Even more sceptical
My head is spinning with more questions than answers
I have some more questions about the experimental design in terms of methodology and correlation. What exactly is a double-filtration apheresis supposed to prove to me if my focus was exclusively on β-amyloid-like clots? I will subgroup this article into two rasing questions.
1. What Is the ThT-Signal Telling, and What Can It Not Tell Without Any Further Validation?
Let me first, once more, start with the Thioflavin T (ThT)-signaling issue. In this regard, I would like to quote Carrol et al. (2025)1:
“Fluoroprobes have also been used as competitors to identify non-fluorescent compounds by displacement. Although fluoroprobes have played critical roles in studying tauopathies, they typically lack specificity for different fibril polymorphs. Indeed, their generality is often a great strength because a single fluoroprobe such as ThT has the versatility to detect a wide range of fibrils, largely independent of sequence or substructures. Yet the field would also benefit from complementary fluoroprobes that are selective for subsets of tau polymorphs.”
“Largely independent of sequence” implies a fundamental lack of proteomic specificity. In biochemistry, the primary structure of a protein, its specific amino acid sequence, is the definitive determinant of its identity, distinguishing unique entities such as Spike protein, fibrinogen, or albumin. Because ThT binding is effectively independent of this primary sequence, the probe is biochemically “blind” to the identity of the target molecule. It does not recognize specific proteins; instead, it reacts exclusively to a common physical motif: the cross-beta-sheet quaternary structure. Since numerous proteins are capable of undergoing conformational transitions into beta-sheet-rich fibrillar structures under physiological or pathological stress2, 3, 4, 5, 6: such as acute systemic inflammation, localized protein misfolding, or shear stress induced by apheresis instrumentation–the resulting fluorescence signal in plasma represents a non-specific aggregate of various amyloidogenic and non-amyloidogenic species, rather than a quantifiable marker of a single distinct pathology.
We’ll examine the reaction of ThT a bit closer: Noormägi et al.7 wrote in 2012:
”(…) Recently, it has been demonstrated that several low-molecular weight compounds like Basic Blue 41, Basic Blue 12, Azure C, and Tannic acid interfere with the fluorescence of ThT bound to Alzheimers’ amyloid-b fibrils and cause false positive results during the screening of fibrillization inhibitors. In the current study, we demonstrated that the same selected substances also decrease the fluorescence signal of ThT bound to insulin fibrils already at submicromolar or micromolar concentrations. (…)”
"(…) It has been demonstrated that ThT binds to the grooves of the cross-beta structure of fibrils [4,7,9]. The binding stoichiometry of bound ThT inducing the characteristic fluorescence is about 0.09 moles of ThT per mole of insulin in fibril form [16]. Our results show that the apparent fluorescence quenching starts at very low submicromolar concentration of selected compounds and is completed at concentrations equal to 0.1 stoichiometry, which is in agreement with the binding stoichiometry for ThT determined earlier [16]. Compounds that interfere with ThT are similar to the structure of ThT (see Table 1), and, therefore, it is realistic that they compete with ThT for common binding sites on amyloid fibrils. Basic Blue 41 and Basic Blue 12 expose high, nanomolar affinity to the insulin fibrils, which is higher than affinity of ThT. This fact could be further exploited for design of novel amyloid probes or potential starting points for discovery of substances inhibiting protein fibrillization process, which are applicable as drug candidates for amyloidogenic diseases. We have to mention that Methylen Blue, which has similar structure to Basic Blue 41 and Basic Blue 12 is currently in clinical trials as disease modifying drug for Alzheimers disease [17,18]. (…)”
The authors demonstrated in 2012 that ThT and ThT-like structures possess a competitive nature, which can lead to significant interference, resulting in both false-positive and false-negative signaling. Furthermore, it has been demonstrated–at the latest since Biancalana et al. (2010)8 –that ThT binds non-specifically to the general hydrophobic β-sheet structures of fibrils:
“Subsequent molecular dynamics analysis of the PSAM in the presence of ThT enabled the first application of dye-binding simulations to a discrete and well-defined ThT binding site [50]. The hybrid experimental and computational approach employed to study the PSAMs has thus provided an important link between dye-binding simulations and experimentally testable hypotheses. Molecular dynamics simulations were conducted in a similar manner as for the eight-stranded KLVFFAE protofibrils described above [44, 45]. In order to maximize computational efficiency, the N- and C-terminal globular domains of the PSAMs were removed, as these have been experimentally demonstrated not to bind ThT. The initial system was composed of a periodic water box containing ~5600 water molecules, the “excised” PSAM flat β-sheet, two ThT molecules, and two neutralizing chloride ions. Simulations were conducted at 310 K over 100 ns, and the resulting populations of bound ThT molecules were clustered into predominant binding modes. These simulations demonstrated that ThT binds primarily to the designed site along the shallow groove formed by cross-strand Tyr side chains, making subtle contacts with the adjacent Leu ladder (Figure 4f-4h, Site a). The striking similarity between the Val-Phe [44] and Tyr-Leu [50] ThT-binding motifs observed in simulations offers support for the validity and potency of such aromatic-mediated ThT binding modes. These results strongly suggest that surface-exposed channels rich in aromatic amino acids are the primary binding sites of ThT. Together, the findings rationalize the broad binding spectrum of ThT toward diverse fibrils.”
