The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Identity verified. The target is human B9D2, also called MKSR2 or B9-domain-containing protein 2—not the related B9D1/MKSR1 or MKS1. Its B9 domain occupies most of the small protein and belongs to the C2-like domain superfamily, consistent with the supplied B9-C2/PF07162 annotation. B9D2 is a non-transmembrane protein; there is no established catalytic reaction or transporter substrate. Its best-supported primary function is as a structural and organizational component of the ciliary transition-zone MKS complex. (caenenbraz2024newfunctionsof pages 1-2, okazaki2020formationofthe pages 5-7, okazaki2020formationofthe pages 1-5)
The transition zone (TZ) lies at the base of the primary cilium, between the basal body and the axoneme. It helps maintain a ciliary membrane composition distinct from the surrounding plasma membrane while permitting regulated protein traffic. In human-cell interaction assays, B9D2 binds both MKS1 and B9D1; MKS1 and B9D1 do not bind one another detectably without B9D2. The supported arrangement is therefore MKS1–B9D2–B9D1, with B9D2 serving as the central molecular bridge. In human retinal pigment epithelial (RPE1) cells, loss of either MKS1 or B9D2 prevents normal TZ localization of the other B9-complex components. (okazaki2020formationofthe pages 7-11, okazaki2020formationofthe pages 5-7, okazaki2020formationofthe pages 1-5)
The clearest functional test is B9D2 knockout and rescue in human RPE1 cells. Knockout produces a moderate reduction in cilium formation and length, but a pronounced defect in ciliary membrane-protein composition: GPR161 is absent under basal conditions, Smoothened (SMO) fails to accumulate after agonist stimulation, and the membrane-associated proteins ARL13B and INPP5E are lost from cilia. Re-expression of B9D2 rescues the abnormal localization. By contrast, the examined IFT88/IFT140 localization and IFT88-particle movements remain largely intact. These observations identify B9D2 primarily as a contributor to TZ-dependent selective retention or gating of membrane-associated cargo, rather than an enzyme, a cargo transporter, or an indispensable component of intraflagellar transport. (okazaki2020formationofthe pages 7-11, okazaki2020formationofthe pages 5-7)
A subsequent study extended this mechanism. Co-immunoprecipitation detected an association of B9D2 and MKS1 with the TZ membrane protein TMEM67; B9D2-knockout cells lost normal TZ enrichment of TMEM67 while retaining the examined CEP290 and RPGRIP1L localization. The authors infer that the soluble B9 complex helps stabilize or anchor TMEM67 within the membrane-proximal MKS assembly. This is an experimentally supported organizational role, not evidence that B9D2 itself spans the membrane or forms a pore. The paper appeared online 30 October 2025, although its journal assignment is Journal of Clinical Investigation 136(2), 2026. (he2026ciliopathyrelatedb9protein pages 4-5, he2026ciliopathyrelatedb9protein pages 1-2)
B9D2 also acts before the TZ forms. Imaging placed B9D2 and MKS1 at the mother centriole in proliferating, predominantly non-ciliated RPE1 cells. Electron microscopy of B9D2 knockouts found fewer mother centrioles associated with preciliary vesicles, while immunostaining showed impaired removal of the centriole-capping protein CP110 after ciliogenesis induction. The data support a role in early preciliary-vesicle docking and initiation of cilium assembly; precisely how B9D2 recruits or docks those vesicles remains unresolved. (he2026ciliopathyrelatedb9protein pages 5-7)
Hedgehog signaling is the most directly interpretable signaling connection: SMO and GPR161 require appropriate ciliary localization for pathway regulation, and B9D2 knockout disrupts both proteins’ observed ciliary localization. This establishes a route by which B9D2 deficiency can perturb Hedgehog signaling; the receptor-localization experiments should not be mistaken for a measurement of every downstream Hedgehog response in B9D2-knockout cells. Hedgehog defects measured in B9D1-mutant mice provide complex-level support but are not B9D2-specific experiments. Reports linking the broader MKS system to Wnt signaling do not establish B9D2 as a direct Wnt receptor or dedicated Wnt-pathway effector. (okazaki2020formationofthe pages 5-7, dowdle2011disruptionofa pages 11-12, hartill2017meckel–grubersyndromean pages 5-6)
