The Uphoff lab


Regulatory fine-tuning of mcr-1 increases bacterial fitness and stabilises antibiotic resistance in agricultural settings
Ogunlana L, Shaw L, Kaur D, Jangir P, Walsh T, Uphoff S, MacLean RC
ISME Journal 17, 2058–2069 (2023)

Phosphorylation by ATR triggers FANCD2 chromatin loading and activates the Fanconi anemia pathway
Kupculak M, Bai F, Luo Q, Yoshikawa Y, Lopez-Martinez D, Xu H, Uphoff S, Cohn M
Cell Reports 112721 (2023)

Phenotypic heterogeneity in the bacterial oxidative stress response is driven by cell-cell interactions
Choudhary D, Lagage V, Foster K, Uphoff S
Cell Reports 112168 (2023)


Adaptation delay causes a burst of mutations in bacteria responding to oxidative stress
Lagage V, Chen V, Uphoff S
EMBO Reports e55640 (2022)

Super-Resolution Microscopy and Tracking of DNA-Binding Proteins in Bacterial Cells
Cassaro C, Uphoff S
Methods in Molecular Biology vol. 2476 (2022)


Cellular heterogeneity in DNA alkylation repair increases population genetic plasticity
Vincent MS, Uphoff S
Nucleic Acids Research 49 (21) 12320–12331 (2021)

Nonrandom segregation of sister chromosomes by Escherichia coli MukBEF
Makela J, Uphoff S, Sherratt DJ
Proc Natl Acad Sci U S A 118 (33) e2022078118 (2021)

Single-molecule imaging of LexA degradation in Escherichia coli elucidates regulatory mechanisms and heterogeneity of the SOS response
Jones EC, Uphoff S
Nature Microbiology 6, 981–990 (2021)

Digging deeper in the biofilm
Choudhary D, Cassaro CJ
Nature Reviews Microbiology (2021)

Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins
Stracy M, Schweizer J, Sherratt DJ, Kapanidis A, Uphoff S, Lesterlin C
Molecular Cell 81, 1-16 (2021)


Pulses and delays, anticipation and memory: seeing bacterial stress responses from a single-cell perspective
Lagage V, Uphoff S
FEMS Microbiology Reviews fuaa022 (2020)

Bacterial phenotypic heterogeneity in DNA repair and mutagenesis
Vincent M, Uphoff S
Biochemical Society Transactions BST20190364 (2020)

DNA ADP-Ribosylation Stalls Replication and Is Reversed by RecF-Mediated Homologous Recombination and Nucleotide Excision Repair
Lawarée E, Jankevicius G, Cooper C, Ahel I, Uphoff S, Tang C
Cell Reports 30, 1373-1384 (2020)


A quantitative model explains single-cell dynamics of the adaptive response in Escherichia coli
Uphoff S
Biophysical Journal 117, 1156-1165 (2019)

Choosing the right label for single-molecule tracking in live bacteria: Side-by-side comparison of photoactivatable fluorescent protein and Halo tag dyes
Banaz N, Makela J, Uphoff S
J Phys D: Applied Physics 52, 064002 (2019)


Filming flagella and pili in action
Lagage V, Uphoff S
Nature Reviews Microbiology 16, 584 (2018)

Real-time dynamics of mutagenesis reveal the chronology of DNA repair and damage tolerance responses in single cells
Uphoff S
Proc Natl Acad Sci U S A 115, E6516-E6525 (2018)
Accompanying commentary

Understanding protein mobility in bacteria by tracking single molecules
Kapanidis A, Uphoff S, Stracy M
Journal of Molecular Biology (2018)

The new microscopy
Briegel A, Uphoff S
Editorial in Current Opinion in Microbiology, 43, 208-211 (2018)


Scc2/Nipbl hops between chromosomal cohesin rings after loading
Rhodes J, Mazza D, Nasmyth K, Uphoff S
eLife e30000 (2017)

Single-molecule analysis of bacterial DNA repair and mutagenesis
Uphoff S, Sherratt DJ
Annual Reviews of Biophysics, 46, 411-432 (2017)

