Project

Part:BBa_K5477051

Designed by: Kate Escobar and Victor Bay   Group: iGEM24_UCopenhagen   (2024-09-29)
Revision as of 11:09, 2 October 2024 by Kateesc1700 (Talk | contribs)


Team UCopenhagen 2024: Parts Collection of MilkClear

Introduction

Our part collection includes 48 total parts: 24 basic parts, 16 composite parts, and 8 devices, with 45 of which are new. This collection is coherent, as all the parts were developed with the specific goal to address contaminants in breast milk. It is also the first collection tackling this purpose.

The parts can be categorized into three main categories:

  1. 1.) Parts for detecting contaminants in breast milk
  2. 2.) Parts for detoxifying contaminants.
  3. 3.) Devices integrating these functions.


Instead of function, we have chosen complexity to group our parts on this page, as multiple parts reappear in each category, due to the interlinked nature of our collection. All parts have been tested in either the Wet-lab or the Dry-lab, which demonstrates their function. We also cloned additional constructs that are not part of this collection.


By contributing a comprehensive collection of receptor, reporter, and detoxification modules, we provide valuable resources that expand current biosensing capabilities and empower future iGEM teams to develop more sophisticated, multi-functional systems.

Devices

The Devices Table outlines the different biosensor devices developed for the detection and detoxification of various environmental contaminants. Each device incorporates specific receptor modules and reporter modules, tailored to detect particular compounds like polycyclic aromatic hydrocarbons (PAHs), dioxins, polychlorinated biphenyls (PCBs), and bisphenol A (BPA). For instance, devices BBa_K5477041 and BBa_K5477042 are biosensors designed to detect PAHs, dioxins, or dioxin-like PCBs, while devices BBa_K5477043 to BBa_K5477045 are specialized for BPA detection. Additionally, BBa_K5477046 introduces the SUPERMOM device, which integrates both detection and detoxification modules to simultaneously identify and neutralize BPA in breast milk. The final device, BBa_K5477047, is a detoxification device targeting PAHs, dioxins, and PCBs through the use of CYP1A1 and UGT enzymes, which metabolize these contaminants into safer, water-soluble compounds. This array of devices demonstrates the versatility of the biosensor platform in addressing diverse environmental and health-related issues.


Part Name Part Type Function
BBa_K5477041 BBa_K5477023: pSTE12-AhR - receptor module, BBa_K5477025: pRET2-ARNT receptor module, BBa_K5477026: pRET2-NCOA - receptor module, BBa_K5477030: XRE-pMEL1-NanoLuc reporter module Device Biosensor device for detection of PAHs, dioxin or dioxin-like PCBs
BBa_K5477042 BBa_K5477024: pRAD27-AhR - receptor module, BBa_K5477025: pRET2-ARNT receptor module, BBa_K5477026: pRET2-NCOA - receptor module, BBa_K5477030: XRE-pMEL1-NanoLuc reporter module Device Biosensor device for detection of PAHs, dioxin or dioxin-like PCBs
BBa_K5477043 BBa_K5477027: pRET2-LexA-ERα(LBD) - receptor module, BBa_K5477031: Lex6Op-pLEU2-NanoLuc reporter module Device Biosensor device for detection of BPA
BBa_K5477044 BBa_K5477028: pPOP6-LexA-ERα(LBD) - receptor module, BBa_K5477031: Lex6Op-pLEU2-NanoLuc reporter module Device Biosensor device for detection of BPA
BBa_K5477045 BBa_K5477029: pRET2-LexA-mERα(LBD) - receptor module, BBa_K5477031: Lex6Op-pLEU2-NanoLuc reporter module Device Biosensor device for detection of BPA
BBa_K5477046 BBa_K5477029: pRET2-LexA-mERα(LBD) - receptor module, BBa_K5477031: Lex6Op-pLEU2-NanoLuc reporter module, BBa_K5477040:UDPD-pPDC1-Lex6Op-pENO1-UGT2B15 Device SUPERMOM: Dual-Function Biosensor for BPA Detection and Detoxification
BBa_K5477047 BBa_K5477037: CYP1A1-pGAL1/10-POR detox module, BBa_K5477036: UDPD-pGAL1/10-UGT1A1 detox module Device Detoxification device against dioxin and PCBs
BBa_K5477048 pRET2-LexA-mERα(LBD) - receptor module, BBa_K5477031: Lex6Op-pLEU2-NanoLuc reporter module, BBa_K5477039: CYP3A4-MYC-pPDC1-Lex6Op-pENO1-POR Device Testing of the SUPERMOM Concept


Composites

The Composites Table showcases the various composite parts that make up the functional modules of each biosensor device. Each composite part consists of a combination of promoters, receptors, or detoxification modules designed for specific detection or detoxification tasks. For example, BBa_K5477023 and BBa_K5477024 feature receptor modules tailored to detect PAHs, dioxins, and dioxin-like PCBs, while BBa_K5477027 and BBa_K5477028 are optimized for BPA detection through engineered estrogen receptor modules. Additionally, the composite parts BBa_K5477035 to BBa_K5477039 focus on detoxification, containing enzymes such as UGT2B15, UGT1A1, and CYP1A1 that metabolize harmful chemicals into less toxic or more easily excretable forms. These composite parts serve as the building blocks of the devices, providing the necessary functionality to detect and detoxify environmental contaminants.