In summary it can be said that the reliance on ThT fluorescence to quantify “amyloid clot burden” in patient plasma is flawed without an orthogonal confirmation due to three primary biochemical constraints:
Lack of Proteomic Specificity (The “Blindness” Problem) ThT is not a targeted probe; it is a structural dye that interacts exclusively with the quaternary architecture of cross-beta-sheet motifs. Because it binds largely independently of the primary amino acid sequence, it cannot distinguish between different proteins. Whether the signal originates from pathogenic amyloidogenic species or benign, functional proteins is indistinguishable to the probe. In a complex matrix like blood plasma—which contains high concentrations of diverse proteins—a ThT signal merely indicates the presence of some structure with beta-sheet characteristics, not the presence of a specific pathological clot.
Susceptibility to Chemical Interference (The Competition Problem) Research by Noormägi et al. (2012) demonstrates that ThT is prone to competitive inhibition. Numerous small-molecule compounds share structural similarities with ThT and compete for the same binding sites on amyloid fibrils. In a clinical or experimental setting, this leads to significant signal distortion:
False Negatives: Competitive displacement of ThT by other substances leads to “fluorescence quenching,” which can be erroneously interpreted as the clearance of amyloid fibrils.
False Positives: Chemical interference can alter the binding kinetics, leading to inaccurate quantifications that do not reflect the actual state of fibrillization.
Structural Ambiguity and Lack of Polymorph Selectivity As underscored by Carrol et al. (2025), ThT lacks the specificity to discriminate between different fibril polymorphs. Its “versatility” in detecting a wide range of fibrils is, in this context, a diagnostic liability. Furthermore, the work of Biancalana et al. (2010)³ reinforces that ThT binding is driven by broad hydrophobic interactions, specifically aromatic amino acid motifs, rather than highly specific molecular recognition.
The use of ThT-based assays to validate the efficacy of procedures like apheresis is methodologically not enough. When biomass is removed from plasma, a reduction in the non-specific ThT signal is an inevitable physical outcome, regardless of whether a disease-causing agent was targeted or if the plasma environment was simply chemically altered. Without independent, rigorous validation, such as mass spectrometry or another orthogonal structure specific fluorescence like Congo red9, to identify the specific protein composition of the material, ThT fluorescence remains an ambiguous indicator that conflates structural detection with specific clinical pathology.
This was further confirmed by Biancalana et al. (2009)10 who detailed the exact structural requirements for ThT binding, reinforcing its reliance on hydrophobic pockets rather than sequence-specific recognition. While Girych et al. (2016)4 discusses how combining probes can attempt to mitigate the shortcomings of using ThT alone. Jamali et al. (2022)11 demonstrated that Z-scan optical method can complement the Thioflavin T assay for investigation of anti-Alzheimer’s impact of polyphenols. This illustrates the necessity of using complementary optical methods, as ThT-only assays are insufficient for characterizing fibrillization inhibitors. Hirata et al. (2024)12 highlight ThT’s utility as a stress-response probe, further emphasizing its non-specificity regarding the type of amyloid structure or underlying disease mechanism. Kalitnik et al. (2025)13 provide a framework for the complex interplay between different amyloid species, debunking the “single-clot” pathology narrative. However, the authors summarize:
“In contrast to ThT and other dyes specific to amyloid fibrils in general, antibodies paired with fluorescence probes can selectively recognize distinct amyloid proteins. Traditional sequence-specific epitopes target defined linear regions, whereas structural epitopes additionally recognize conformational features associated with particular stages of fibrillation (Perchiacca et al., 2012). Due to their regional specificity, antibodies can elucidate the mechanisms of cross-interactions as in the case of AαSyn and lysozyme (Vaneyck et al., 2021). Additionally, conformationally sensitive antibodies map transitions through assembly states, expanding the understanding of the fibrillation kinetics as shown in the case of interactions between Aβ and TDP-43 (Shih et al., 2020).”
