Cluster: Synthetic biology

Synthetic Biology Fundamentals

Synthetic biology involves designing, engineering and building biological systems using standardized biological parts. Standardized biological parts include DNA fragments that code for proteins and DNA elements that regulate transcription. There are common techniques for identifying, isolating, storing and manipulating these biological parts. The generation of customized cells with fully synthetic genomes is another area of synthetic biology.

• Synthetic Biology
• Synthetic cell
• DNA
• RNA
• Transcription
• Translation
• Reverse Transcription
• DNA Synthesis
• Synthetic genomes
• DNA Sequencing
• RNA Sequencing
• Bioinformatics
• Synthetic Circuit Design
• DNA transfection
• Optogenetics
• Directed Evolution
• Recombinant DNA
• Recombinant protein
• Recombineering
• Lambda red recombination
• Programmed chromosome fission and fusion
• Registry of Standard Biological Parts
• Phenomics
• Phosphorylation
• Kinase
• Inverton (invertible DNA region)
• Aptamer
• chimeric antigen receptor (CAR)
• engineered regulatory T cells (Tregs)

DNA Synthesis

DNA synthesis is the linking together of nucleotide bases such as the four naturally occurring ones, Adenine, Thymine, Cytosine and Guanine, to form a DNA molecule. During DNA synthesis non-natural nucleotide bases may also be incorporated into DNA.

• Cambrian Genomics
• Ansa Biotechnologies
• Twist Biosciences
• DNA Script
• Evonetix
• Integrated DNA Technologies
• Genewiz
• SGI-DNA

DNA Sequencing

DNA sequencing is the determination which nucleotide bases are present and in which precise order they occur within a segment of DNA.

• Review of Sequencing Technologies

• Illumina
• Oxford Nanopore

https://www.genome.gov/about-genomics/fact-sheets/DNA-Sequencing-Fact-Sheet

Gene editing techniques

Gene editing techniques are used to alter specific DNA sequences in the genome or RNA molecules, which are transcripts or copies of the DNA sequence that will be translated into the amino acid sequence of the protein.

• CRISPR
• ​CRISPR/Cas Tools​
• CRISPR-Cas3
• CRISPR-Cas9
• CRISPR-Cas 13

• CRISPR-Cas13a
• CRISPR-Cas13b
• CRISPR-Cas13c
• CRISPR-Cas13d

• CRISPR-Cas12a
• CRISPR-Cas12d
• CRISPR-Cas12e
• Epigentic CRISPR
• CRISPR interference
• anti-CRISPR proteins
• Transfection
• RNA Transfection
• Vortex Shedding
• Chimeric antigen receptors (CAR-T)
• Gene Drive
• Codon optimization
• Perturb-seq

Bioinformatics and modeling

Bioinformatics is the use of computational techniques to organize and search biological data as well as model biological systems and solve biological problems.

• Bioinformatics
• iBioSim
• Systems Biology Markup Language (SBML)

Synthetic Circuit Design

Synthetic circuit design is based on knowledge about genetic circuits used by cells, whereby genes and the proteins they encode interact with each other, respond to internal and environmental cues and switch on and off cellular processes like gene expression and cell division. Synthetic circuit design uses a bottoms-up approach to put together well-characterized genes and proteins to produce synthetic gene circuits that perform desired functions.

• iGEM
• iBioSim
• Synthetic Biology Open Language (SBOL)
• Recombinase logic device
• Distributed Multicellular Computation
• Asymmetric plasmid partitioning

Transfection of Nucleic Acids

Transfection is a procedure used to introduce nucleic acids which may be DNA, RNA or oligonucleotides into eukaryotic cells.

• Transfection
• RNA Transfection

Optogenetics

The optogenetics field has adapted the use of light-responsive proteins to control a variety of cellular functions which can be further engineered or built into biological systems through synthetic biology. Optogenetics uses light as a trigger to cause a photosensitive protein to respond by switching on or off a molecular event that can be measured or detected. Photosensitive proteins used in this way are called optogenetic actuators.

• Optogenetics

Directed Evolution

Directed evolution methods mimic natural selection, but the process is sped up in the laboratory. The system is a method of engineering proteins with desired features because it is set up so certain protein structures or functions have a selective advantage.

• Directed evolution
• Phage-assisted continuous evolution (PACE)

Theoretical biology and artificial life

• Artificial life (ALife)
• Autopoiesis
• Chemoton

Whole genome engineering

• Genome Project-write (GP-write) is an open international research project that plans to reduce costs of engineering and testing large genomes in cell lines. Through synthesizing whole genomes, GP-write aims to better understand the human genome and other genomes.