Recent experiments identify a second consequence of defective TZ organization: axonemal microtubule homeostasis. In B9D2-knockout human cells, ciliary tubulin acetylation and polyglutamylation fell despite no corresponding decrease in whole-cell levels of those modifications. HDAC6, a tubulin deacetylase, was detected in some mutant cilia where it was absent from controls, while ciliary distribution of the glutamylase TTLL5 was altered. HDAC6 inhibition or depletion restored axonemal acetylation. After six hours of serum-induced disassembly, 77.8% of wild-type versus 41.5% of B9D2-knockout cells retained cilia. Maternal–zygotic b9d2-mutant zebrafish also had reduced axonemal modifications. Thus B9D2 affects the distribution of at least some soluble ciliary proteins as well as membrane cargo, although the disassembly findings do not fully account for its reduced ciliogenesis rate. (he2026ciliopathyrelatedb9protein pages 4-5, he2026ciliopathyrelatedb9protein pages 2-4)
This soluble-cargo result refines—not simply overturns—the 2020 observation of apparently normal IFT movement: intact movement of the tested IFT particles does not prove that every soluble protein is correctly compartmentalized. Authoritative TZ reviews likewise caution that a proposed diffusion barrier, lipid organization, and active cargo transport work together, and that their exact molecular contributions remain unresolved. (okazaki2020formationofthe pages 7-11, moran2024transportandbarrier pages 3-5, park2022compositionorganizationand pages 1-3, he2026ciliopathyrelatedb9protein pages 4-5)
Domain-based biochemical inference requires restraint. The B9/C2-like classification is compatible with a membrane-associated scaffold, but does not establish calcium-dependent lipid binding or enzymatic activity. A 2024 lipid-overlay experiment using extracts from B9D2–GFP-expressing HEK cells found its strongest signals with PI4P and PI(3,4,5)P₃, and a weaker signal with PI(4,5)P₂. Because the assay used immobilized lipids and cell extracts rather than purified B9D2, it does not determine direct binding, native-membrane specificity, affinity, or a physiological lipid substrate. (okazaki2020formationofthe pages 1-5, caenenbraz2024newfunctionsof pages 8-10, caenenbraz2024newfunctionsof pages 10-12)
A 2024 study observed B9D2 at ZO-1- and claudin-4-associated tight junctions in normal rat cholangiocyte and kidney epithelial cultures, rather than exclusively at cilia. The authors used serum-maintained conditions in which fewer than 5% of cells were ciliated. Three B9D2-targeting shRNAs disrupted junctional ZO-1 organization and the distribution of claudin-4 and E-cadherin. In cholangiocyte monolayers, control transepithelial electrical resistance reached approximately 2,000–2,500 Ω·cm² on days 8–10, whereas knockdown cultures remained below 500 Ω·cm². In three-dimensional culture, depleted cells still formed cysts, but mean cyst diameter was approximately half that of controls. These results implicate B9D2 in epithelial junction maturation, barrier integrity, and lumen expansion, offering a plausible contributor to biliary abnormalities in ciliopathies. They do not yet establish the same extraciliary role in normal human tissue: the principal models were rat cells, residual cilia were possible, and a direct junctional molecular mechanism was not established. (caenenbraz2024newfunctionsof pages 8-10, caenenbraz2024newfunctionsof pages 1-2, caenenbraz2024newfunctionsof pages 2-3, caenenbraz2024newfunctionsof pages 10-12)
The evidence and its limitations can be summarized by functional site:
| Site and molecular role | Best experimental evidence/date | Confidence and caveat |
|---|---|---|
