Semester-in-Residence Projects

The Semester-in-Residence (SIR) program is a unique part of the California State University San Marcos’ Professional Science Master’s in Biotechnology. The program provides students with the opportunity to work in a biotechnology or related life sciences business to address a real-world issue, project or problem by integrating new skills and information gained from their coursework.

The project functions as a capstone experience in lieu of a Master’s thesis, and runs for approximately 15 weeks requiring 300 hours of work. It is similar to a structured internship with a very specific, comprehensive schedule of deliverables established by the student, in consultation with the CSUSM Biotechnology Advisory Committee and the community partner.

Past Projects

• Company Listings

  Abbott Vascular | ACI Biomedical | Active Motif | Advanced BioMatrix | Alere Inc. | Althea |  Technologies | Amplyx Pharmaceuticals | Ambryx Inc. | Aragene | Ardea Biosciences | Autogenomics | BD Biosciences | Beckman Coulter, Inc. | Carlsbad Aquafarm | Cliniqa Corporation | Cosmo Bio USA | DNA Electronics | Encina Waste Water Authority | Genentech, Inc | Genmark Diagnostics, Inc. | Genoptix | Gilead Sciences | Howard Hughes Medical Institute | Ibis Biosciences, an Abbott Company | Illumina Inc. | Imgenex Corporation | Inova Diagnostics | Let’s Go Robotics | Librede Inc. | Life Technologies | Local Urban Vegetables | MarDx Diagnostics | Myron L Company | MicroBio Products | Millipore | nanoComposix Inc. | Navigate BioPharma | Neogenomics | Neuropore | Quidel Corporation  | Pfenex Inc. | Plantible Foods Inc. | Point Loma Wastewater Treatment Plant | Promethean Biofuels Cooperative Corp. | Rady Children’s Institute for Genomic Medicine | Rare Science | Roushka Bio LLC | San Diego Zoo Global Institute for Conservation Research | San Diego Sheriffs Department, Crime Lab | Sapphire Energy | Seacoast Science, Inc.   | Sirigen/BDB. | Sigma Millipore | Syntron Bioresearch, Inc | T2 Energy | Thermofisher Scientific Inc | The Scripps Research Institute | Time Logic | Valicor Renewables | Zoetis

