...Apoptosis or “programmed cell death" plays a pivotal role in an array of biological processes including...development, the immune system, and cell turnover. Apoptosis is a highly controlled process that is triggered...fragmentation and death (Elmore, 2007). To study apoptosis in vivo, scientists have used genetically encoded...fluorescent executioner caspase reporters. Several apoptosis reporters have been developed, such as the Forster...Zhang et al., 2019). Thus to effectively study apoptosis in vivo scientists need a protease reporter that...brightness. The Shu Lab from UCSF designed an improved apoptosis reporter, ZipGFP, which utilized the self-assembling... better study the spatio-temporal dynamics of apoptosis in living animals. To do this they modified a ...

...Genome Institute of Singapore. Chapter 3: Biology research and resources in Singapore. Chapter 4: Life as...Chew, a researcher at the Genome Institute of Singapore who recently started his own lab. We discuss some...Principal Investigator at the Genome Institute of Singapore. His lab focuses on producing biotechnologies ... singapore...

...pGL3Basic_ME.1/ApoEpromoter APOE ApoE Alzheimer's Sohail Tavazoie 51436 pGL3Basic-ME.2/ApoEpromoter APOE ApoE Alzheimer's...190810 FUGW-APOE-E4-T2A-Puro APOE UbC Alzheimer's Ronald Hart 190811 pTet-O-APOE-E2-T2A-Puro APOE UbC Alzheimer's... pTet-O-APOE-E3-T2A-Puro APOE UbC Alzheimer's Ronald Hart 190813 pTet-O-APOE-E4-T2A-Puro APOE UbC Alzheimer's...190807 FUGW-APOE-E2-T2A-mCherry APOE mCherry UbC Alzheimer's Ronald Hart 190808 FUGW-APOE-E3-T2A-mCherry...T2A-mCherry APOE mCherry UbC Alzheimer's Ronald Hart 190809 FUGW-APOE-E4-T2A-mCherry APOE mCherry UbC Alzheimer's...41846 psiCheck-ApoE3'UTR APOE SV40 Alzheimer's Sohail Tavazoie 41848 psiCheck-ApoECDS APOE Luc SV40 Alzheimer's...Schwamborn 87085 pCMV4-ApoE2 APOE CMV Alzheimer's Bradley Hyman 87086 pCMV4-ApoE3 APOE CMV Alzheimer's Bradley...

...environmental factors. For example, variations of Apolipoprotein E (APOE), such as the ε4 allele, are a risk factor...

...necrosis factor (ligand) superfamily, member 10 APO2L, Apo-2L, CD253, TL2, TRAIL TNFSF11 tumor necrosis ...necrosis factor (ligand) superfamily, member 10 APO2L, Apo-2L, CD253, TL2, TRAIL TYROBP TYRO protein tyrosine... necrosis factor receptor superfamily, member 25 APO-3, DDR3, DR3, LARD, TNFRSF12, TR3, TRAMP, WSL-1, ...Fas (TNF receptor superfamily, member 6) ALPS1A, APO-1, APT1, CD95, FAS1, FASTM, TNFRSF6 FASLG Fas ligand...involved in proliferation, cell differentiation, and apoptosis. Plasmid Tables The gene names in these tables...

...tetracyclin-dependent transgene/shRNA expression ApoE.HCR.hAAT Mammalian Ehmer 85578 pTC-ApoE-Tet CreER expression and tetracyclin-dependent...tetracyclin-dependent transgene/shRNA expression ApoE.HCR.hAAT Mammalian Ehmer 85797 pSkipFlox split Cre Pfcrt...

...capability of the seven human APOBEC3 proteins, finding that APOBEC3A and APOBEC3bctd are the most efficient ...editing by a APOBEC-Cas9n-UGI complex. So how exactly does this work? Figure 1: APOBEC- and Cas9-mediated...that have been successfully edited with APOBEC3A and APOBEC3B (St. Martin et al., 2018). TLDR: The ACE...to monitor APOBEC-Cas-9 mediated editing. eGFP reporters for single base editing by APOBEC-Cas9 Though...reporters that can help you do just that. Monitoring APOBEC and Cas9-mediated editing in real time The Harris...Harris lab created ACE, a reporter that monitors APOBEC (a family of cytidine deaminase proteins) and Cas9... action. Image from St. Martin et al., 2018. APOBEC-Cas9n-UGI targets its preferred trinucleotide motifs...