| Ciliary transition zone (TZ): membrane-protein gate. Human B9D2/MKSR2 (Q9BPU9) is the central linker in a soluble, linear MKS1–B9D2–B9D1 complex. Interdependent TZ localization of all three proteins supports selective ciliary membrane composition. | Interaction and three-hybrid assays showed that B9D2 binds MKS1 and B9D1, whereas MKS1 and B9D1 do not bind directly. In B9D2-knockout human RPE1 cells, ciliary GPR161, agonist-induced SMO, ARL13B and INPP5E were lost, while IFT88/IFT140 localization and IFT movement remained largely normal; wild-type B9D2 rescued the phenotype (2020). (okazaki2020formationofthe pages 5-7, okazaki2020formationofthe pages 7-11) | High. Direct human-cell knockout, rescue, interaction and localization evidence. “Gate” denotes a component of the larger MKS/TZ compartmentalization system—not a pore or independently sufficient barrier. Current reviews emphasize that passive diffusion restriction, lipid organization and active trafficking remain mechanistically intertwined. (moran2024transportandbarrier pages 5-6, park2022compositionorganizationand pages 1-3) |
| TZ membrane anchoring and axonemal homeostasis. The B9 complex recruits or stabilizes TMEM67 at the TZ and helps exclude inappropriate soluble enzymes, thereby maintaining axonemal tubulin acetylation and polyglutamylation. | Co-immunoprecipitation showed TMEM67 interaction with B9D2 and MKS1; B9D2 loss disrupted TMEM67—but not CEP290 or RPGRIP1L—localization. HDAC6 entered B9D2-deficient cilia, TTLL5 distribution changed and axonemal modifications declined without a corresponding global cellular decrease. After 6 hours of serum-induced disassembly, 77.8% of wild-type versus 41.5% of B9D2-knockout cells retained cilia; HDAC6 inhibition or depletion restored acetylation. Published online October 30, 2025 and assigned to JCI volume 136 (2026). (he2026ciliopathyrelatedb9protein pages 4-5, he2026ciliopathyrelatedb9protein pages 1-2) | High for cultured cells; moderate for the complete in-vivo mechanism. Supported across human and mouse cells and maternal–zygotic zebrafish mutants, but much of the mechanistic chain derives from engineered knockout and overexpression systems. |
| Mother centriole before TZ assembly: initiation of ciliogenesis. B9D2 and MKS1 localize to the mother centriole in non-ciliated proliferating cells and facilitate preciliary-vesicle docking and CP110 removal. | Electron microscopy found fewer mother centrioles with associated ciliary vesicles in B9D2-knockout RPE1 cells; CP110 removal after serum starvation was impaired. Structured-illumination microscopy placed B9D2 near the mother-centriole marker CEP164 before cilium formation. Published online in 2025 and assigned to JCI volume 136 (2026). (he2026ciliopathyrelatedb9protein pages 5-7) | Moderate–high. Direct imaging and knockout evidence establish an early ciliogenesis role, but the vesicle-recruitment mechanism and direct binding partners remain incompletely defined. |
| Extraciliary epithelial tight junctions and lumen expansion. In rat cholangiocyte and kidney epithelial models, B9D2 associates with ZO-1/claudin-4-positive junctions and supports junction maturation, barrier tightness and biliary-cyst lumen expansion. | Under conditions with fewer than 5% ciliated cells, B9D2 localized at cell contacts and colocalized with ZO-1 and claudin-4, but not adherens-junction or desmosomal markers. shRNA depletion broadened or disrupted ZO-1 and dispersed claudin-4 and E-cadherin. During days 8–10, control transepithelial resistance was approximately 2,000–2,500 Ω·cm², whereas all B9D2-depleted conditions remained below 500 Ω·cm²; 3D cyst diameter fell to approximately half of control without significantly preventing cyst formation or secretion (October 2024). (caenenbraz2024newfunctionsof pages 8-10, caenenbraz2024newfunctionsof pages 2-3, caenenbraz2024newfunctionsof pages 10-12) | Moderate for rat epithelial models; low–moderate for normal human physiology. Three shRNAs and low-ciliation conditions support an extraciliary interpretation, but no human-tissue confirmation or junctional rescue was reported; residual cilia and indirect polarity effects cannot be fully excluded. |
