independent projects.

Jairaj Acharya

Research Goals/Purpose:

Our group studies sphingolipid/phospholipid signaling using Drosophila and mouse as model organisms. We use a combination of genetic, biochemical and cell biological approaches to evaluate the role of genes of sphingolipid metabolism/signaling in physiologcial and pathological conditions

Training Plan:

The student will be trained in all basic methodologies required in our studies. The student will work under the supervision of a post-doctoral fellow. The student will have the opportunity to pursue small independent projects.

Matthew Anderson

Research Goals/Purpose:

The goal our lab is to understand the functions of the genes that guide embryonic development that when mutated lead to cancer. We use mouse models to study these genes during embryogenesis. Recently we have employed cutting edge multiplex fluorescent mRNA detection techniques to analyze gene expression and embryonic patterning. For this project we want to continue our analysis of gene expression in embryos focusing on a few genes previously shown to be expressed in a gradient within an embryonic progenitor tissues.

Training Plan:

Students will learn to dissect mouse embryonic tissues, perform whole mount fluorescent in situ mRNA labeling, confocal imaging of labeled tissues, and computer modeling of gene expression.

Roxanne Angell

Research Goals/Purpose:

Project Management (PM): Enterprise Information Technology Program (EIT) and Information Technology (IT) Projects using Project Management best practices based on the Project Management Body of Knowledge (PMBOK). Current IT projects will be included in addition to new EIT projects or initiatives. These projects will be built out and followed through the processes and techniques for initiation, planning, implementation, monitoring and controlling, and closing. IT Service Improvement: The purpose is to improve upon processes and practices within the IEIT/IT Operations Group (ITOG) by using the Information Technology Infrastructure Library (ITIL) methodology of service strategy, service design, service transition, service operations and continual service improvement.

Training Plan:

Project Management (PM): The student intern will work with an EIT Project Manager on current and new IT centric project initiatives. Student will be exposed to the 47 processes, the 5 process groups, and the 10 knowledge areas of project management. Training includes biweekly Project Management Meetings, independent reading, and other project management training opportunities. IT Service Improvement: The student intern will work with the project manager on exploring and improving existing incident management, change management, configuration management, and problem management processes and procedures based on ITIL standards for continuous service improvement. Includes independent reading of best practices for IT Service Management, weekly change management meetings, and communication meetings with different groups aimed at achieving goals and preventing problems.

B

Ulrich Baxa

Research Goals/Purpose:

NCEF provides high end cryo-EM imaging for extramural users. Imaging sessions are usually 48 hours and each produces about 5 TB of uncompressed image data. There data and the corresponding metadata (microscope settings, position targeting, etc.) have to be collected, archived, analyzed for QC, and reported back to the users. We want to standardize and automate this process as much as possible so that we can increase our imaging efficiency. Automation of quality control and reporting will lift work load off microcopists and allow us to eventually switch to 24 hour imaging sessions which will increase the efficiency and reduce wait times.

Training Plan:

The student will be involved in creating software, scripts, and templates for automated image analysis and imaging quality control. He/She will be creating a report template that automatically fills in the metadata from a database and the quality control results. We are looking for somebody with a strong interest in programming and data analysis.

Kajal Biswas

Research Goals/Purpose:

The student will learn basic laboratory safety and basic biological techniques. The student will then be exposed to various molecular biological techniques like PCR, cloning, gel-electrophoresis, sequencing, western blot as well as cell culture techniques. In addition, the student will also be trained to obtain scientific information as well as maintaining and presenting experimental data in laboratory and scientific meetings.

Training Plan:

BRCA2 is a known tumor suppressor and presence of mutations are associated with predisposition to breast, ovarian and pancreatic cancers. Many variants with unknown significance has been identified in this gene from genetic screening of susceptible families. In an attempt to identify the pathogenic significance of those variants, our lab has developed an mouse embryonic stem cell based technology. We are now improving that technology using highthroughput mutation generation and next generation sequencing. The students will use this technology to generate mutations in mouse ES-cells using recombineering.

Mia Bjelogrlic

Research Goals/Purpose:

Serve as a member of the Occupational Health Team. Performing in the role of clinical staff performing activities in the clinic with the professional staff including: patient triage, taking vital signs, measuring height and weight, obtaining past medical history, planning and participating in wellness activities. (Take a Hike, wellness emails)

Training Plan:

Performing the following skills: Vital Signs (temperature, blood pressure, pulse, respirations, pulse oximetry), visual acuity, whispered voice testing, color vision, medication reconciliation, electronic medical record, venipuncture, informed consent, collection of specimens (midstream urine, venous blood sampling), intramuscular injections, intradermal skin testing, EKG, ear irrigation, eyewash, cardiopulmonary resuscitation, automatic external defibrillator AED) Independently plan, execute and evaluate a Wellness activity. (Take your child to work day, Take a Hike, Monthly wellness topics, Take Back your Lunch, Stairway to Wellness, or Stop the Bleed Education) Perform office adminisrative practices: answering telephone, scheduling appointments, scanning, participating with the quality control audit for scanning and assisting with medical records storage. Writing an occupational health article for the Poster. Deliver one presentation to the OHS staff at the weekly staff meeting in regard to one of the following topics: 1. Travel Medicine Topic 2. Evidence Based Practice Finding on Musculoskeletal System

