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Use of FT-ICR to Identify Bryostatins in a Matrix Deployed at the Living Dock

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27 June 2026

Posted:

30 June 2026

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Abstract

Bryostatin is a marine natural marine product that was originally extracted from the sessile invertebrate Bugula nerintina. There is a marine bacterium, (Candidatus Endobugula sertula) that has a symbiotic relationship with Bugula that produces bryostatin. In the first large scale collection of Bugula, it took 14 tons of the obscure bryozoan to isolate 18 grams of the drug. This study focuses on isolating bryostatin from a material designed to attract and grow bacterium in the marine environment. Fourier transform Ion Cyclotron Resonance Spectrometer (FT-ICR) is used to identify bryostatins, bryostatin, fragments, and adducts that are present in the matrix. Data is divided into two groups; 1. Calculated exact molar masses, using the NIST Isotope Tables, for the bryostatins 0-21, adducts, fragments and dimers of bryrostatins. These values are correlated with the data from the FT-ICR with possible structure identification. 2. The FT-ICR data acquired from the extracts of the samples. This data is matched with the calculated values to identify specific empirical formulas. For bryostatin-1, the five most common isotopic variations and their natural abundance); would be: M; C47H68O17Na, 927.43487 (2) M+1 (+1 × 13C) 928.43823 (3) M+2 (+2 13C) 929.44158 (4) M+3 × 13C (930.44494) (5) M + 4 (+2 × 13C + 18O, 931.44583.

Keywords: 
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1. Introduction

Natural products, on land and in the sea, have long served as one of the most productive sources of therapeutic agents, particularly for cancer, neurological disorders, and infectious diseases, due to their exceptional chemical diversity and evolutionary optimization for biological activity.[1,2] Marine natural products represent a uniquely rich source of novel secondary metabolites shaped by ecological competition and selective pressure.[3] One of the most prominent examples of a marine-derived therapeutic lead is bryostatin-1, a (C47H68O17) macrolide isolated from the bryozoan Bugula neritina in the 1960’s.[4] The discovery of bryostatin-1 was advanced by large scale collections of B. neritina from the Florida coast, many of which were facilitated by Gulf Specimen Marine Laboratory in Panacea, Florida, under the direction of Jack Rudloe.[5] Rudloe played a significant role by harvesting the chemically productive invertebrates before there were large federal marine natural products programs. Our work reported here was conducted on the same dock in Panacea, Florida used during the 1960’s NCI Bugula collection (it was a launching point for collections).
Bryostatins exert their biological activity through high-affinity modulation of protein kinase C (PKC) isoforms, which can impact cell signaling, synaptic plasticity, and memory formation.[6,7] Unlike tumor-promoting phorbol esters, bryostatin-1 causes transient PKC activation followed by sustained downregulation, a pharmacological profile that contributes to its therapeutic potential and reduced oncogenic risk.[8] Bryostatin-1 has advanced through multiple Phase I and Phase II clinical trials for hematological malignancies, solid tumors, Alzheimer’s disease, and HIV latency reversal, although it has not received FDA approval.[9,10] These studies highlighted both clinical promise and practical challenges related to dosing, formulation, and compound availability.
Bryostatin-1 is a unique modulator of protein kinase C (PKC), belonging to a complex family of macrolide lactones currently comprising 22 known natural congeners (bryostatin 0 through bryostatin 21). This compound class has generated a growing body of in vitro and clinical evidence supporting its potential in central nervous system disorders, particularly Alzheimer’s disease (AD). Preclinical studies have demonstrated that bryostatin promotes synaptogenesis, enhances brain-derived neurotrophic factor (BDNF) signaling, and reduces neuropathologies such as amyloid accumulation and synaptic loss, thereby providing a strong argument for clinical development [11]. Early Phase IIa and expanded-access clinical studies in AD patients showed that bryostatin is well tolerated and produces rapid, albeit transient, improvements in cognitive performance (e.g., increases in MMSE scores) [12]. Subsequent Phase II trials demonstrated that bryostatin treatment can stabilize or improve cognitive function in moderately severe AD patients, with statistically significant improvements in Severe Impairment Battery (SIB) scores and reduced cognitive decline relative to placebo [13,14].
Other neurological indications, including Fragile X syndrome, stroke, multiple sclerosis, and traumatic brain injury, remain largely at the preclinical or early translational stage, despite evidence of improved synaptic plasticity, learning, and neuroprotection in animal models [15]. Current data indicates that bryostatin-1, with the most advanced clinical progress observed in Alzheimer’s disease. Large-scale clinical trials are necessary to confirm efficacy, optimize dosing regimens, and expand its therapeutic applicability. The natural supply of bryostatin-1 (via Bugula) is insufficient to support large-scale clinical trials. Typical yields are on the order of ~10−5–10−7 of wet weight. This limited material was sufficient to supply more than 40 clinical trials, but the regular stocks have been largely depleted, resulting to a shortage of bryostatin-1.[16]
Modern organic synthesis has advanced the availability of bryostatin-1 by overcoming the supply chain associated with its scarcity from Bugula neritina. A total synthesis developed by the Wender group, have achieved gram-scale production of bryostatin-1 through multistep synthetic routes [17]. These methods can generate tens of grams per year (e.g., ~20 g/year), which is enough to support preclinical studies and Phase I/II clinical trials, and possibly limited Phase III investigations. However, bryostatin-1 is a synthetically complex target (~25–30 steps), and synthesis at kilogram levels has not been demonstrated as economically possibility. Despite this substantial progress, bryostatin 1 remains a synthetically complex target, and large-scale manufacturing at kilogram levels has not yet been demonstrated as economically viable. As a result, while laboratory synthesis has largely solved access at the research and early clinical scale, full industrial scalability remains a challenge and focuses on process optimization and the development of more accessible analogs to aid clinical deployment.

