Library · Biology & lab methods
What Cellular Membrane Transport Probing got wrong, from 11 theses
Summary written by a model from the records below: The records describe methodological failures and technical limitations encountered when investigating membrane transporter proteins and ion channels. Researchers faced challenges with surrogate functional assays, background interference, in vitro vesicle reconstitution, and electrophysiological detection limits. These records come from graduate theses, 2021 to 2026, each labeled with its degree where the repository states it, and each links to its thesis. They were extracted by language models reading the full text, so treat each as a lead to read, not a verdict.
Plus 10 problems the authors left open, listed at the end.
Failure modes, by theses reporting them
Select a mode to jump to its records.
Surrogate assays and indirect proxies fail to reliably reflect transport activity
Researchers found that fluorescent substrate analogs and transmembrane homology failed to validate direct transport or drug efflux functions. Similarly, agar clearing assays reflected lysis and diffusion rather than transporter display, while membrane localization assays did not account for observed nutrient uptake variability.
Tried and failed
fluorescent substrate analog uptake assay applied to transporter substrate specificity validation. Outcome: did not generalise. Reason: fluorescent analog uptake failed to reproduce previously reported direct transport activity
Tried and failed
assigning drug efflux function based on transmembrane homology applied to bacterial antibiotic susceptibility determinants. Reason: candidate transporters functioned in cell wall maintenance rather than direct active drug extrusion
Genetic determinants of antibiotic susceptibility reveal novel mechanisms of action and resistance in mycobacteria · Harvard · PhD
Considered and rejected
Considered and rejected: Rejected the tributyrin emulsion agar clearing assay for measuring lipase (LipA) autotransporter display efficiency, as it primarily reflects enzyme diffusion and bacterial lysis rather than surface display.
Engineering synthetic adhesins for biophysical investigation and rewiring of host-microbe interactions · EPFL · PhD
Tried and failed
membrane transporter localization assays applied to nutrient uptake variability across aneuploid strains. Outcome: did not generalise. Reason: Uptake variability occurred without the membrane localization changes observed in other aneuploid strains
Exploring the role of aneuploidy in phenotypic variability · MIT · PhD
Endogenous background flux and dye permeability variations confound transport measurements
Radioactive tracer uptake was obscured because target cation flux was indistinguishable from background endogenous flux. Optical calcium biosensor recordings were similarly disrupted by confounding intracellular transport and dye permeability variations along physical channel dimensions.
Tried and failed
radioactive tracer uptake assay applied to measuring transporter-mediated cation flux. Outcome: no signal. Reason: tracer uptake was indistinguishable from background endogenous ion flux
Molecular mechanisms of Sonic hedgehog release and delivery · Harvard · PhD
Tried and failed
somata fluorescence imaging of calcium biosensors applied to quantifying single-channel ion transport. Outcome: no signal. Reason: confounding intracellular calcium transport masked correlation with transported charge during depolarizing stimuli
Single-channel physiology in small compartments · Harvard · PhD
Considered and rejected
Considered and rejected: Rejected using absolute fluorescence intensity to compare calcium levels across different channel dimensions due to dye permeability variations along narrow/long channels.
CELL MIGRATION UNDER CONFINEMENT: HYDRAULIC RESISTANCE IN PATH NAVIGATION AND PHENOTYPIC TRANSITION · Johns Hopkins · PhD
In vitro proteoliposome reconstitution fails to provide reliable transport signals
Reconstitution of transmembrane solute transporters into proteoliposomes failed to yield detectable functional transport activity. In stopped-flow fluorescence assays, empty control vesicles exhibited higher proton flux and fluorescence changes than vesicles containing the transporter protein.
Tried and failed
proteoliposome reconstitution for in vitro transport assay applied to transmembrane solute transporter proteins. Outcome: no signal. Reason: functional reconstitution and transport activity could not be detected in proteoliposomes
New tools for the discovery of pigment gene function · MIT · PhD
Tried and failed
stopped-flow fluorescence kinetics with reconstituted proteoliposomes applied to membrane transporter proton flux quantification. Outcome: worse than baseline. Reason: empty control vesicles exhibited higher proton flux and fluorescence changes under acidic conditions than protein-containing vesicles
Understanding antimicrobial resistance mechanisms and the production of antimicrobial peptides in E. coli · UT Austin · PhD
Electrophysiological patch-clamp recordings are limited by cell identification requirements and electroneutral kinetics
Cell-attached voltage clamp could not be used alone because identifying neuronal subtypes required prior whole-cell current clamp recording. In other studies, patch-clamp electrophysiology failed to detect transport because the transport mechanism was electroneutral or the kinetics were too slow to produce measurable current.
Considered and rejected
Considered and rejected: Cell-attached voltage clamp was rejected for studying naturalistic HCN channel kinetics because whole-cell current clamp is required first to identify LTH vs OLM neurons by ISI ratio.
Subtype specific dysfunction of inhibitory interneurons in Fragile-X syndrome · UT Austin · PhD
Tried and failed
patch-clamp electrophysiology applied to copper transporter protein functional characterization. Outcome: no signal. Reason: transport mechanism is electroneutral or transport kinetics are too slow to generate measurable current
DEVELOPMENT OF A PLANT MEMBRANE-ON-CHIP PLATFORM FOR INTERROGATING PROTEIN-MEDIATED METAL TRANSPORT · Cornell · PhD
Left open by the authors
Problems the authors named and did not get to.