• Minimal bacterial genome
• Synthetic Yeast 2.0

Biofuel

Synthetic biology approaches are used to modify microbes for better production of biofuels.

• Cellulosic biofuel

Cellular Agriculture

Synthetic biology is applied to cellular agriculture to genetically engineer cell cultures to provide new or enhanced capabilities to produce agricultural products that we otherwise obtain from animal and plant farming. For companies, see cellular agriculture subsection under companies heading.

Biosensors

In medicine synthetic molecular and cellular biosensors hold potential in diagnostics and theranostics, whereby gene circuits could act like an intracellular molecular prosthesis, monitoring disease-associated biomarkers and adjusting therapeutic response accordingly.Biosensors can also be used for targeted delivery of therapeutics.

DNA nanorobots – Described in Nature Biotechnology in 2018, DNA nanorobots were constructed using DNA. A DNA aptamer binds nucleolin, a protein expressed in tumor-associated endothelial cells, and binding causes a molecular trigger to open the DNA nanorobot and release the payload at the tumor site.

• RNA-based biosensing
• Phage-based diagnostics
• Paper-based synthetic gene networks
• Bacterial biosensors
• Mammalian cell biosensors

Synthetic Tissue Development

Synthetic biology is applied to tissue engineering and morphogenetic engineering to make genetic manipulations that control the self-organization programs used by multicellular organisms during development and regeneration for the purpose of generating self- assembling structures. A method for construction of self-assembling structures would use the sequence, 1) form a pattern, 2) change gene expression, 3) trigger morphogenesis. Researchers from University of Edinburgh described their construction of a net-like structure by two cell types which formed a pattern, resulting in differential gene expression between the two cell types. The holes in the “net” were formed when a morphogenic effector was used to drive cell death in one cell type.

Engineered Living Materials

Engineered living materials (ELMs) are engineered materials made of living cells able to form or self-assemble material or modulate the functional performance of material. The foundations of ELMs come from synthetic biology and materials engineering.

Mapping Projects

Since synthetic biology aims to redesign or build biological entities using biological parts, mapping how those parts fit together in natural living systems can serve as a guide for how to put parts together to attain a desired function. Mapping and reading genomes has lead to writing synthetic genomes that function in bacteria. Systems biology is involved in creating maps of biological interactions involving cells, genes, proteins and metabolic pathways in healthy and diseased living systems which can serve as a reference point for synthetic biology. At a meta level, mapping how different areas of synthetic biology and biological engineering are developing and could evolve in the future can help to identify promising areas for research

'Omics' Projects and Biological Atlases

• Human cell atlas
• Allen Brain Atlas
• Human Connectome Project
• Human Protein Atlas
• Human Genome Project
• Mitotic Cell Atlas

Technical Roadmaps

• Engineering Biology Research Consortium (EBRC) Roadmap

Standardization

• ​Systems Biology Graphical Notation (SBGN) Project
• BioBricks Foundation
• Registry of Standard Biological Parts (iGEM)
• Synthetic Biology Open Language (SBOL)

Facilitating access to DNA sequences

• The Free Genes Project
• Addgene

Blockchain and biology

The ability of blockchain to facilitate transparency, control and sharing of information, while keeping data secure, is being applied to biotechnology with companies like Nebula Genomics aiming for homomorphic encryption of people's genomic data. Blockchain technology in data storage and online platforms can improve sharing and access to information and also provide quicker ways for tracking and managing various steps in drug development.

For immunotherapies such as CAR-T cell therapy, blockchain can provide ways to store, maintain, track and secure information about cells derived from a donor patient like editing performed, storage conditions and transport from donor to recipient. Information must be accessible to patients, physicians, laboratory scientists, logistics companies, supply chains and infusion centers. For blockchain companies in this area see subsection under "Companies" heading below.

Conferences

• SynBioBeta
• iGEM Giant Jamboree
• Biosummit
• Engineering Biology Research Consortium (EBRC)
• Synthetic Biology: Engineering, Evolution & Design (SEED)
• London Calling Conference
• Damp Lab

Organizations and projects

• SynBio Canada

Startup Incubators and Accelerators

• Indiebio
• Rebelbio
• Y Combinator Bio
• SynbiCITE
• Johnson & Johnson Innovation
• McKinsey & Company

Nonprofits

• BioCurious
• Diybio
• Parker Institute for Cancer Immunotherapy
• Revive & Restore
• SRI International
• Thought for Food Foundation

Companies

Aquaculture

• Calysta
• KnipBio
• Microsynbiotix
• NovoNutrients

Biological control system

• Oxitec (Insect-based)

Bioplastics

• Bluepha

Biopharma and health

Aging and senescence

Senescence is a state of permanent growth arrest that cells can enter when they are damaged or stressed where they lose the ability to divide but do not undergo cell death. Cellular senescence is both an anticancer mechanism and contributor to loss of tissue and organ function over time in aging and age-related disease.