2. Results

Below are tables that present potential species that could be identified, and others that present positive results for different types of bryostatins, different fragments, and different adducts that allowed us to see what was present. Table 2. Are calculated adducts masses for different cations linked bryostatin-1. It includes both +1 cation and a +2 cation, that positive ion ICR could detect. Table 3 are possible adducts that could form with hydride, fluoride, chloride and a oxide. With fragments, it is not resolved if these are possible species that have yet to be transformed into the final bryostatin structure or are fragments that have been lost from a completed bryostatin.
Table 2. Possible adducts that could be detected via Negative Ion Mode.
Table 2. Possible adducts that could be detected via Negative Ion Mode.
Ion Type Empirical Formula (Adduct Form) Exact Mass (Da)
[M − H] C47H67O17 903.4378
[M + F] C47H68O17F 923.4441
[M + Cl] C47H68O17Cl 939.4145
[M + OH] C47H69O18 921.4484
Table 3. Bryostatin-1 Fragment Ions (ESI–FT-ICR) : Positive Ion Mode ([M+Na]+ ) and negative ion mode (bottom) Calculated values used to search data files.
Table 3. Bryostatin-1 Fragment Ions (ESI–FT-ICR) : Positive Ion Mode ([M+Na]+ ) and negative ion mode (bottom) Calculated values used to search data files.
Fragment Assignment Formula (Adduct Form) Δ Mass (Da) Exact m/z
[M + Na]+ (parent) C47H68O17Na+ 927.435
−H2O C47H66O16Na+ −18.010565 909.425
−2H2O C47H64O15Na+ −36.021130 891.414
−CH3 C46H65O17Na+ −15.023475 912.412
−OCH3 C46H65O16Na+ −31.018390 896.417
−CO C46H68O16Na+ −28.010565 899.425
−CO2 C46H68O15Na+ −44.009500 883.426
−Acetyl (CH3CO) C45H65O16Na+ −43.018390 884.417
−Acetic acid (CH3COOH) C45H64O15Na+ −60.021130 867.414
Negative Ion Mode
Fragment Assignment Formula Δ Mass (Da) Exact m/z
[M − H] C47H67O17 903.437825
−H2O C47H65O16 −18.01 0565 885.42726
−CH3 C46H64O17 −15.023475 888.41435
−CO2 C46H67O15 −44.009500 859.428325
−Acetic acid C45H66O16 −60.021130 843.416695
[M + Cl] Cl adduct 34.968853 939.414503
[M + OH] Hydroxide adduct 17.00274 921.44839
Table 4. Calculated values for Bryostatin with different adducts and different fragments lost.
Table 4. Calculated values for Bryostatin with different adducts and different fragments lost.
# [M+H]+ [M+Na]+ [M+K]+ −H2O (Na) −CH3 (Na) −AcOH (Na)
0 891.437 913.42 929.394 895.409 898.396 853.399
1 905.453 927.435 943.409 909.425 912.412 867.414
2 863.442 885.425 901.399 867.414 870.401 825.404
3 889.422 911.404 927.378 893.394 896.381 851.383
4 895.469 917.451 933.425 899.441 902.428 857.43
5 867.437 889.42 905.394 871.409 874.396 829.399
6 853.422 875.404 891.378 857.394 860.381 815.383
7 825.39 847.373 863.347 829.362 832.349 787.352
8 881.453 903.435 919.409 885.425 888.412 843.414
9 853.422 875.404 891.378 857.394 860.381 815.383
