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Extended Learning

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 ´ó·¢ Biotechnology Advisory Committee and the community partner.

Past Projects

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  • 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 VioletTM 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-BLASTâ„¢ 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
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  • 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