C

Raul Cachau

Research Goals/Purpose:

Compile a series of procedures to improve the processing of electron microscopy data to generate molecular structures. The rapid evolution of electron microscopy (Cryo-EM and other modalities) have resulted in severe bottlenecks in the data processing. One way to improve the processing of electron microscopy data is by using modeling and machine learning tools, yet the integration of these tools is incomplete at present. The student will learn tools for image processing (Relion) for the reconstruction of electron density maps and help asses procedures to accelerate the processing of electron microscopy data.

Training Plan:

The student will first be made familiar with the process of electron microscopy data acquisition. Then she/he will be introduced to electron density maps reconstruction and become proficient with this process. Finally, the student will operate on model data (using the protocols previously learned) to asses the feasibility of using model data to accelerate the reconstruction of electron density maps. The student will be involved in projects related to immuno-oncology and cell receptors structure analysis.

Raul Cachau

Research Goals/Purpose:

Low temperature (cryo) electron microscopy (Cryo-EM) is a powerful tool to study the shape of macromolecules and explore the multiplicity of shapes they can adopt. A limitation of Cryo-EM is that molecules are frozen in place and the time evolution of the biological processes can only be followed using complex setups. Advanced modeling tools can dynamize these structures by exploring their flexibility and the way their shapes relate. The student will learn the method used for these types of studies (called stochastics dynamics) and help implement it for the study of immuno-oncology and cell receptors structure analysis.

Training Plan:

The student will first be made familiar with the process of molecular modeling. Then she/he will be introduced to molecular dynamics simulations and become proficient with this tool. Finally, the student will explore the dynamic behavior of a membrane protein (using the protocols previously learned) to asses the determinant features in the structure that are responsible for their function in the cell.

Ravindra Babu Chalamalasetty

Research Goals/Purpose:

Wnts are powerful secreted signaling molecules required for stem cell potency and cell-fate decisions in embryonic stem cells, early embryonic development and tumorigenesis. The current focus of our laboratory is to identify the key lineage determinants downstream of Wnt signaling pathway during embryonic stem cell differentiation.

Training Plan:

The Student will be trained under my supervision and will learn the concepts of the project. Selected student will be taught basics of Molecular Biology, Biochemistry, Cell Biology, Embryonic stem cell culture system, Developmental biology and Bioinformatics. They will then participate in independent projects with the expectation of experimental set-up, data analysis and record keeping and presentation.

Elena Cornejo Castro

Research Goals/Purpose:

The Viral Oncology Section (VOS) has developed a genome capture approach for the generation of Kaposi's sarcoma herpesvirus (KSHV) whole genome sequences using next generation sequencing. This virus is the causative agent of multiple malignancies observed throughout the world. Previously, very limited genetic characterization of KSHV was possible and strains were categorized based on few genes.

Training Plan:

The generation, characterization and downstream analysis of these data requires the use and adaptation of open-source bioinformatic tools. The student will assist in the comparative analysis of herpesvirus genomes, including the identification of sequence variations and recombination analysis. Further the student will validate and if necessary adapt a newly developed computational pipeline for the assembly of viral genomes.

Cathleen Cullen

Research Goals/Purpose:

Project Description The WHK Intern will work at the Office of Scientific Operations (OSO) within the NCI at Frederick. The WHK intern will spend time working with the public affairs specialist, administrative officer, and educational outreach specialist on his/her primary goal of communicating scientific and health information from the NCI at Frederick. Official projects will include 1) developing articles for the NCI at Frederick online newsletter The Poster, 2) creating and presenting a scientific research poster at the NCI at Frederick Poster Day, NIH Student Poster Day, and the NICBR Spring Research Festival and 3) additionally assisting in various internal and external outreach events that focus on communicating health and well-being, the NCI mission, and advantages of STEM education for Frederick County youth.

Training Plan:

Goals The overall goal of this internship is for the WHK intern to obtain an appreciation for communicating scientific discovery in plain language to the larger public. He/she will leave the internship with a greater understanding of how to communicate complex scientific topics to a lay audience. The intern will develop specific skills sets throughout the course of the internship to achieve this goal. The skills will include but are not limited to the following: • Written communication o The intern will write a series of articles highlighting various researchers at the NCI at Frederick for the Poster which will help the WHK intern experience the variety and breadth of science at the NCI at Frederick. He/she will have the opportunity to explore various areas and interests in science. Additionally, this will also help the student develop writing skills, including writing in plain language. • Oral Communication o The WHK intern will be responsible for developing and presenting a scientific research poster to a public audience several times through the course of the internship. These occurrences will give him/her the opportunity to orally present the various ways of communicating scientific discoveries to the public. It will also give the intern an opportunity to accept constructive feedback from peers and mentors about his/her presentation skills. o The WHK intern will also be responsible for developing and presenting a presentation at the NICBR teachers NECSES event. This presentation should include input from other students in the WHK intern program and potentially interns in other NICBR partner programs on scientific education. • Public Affairs & Outreach o The WHK intern will assist with various outreach events throughout the course of his/her time in the internship. The inter will gain experience with developing programs, handling professional interactions with the public, and advocating and promoting the proper communication of complex scientific discoveries and STEM education for Frederick County youth. The opportunities will enhance experiential learning for the WHK student in his/her develop in scientific communication. Timeline 1st quarter ( May/June – August/Sept) – learn the various tools for communicating with the public and within the NCI at Frederick. Develop a poster for presentation at various poster days. 2nd quarter (Sept/Oct. – Nov/Dec) – Select a scientist or professional at the NCI at Frederick to profile and work with communications staff on developing interview questions, setting up and conducting the interview, doing background research and writing an article to be published in the Poster. Write the beginning in a series of posts on the WHK student experience incorporating self-experience as well as experiences from other WHK students. 3rd quarter (Dec/Jan.- March/April) – conduct the second individual profile to be published in the Poster. Continue to develop student experience series. Research and suggest new potential articles or outreach activities for communicating scientific information. 4th quarter (March/April- May/June) – conduct the third individual profile for publication in the Poster. Help to develop the WHK student incoming/outgoing ceremony for enhancing the student experience in the WHK program.

D

Ira Daar

Laboratory of Cell and Developmental Signaling

Research Goals/Purpose:

The mechanisms controlling morphogenetic movements during development involve modifications of cell-cell and cell-matrix adhesion. Abnormal modifications of these adhesion systems are often associated with metastatic progression. Our present focus is on a subset of the Eph family of molecules that are de-regulated in a wide variety of metastatic cancers.

Training Plan:

The student will be taught to use the Xenopus system under my supervision or that of a postdoctoral fellow in the Cancer and Developmental Biology Laboratory. The project will involve completing the functional characterization of the cellular and developmental effects mediated by the intracellular portion of the EphrinB transmembrane Eph ligand. 1) EphrinB mutants will be expressed in developing embryos to determine structural motifs that are important for EphrinB-induced developmental effects. 2) EphrinB will be co-expressed with proteins found to be associated with EphrinB. The ability of these proteins to physically interact with EphrinB will be assayed. The ability to modulate EphrinB-induced developmental effects will also be assessed. 3) The ability of EphrinB to modulate the protein’s activity will also be tested.

Natalia De Val Alda

Research Goals/Purpose:

CMM offers investigators access to unique expertise and EM technologies that allow our partners to explore new avenues of research in order to enhance the knowledge of biological systems. Our lab provides high-resolution Transmission Electron Microscopy (TEM) with the use of our 300kEV Titan Krios electron microscope coupled with a direct detector k2 camera. Supporting equipment includes 2 FEI Vitrobot, as well as several FEI scopes to assess sample quality. The research goals for the WHK student will be to be able to understand all the EM pipeline, from sample preparation to data collection. The purpose will be for the student to become an independent user in our lab.

Training Plan:

The training plan is to become familiar with all the main procedures used in Electron Microscopy. He or she will be mainly working with myself as well as Htet Khant. He or she will learn how to work with cells, viruses as well as protein-protein complexes. This will give him/her a broad spectrum of the type of samples we work with at the CMM. He or she will focus mainly in the TEM technique. After the two months training, he or she will be able to do some of the sample preparations and data collection by himself/herself. Of course, he or she will be always monitored by me or Htet. He or she will start with some theoretical training about what is a TEM scope (this will take one or two days) and after that he or she will start working on the bench with Htet. At the end of his/her training, he or she will understand the main points of the EM technique and being able to prepare some of the easy samples by himself/herself.

F

John Fenimore

Research Goals/Purpose:

Our lab specializes in cancer and inflammation biology, with a focus in the cytokine, interferon gamma. It will also be a vital duty of our students to assist in helping support our mouse colony via regular genotyping and other lab duties. My work focuses on mitochondrial defects in our mouse model and how it related to human diseases with examinations of fatigue, metabolic and functional changes. Our students will work with model cell lines to examine underlying factors and questions in our inflammatory model.

Training Plan:

Along with basic laboratory skills, we hope to promote critical thinking and other tasks that will answer questions regarding this model of disease. We wish to promote a feeling of inclusion in our lab. Instruction on genotyping, cell culture, staining and working with your mentor on experimental design will be a large part of your experience.