Part Name Part Type Length (bp)
BBa_K5477023 pSTE12-AhR - receptor module Composite Promoter and Receptor for detection of PAHs, dioxin or dioxin-like PCBs 3117
BBa_K5477024 pRAD27-AhR - receptor module Composite Promoter and Receptor for detection of PAHs, dioxin or dioxin-like PCBs 1900
BBa_K5477025 pRET2-ARNT receptor module Composite Promoter and nuclear translocator detection of PAHs, dioxin or dioxin-like PCBs 2155
BBa_K5477026 pRET2-NCOA - receptor module Composite Promoter and nuclear receptor co-activator for the detection of PAHs, dioxin or dioxin-like PCBs 5032
BBa_K5477027 pRET2-LexA-ERα(LBD) - receptor module Composite Promoter and Receptor for detection of BPA 2389
BBa_K5477028 pPOP6-LexA-ERα(LBD) - receptor module Composite Promoter and Receptor for detection of BPA 2389
BBa_K5477029 pRET2-LexA-mERα(LBD) - receptor module Composite Promoter and Receptor for detection of BPA 2389
BBa_K5477030 XRE-pMEL1-NanoLuc - reporter module Composite A xenobiotic response element, a promoter, and a luciferase reporter gene for the detection signal against PCBs, dioxins, and dioxin-like compounds 868
BBa_K5477031 Lex6Op-pLEU2-NanoLuc reporter module Composite DNA-binding domain, promoter, and luciferase reporter gene for the detection signal against BPA 880
BBa_K5477035 UDPD-pGAL1/10-UGT2B15 Composite Detoxification module against BPA 3724
BBa_K5477036 UDPD-pGAL1/10-UGT1A1 Composite Detoxification module against PAHs, dioxin and PCBs 3726
BBa_K5477037 CYP1A1-pGAL1/10-POR Composite Detoxification module against PAHs, dioxin and PCBs 4312
BBa_K5477038 CYP3A4-pGAL1/10-POR Composite Detoxification module against a wide array of contaminants 4250
BBa_K5477039 CYP3A4-MYC-pGAL1/10-POR Composite Detoxification module against a wide array of contaminants 4286
BBa_K5477040 UDPD-pPDC1-Lex6Op-pENO1-UGT2B15 Composite Detoxification module for the detoxification of BPA 3631
BBa_K5477032 CYP3A4-MYC-pPDC1-Lex6Op-pENO1-POR Composite Detoxification module for BPA 4193



Parts

The Parts Table lists individual genetic components, including promoters, coding sequences (CDS), and regulatory elements, that make up the biosensor and detoxification systems. Promoters such as pRET2 and pSTE12 are used to drive constitutive or inducible expression of the receptor and detoxification modules, ensuring that the biosensors are responsive under the desired conditions. The table also includes various coding sequences for receptors like AhR, ARNT, and LexA-ERα, which are central to detecting endocrine disruptors like BPA and other toxic chemicals. Detoxification enzymes such as CYP1A1, UGT2B15, and CYP3A4 are also featured, responsible for metabolizing and neutralizing harmful substances. These individual parts allow the biosensors to be highly modular, enabling customization for different contaminants while maintaining efficiency and compatibility with standard assembly methods.


Part Name Part Type Length (bp)
BBa_K5477000 pRET2 - Medium strong constitutive promoter in Saccharomyces cerevisiae Regulatory (Promoter) 700
BBa_K5477001 pSTE12 - Constitutive promoter in Saccharomyces cerevisiae Regulatory (Promoter) 557
BBa_K5477002 pRAD27 - Weak constitutive promoter in Saccharomyces cerevisiae Regulatory (Promoter) 694
BBa_K5477003 pMEL1 - Constitutive core promoter in Saccharomyces cerevisiae Regulatory (Promoter) 256
BBa_K5477004 pLEU2 - Constitutive core promoter in Saccharomyces cerevisiae Regulatory (Promoter) 130
BBa_K5477005 pGAL1/10 - Bidirectional inducible promoters from Saccharomyces cerevisiae Regulatory (Promoter) 664
BBa_K5477006 pPDC1-Lex6Op-pENO1 - Bidirectional synthetic promoters with Lex6Op Regulatory (Promoter) 571
BBa_K5477007 pPOP6 - Weak constitutive promoter in Saccharomyces cerevisiae Regulatory (Promoter) 700
BBa_K5477008 XRE - Xenobiotic Response Element Regulatory Binding Element 82
BBa_K5477009 Lex6Op - six tandem copies of LexA operator Regulatory Binding Element 220
BBa_K3793004 AhR - Aryl hydrocarbon Receptor CDS - receptor 2547
BBa_K3793005 ARNT - Aryl hydrocarbon Nuclear Transporter CDS - receptor 2370
BBa_K1680009 NanoLuc - NanoLuciferase reporter gene CDS - Reporter gene 516
BBa_K5477012 NCOA - Nuclear receptor coactivator CDS - receptor 4326
BBa_K5477013 LexA-ERα chimeric activator CDS - receptor 1683
BBa_K5477014 LexA-mERα chimeric activator CDS - receptor 1683
BBa_K5477015 LexA-ERRγ chimeric activator CDS - receptor 1602
BBa_K5477016 UGT2B15 CDS - enzyme 1593
BBa_K5477017 UGT1A1 CDS - enzyme 1602
BBa_K5477018 UDPD CDS - enzyme 1446
BBa_K5477019 CYP1A1 CDS - receptor 1575
BBa_K5477020 CYP3A4 CDS - enzyme 1512
BBa_K5477021 CYP3A4-MYC CDS - enzyme 1548
BBa_K5477022 POR CDS - enzyme 2061
[edit]
Categories
Parameters
None