• Senolytic
• Oisin Biotechnologies
• Deinove

Autoimmune diseases

• Synthorx

Cancer

• Circle Pharma
• OncoSenX
• Synthorx

Immunotherapy

• Senti Biosciences

Vaccines and infectious disease treatments

• Meissa Vaccines
• Swiftscale Biologics

Other areas

• A-Alpha Bio - yeast-based screening of protein-protein interactions for drug development
• AO Biome
• Amprologix
• Autolus
• Azitra
• BiomeX
• Biosyntia
• Bluepha
• Chain Biotech
• Deep Genomics
• Deinove
• Distributed Bio
• Editas Medicine
• Egenesis
• Evolve Biosystems
• GenScript
• Humane Genomics
• Hyasynth
• Intellia Therapeutics
• LifeMine Therapeutics
• Meridian Management Consultants
• Mother Dirt
• Obsidian Therapeutics
• Oxford BioMedica
• Oxford Genetics
• Poseida Therapeutics
• Protea Biosciences Group
• Prokarium
• ​Renew BioPharma
• Siolta Therapeutics
• Synlogic
• SyntheX
• Teewinot Life Science
• Tierra Biosciences
• ViThera Pharmaceuticals
• Wave Life Sciences
• Zbiotics
• CHAIN Biotechnology
• Eligo Bioscience
• Cell Design Labs
• Juno Bio - microbiome

Bio-Manufacturing

• Cargill
• Catapult Cell and Gene Therapy
• Deinove
• Faber Futures
• Genomatica
• Gilson
• Indee labs
• Kraig Biocraft Laboratories
• Linear Diagnostics
• Nanocellect Biomedical

• Science Exchange

• Sphere Fluidics
• Stratophase
• Synlife

Bio-Materials

• Bolt Threads
• Ecovative Design
• Kraig Biocraft Laboratories

Bio-Mining (Biomining)

• Universal Bio Mining

Blockchain

Blockchain applied to tracking and security of biological data

• Nebula Genomics (genome sequencing company)
• Genexi (blockchain and cryptocurrency marketplace)
• Orvium (scientific publishing)

Carbon capture and conversion

• Oakbio
• NovoNutrients

Cellular agriculture

• Clara Foods
• Finless Foods
• Geltor
• Memphis Meats
• MosaMeat
• New Harvest
• Perfect Day Foods
• Aleph Farms
• SuperMeat
• Mission Barns
• MuuFri
• Afineur
• VitroLabs
• Real Vegan Cheese

Chemicals production

• METabolic EXplorer (petrochemical process alternatives)

Food and agriculture

• AgriMetis
• Asilomar Bio
• 3F Bio
• Bayer
• Calyxt
• Evolva
• GreenLight Biosciences
• MiProbes (biosensor for food contamination)
• Provivi
• Yield10 Bioscience

Gene/Genome synthesis

• DNA Script
• Evonetix
• Integrated DNA Technologies
• Molecular Assemblies
• Synbio Technologies
• Synthego
• Twist Bioscience

Genome/protein engineering

• Arzeda
• Codexis
• LabGenius
• Oxford Biotrans
• Touchlight
• Inscripta

Lab tools

• Bento Lab by Bento Bioworks
• Chai Biotechnology
• Cytera Cellworks
• Labcyte
• Mission Bio
• Opentrons
• Sleight Beer Lab
• Scaled Biolabs
• ​Elemental Machines

Lab space

• LabCentral Inc.

Organism Engineering

• Benchling
• Evolva
• Ginkgo Bioworks
• Inscripta
• Lumen Bioscience
• The ODIN
• Prellis Biologics

Phage engineering

Phages are engineered for use as phage therapies as antimicrobial agents and also for delivery of drugs and vaccines. Phages can also be engineered to assemble new materials.

• Locus Biosciences
• Eligo Bioscience
• Nextbiotics

Research labs

• MIT Media Lab
• DAMP Lab
• InnovationLab

Federal organizations

• Intelligence Advanced Research Projects Activity
• National Institute of Standards and Technology

Software

• A-Alpha Bio
• Asimov
• Codagenix
• Cyrus Biotechnology
• Digi.bio
• Synthace
• Radix Labs
• Visolis

Venture Capital

• Better Ventures
• Bioeconomy Capital
• DCVC Bio
• Inevitable Ventures
• The Longevity Fund
• Lux Capital
• Mayfield Fund
• Mubadala Ventures
• Refactor Capital
• Spruce Capital Partners

Biosafety Organizations

• AMEXBIO