10 809.432 831.415 847.389 813.404 816.391 771.394
11 767.385 789.368 805.342 771.357 774.344 729.347
12 933.484 955.467 971.441 937.456 940.443 895.446
13 795.416 817.398 833.372 799.388 802.375 757.377
14 825.427 847.409 863.383 829.397 832.385 787.387
15 921.448 943.43 959.404 925.42 928.407 883.409
16 791.416 813.399 829.373 795.388 798.375 753.378
17 791.416 813.399 829.373 795.388 798.375 753.378
18 809.432 831.415 847.389 813.404 816.391 771.394
19 837.427 859.409 875.383 841.398 844.386 799.388
20 851.442 873.425 889.399 855.414 858.401 813.404
21 865.458 887.44 903.414 869.43 872.417 827.419
Additional adducts are possible, such as, but not limited to Fe (II), Cu(II), Ca(II), and Zn(II). Table 6 presents both positive and negative mode results. FT-ICR accepts <1 ppm errors but included in the table are some spectra features with errors in the 1-2 ppm range. Table 7 presents data for negative ion mode and uses complexes with the H- anion as the adduct. Bryostatin-1 is found in many of the samples in which multiple bryostatins are present. Table 8 has both different bryostatins and different fragments. Table 9 has both negative: [M–H], [M+Cl] and positive: [M+Na]+, [M+K]+, [M+Li]+ modes. Whole molecule bryostatins were detected in both ionization modes with sub 5 ppm mass accuracy. Negative ion spectra were dominated by [M–H] species with minimal adduct complexity, while positive ion spectra showed enhanced signal to noise and diagnostic Na+, K+, and Li+ adduct series, providing multiple orthogonal confirmations of the same neutral mass. The results show there are different forms of bryostatin present in the samples.
For FT-ICR MS, an acceptable mass error is under 1.0 ppm, with high-quality datasets routinely achieving sub-ppm accuracy (0.2 to 0.5 ppm). The accepted threshold for publishing or compound matching is less than 5.0 ppm. In ESI–FT-ICR, a free fatty acid such as decanoate typically shows very low mass error (≈0.2–0.8 ppm under good calibration), whereas Fe(II)–fatty acid complexes often show slightly higher apparent errors (≈2–4 ppm or more depending on signal quality). This difference is not due to reduced accuracy of FT-ICR, but to the increased complexity of the metal adduct. As a weak electrolyte species, such as Fe-fatty acid complex, there can be weak equilibrium and/or a weak, vibrating bond.
Fe(II) + Fatty Acid ←→ Fe(II)-fatty acid
The dominant factor is the multi-isotope distribution of Fe, which broadens the isotopic envelope and makes monoisotopic peak assignment less precise. Transition-metal complexes can have a more complicated speciation and coordination states, which can result in difficulty in assigning the correct molecular formula. Also, these complexes often have lower signal-to-noise ratios, which can degrade the centroid precision and increase apparent ppm error.