Left open
Design optimal voltage protocols and collect experimental patch-clamp data to eliminate remaining candidate drug-binding models. Blocker: Requires a wet lab with patch-clamp electrophysiology apparatus and cell lines to collect experimental ion channel data.
Modelling drug binding to biological ion channels · Nottingham · PhD
Left open
Perform automated patch-clamp (SyncroPatch) experiments at 37°C to verify drug-trapping behavior in ion channels. Blocker: Requires a wet lab with automated patch-clamp electrophysiology equipment (SyncroPatch) and biological cell lines.
Modelling drug binding to biological ion channels · Nottingham · PhD
Left open
Integrate patch-walking with Channelrhodopsin-assisted circuit mapping (CRACM) and test on PV-interneuron stressors in Alzheimer's disease models. Blocker: Requires wet lab facilities, electrophysiology patch-clamp rig, optogenetics setup, and transgenic Alzheimer's disease animal models.
Towards automation of multimodal cellular electrophysiology · Georgia Tech · PhD
Left open
Identify the specific transporter mediating D-2HG uptake in mouse CD8+ T cells experimentally. Blocker: Requires wet lab experiments, mouse CD8+ T cells, and biochemical assays to identify the transporter.
Environmental Barriers to T Cell Metabolism and Function · Harvard · PhD
Left open
Use distinct fluorescent emission wavelengths (red in gel, green in suspension) to eliminate background noise in confocal channels during traction rheoscopy. Blocker: Requires a wet lab, flow cell apparatus, fluorescent particles/gel preparation, and confocal microscope
Spatio-temporal Measurements of Dynamic Suspensions · Harvard · PhD
Left open
Determine the counter-substrate for mitochondrial NAD+ transporter SLC25A51 using proteoliposome transport or DRaCALA binding assays. Blocker: Requires a biochemistry wet lab, radioactive reagents, purified SLC25A51, and proteoliposome transport assays.
Labeled nicotinamide adenine dinucleotide reveals the mechanism of mitochondrial NAD⁺ replenishment · UT Austin · PhD
Left open
Validate proton transport function of GDT1 and TMEM165 using resistance measurements and encapsulated fluorescent pH-sensitive dyes under varying buffer pH. Blocker: Requires a wet lab, purified/expressed ion transporter proteins, liposomes, and electrophysiological/fluorescence assay apparatus.
Cell-free platform for the functional characterization of intracellular ion transporters · Cornell · PhD
Left open
Investigate yeast transporters PDR5 and ERG6 to explain the 180-fold yeast-specific IC50 discrepancy between acalabrutinib and ibrutinib. Blocker: Requires wet-lab yeast genetics and biochemical transport assays.
High-throughput screen reveals novel resistance mechanisms of Bruton’s Tyrosine Kinase to targeted therapeutics · UT Austin · PhD
Left open
Characterize P-ATPase1 to verify whether it functions as a Zn2+ efflux transporter in Chaetoceros neogracile. Blocker: Requires wet-lab culturing, genetic manipulation, or biochemical transport assays on C. neogracile.
Left open
Determine if AAT7610 and AAT7650 form a functional heterodimeric glutamine transporter using transport kinetics, inhibition, and peptide SRM turnover assays. Blocker: Requires a biochemistry/molecular biology wet laboratory and physical parasite/protein samples
Uncovering the Role of 5'-Nucleotidases in Pyrimidine Metabolism in Trypanosoma brucei · UT Southwestern · PhD
Who has worked on this
Authors of the public theses cited on this page, most-cited first.
- Frankie Patten-Elliott · Nottingham · PhD · 2026
Modelling drug binding to biological ion channels - Madeleine Rose Howell · Harvard · PhD · 2026
Single-channel physiology in small compartments - Barituziga Banuna · Cornell · PhD · 2025
DEVELOPMENT OF A PLANT MEMBRANE-ON-CHIP PLATFORM FOR INTERROGATING PROTEIN-MEDIATED METAL TRANSPORT - Alexis Ostwalt · Cornell · PhD · 2024
Cell-free platform for the functional characterization of intracellular ion transporters - Kerry Alexandra McGowen · Harvard · PhD · 2024
Genetic determinants of antibiotic susceptibility reveal novel mechanisms of action and resistance in mycobacteria - Mighten C. Yip · Georgia Tech · PhD · 2023
Towards automation of multimodal cellular electrophysiology - Yue Wen Deng · UT Southwestern · PhD · 2023
Uncovering the Role of 5'-Nucleotidases in Pyrimidine Metabolism in Trypanosoma brucei - Erick Ruiz · Harvard · PhD · 2022
Spatio-temporal Measurements of Dynamic Suspensions - Douglas R. Brown · MIT · PhD · 2022
MFSD7C is an ATP Transporter that Supports Bacterial Killing by Alveolar Macrophages in a Lipid-Rich Microenvironment - Riss Morgan Kellogg · MIT · PhD · 2022
Assessing the potential for zinc limitation of marine primary production: proteomic characterization of the low zinc stress response in marine diatoms - Giulia Notarangelo · Harvard · PhD · 2022
Environmental Barriers to T Cell Metabolism and Function - Christine Anne Moomau · MIT · PhD · 2022
Exploring the role of aneuploidy in phenotypic variability
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