...formation of atherosclerotic plaques. ApoB bound lipoproteins (ApoB-LPs) are indirectly measured through...great model for high throughput study of ApoB-LPs because their ApoB homologes are functionally conserved,...endogenous ApoB-NanoLuc reporter by inserting the NanoLuc luciferase downstream of the apoB gene. Using...PMID: 30639098. LipoGlo: A reporter for measuring ApoB bound lipoproteins Article contributed by Leah Schwiesow...lipoproteins that accumulate within the vascular wall. ApoB, the main structural component of atherogenic lipoproteins... However, size distribution and concentration of ApoB-LPs has been shown to have a strong correlation ...cardiovascular disease and indirect measurement of ApoB-LPs through triglyceride/cholesterol does not provide...

...marmosets, green monkeys, rhesus macaques N/A Chuapoco et al., 2023 AAV-F CNS: neurons and astrocytes...effectively transduces vasculature in adult marmosets (Chuapoco et al., 2023). AAV.CAP-B10 shows similar behavior...neurotropic in infant rhesus macaques and green monkeys (Chuapoco et al., 2023). However, in adult macaques, it ...tropism with a potential bias toward astrocytes (Chuapoco et al., 2023). Additionally, AAV.CAP-Mac has a...in physiological conditions (Chen et al., 2023, Chuapoco et al., 2023). Among the capsids tested, AAV9-...Chen X., Goertsen D., Coughlin G.M., Hori A.M., Chuapoco M.R., Otis T.S., Miles T.F., Gradinaru V. Adeno-Associated...10.3389/fimmu.2021.730825 Campos LJ, Arokiaraj CM, Chuapoco MR, Chen X, Goeden N, Gradinaru V, Fox AS. (2023...

...Reference CBE SpCas9 rAPOBEC1 NGG 6 SpCas9 Target-AID (PmCDA1) NGG 5 SpCas9-VQR rAPOBEC1 NGA 8 SaCas9-... plant systems. Target-AID based (CBE-2)-  and rAPOBEC based (CBE-1)-  CBEs are successful base editors...rice, tomato, wheat, and potato. Target-AID and rAPOBEC based CBEs are known to deaminate cytosine placed...closer to the PAM site? CBE developed using the hAPOBEC3 deaminase can edit in a stretched window ranging...SaCas9-KKH rAPOBEC1 NNNRRT 8 ABE SpCas9 TadA-TadA* NGG 9-12 SpCas9-VQR TadA-TadA* NGA 8 SaCas9 TadA-TadA...editing in plants using a fusion of nCas9 and human APOBEC3A." Nature biotechnology (2018). PubMed PMID: 30272679...

... like APOBEC. To achieve this they created a lentiviral vector system that monitors both APOBEC- and Cas9..., the Harris lab showed that human APOBEC3A-Cas9n-UGI and APOBEC3B-Cas9n-UGI base editing complexes are...abundance, and mCherry fluorescence is activated when APOBEC-Cas9n-UGI-mediated activity edits out a frame-shift... efficient than the BE3 plasmid containing rat APOBEC1. Finally, they show that the ACE reporter can also...

...post was contributed by guest blogger Daniel M. Sapozhnikov, a graduate student in the laboratory of Dr. ...leading to unpredicted gene expression changes (Sapozhnikov and Szyf 2021, Charlton et al. 2020). Most importantly...between DNA demethylation and gene expression (Sapozhnikov and Szyf 2021).    Figure 3: A simpler...leaving the target CpG unmethylated. Adapted from Sapozhnikov and Szyf 2021.   Let me leave you with a...  Thank you to our guest blogger!Daniel M. Sapozhnikov is a graduate student in the laboratory of Dr...1060–1065. https://doi.org/10.1038/nbt.3658. Sapozhnikov DM, Szyf M (2021) Unraveling the functional role...