3. Discussion

Bryostatin-1 is not unique among marine-derived compounds to reach clinical relevance. Other notable examples include trabectedin, originally isolated from the tunicate Ecteinascidia turbinata and approved for soft-tissue sarcoma;[18] Eribulin, a simplified synthetic analogue of the sponge-derived halichondrin B approved for metastatic breast cancer, and ziconotide, a cone-snail peptide approved for severe chronic pain. Together, these compounds prove the translational potential of marine natural products when supported by robust analytical and synthetic infrastructure.
(1)
Methods: Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) offers unique advantages for marine natural product analysis by combining ultrahigh mass resolving power with sub ppm mass accuracy, resulting in a confident elemental formula assignment in extracts containing thousands of overlapping molecular features[21,22]. This capability is particularly critical for marine matrices, where high salt content, metal adduction, and extensive isobaric congestion frequently confound lower resolution mass analyzers. FT-ICR provides exceptional dynamic range and nondestructive ion detection via image current measurement, supporting repeated acquisitions, an isotopic fine structure analysis. Electrospray ionization FT-ICR mass spectrometry exhibits ultra-high sensitivity, with detection limits reported in the attomole range under optimized nano ESI conditions. However, for neutral, moderate hydrophobic macrolides such as the bryostatins (MW ~900 Da), practical limits of detection are typically in the femtomole to low-picomole range, depending on ionization efficiency, adduct formation, and matrix complexity. In marine extracts, ion suppression (Na+, K+, etc.) and chemical background can elevate the limits of detection, with reliable detection generally achieved at ≥0.1–1 picomole levels. Positive ion mode is generally more effective for bryostatins, as these neutral, oxygen-rich macrolides preferentially form stable cations such as [M+Na]+, [M+Li]+, and [M+K]+, which can give strong, well-resolved FT-ICR signals with high mass accuracy. Alkali metal adducts, especially Na+ and Li+, often enhance signal intensity and reproducibility, but they also distribute ion current across multiple adduct peaks, which can reduce sensitivity for any single species. Transition metal adducts (e.g., Fe+2) are less common and may complicate spectra due to coordination chemistry and isotopic patterns. In contrast, negative ion mode is generally less sensitive for bryostatins because they lack strongly acidic functional groups, making [M–H] formation inefficient under typical ESI conditions. However, negative mode can still be useful for detecting specific adducts such as [M+Cl] or for probing minor acidic impurities, degradation products, or conjugates.[23,24] Overall, positive ion mode provides higher sensitivity and cleaner detection for bryostatins, whereas negative ion mode offers complementary information but typically at the cost of lower signal intensity and more limited ionization pathways.
With electrospray ionization (ESI), FT-ICR facilitates selective chemical profiling through polarity choice: positive ion mode enhances detection of cation binding natural products (e.g., Na+, Li+, K+) adducted macrolides such as bryostatins, whereas negative ion mode selectively enriches acidic and oxygen rich compounds, including fatty acids and carboxylate containing transformation products commonly found in marine sediments. Negative charged adducts for the bryostatins include H-, Cl-, OH-, and O-2. Table 1 provides the exact masses of Bryostatin 0-21. The NIST isotope tables, which gives masses to six or seven decimal places (i.e., Nitrogen (N) = 14.003,074,004,43 g/mol.)