And this finally leads me to an answer, shocking me a little bit:
”specificity of ThT signal in plasma matrices
reproducibility across samples
correlation with symptom burden
modulation with intervention”
Is it obvious or do I need to spell it out? The loss of a signal (or a reduction in biomass) following a massive intervention like a double filtrated apharesis (including Immusorba TR) does not imply that the removed material was the causative agent of the disease. This is a classic methodological trap: equating the clearance of an aggregate with the resolution of a pathology. Because the ThT signal is essentially a readout of non-specific structural motifs in a fluctuating plasma environment, any significant physical filtration process will inevitably lower the fluorescence intensity. This reduction is a physical artifact of biomass removal, not a validated clinical indicator of “amyloid clearance.”
By relying on such an imprecise proxy, the entire premise of “clot clearance” as a therapeutic endpoint collapses. Without establishing a direct, sequence-specific correlation between the removed proteins and the patient’s symptomatic burden, these protocols remain exploratory at best, and medically reckless at worst. We are seeing a confusion of “cleaning the fluid” with “curing the biology”.
So much for my first question, which Maria Gutschi recently expanded upon from a pharmacological perspective with several extremely important aspects.
2. Are we dancing on an active volcano?
The study by Sheik et al.14 from 2017 investigated a new approach to neutralizing SEVI (Semen-derived Enhancer of Virus Infection) amyloid fibrils, which can massively increase HIV infectivity. This demonstrates that amyloid fibrils occur naturally and can facilitate certain viral infections. The authors used hydrophobic nanoparticles to drastically reduce this effect.
Here are the key findings of the work:
The authors demonstrate that polymers with hydrophobic side chains are capable of interacting with SEVI and significantly disrupting its β-sheet structure. The β-sheet content was reduced by approximately 45% through the use of these hydrophobic materials compared to SEVI in the presence of hydrophilic control polymers.
“Herein, we show that polymers containing hydrophobic side chains can interact with SEVI and reduce its β-sheet content by ~45% compared to the β-sheet content of SEVI in the presence of polymers with hydrophilic side chains, as estimated by Polarization Modulation-Infrared Reflectance Absorption Spectroscopy Measurements.”
This structural change led to a measurable reduction in SEVI-mediated HIV infection in TZM-bl cells. A nanoparticle formulation of the hydrophobic polymer reduced SEVI-mediated HIV infection by 60% compared to control treatment.
“A nanoparticle formulation of this hydrophobic polymer reduced SEVI-mediated HIV infection in TMZ-bl cells by 60% compared to control treatment.”
A crucial point is that these nanoparticles did not require specific amyloid-targeting groups. Although this required high concentrations to observe biological activity, this approach highlights the potential of using hydrophobic interactions to specifically modify the secondary structure of amyloids.
“While these nanoparticles lacked specific amyloid-targeting groups, thus, requiring high concentrations to observe biological activity, the use of hydrophobic interactions to alter the secondary structure of amyloids represents a useful approach to neutralizing SEVI function.”
Interestingly, the authors used hydrophobic polymer nanoparticles with a nearly neutral charge and covalent bonding, as they emphasized in their study, to demonstrate that the hydrophobic properties of nanoparticles alone are sufficient to actively interact with β-sheet structures.
This raises a huge question: How on earth would actually used LNPs act with fibril-structures? However, as demonstrated by the authors, β-amyloid sheet structures occur naturally and are not necessarily an indicator of amyloid-driven pathogenicity. As allways in systems biology terms: Context, space, place and threshholds matter.
And here is the real dance on the volcano.
In their paper, Hammarström and Nyström (2023)15 assumed the dangerous interplay between viral infections, amyloid formation, and neurodegeneration. The authors claim that many viral proteins are inherently amyloidogenic and that direct cooperation or “cross-seeding” can occur between human and viral proteins. A key example in their work is SARS-CoV-2: The abnormal blood clotting observed in severe COVID-19 cases or Long COVID was directly associated to the amyloid formation of human fibrin as well as the viral spike protein. The study concludes that virus and amyloid research must collaborate more closely to develop drugs against long-term neurological and systemic damage caused by such viral infections.