H

Maryellen Hackett

Research Goals/Purpose:

1. Project Description – The WHK Intern will be stationed in the Office of Public Affairs, Frederick National Laboratory for Cancer Research. The intern will work closely with the director of public affairs to become acquainted with institutional public outreach in a national laboratory environment. The intern will interact with staff at all levels of the organization and with constituents in the Frederick community. The intern will gain experience with outreach projects to support institutional goals, crafting institutional messages for various audiences, writing, editing, photography, videography, using graphics and other visuals to communicate, website content management, social media best practices, face-to-face community interactions, and interacting and working with a creative services staff. The intern will also gain experience in internal business communications and intranet content management. Goal – The project is designed to give the WHK intern an understanding of how a public affairs office operates within a national laboratory environment and how communications can be used strategically to support the mission, and enhance the reputation, of a biomedical research organization. The internship will also provide experience with internal communications supporting best business practices and staff engagement. The intern will develop specific skill sets with opportunities for writing for a mass audience; writing for a website; use of multimedia; producing material for social media; business communication; tailoring messages for target audiences; converting scientific jargon into everyday language; researching and writing a news story; working with designers, photographers, and other creative individuals to produce successful outreach materials; and preparing for a trade show exhibit.

Training Plan:

2. Student Plan – The WHK intern will receive assignments as they arise throughout the year. For a general overview: Jun – Aug: Introduction to staff, community contacts. Writing exercises with a focus on the fundamentals of news-writing. Write 2-3 stories for Insite, including at least one scientific article, and explore multimedia options to accompany texts. Repurpose/recast as warranted to the Poster, FNL website, social media, handout, etc. Sep – Nov: Assist in preparing for In The Streets exhibit and other community events as they are available. Assisting in materials development. Opportunity to attend and participate in community outreach events. Continue to pursue outreach assignments as they arise. Work with creative service professionals on a variety of projects. Dec – Feb: Work on integrated communications to support institutional goals. For example: Write profile articles or produce videos on WSK interns for publication in Insite and the Poster. Continue with multimedia assignments. Mar – May: Assist in preparing exhibit, handout, and talking points for community events as they arise. Contribute to design of a sponsorship advertisement, i.e. the Weinberg speaker series. Work with SPGM on production. Continue producing materials for Insite, Poster, other channels.

Sarah Hooper

Research Goals/Purpose:

To explore occupational medicine and learn skill set and critical thinking to build a medical career.

Training Plan:

Performing the following skills: Vital Signs (temperature, blood pressure, pulse, respirations, pulse oximetry), visual acuity, whispered voice testing, color vision, medication reconciliation, electronic medical record, venipuncture, informed consent, collection of specimens (midstream urine, venous blood sampling), intramuscular injections, intradermal skin testing, EKG, ear irrigation, eyewash, cardiopulmonary resuscitation, automatic external defibrillator AED) Independently plan, execute and evaluate a Wellness activity. (Take your child to work day, Take a Hike, Monthly wellness topics, Take Back your Lunch, Stairway to Wellness, or Stop the Bleed Education) Perform office adminisrative practices: answering telephone, scheduling appointments, scanning, participating with the quality control audit for scanning and assisting with medical records storage. Writing an occupational health article for the Poster. Deliver one presentation to the OHS staff at the weekly staff meeting in regard to one of the following topics: Occupational medicine

K

Suhas Kharat

Research Goals/Purpose:

Student will learn basic molecular biology techniques such as plasmid isolation, primer designing, PCR reaction setup, restriction digestion, DNA ligation, bacterial transformation. Apart from molecular biology students will also work on some bioinformatic assignments such as analyzing DNA and protein sequences in BLAST and ClustalW tools. As part of specialized training students will learn fluorescence microscopy.

Training Plan:

Similar to Research goals.

Jay Knight

Research Goals/Purpose:

Basic understanding of IT Infrastructure including Networking, Server Operating Systems and Storage.

Training Plan:

Work side by side with the various infrastructure groups to learn day to day tasks associated with supporting and maintaining the IT infrastructure for FNLCR.

Ron Kunz

Research Goals/Purpose:

Assessment and planning for Emergency Operations.

Training Plan:

1. Research the standards for Emergency Management. 2. Learn the Operations of Environmental, Health and Safety 3. We will partner with the Occupational Health Services to plan and execute the Stop the Bleed Program. 4. Complete the basic FEMA training.

L

Stephen Lockett

Research Goals/Purpose:

Solid tumors contain a wide variety of cell types that are interacting with their neighbors and more distantly through cytokine signaling. To understand this complexity, it is necessary to label tumors with fluorescence antibodies to identify the scores of different cell types and then to image them microscopically. Next the images must be analyzed to quantify the numbers of each cell type and elucidate the cellular organization of the cells by determining which cell types are neighbors to other cell types. Currently these analyses are being performed in mouse models and changes in the spatial organization of cells, particularly immune cells are being discovered when the mice are treated with experimental therapies. The expertise for understanding these changes in cellular organization of tumors, the capabilities for growing and treating mouse tumors, performing the fluorescence labeling, acquiring the images and analyzing the images with existing algorithms are all in place and underway. However, currently there is a lack of personnel to apply the algorithms to images and to present the quantitative results from analysis in the form of tables, graphs and annotated images.