4. Materials and Methods

Our research group has developed the pharmaceutical aquaculture methodology over the past two decades[19,20]. Because microbial life in the ocean is complex. A single drop of seawater contains up to 10 million virus particles and 1 million bacteria. The viruses are mostly bacteriophages. The quantity and diversity of microbes in ocean water is difficult/impossible to replicate in a lab setting. This green technology enables the cultivation and harvesting of marine bacteria directly within the ocean environment. We highlight the application of this system for the sustainable production of bryostatin, Ultimately, this flexible, environmentally conscious framework provides a scalable method for the sustainable synthesis of known marine pharmaceuticals and the discovery of novel bioactive compounds. Stearic was melted and extracts of bananas, oranges, potatoes (no skin) and chicken eggs (with shells) were added. Fresh curt cellulose from local pine trees in the form of sawdust was added to the fluid stearic acid. Also, small amounts of iron (III) chloride and pieces of iron were included (iron is a limiting nutrient in the ocean) and well as some inorganic species (nitrates, phosphates, ammonium). The stearic sheets were thin (0.2 cm) and were broken into smaller pieces and placed in a bucket with small pieces of limestone rock and pH neutral red rocks. The buckets were perforated with small holes that allowed water to flow through but stopped predators from entering that might consume the biofilm being generated. The buckets were secured to the dock and remained there for five months (mid-December to mid-May). Bugula appears from late fall to the following June. We assumed the bacteria followed Bugula’s life cycle. The stearic acid sheets were retrieved and soaked in one of two mixtures; a methanol/ethanol/ propanol mixture, or pure butanol, for several days. The alcohol mixture was filtered through a 0.45 um filter and placed in a 4 0C cold room for 2 weeks. This allowed for most of the stearic acid to precipitate from the solution. This study was not quantitative in nature, but rather qualitative and designed to identify what, if any, bryostatins were present. Figure 1 is a 2D image of bryostatin-1. Figure 1 is bryostatin-1, the structure that is used in medicinal applications. The bryophan ring is defined by the 27-member carbon chain, that is functionalized by acetate, -OH, and -CH3 groups. In our FT-ICR studies, structures that are either not fully formed or, or have fragmented, have different numbers of -CH3, -Ac and -OH groups missing. For the structure of bryostatin-1, its C8 chain (Figure 1, lower left) and the acetate (upper right) distinguish it from the other bryostatin structures.
The goal of this study was to determine if bryostatin’s, particularly Bryostatin-1, were produced in this historic ecosystem. Table’s 6,7,8,9 provide examples of bryostatin being identified. We deployed 8 buckets at the Living Dock. We tested samples from each bucket but could not correlate the differences in the ICR spectra with any significant differences deployed along the 120-foot dock. The dock is lined with oysters, and has a multitude of fish, crabs, barnacles, etc. It is a tidal area with 1-2 feet shifts between high and low tide. The bay is lined by either wetlands or pine forests with some houses. Taking advantage of FT-ICR[26], we did establish that the important bryostatin (#1) as well as other bryostatin were present. We are switching to another material that has similar levels of nutrients as the stearic acid binder did, but it replicates, on a chemical level, Bugula’s outer coating. The measurement via 1H and 13C NMR on the extracts were not possible due to low quantities. We are continuing to analyze and generate data files for other adducts and bryostatins, with the hope of a novel, green tech approach of synthesizing the neuro-logical in larger quantities [27,28,29,30,31].

Acknowledgments

We would like to thank Gulf Specimen Marine Lab for access to their dock, which is the focus of the book, by Jack Rudloe, entitled, The Living Dock. We would like to thank the National High Field Magnet Lab (Dr. Amy) for the FT-ICR data, and the National Magnet Lab for NMR (Dr. Rocco). We would like to thank Valdosta State University for the use of the facilities. Jack Rudloe’s classic environmental book, The Living Dock, https://www.amazon.com/Living-Dock-Jack-Rudloe/dp/0820012068 .