• Research and Development Projects
  • Endoplasmic Reticulum Stress in Rodent Models: Interface with Metabolic Disease
  • Vivianite Investigation at the Point Loma Wastewater Treatment Plant by Phosphate Fractionation
  • Determining the Membrane Topology of CsgG Protein in Escherichia Coli
  • Gene Regulation Using Transcription Activator-like Effectors in Mammalian Cell Lines
  • Comparison of Four Bioanalystical Methods for the Quantitation of a PEGylated Therapeutic
  • Evaluation of Glutaraldehyde Crosslinking Reactions to Enhance the Efficiency of an Anti-Streptolysin O Purification Column  Christopher Heisinger
  • Effects of Zinc on Ethanol Drinking, Behavior, and Oxidative Stress Following Chronic Intermittent Ethanol Exposure  Chelsea Cates-Gatto
  • Improving Photophysical Properties of Brilliant Violet^TM Polymers Via Structural Modifications  Lan Tran
  • A Target Enrichment and Fast PCR Method for Rapid Detection of Infectious Pathogens  Joseph Musmacker
  • Piecing Together the Visual Corticothalamic Retinotopic Map of the Mouse  Jamie Evora
  • Evaluation of Pollen Tube Growth from Liliaceae Flowers  Harika Sokkam
  • Characterization of Stem Cells Using CDy 1 a Stem Cell-Specific Dye  Rhoda Mondeh-Lowor
  • Epigenetics and Exercise in Relation to Atherosclerosis  Sukhdeep Sandhu
  • Chicken Fibroblast Cell Fusion with Avian Germline Stem Cells: A Model for Conservation of Exotic Bird Germplasm  Madhawi Alohali
  • Creating and Screening Mutant Populations to Enhance Astaxanthin Production in Haematococcus Pluvialis  Rohit Patel
  • Engineering a Cell Line for Analysis of Type I Interferon Signaling  Nahn Nguyen
  • Direct Conversion of Human Fibroblasts into Defined Neuronal Subtypes Using Lineage-Specific Factors  Nina Rander
  • The Effects of Aurintricarboxylic Acid in CHO Cultures in Chemically Defined  Elaine Lee
  • Gene Regulation Using Transcription Activator-Like Effectors in Mammalian Cell Lines  Vinita Kapur
  • Optimizing Adsorption Capacity of Activated Carbon: A Study of Effects of Arene Concentration Nana Banafon  Alicia Smith
  • Decreasing product heterogeneity by removal of the heavy chain terminal lysine from Mab1  Jennipher Rose Jose
  • Characterization of crude glycerol transesterfication methods and their effects on the growth of Chlorella vulgaris and Chlorella protothecoidesAndre Domingo & Jennifer Zarzoso
  • Characterization of the interation of CsgF and Human Islet Amyloid PolypeptideMaryAm Alshulah
  • Monitoring Sendai viral backbone clearance in newly established induced pluripotent stem cells  Akili Tcha Binidi
  • Using Peptide Nucleic Acid Capture Probes to Identify 16s rRNA Gene of Sepsis causing Bacteria in Whole Blood Specimens  Soujanya Mamidi
  • Determining the regions involved in CsgE interation with HIAPP  Ashwag Binmahfooz
  • Evaluation of Enhancers that Increase Generation of Induced Pluripotent Stem Cells Under Xeno-Free Culture Conditions  Nikki Wetton
  • Translocation of Cell-Penetrating Peptides into  Emiliania huxleyi: Developing Novel Methods for Genome-Editing in Algae  Ryan Wallace
  • Identification of oogonial stem cells in adult quail ovaries: A model for conservation research of endangered avian species  Sara Jabalameli
  • Efficient Genome Editing Through Identification of a Universal Cell-Penetrating Peptide Conjugated to CRISPR/Cas9 System  Trae Reighert & Hirak Chavada
• Bioinformatics Projects
  • Comparison Evaluation of Various Software Tools and Methodologies for Chromatin-Immunoprecipitation (ChIP) Data Analysis
  • A Methodology for the Analysis of Metagenomics Data Using DeCypher System
  • A Comparative Analysis of the Tera-BLAST™ Algorithm
  • Efficient and Multiplex Genome Editing Using GeneArt CRISPR Nuclease mRNA.  Johan Garza
  • Functional Annotation of the Emiliana Huxleyi, Isochrysis Galbana, and Gephyrocapsa Oceanica Genomes  Jonathan Dy Albay
• Marketing Projects
  • Commercialization of Biopellet Fertilizer: Marketing Plan for Encina Waste Water Authority
  • Increasing the Knowledge Base for Neutrophil Gelatinase-Associated Lipocalin (NGAL) as a Biomarker for Acute Renal Injury and Cardiorenal Syndrome
  • Development and Market Analysis of an Educational Mini-Bioreactor  Christopher Kensinger and Eric Gudorf
  • Online Market Survey to Assess the Need for an Educational High Performance Liquid Chromatograph (HPLC)  Jennifer Cunningham
  • Research and Analysis of the Market’s Interest for the Pollen Grwoth Cell Fertilization Kit  Minh Huynh
  • Developing Trial-Size Products to Offer More Effective Solutions for Experimental Design  Matt Miceli
  • Optimizing Website Design to Enhance Company Visibility  Kyle LeBlanc
  • FermSys Marketing Plan
• Business Development Projects
  • A Business Plan: Bioinformatic Services
  • Becoming a CRO: A Business Plan   
  • Increasing Efficiency in Complaint Handling by Implementation of Investigation Report  Denisse Reyes
  • Advancing Operation and Internal Capabilities through Documentation
  • Phase Zero Research for Market Feasibility of a New Diagnostic Test in the Biotechnology Industry  Jillian Lai
• Product/Assay Development Projects
  • Use of Oligonucleotide Capture Probes to Increase Bacterial Sensitivity on the Ibis PLEX-ID BAC Assay in Whole Blood Specimens
  • Optimizing TnT and TnC Cross-Linking to Increase Antibody Affinity and TnT, Yield, and Stability
  • Novel Multiplex PCR Technology Using Universal Primer in a Statin Assay  Perna Singh
  • Detection of Toxin Producing Clostridium Difficile Using Multiplex PCR  Jaya Ramrakhyani
  • Mouse Global LINE Methylation Assay  Patty Valesco
  • Optimizing the Asymmetric Primer Extension Assay Using the Infiniti Platform Kathleen Borst
  • Development of Cost-Effective Multiplex PCR Detection of MRSA  Abhisek A. Naik
  • Detection of Cancer Variants in Clinical Studies of a Next-Generation Sequencing Based Assay  Foram Rathi
  • Introducing an initialization step to optimize the signal to noise ratio on the eSenor Chip  Vanessa Mendez
  • Development of a multiplex PCR assay to detect drug resistant Helicobacter pylori  Abdullah Althuwaybi
  • Screening of anti-human VEGFR-1 and anti-human VEGFR-2 antibodies with different in-house clones, for flow cytometry and immunohistochemistry applications  Tannaz Rafizadeh
• Training/Process Development Projects
  • Optimizing Clean In Place Procedures for Oceanside Manufacturing
  • Chromatograghy DeltaV Overview: Creating an E-learning Module
  • Lean Manufacturing Principles: Optimization of Workflow and Production Lead Time Reduction
  • Implementation of the BenchPro 2100 for the Production of Low Demand Plasmids
  • Developing Mammalian Cell Culture Capabilities for Process Science at Ajinomoto Althea, Inc.  Berlin Siador
  • Cleanroom Training to Decrease Deviations Related to Process Error and Operator Error  Jaycee Nguen
  • Establishing amplicon monitoring program and implementing improved cleaning procedures to reduce contamination in pre- and post-PCR laboratories  Mayur Jain
  • Implementing a Curriculum for Improving Accuracy of Real-time Comments in Electronic Batch Records for Genentech, Inc. Kirstie Hunt