Training Plan:

The student will fulfill the aforementioned need. In doing so, (s)he will gain knowledge and understanding about tumors at the single cell level, about the process of labeling and acquiring microscope images and about the algorithms for analyzing the images. In terms of the analysis, the student will learn about the process of segmentation (separation of images into objects (cells) versus background), noise and distortions in images that affect quantification, statistical methods for determining probabilities and significance of results and methods to visually present results. The student may be trained in how to modify / extend existing algorithms if this is necessary and (s)he appears to have such ability. If the work involves images of human tumors, these images will have been deidentified before the student has access to them.

M

Tyler Malys

Research Goals/Purpose:

Application of statistical methodologies in collaboration with NCI-F investigators.

Training Plan:

Undergo mentoring to improve: data characterization, database interface, application testing, file conversion, data re-structuring, analytical graphic generation and statistical method implementation, in addition to quality assurance and completeness of tasks.

Arun Mishra

Research Goals/Purpose:

BRCA2 is a huge protein involved in DNA damage repair via homologous recombination. It does this by loading RAd51 nucleofilaments on the damaged DNA. BRCA2 has 8 BRC repeats which are known to interact with RAD51 and bring it near to the damaged DNA site. The redundancy of these repeats is not known. The student will be making multiple mutants of these repeats in human BRCA2 in a mouse ES cell system.

Training Plan:

The student is expected to learn basic lab techniques like PCR, western blotting, microbial cultures and a bit of microscopy, which would enhance his/her knowledge and expertise in molecular biology. The purpose is to induce him/her with critical thinking and designing small experiments for the project he/she is assigned.

Joelle Mornini

Research Goals/Purpose:

Researching and implementing effective methods for Library outreach and meeting the information needs of key user groups, including scientists, postdoc and postbac researchers, lab support staff, and students and interns.

Training Plan:

The Library Intern will job shadow Library staff members, assist with covering the front desk and interacting with Library patrons, assist with Library marketing and outreach (through the TV monitor, bulletin board, flyers, event emails, Library newsletter, analysis of users statistics and demographics, and other marketing and outreach methods), assist with collection development (through book inventory, processing donated books, and shelf reading), assist with Library events (including Student Jeopardy, Winter/Summer Video Series, Take Your Child To Work Day, and Book and Media Swap), and assist with creation and teaching Library trainings.

N

Kedar Narayan

Research Goals/Purpose:

At the Center for Molecular Microscopy, 3-D electron microscopic imaging of large cellular and tissue samples at nanoscale resolutions is carried out primarily by a technique called FIB-SEM, or Focused Ion Beam Scanning Electron Microscopy. Extraction of features of interest from these large image datasets, called “segmentation”, reveals new biology and helping confirm hypotheses. However, segmentation is a manual and a relatively slow step. In this research goal, we aim to set up and streamline manual and semi-automated segmentation of FIB-SEM datasets with the aim of efficiently visualizing biological structures in 3-D. Additionally, we aim to feed these "ground truthed" segmentation datasets to train a separately designed neural network, with the ultimate goal of accurate automated segmentation of FIB-SEM data.

Training Plan:

The WHK SIP students will be trained by CMM personnel to use segmentation software, and will be given training FIB-SEM datasets to practice and sharpen their skills. The CMM is highly collaborative, so there is a variety of interesting projects that require segmentation of specific cellular features, such as mitochondria, bacteria etc. The students will be expected to segment out these features as required, both for direct analysis, as well as for training the neural network.

P

Lorena Parlea

Research Goals/Purpose:

As scientific understanding of human diseases and their treatments expands, there is an ever-increasing focus on developing therapeutics that function on the smallest of scales. Nanomedicine can be used to fight afflictions from the moment they are expressed using gene-silencing therapy. The discovery of RNA interference (RNAi) served as a key to open the door for human gene therapy based on small interfering RNAs (siRNAs). Ever since, harnessing the silencing functions that siRNAs carry out within cells has become an endeavor of great importance; RNA itself may offer the most convenient method of delivering therapeutics to cells through the construction of functionalized RNA-based nanostructures. Student intern will be part of projects related to experimental RNA nanobiology working in conjunction with the computational RNA structure nano design component of our laboratory. Some potential projects are enumerated below. Final decisions on specific topics will be made after detailed discussions with the intern after arrival.

Training Plan:

Experimentally test and validate various RNA Nanoparticles self-assembly. Specific steps in the training will involve: 1) Independent search of literature in order to identify, read and possibly present relevant papers on RNA structure, nanobiology, and experimental approaches; 2) Learn experimental techniques used in our laboratory; 3) Aid in running experimental protocols used in RNA nano assembly; 4) Run various experiments to analyze and determine the structural features and functionalities of the designed nanoparticles; 5) Attend seminars when possible; 6) Collaborate with other scientists; 7) Aid in writing results in scientific papers.