What is more, the central reference that Hammarström & Nyström rely on in their 2023 review for the spike-amyloid claim is their own preceding paper from 2022 (JACS). And what exactly did they do there? In the 2022 JACS paper, amyloidogenic sequences in the spike protein were identified using ThT kinetics, Congo red staining, and TEM ultrastructure. What initially sounds valid here turns out to be a methodological extrapolation: Because they did this on isolated synthetic 20-amino acid peptides, incubated at 37°C in vitro.16
This represents a methodologically enormous leap: they demonstrate that isolated peptide fragments can be amyloidogenic under artificial conditions in vitro, and then extrapolate in the 2023 review that this constitutes a mechanism for Long COVID coagulation pathology.
While the former paper emphasizes the pathogenic dangers of naturally occurring amyloids, the study by Dodd-o et al. (2024)17 demonstrates how this very architectural principle can be specifically utilized to combat viruses. The researchers developed a tunable antiviral platform made of synthetic peptides that self-assemble into functionalized β-sheet fibrils. These specific peptides possess two distinct domains: one forces the molecule to self-assemble into a stable fibril structure, while the other domain specifically binds to viral proteins (such as the SARS-CoV-2 spike protein). This fibril structure creates a “multivalent” binding surface that neutralizes viral complexes extremely efficiently and, due to its structure, exhibits particularly high resistance to viral mutations.
To understand the contradiction, one must examine the methodologies in detail:
Hammarström & Nyström(2023): Their work serves as a comprehensive review and a conceptual hypothesis formulation (the "Vicious Liaison"). They frequently rely on literature data derived primarily from ThT assays, high dosage in vitro experiments with no physiological comparable parameters (e.g.: Christ et al.18; 150µl of 4 mM ThT19), and, for another example, case reports n=1. While such data are useful for identifying correlations between viral load and amyloid presence, they do not constitute mechanistic proof of the structural integrity of the amyloids, nor does the study provide direct evidence of neurodegenerative clinical signs.
Sheik et al. (2017): In contrast to the weak evidence given by Hammarström & Nystöm, they used Polarization Modulation-Infrared Reflectance Absorption Spectroscopy (PM-IRRAS) to measure β-sheet content directly. This is a much more robust line of evidence than a simple fluorescence signal, as it analyzes the molecular vibration of peptide bonds (Amide I band), thereby allowing for a direct assessment of secondary structure.20
Dodd et al. (2024): The researchers use “tunable compositions,” a modular approach. They separate the physical property of fibril formation (self-assembly via a self-assembly domain) from the biological function of viral neutralization (via a specific targeting domain). This is a decisive difference: they leave nothing to chance (or a vague ThT signal) but instead design the amyloid structure intentionally. Unlike smaller molecules that might only block a single site, this platform exploits the multivalent nature of the fibril. The fibril serves as a “scaffold” presenting numerous antiviral units. This ensures enormous binding density and robustness. To support their claims, the group does not rely solely on ThT. They characterize their artificial fibrils using electron microscopy (TEM/AFM) and CD-spectroscopy (circular dichroism) to provide genuine proof of the structural integrity of their β-sheet constructs.
Summary: The Methodological Dubiousness of ThT-Based Apheresis
The current use of Thioflavin T (ThT) fluorescence to quantify “amyloid burden” in apheresis therapy is methodologically insufficient and clinically misleading. Because ThT reacts solely to quaternary structure (cross-beta-sheets) and is blind to primary sequences, it cannot differentiate between pathological protein aggregates and functional, systemically relevant protein structures.
A significant reduction in the ThT signal following double-filtration apheresis is, therefore, not evidence of selective “amyloid clearance,” but merely a physical artifact of biomass reduction. Without the use of orthogonal, sequence-specific analytics (such as mass spectrometry or structure-specific antibodies), this therapeutic approach fails to address the underlying causal pathology. Furthermore, the non-specific removal of amyloids ignores systems biological complexity: amyloid structures are not inherently toxic, but rather operate in a dynamic equilibrium between physiological function (e.g., antiviral defense) and pathological aggregation. Even more, post-viral syndrom is no new mechanism21, 22, 23 and up today not fully understood24, 25, 26, 27, 28. Furthermore, it has not been conclusively clarified whether amyloid proteins exclusively promote pathogenic states.29, 30
Conclusion
The current trend of “cleaning the fluid” without validating the proteomic identity of the target structures represents a medically risky oversimplification that substitutes scientific evidence with a non-specific fluorescence marker.