  BACK TO T
• Operations and Internal Capabilities Projects
  • Performance Improvement and Outcome Monitoring for Urinalysis Drug Test Breaking  Zeena Jahani
  • Manufacturing Bottlenecks: A Document Control Project  Brian Pizano
  • An Enabling High Throughput Process for Discovery of Specific Peptide Drug  Ross Fellows
  • Creation, Implementation and Assessment of a Mastery-Level Curriculum for Bioprocess Technicians  Martha James
  • Identifying the Competitive Landscape and End-User Requirements for the Development of a Novel GMP 500L Single-Use Bioreactor System
  • Implementartion of Lean Principles for the Re-Organization of the Quality Control Laboratories for Optimizing Associate Efficiency, Eliminating Waste and Controlling Inventory  Germalaine Arenas
  • The Advantages of Single Use Bioreactors and its Use as an Inoculum Seed Reactor  Bayan Awwad
  • Reducing HiSeq Setup Times in Sequencing Services Laboratory with 5S: Implications for Productivity and Quality  Ashley Ginbey
  • Chemical Utilization Analysis Used in DNA Sequencing: A Proposal for Optimization and Cost Reduction  Wallace Keau Wong
  • Bringing Gracilaria From Tank to Market: Optimization of Growth and Dehydration Methods  Thomas Pillsworth
  • Flow Cytometry Workflow Optimization through Implementation of Lean/Six Sigma Methodologies  Robert Andrews
  • Developing Addiction/Pain Management Genotyping Panel using Technology Platform  Azadeh Farahmand
  • Developing a Device for Self-Monitoring of Progesterone During In- Vitro Fertilization (IVF)  Marziyeh Tehraniyekta
  • A Web-Based Training Module for Manufacturing Process Comment Writing  Natalie Mabrey
  • Lean Manufacturing Principles: Optimization of Workflow and Production Lead Time Reduction  Manuel A. Perez
• Quality Projects
  • Determining the Trans Fat Content of Cakes and Doughnuts Sold in San Diego Grocery Store Bakeries
  • Guidelines for a Companion Diagnostic in a Regulated Environment
  • Microbial Survey of Althea Technologies 2011/2012 Environmental Isolates  Gabriel Rodriguez
  • Development of a Universal Contamination Testing Protocol for Index Adaptors used for Multiple Platforms  Rita Pitts
  • Equipment Validation of the 3 mm Bioprocess System  Joey Stark
  • Ensuring Genoptix Compliance with FDA Guidelines for Laboratory Developed Tests  Kevin Nguyen
  • Cost Analysis of Terminal Sterilization and Aseptic Processing Methods of Sensitive Implantable Combination Drug Device Products  Zenabu Bawa-Mamudu
  • Optimizing Adsorption Capacity of Activated Carbon  Alicia Smith
  • A Study of Effect of Arene Concentration  Nana Banafon
  • Development of a Real Time Molecular Surveillance Tool for Algal Pond Contaminants  Hee Cheol Kim
  • Quality Manual for Employees  Jeffery Ly
• Other Projects
  • Communication: The Driving Force for Continuous Improvement Wave Reactor Proof of Concept
  • Evaluating Communication Channels and Practices Within and Across the Ardea Phase 3 Clinical Program  Kathy Truong
  • Development and Pilot Experiment of a Project Portfolio Management Tool for Supplier Quality  Jessie Wood
  • Installation of a Fertigation Monitoring System to Control the Nutritional Flow of Hydroponic Plants  Mike Vo
  • Optimizing Metabolic Efficiency through Manipulation of Surfboard Design  Taylor Frazee
  • Calibration and Testing of Electrodes for Use in a Hydroponic System  Jack Hattaway