Lorena Parlea

Research Goals/Purpose:

Our lab's research goal is to understand the characteristics of RNA folding and self-assembly, and to explore the immuno/therapeutic potential of functionalized RNA-based nanoparticles.

Training Plan:

Students will learn how to perform various experimental techniques pertaining to RNA Nanoparticles production, such as PCR and transcriptions, purification, assembly and analysis. Students will also prepare native and denaturing gels and run gel electrophoresis. Additionally, students will be involved in maintaining cell lines, testing the RNA Nanoparticles on several cell types, and assessing their effect through various cell-based assays.

Vladimir Popov

Research Goals/Purpose:

The Partnership Development Office works to establish partnerships and collaborations among Frederick National Laboratory scientists and external researchers in government, academia, industry, and the nonprofit research community. The intern will work on projects related to marketing and outreach (internal and external), business development, intellectual property and technology transfer, and strategic partnership development. The intern will get a unique view into the business side of operating a national laboratory.

Training Plan:

The intern will work with the individual members of the PDO on a variety of projects: development of strategic outreach materials (including articles and social media content), work on various partnership agreements, intellectual property research and technology transfer projects, and more. The student will attend a variety of meetings related to various partnership development work. The internship will involve a few large projects as well as several smaller projects throughout the year. One large projects will culminate in a poster that the student can present at the student poster session. This project can be tailored to the intern’s specific interests as the PDO covers a large spectrum of work.

Anu Puri

Research Goals/Purpose:

Development of Tunable & On-demand Deliverable RNAi-based Nanotherapeutics for Treatment of Cancer

Training Plan:

Student will be involved in the development of lipid-based and polymeric nanoparticles, optimize methods for siRNA encapsulation. He/she will perform in vitro screening of these delivery vehicles. He/she will learn various techniques which include: nanoparticle fabrication, characterization of nanoparticles, tissue culture, FACS, cell toxicity assays, fluorescence microscopy, lipid handling, and gel electrophoresis and ELISA assays.

S

Sounak Sahu

Research Goals/Purpose:

Germline inheritance of a mutation in one of breast cancer susceptibility genes, BRCA1 or BRCA2 leads to breast and ovarian cancer. Our lab is interested to understand the function of BRCA2 in breast tumorigenesis with an aim to functionally characterize different BRCA2 variants in mouse embryonic stem cells (mESCs). We are currently using CRISPR-Cas9 based genome editing in mESC to generate different BRCA2 variants to functionally characterize the effect of single nucleotide variants (SNVs). The mESCs with various SNVs are reprogrammed in the presence of different growth factors and cultured in 3D matrix to form organoids or “mini-breasts in a dish”. The succesful generation of mammary organoids from ES cells expressing BRCA2 SNVs will be a powerful model to study mammary cell fate and could be used as a complementary system to remodel breast cancer tumorigenesis.

Training Plan:

The student will learn basic molecular biology techniques like PCR, Cloning and sanger sequencing, Agarose gel electrophoresis, DNA/RNA/Protein isolation, western blot, immunofluorescence in embryonic stem cells and mammary organoids and will be trained in confocal microscopy and image analysis. In addition, the student will be exposed to basic bioinformatic tools like BLAST, analysing DNA sequences as well as image analysis tools. The student should maintain a record of experiments in laboratory notebook and will be encouraged to attend the weekly lab meetings with other lab members and present their data during the internship.

Tanmoy Sarkar

Research Goals/Purpose:

Studying the role of Id2 protein in hematopoietic stem cell development and cancer. Id proteins play important role in the maintenance of hematopoietic stem cell population and also play an important role in hematopoietic malignancies. This project will particularly designed to identify the molecular mechanism of Id2 protein in normal and oncogenic hematopoiesis

Training Plan:

Student will study the genotype of Id2 Knock out mice and will be associated with cloning of Id2 cDNA using bacterial system. Students will be exposed to molecular techniques namely DNA isolation, PCR, Cloning and plasmid isolation.

Satheesh Sengodan

Research Goals/Purpose:

BRCA2 is a tumor suppressor primarly involved in DNA repair via homologous recombination. Pathogenic mutation in BRCA2 gene portion has been shown to predispose cancers mainly to breast and ovary. Also, BRCA2 loss leads to synthetic lethality in mouse embryonic stem cells (mESCs). However, recently it was shown that BRCA2 deficient mESCs can be rescued when parp or MRE11 was inhibited before BRCA2 loss. Parp by interacting with MRE11, an endonuclease promotes the degration of stalled replication fork and fork degration has been shown to be lethal to BRCA2 deficient mESCs. When fork is protected before BRCA2 loss by parp inhibitor, Olaparib or MRE11 inhibitor, Mirin, the cell survives. Even transient exposure to parp inhibitor, Olaparib or MRE11 inhibitor, Mirin before BRCA2 loss can rescue the cells. Though the effect of Olaparib or Mirin is transient and the fork is no longer protected, the cell continues to survive which is highly intriguing. Also it raises the concern of BRCA2 proficient cells to become neoplastic when these cells undergo LOH after parp inhibition in patient cases. So what contributes to the survival advantage for BRCA2 deficient mESCs is highly puzzling. To address this, we carried out RNA seq and Whole genome sequencing in Mirin rescued mESCs. We found that several of the cancer associated pathways were up regulated in mESCs as expected as these cells are BRCA2 deficient. We would like to evaluate few of these genes and its role role in fork protection to determine what contributes to cell survival in BRCA2 null condition.

