Synpoptosis & Synthetic Cell Death: Vocabulary Review

Vocabulary flashcards covering key synthetic biology, immunology, and cell-death terms from the lecture notes.

Synpoptosis

Engineered, programmable circuits that trigger apoptosis-like cell death on demand.

Apoptosis

Programmed cell death involving cell shrinkage, DNA fragmentation, and membrane blebbing; typically immunologically ‘cold.’

Immunologically “cold”

A state in which dying cells provoke little or no immune response.

Pyroptosis

Inflammatory programmed cell death driven by gasdermin pore formation; immunologically ‘hot.’

Immunologically “hot”

Tissue or tumor with high immune-cell infiltration and strong inflammatory signals.

GSDMD (Gasdermin D)

Pore-forming protein cleaved by caspase-1/4/5/11; N-terminal fragment forms membrane pores that cause pyroptosis.

GSDME (Gasdermin E)

Gasdermin activated by caspase-3; switches apoptotic signaling to pyroptosis after cleavage.

MBP (Maltose-Binding Protein)

Bacterial periplasmic protein often used as a solubility tag in recombinant protein expression.

Protease

Enzyme that cleaves peptide bonds, activating or inactivating target proteins in signaling pathways.

Executioner proteins

Terminal effectors of cell-death pathways, e.g., caspase-3 in apoptosis.

DAMP (Damage-Associated Molecular Pattern)

Intracellular molecules released by stressed or dying cells that trigger innate immunity.

CAR-T Cells

T lymphocytes engineered to express chimeric antigen receptors for antigen-specific tumor killing.

scFv

Single-chain variable antibody fragment that confers antigen specificity in CAR constructs.

CD3ζ

T-cell receptor signaling domain incorporated into CARs to initiate T-cell activation.

CAR co-stimulatory domain

Secondary signaling module (e.g., CD28, 4-1BB) that enhances CAR-T persistence and function.

Granzyme B

Serine protease released by cytotoxic lymphocytes to activate apoptosis or pyroptosis in target cells.

TRAIL

TNF-related apoptosis-inducing ligand that activates death receptors DR4/DR5 to trigger caspase-8/10.

BID

BH3-only pro-apoptotic protein; truncated form activates BAX/BAK at mitochondria.

Cytochrome c

Mitochondrial protein whose cytosolic release activates caspase-9 and downstream apoptosis.

BH3 domain

Bcl-2 Homology 3 motif that mediates interactions among pro- and anti-apoptotic Bcl-2 family members.

BAX

Pro-apoptotic Bcl-2 family protein that forms mitochondrial pores after activation.

BAK

Pro-apoptotic Bcl-2 family protein functioning similarly to BAX in mitochondrial permeabilization.

Caspase

Cysteine-aspartic protease family orchestrating apoptotic and inflammatory cell-death cascades.

Caspase-3

Executioner caspase activated by intrinsic/extrinsic signals; cleaves numerous substrates during apoptosis.

CAD

Caspase-Activated DNase; degrades nuclear DNA once released from its inhibitor (iCAD).

Xkr-8

Caspase-cleaved phospholipid scramblase that flips phosphatidylserine to the outer membrane during apoptosis.

Annexin V

Calcium-dependent protein that binds exposed phosphatidylserine on apoptotic cells.

Phosphatidylserine (PS)

Anionic phospholipid normally on inner leaflet; externalized during apoptosis.

Sytox

Membrane-impermeant DNA dye that stains pyroptotic or membrane-ruptured cells.

Leucine zipper (LZ/ZIP)

Protein dimerization motif with leucine at every seventh residue.

TEVP

Tobacco Etch Virus protease; site-specific protease used in synthetic circuits.

TVMVP

Tobacco Vein Mottling Virus protease; orthogonal viral protease for protein engineering.

HCVP

Hepatitis C virus protease; another orthogonal protease in synthetic biology.

Coherent feed-forward loop

Network motif where a regulator controls a target both directly and through an intermediate, with concordant effects.

Incoherent feed-forward loop

Network motif where direct and indirect paths have opposite effects on the target.

Q-VD-OPh

Broad-spectrum caspase inhibitor blocking apoptosis (not pyroptosis).

TO-PRO-3

Nuclear dye that enters apoptotic (via pannexin channels) or pyroptotic cells (via pores).

Interleukin-1 family

Group of 11 cytokines (e.g., IL-1β, IL-18) mediating inflammation.

LDH release

Extracellular lactate dehydrogenase, a common marker of membrane-disruptive death like pyroptosis.

ATP (extracellular)

Indicator of cell lysis; high levels signify loss of viability, often via pyroptosis.

Jurkat cells

Immortalized human T-cell leukemia line used in apoptosis studies.

THP-1 cells

Human monocytic leukemia line capable of differentiating into macrophage-like cells.

RAS oncogene

Mutated GTPase driving proliferation and altering apoptotic balance in cancers.

CAAX motif

C-terminal sequence that directs prenylation and membrane localization of proteins like RAS.

Necroptosis

Inflammatory programmed cell death involving RIPK3 and MLKL-mediated membrane rupture.