...a paper profiling four base overhang ligation (Potapov et al., 2018), which showed that the five traditional... for the job compared to T7 ligase (it was—see Potapov et al., 2018). More complex reactions benefited... forget to ask DAD for some help! References Potapov, V., Ong, J. L., Kucera, R. B., Langhorst, B. W...doi.org/10.1021/acssynbio.8b00333 Pryor, J. M., Potapov, V., Bilotti, K., Pokhrel, N., & Lohman, G. J. ...doi.org/10.1021/acssynbio.1c00525 Pryor, J. M., Potapov, V., Kucera, R. B., Bilotti, K., Cantor, E. J.,...

...detergents, such as Triton X-100, Tween-20, or saponin. Each detergent has different chemical properties... and membrane integrity (Fig. 2). For example, saponin interacts with cholesterol in cell membranes and...) Permeabilizing with the selective detergent, saponin, keeps membrane-associated proteins in place, while...fixing with formaldehyde and permeabilizing with saponin. However, if you are not worried about washing ...

...variants with other deaminases: AID, CDA1, and APOBEC3G (Komor et al., 2017). CDA1-BE3 and AID-BE3 edited...Cs following a G more efficiently than BE3, but APOBEC3G displayed less predictable sequence preferences...editing product purity. The lab also extended the APOBEC1-Cas9n and Cas9n-UGI linkers to improve product ...Komor et al., 2017 BE4 and BE4-Gam; AID, CDA1 and APOBEC3G BE3 variants A second copy of UGI improves product...

...generate and screen a library of AAV9 variants (Chuapoco et al., 2023). They found the best-performing ...characterization of AAV.CAP-Mac. Image reproduced from Chuapoco, Flytzanis, Goeden, et al. 2023, under CC-BY license...license.   Find the AAV.CAP-Mac plasmid here!   Chuapoco, M.R., Flytzanis, N.C., Goeden, N. et al. Adeno-associated...

...awry. The process of programmed cell death, or apoptosis, is one such mechanism. When a cell or its genetic...that cell will most often commit itself to the apoptotic pathway and be eliminated from the body. In the...the case of cancer, however, the apoptotic pathway is circumvented because of the specific genes involved...

...of T4 DNA Ligase fidelity studies conducted by Potapov et al. at NEB (1, 2). While T4 DNA Ligase, the ...England Biolabs, Inc.       References 1. Vladimir, Potapov, et al. "Optimization of Golden Gate assembly through...and bias profiling." bioRxiv (2018): 322297. 2. Potapov, Vladimir, et al. "A single-molecule sequencing...

... HIV-1 toxic proteins, CRISPR/Cas9 SAM caused apoptosis, indicating a true “shock and kill” response. ...on cell viability, cell cycle progression, or apoptosis with Cas9/gRNA expression. A pooled analysis found...Addgene. Kaminski R, Chen Y, Fischer T, Tedaldi E, Napoli A, Zhang Y, Karn J, Hu W, Khalili K. Elimination...

...agonist CASP3 Caspase 3, apoptosis-related cysteine peptidase CASP8 Caspase 8, apoptosis-related cysteine peptidase...effects of p53 are in promoting cell cycle arrest, apoptosis, or senescence in damaged cells. The p53 name ...oligomerization. In particular, the loss of p53’s pro-apoptotic effects is especially important to tumorigenesis... below. Symbol Name 14-3-3-σ Stratifin Apaf-1 Apoptotic peptidase activating factor 1 ATM ATM serine/threonine...peptidase CASP9 Caspase 9, apoptosis-related cysteine peptidase Cyclin B CCNB1 CCNB2 CCNB3 Cyclin B1, ...protein p53 p53AIP1 Tumor protein p53 regulated apoptosis inducing protein 1 p53R2 p53 inducible, ribonucleotide...activator inhibitor type 1), member 1 PERP TP53 apoptosis effector PIDD p53-induced death domain protein...