Training Plan:

Protege will learn and understand safety protocols which needs to be followed in laboratory. Initial training will include learning molecular biology techniques such as agarose gel electrophoresis of DNA, DNA/RNA isolation, cDNA synthesis, Real time PCR and Western blotting. Upon acquiring essential molecular biology techniques, protégé will learn certain basic cell biology techniques such as immunofluorescence staining of fixed cells (ICC), DNA fiber assay staining and analysis. Once trained, the prime aim of the student is to analyze the DNA fibers by ICC to understand the contribution of fork protection in cell survival.

Bruce Shapiro

Research Goals/Purpose:

The study of the structure and function of ribonucleic acids (RNA) is an important area of biological and computational research. Understanding of the role that these molecules play in a cell's life cycle has become very important. The various types of RNAs that control a cell's normal function are tRNA, mRNA, rRNA and most recently discovered RNAi. RNAs, such as the viruses HIV, polio and the common cold, to name a few, are detrimental to living organisms. Our research deals with the basic biological concepts associated with RNA structure function relationships and also the development of computational and experimental methodologies and tools to unravel these relationships. Included are algorithms for RNA folding and analysis of the folding results. We also employ machine learning techniques encompassing techniques such as neural network methodologies. We do molecular mechanics and molecular dynamics simulations on RNA and RNA/protein complexes to understand atomic scale interactions that determine the functionality of these molecules. We also explore ways of using RNA structure/function relationships to define RNA-based nanobiology entities. These RNA based structures have the potential for therapeutic uses amongst other possibilities. Several software approaches are being explored and developed to assist in the design of these RNA-based therapeutic nanoparticles. Student intern will be working on projects related to computational approaches to RNA structure and function. Student will not only learn and apply computational techniques, but will also learn how physics, chemistry, mathematics and biology all interplay to solve the research problems associated with the lab.

Training Plan:

Some potential projects are enumerated below: 1) Apply several software tools developed by our laboratory, and others to explore RNA structure and function. 2) Carry out molecular mechanics and molecular dynamics simulations of RNA using high performance computing facilities. 3) Develop computer algorithms for improving RNA structure prediction and analysis methods for both secondary and tertiary structure. 4) Searches for interesting functional features in RNA sequences and their structures. 5) Find and understand RNA folding patterns using various algorithms. 6) Enhance and help develop new algorithms for our computational RNA-based software. This includes adding features for prediction and characterization of our RNA nanobiology structures for potential therapeutic use. 7) Apply coarse-grained simulation techniques to RNA nano-constructs to understand their dynamic behavior. 8) Help to develop and maintain our web servers. Specific steps in the project will involve: 1) Library work to find and read relevant papers on RNA structure, nanobiology, computational and experimental approaches. 2) Familiarization with computers and software in our lab and experimental techniques. 3) Learn about software development methods

Chunmei Shi

Research Goals/Purpose:

We are interested in studying the processing and maturation of miRNAs. The final goal of our research is to investigate the mechanism of miRNA biogenesis and miRNA decay on tumorigenesis. In particular, the student will explore how different terminal uridylyl transferase family members involved in miRNA decay.

Training Plan:

The student will learn the basic concepts of miRNA biology such as the non-canonical biogenesis pathway and mRNA targeting. Student will do regular and/or challenge experiments to gain the insight of biology research. Student will also read relevant literatures and participate in scientific discussions in the lab meeting once a week. Student will also present his/her work in group meetings and listen to the presentations of others. The goal is to help student to accumulate the knowledge of biology and learn most RNA biology related techniques. Moreover, the student will get training for improving his/her critical thinking skill and efficiently plan the experiments, as well as scientific interpretation of the results.

Yurong Song

Research Goals/Purpose:

To characterize mouse cancer cell lines in in vitro and in vivo system for preventative cancer vaccine test

Training Plan:

The student will learn to culture cells using aseptic technique, perform viability analysis of cells, bank cells as master stock and working stock, analyze vaccine target expression by Western blot or flow cytometry, determine the haplotype expression by flow cytometry, assess the proliferation rate by XTT assay, and prepare cells for in vivo subcutaneous injection into mice. The student will also learn data analysis, preparing data for presentation, and data presentation in our weekly lab meeting. Furthermore, he/she will learn time management skill and project management skill, effective teamwork skill, and also get to know what a biomedical scientist's life is like.