Frequent exchange of the DNA polymerase during bacterial chromosome replication
Beattie TR, Kapadia N, Nicolas E, Uphoff S, Wollman AJM, Leake MC, Reyes-Lamothe R
eLife, e21763 (2017)


Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli
Stracy M, Jaciuk M, Uphoff S, Kapanidis AN, Nowotny M, Sherratt DJ, Zawadzki P
Nature Communications, 7, 12568 (2016)

Imaging cellular structures in super-resolution with SIM, STED and Localisation Microscopy: A practical comparison
Wegel E, Göhler A, Lagerholm BC, Wainman A, Uphoff S, Kaufmann R, Dobbie IM
Scientific Reports, 27290 (2016)

Stochastic activation of a DNA damage response causes cell-to-cell mutation rate variation
Uphoff S, Lord ND, Potvin-Trottier L, Okumus B, Sherratt DJ, Paulsson J
Science, 27290, 1094-1097 (2016)

Super-resolution microscopy and single-molecule tracking for quantitative analysis of DNA repair in bacteria
Uphoff S
Methods in Molecular Biology, Chromosome Architecture, 221–234 (2016)


Live-cell superresolution microscopy reveals the organization of RNA polymerase in the bacterial nucleoid
Stracy M, Lesterlin C, Garza de Leon F, Uphoff S, Zawadzki P, Kapanidis AN
Proc Natl Acad Sci U S A, 112(32), E4390–E4399 (2015)


In vivo single-molecule imaging of bacterial DNA replication, transcription, and repair
Stracy M, Uphoff S, Garza de Leon F, Kapanidis AN
FEBS Letters, 588(19), 3585–3594 (2014)

Visualizing protein-DNA interactions in live bacterial cells using photoactivated single-molecule tracking
Uphoff S, Sherratt DJ, Kapanidis AN
J Vis Exp, 85 (2014)

Studying the organization of DNA repair by single-cell and single-molecule imaging
Uphoff S, Kapanidis AN
DNA Repair, 20, 32-40 (2014)

The SMC complex MukBEF recruits topoisomerase IV to the origin of replication region in live Escherichia coli
Nicolas E, Upton AL, Uphoff S, Henry O, Badrinarayanan A, Sherratt DJ
MBio, 5(1), e01001-13 (2014)


Long-lived intracellular single-molecule fluorescence using electroporated molecules
Crawford R, Torella JP, Aigrain L, Plochowietz A, Gryte K, Uphoff S, Kapanidis AN
Biophysical J, 105(11), 2439-2450 (2013)

Single-molecule DNA repair in live bacteria
Uphoff S, Reyes-Lamothe R, Garza de Leon F, Sherratt DJ, Kapanidis AN
Proc Natl Acad Sci U S A , 110(20), 8063-8068 (2013)


In vivo architecture and action of bacterial structural maintenance of chromosome proteins
Badrinarayanan A, Reyes-Lamothe R, Uphoff S, Leake MC, Sherratt DJ
Science, 338(6106), 528-531 (2012)


DAOSTORM: an algorithm for high- density super-resolution microscopy
Holden SJ, Uphoff S, Kapanidis AN
Nature Methods, 8(4), 279-280 (2011)

Improved temporal resolution and linked hidden Markov modeling for switchable single-molecule FRET
Uphoff S, Gryte K, Evans G, Kapanidis AN
ChemPhysChem, 12(3), 571-579 (2011)


Defining the limits of single-molecule FRET resolution in TIRF microscopy
Holden SJ, Uphoff S, Hohlbein J, Yadin D, Le Reste L, Britton OJ, Kapanidis AN
Biophysical J, 99(9), 3102-3111 (2010)

Monitoring multiple distances within a single molecule using switchable FRET
Uphoff S, Holden SJ, Le Reste L, Periz J, van de Linde S, Heilemann M, Kapanidis AN
Nature Methods, 7(10), 831-836 (2010)