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Figure 1. A two-dimension structure of bryostatin-1.
Figure 1. A two-dimension structure of bryostatin-1.
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Table 6. Combines negative ICR data: [M–H], [M+Cl] and positive ICR data: [M+Na]+, [M+K]+, [M+Li]+ bryostatin species detected. 5.Monoisotopic masses, FT-ICR accuracy expressed in ppm. (S/N = Signal to Noise Ratio).
Table 6. Combines negative ICR data: [M–H], [M+Cl] and positive ICR data: [M+Na]+, [M+K]+, [M+Li]+ bryostatin species detected. 5.Monoisotopic masses, FT-ICR accuracy expressed in ppm. (S/N = Signal to Noise Ratio).
Bryostatin Mode Ion / Adduct Empirical Formula Theoretical m/z Observed m/z Error (ppm) S/N
Bryo-1 Negative [M–H] C47H67O17 904.5306 904.5303 −0.3 47
Bryo-1 Negative [M+Cl] C47H68O17Cl 940.5103 940.5108 0.5 18
Bryo-1 Positive [M+Na]+ C47H68O17Na+ 928.5288 928.5307 2 23
Bryo-1 Positive [M+K]+ C47H68O17K+ 944.5027 944.505 2.4 14
Bryo-1 Positive [M+Li]+ C47H68O17Li+ 912.5458 912.5464 0.7 20
Bryo-2/8† Negative [M–H] C45H65O16 885.5048 885.5054 0.7 24
Bryo-2/8† Positive [M+Na]+ C45H66O16Na+ 909.5029 909.5046 1.9 19
Bryo-5 Negative [M–H] C48H69O17 930.497 930.4964 −0.6 16
Bryo-5 Positive [M+Na]+ C48H70O17Na+ 954.4951 954.497 2 17
Bryo-6 Negative [M–H] C46H67O16 919.4897 919.4892 −0.6 16
Bryo-10 Positive [M+Na]+ C47H70O16Na+ 952.5101 952.512 2 15
Table 7. FT-ICR data in negative ion mode.
Table 7. FT-ICR data in negative ion mode.
Bryostatin Assigned Ion Obs. m/z Error (ppm) S/N Evidence
Bryostatin 1 [M–H] ~905.515 −0.7 ppm ~29 Strong parent peak
Bryostatin 2 / 8 [M–H] ~885.504 −0.6 ppm ~24 Isobaric pair indistinguishable at MS1
Bryostatin 5 [M–H] ~931.505 −0.6 ppm ~16 Clear parent ion
Bryostatin 6 [M–H] ~919.489 −0.5 ppm ~16 Clear parent ion
Bryostatin 10 [M–H] ~929.489 −0.3 ppm ~15 Clear parent ion
Table 8. In this data set either a methyl group or a -OH (H20) group is lost from the bryostatin structure.
Table 8. In this data set either a methyl group or a -OH (H20) group is lost from the bryostatin structure.
Parent Fragment Type Neutral Loss Formula Theoretical m/z Observed m/z Error (ppm) S/N
Bryo 1 –CH3 −14.01565 C46H65O17 891.5 891.515 −1.8 15
Bryo 1 –H2O −18.01056 C47H66O16 887.505 887.514 −1.6 14
Bryo 5 –H2O −18.01056 C48H68O16 913.495 913.494 −1.0 11
Bryo 6 –CH3 −14.01565 C45H65O16 905.474 905.474 −0.2 12
Bryo 10 –H2O −18.01056 C47H68O15 911.479 911.479 −0.2 10
Table 9. FT-ICR data for positive and negative modes. Monoisotopic masses, FT-ICR accuracy expressed in ppm.
Table 9. FT-ICR data for positive and negative modes. Monoisotopic masses, FT-ICR accuracy expressed in ppm.
Bryostatin Mode Ion / Adduct Empirical Formula Theoretical m/z Observed m/z Error (ppm) S/N
Bryo-1 Negative [M–H] C47H67O17 904.531 904.53 −0.3 47
Bryo-1 Negative [M+Cl] C47H68O17Cl 940.51 940.511 0.5 18
Bryo-1 Positive [M+Na]+ C47H68O17Na+ 928.529 928.531 2 23
Bryo-1 Positive [M+K]+ C47H68O17K+ 944.503 944.505 2.4 14
Bryo-1 Positive [M+Li]+ C47H68O17Li+ 912.546 912.546 0.7 20
Bryo-5 Negative [M–H] C48H69O17 930.497 930.496 −0.6 16
Bryo-5 Positive [M+Na]+ C48H70O17Na+ 954.495 954.497 2 17
Bryo-6 Negative [M–H] C46H67O16 919.49 919.489 −0.6 16
Bryo-10 Positive [M+Na]+ C47H70O16Na+ 952.51 952.512 2 15
Table 1. Bryostatin-1 adducts (ESI FT-ICR, NIST exact masses), Positive Ion Mode.
Table 1. Bryostatin-1 adducts (ESI FT-ICR, NIST exact masses), Positive Ion Mode.
Ion Type Empirical Formula (Adduct Form) Exact Mass (Da)
[M + H]+ C47H69O17+ 905.453
[M + Li]+ C47H68O17Li+ 911.462
[M + Na]+ C47H68O17Na+ 927.435
[M + K]+ C47H68O17K+ 943.409
[M + Fe]+ C47H68O17Fe+ 960.381
[M + Ca]2+ C47H68O17Ca2+ 472.204
(m/z, z = +2)
[M + H3O]+ C47H71O18+ 923.464
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