Vibrant DiD

Lipophilic fluorescent dye used for cell tracking and identification.

ACTG1

Gene encoding gamma-actin; common housekeeping transcript for normalization.

GAPDH

Glycolytic enzyme frequently used as a housekeeping gene control.

VLP (Virus-like particle)

Self-assembled viral shells lacking genomic material, useful for delivery or vaccines.

Escherichia coli MG1655

Lab strain approximating wild-type E. coli; used with F helper plasmid in ADEPT.

ADEPT

Amplification of Dynamic Expression by Programmable Transfer; population-level gene control via plasmid transfer.

Fp

Plasmid-carrying cell fraction; proportion of cells harboring a given plasmid.

Fc

Average plasmid copy number within plasmid-bearing cells.

FE

Gene expression driven by a single plasmid copy, often monitored via GFP.

CRISPR

Bacterial adaptive immune DNA repeat system leveraged for genome editing.

Cas9

CRISPR-associated nuclease that creates double-strand DNA breaks at gRNA-specified sites.

CRISPR-Cas9

Genome-editing platform combining Cas9 with guide RNA for targeted DNA modification.

gRNA

Guide RNA containing 20-nt spacer that directs Cas9 to complementary DNA next to PAM.

PAM site

Protospacer adjacent motif required for Cas9 recognition and cleavage (e.g., NGG for SpCas9).

NHEJ

Error-prone double-strand break repair causing indels; exploited for gene knockouts.

HDR

High-fidelity repair pathway using donor template; enables precise genome edits.

HGT (Horizontal gene transfer)

Movement of genetic material between organisms outside parent-offspring lineage.

Transduction

Phage-mediated horizontal gene transfer between bacteria.

Transformation

Uptake of free DNA from the environment by bacteria.

Conjugation

Direct cell-to-cell transfer of plasmids through pilus-mediated contact.

F plasmid

Fertility plasmid encoding all genes needed for self-transfer via conjugation.

FHR plasmid

Fertility helper plasmid providing conjugation machinery but lacking self-transfer capability.

F conjugation machinery

Protein set enabling pilus formation and plasmid transfer in bacteria.

Orthogonal control

Independent regulation of multiple biological modules without crosstalk.

Tetrathionate (TTR)

Inflammation-associated molecule used as gut biomarker and inducer of pTtrB promoter.

ROS (Reactive Oxygen Species)

Reactive molecules derived from oxygen; overproduced during inflammation.

pTet promoter

Tetracycline-inducible promoter repressed by TetR and activated by doxycycline/ATc.

Tetracycline (Tet)

Antibiotic ligand that induces pTet by inhibiting TetR.

pLac promoter

Lactose/IPTG-inducible promoter with LacI repression; known for basal leakiness.

Lactose (Lac)

Sugar that relieves LacI repression to activate pLac.

pLux promoter

AHL/LuxR-responsive promoter used in quorum-sensing circuits.

LuxR

Transcription factor binding AHL to activate pLux promoters.

AHL

Acyl-homoserine lactone quorum-sensing signal that binds LuxR.

pAra (pBAD) promoter

Arabinose-inducible promoter repressed by glucose; activated by AraC-arabinose complex.

Arabinose (Ara)

Sugar inducer of pBAD promoter.

pRha promoter

Rhamnose-inducible promoter; repressed by glucose.

Rhamnose (Rha)

Sugar that activates pRha promoter.

pTtrB promoter

Tetrathionate-responsive promoter regulated by TtrS/TtrR two-component system.

TtrS/TtrR

Histidine kinase/response regulator pair sensing tetrathionate and controlling pTtrB.

Chloramphenicol (Cm)

50S ribosome inhibitor; bacteriostatic antibiotic blocked by acetylation resistance.

CmR

Chloramphenicol resistance, often via chloramphenicol acetyl-transferase.

Kanamycin (Kan)

Aminoglycoside antibiotic binding 30S ribosome, causing mis-translation.

KanR

Kanamycin resistance conferred by aminoglycoside-modifying enzymes.

Linoleic acid (Lin)

Fatty acid that disrupts bacterial conjugation efficiency.

Periodic forcing

Temporal modulation of gene expression via repeated inducer pulses.

LIDAR

Ligand-Induced Dimerization-Activating RNA editing platform controlling gene expression post-transcriptionally.

cLIDAR

Cytosolic binder-based LIDAR using rapalog-dependent FRB/FKBP dimerization.

FKBP

Immunophilin domain binding FK506/rapamycin; used in inducible dimerization systems.

FRB

mTOR domain that binds FKBP in presence of rapamycin.

mTOR

Kinase regulating growth and metabolism; inhibited by rapamycin.

Rapamycin

mTOR inhibitor that mediates FKBP-FRB dimerization.

eLIDAR

Extracellular binder-based LIDAR incorporating CD28 transmembrane domains.

VEGF

Vascular endothelial growth factor promoting angiogenesis.

IL-2

Cytokine driving T-cell proliferation and survival.

gLIDAR

GPCR-based LIDAR harnessing β-arrestin2 recruitment to activated GPCRs.