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On the page of his website where McCairn advertises his "amyloid burden" detection service, there are two images of the same fiber that he found in Lyndsey's blood in 2024, where both images show the fiber after ThT staining but the other image is taken in UV mode. [https://synapteklabs.com/protocol-on-sending-blood-samples-2/] In the stream where McCairn showed the fiber, he only showed the sample after ThT staining, but he didn't show if the fiber was already autofluorescent before the staining, so the fluorescence may have not even been because of the ThT. [https://rumble.com/v5zq84w-operation-blue-drone-and-lessons-in-fluorescent-microscopy-amyloid-signals-.html?start=7301] Some other fibers McCairn has shown have already been autofluorescent before ThT staining, but McCairn seems to consider that to be sufficient evidence that the fibers are made of "amyloidogenic fibrin", even though for example textile fibers that have been bleached white can be strongly autofluorescent, like how white t-shirts are fluorescent under UV light.
In one stream McCairn even found some random autofluorescent fibers in a Moderna vaccine sample. [https://sars2.net/clot3.html, search for Moderna] At one point of the stream, he showed a fiber in non-UV mode and without ThT staining, and then when he applied ThT on the sample and switched to UV mode, he said that the fiber now glowed brighter than the background. However he failed to mention that a few minutes earlier when he had not yet applied the ThT, he panned past the fiber in UV mode, so you could see the fiber was already autofluorescent even without the ThT. Later he said "I can't explain the takeup of Thioflavins", but he didn't mention that the same fiber that supposedly took up Thioflavin was autofluorescent even without the ThT.
Last year when Nicolas Hulscher said that McCairn found "amyloid fibrils" in the 3-year-old's blood, Ian Musgrave replied: "That's a cellulose fibre, not amyloid." [https://x.com/KevinMcCairnPhD/status/1959430726237168121] Then McCairn said: "No it isn't. It's amyloidogenic fibrin." And Musgrave said: "No, it is not. It's just a cellulose fibre. I've EMed enough real amyloids and sighted enough cellulose fibres under the microscope to know which is which." And Musgrave said: "Thioflavin will stain almost anything if you don't use the right conditions, I have long experience with thioflavin and amyloids."
Then McCairn said: "No it doesn't when used at the right molar concentration, coupled with use of microinjection techniques to target the object. Besides cellulose doesn't auto-fluoresce. If you think it cellulose why don't recapitulate the slide with the fibrous clot being in-situ with the blood layer, and with connecting micro clot globular forms connecting each ends."
What he called the "globular forms" connected to the ends of the fiber were some random blobs on the slide that didn't even look connected to the fiber, and I don't think McCairn even verified if the blobs were made of fibrin or not. [https://sars2.net/clot3.html#Substack_post_about_SEM_images_of_the_3_year_olds_fiber] And McCairn forgot to mention that cellulose can be strongly fluorescent if it has been bleached white.
McCairn then replied that in order to eliminate false positives, "I run antibodies, use SEM/EDX, and Raman on samples". [https://x.com/KevinMcCairnPhD/status/1959414465293959358] I have told him to verify that his fibers are actually made of fibrin by doing either immunostaining with anti-fibrin antibodies or Raman spectroscopy, but I haven't seen him ever actually publish the results of either type of analysis (even though I don't know if by antibodies he meant anti-fibrin antibodies or antibodies to recognize amyloid proteins).
Last year McCairn published two Substack posts about the 3-year-old's fiber. In the first post he showed light microscope images of the sample, and he indicated that he was next going to run SEM, EDX, and Raman on the sample. [https://substack.com/@kevinwmccairnphd282302/p-164383206] In the second post he posted SEM images of the sample but he didn't describe EDX or Raman results. When I asked him why he didn't publish the EDX or Raman results, he responded to me by doing a stream where he showed the EDX results, but he said that he couldn't do Raman "because the sample was sent on a glass slide, and you need quartz slides for Raman". [https://x.com/KevinMcCairnPhD/status/1961314002304438763] But then I pointed out that McCairn had earlier said that the sample was preserved for Raman, and a glass slide may have been acceptable for Raman according to LLMs. And he already knew in advance that the sample was on a glass slide, so why did he even say he was going to do Raman?
I still suspect that he did actually run Raman on the sample, but the results showed that the fiber was not made of fibrin, so he decided to not publish the results. And if McCairn did immunostaining with anti-fibrin antibodies, it would be an easy way to verify if the fibers that look like textile fibers are actually made of fibrin.