Monalisa Swain

Research Goals/Purpose:

The project involves the structural and functional studies of RNA / RNA-protein / RNA-small molecule interaction using various biochemical and biophysical techniques.

Training Plan:

The student will be trained in protein and RNA biochemistry and structural biology. All necessary instrumentation is available in the laboratory. Upon successful protein / RNA purification, the student will be trained in (i), setting up crystallization trays using robots (ii) evaluating crystal quality by microscopy, and (iii) and optimization to obtain high quality crystals. Several potent small molecule inhibitors have already been identified for several RNA and the student will work on finding the small molecule interaction with RNA.

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Julio Valencia

Research Goals/Purpose:

To study the impact of cancer acting as a comorbid condition in pre-existent autoimmunity.

Training Plan:

Primary goal is provide accurate genotyping of mice with different levels of autoimmunity. Develop different skills to grow immune cells and test their different responses to immune-stimulating and -suppressing drugs.

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Abdul Waheed

Research Goals/Purpose:

The goal of the research in our lab is to understand the molecular biology of HIV-1 replication, in particular, mechanisms of HIV-1 assembly and release. Several host-factors are involved in the process of virus assembly and release. Understanding the molecular mechanisms of HIV-1 assembly and release would eventually help to design the drugs that inhibit the late stages of the HIV-1 replication cycle. Several drugs have been tested in the lab that showed antiviral activity for HIV-1. We would also test these compounds for its anti-viral activity in other viruses like MLV, EIAV, FIV, etc. The ultimate goal of our research is to identify novel targets for the development of anti-HIV therapies that can be used to treat infected patients.

Training Plan:

The student will be trained to learn a variety of techniques in the fields of molecular and cell biology, biochemistry, bioimaging, and virology. These include recombinant DNA techniques involving cloning of genes in plasmid vectors, mammalian cell culture maintenance, transfection of plasmids in mammalian cells, immunoblot analysis, fluorescent microscopy, etc. The student will learn how to use general laboratory equipment and the basics of many of the assays used in the laboratory. The student will gain experience in designing the experimental plan, performing the experiments and trouble-shooting the potential problems. The student will learn how to maintain the records of their data, and trained to present their work in both formal and informal lab meetings and poster presentations in scientific meetings.

Kylie Walters

Research Goals/Purpose:

Project goals include defining new mechanisms of protein function and reagents to manipulate function.

Training Plan:

The student will learn how to make samples for structural biology projects, collect structural biology data, and analyze results.

Tina Watts

Research Goals/Purpose:

Serve as a member of the Occupational Health Team. Performing in the role of clinical staff performing activities in the clinic with the professional staff including: patient triage, taking vital signs, measuring height and weight, obtaining past medical history, planning and participating in wellness activities. (Take a Hike, wellness emails)

Training Plan:

Performing the following skills: Vital Signs (temperature, blood pressure, pulse, respirations, pulse oximetry), visual acuity, whispered voice testing, color vision, medication reconciliation, electronic medical record, venipuncture, informed consent, collection of specimens (midstream urine, venous blood sampling), intramuscular injections, intradermal skin testing, EKG, ear irrigation, eyewash, cardiopulmonary resuscitation, automatic external defibrillator AED) Independently plan, execute and evaluate a Wellness activity. (Take your child to work day, Take a Hike, Monthly wellness topics, Take Back your Lunch, Stairway to Wellness, or Stop the Bleed Education) Perform office administrative practices: answering telephone, scheduling appointments, scanning, participating with the quality control audit for scanning and assisting with medical records storage. Writing an occupational health article for the Poster. Deliver one presentation to the OHS staff at the weekly staff meeting in regard to one of the following topics: Travel medicine topic, Evidence based practice finding on Musculoskeletal system.

Christopher Westlake

Research Goals/Purpose:

Ultrastructure Analysis of Primary Cilium assembly Almost every cell in the human body contains at least one cilium. While some cilia in human cells function in locomotion, not unlike cilia on the surface of the single celled organism paramecium, most of our bodies cilia are immotile and function in cellular signaling. Hence the cilium is often referred to as the cell’s antennae. In humans cilia are critical for reproduction and embryonic development and are needed for vision and for our sense of smell. Defects in cilia function are associated with more than 20 genetic disorders and cancer. We are investigating how membrane transport regulators function in the building of the cilium, a process termed ciliogenesis. Through the use of various genetic approaches in cells and zebrafish embryos and cellular imaging we are able to understand how ciliogenesis occurs and to determine what proteins regulate this process.

Training Plan:

Students will use computer based analysis programs to map and identify structures involved in the assembly of the primary cilium. Electron microscopy images captured from cells will be converted into three-dimensional representations of the developing cilium. Students will become proficient at using imaging software to generate 2D and 3D animation structure models for presentations and publications. Through this work students will be gain a deeper understanding of various aspects of cell biology. Students may also have the opportunity to gain wet laboratory experience in cell biology techniques, including cell culture and microscopy imaging (epifluorescence and confocal microscopy).