| B9/C2-like domain and membrane association. B9D2 is a small non-transmembrane B9-family protein whose domain belongs to the C2-domain superfamily; it may associate with phosphoinositide-rich membranes. No catalytic reaction is known. | Human-protein studies show that the B9 domain occupies nearly the entire B9D2 sequence and mediates B9-complex assembly. A 2024 lipid-overlay assay using extracts from B9D2–GFP-expressing HEK cells produced the strongest signals with PI4P and PI(3,4,5)P3 and a weaker signal with PI(4,5)P2. (okazaki2020formationofthe pages 1-5, caenenbraz2024newfunctionsof pages 8-10, caenenbraz2024newfunctionsof pages 10-12) | High for domain-family assignment and complex assembly; low for lipid specificity. The overlay used whole-cell extract and immobilized lipids—not purified B9D2—so it does not establish direct binding, native-membrane affinity or physiological specificity. The C2-like fold is not evidence of enzymatic activity. |
| Human disease variants: recessive Meckel and Joubert syndromes. Variant severity appears to reflect differential disruption of B9-complex stability, TZ localization and ciliogenesis. | In one consanguineous family, two Meckel-syndrome fetuses were homozygous for p.Ser101Arg; the variant was absent from 300 ancestry-matched controls, failed to rescue zebrafish b9d2 suppression and abolished MKS1—but not B9D1—binding (2011). (dowdle2011disruptionofa pages 9-11, dowdle2011disruptionofa pages 8-9) A later screen identified biallelic B9D2 variants in 2 of 151 Chinese Joubert patients: c.215-1G>T plus p.Asp47Val and p.Arg75Trp plus p.Asp53_Trp57del; parental segregation and aberrant splicing were confirmed. Joubert missense variants retained B9-complex binding and rescued ciliogenesis but impaired TZ function, whereas p.Ser101Arg was unstable and failed to rescue ciliogenesis. Published online October 30, 2025 and assigned to JCI volume 136 (2026). (he2026ciliopathyrelatedb9protein pages 7-9, he2026ciliopathyrelatedb9protein pages 5-7, he2026ciliopathyrelatedb9protein pages 9-11) | High for recessive disease association; moderate for genotype–mechanism generalization. Patient numbers are very small, and functional tests rely heavily on engineered cells and animal models. B9D2 should not be conflated with B9D1/MKSR1 or MKS1, despite their shared domain and complex membership. |
Table: Evidence-based functional annotation of human B9D2/MKSR2 (Q9BPU9), covering its ciliary and proposed extraciliary roles, disease variants, quantitative findings and evidentiary limitations.
Biallelic B9D2 variants are implicated in Meckel syndrome and Joubert syndrome, disorders consistent with loss or impairment of TZ-associated ciliary function. In one consanguineous Meckel-syndrome family, two affected fetuses carried homozygous c.301A>C (p.Ser101Arg); the variant was absent from 300 ancestry-matched controls. Wild-type human B9D2 partially rescued the studied b9d2-suppressed zebrafish phenotype, whereas p.Ser101Arg did not. Biochemical experiments found that p.Ser101Arg lost detectable MKS1 interaction while retaining B9D1 interaction. These observations connect a patient variant specifically to B9-complex disruption; the extensive mouse developmental and Hedgehog experiments in that publication examined B9d1, and should not be attributed to B9D2 knockout. (dowdle2011disruptionofa pages 1-2, dowdle2011disruptionofa pages 9-11, dowdle2011disruptionofa pages 8-9)
More recently, exome sequencing of 151 Chinese Joubert-syndrome patients identified two affected individuals with biallelic B9D2 variants: one had c.215-1G>T and p.Asp47Val, and the other p.Arg75Trp and p.Asp53_Trp57del. Parental segregation was confirmed; the splice-site variant produced aberrant transcripts. In engineered B9D2-knockout cells, the tested Joubert-associated missense variants restored ciliogenesis but failed to restore normal TZ-associated cargo localization and axonemal modifications. In contrast, the Meckel-associated p.Ser101Arg variant was less stable under stable-expression conditions and failed to fully rescue ciliogenesis. This supports a variant-dependent separation between early cilium assembly and subsequent TZ function, but two newly identified patients cannot establish a general genotype–phenotype rule. Earlier C. elegans editing of Joubert-associated P74S and G155S likewise produced variant-dependent TZ phenotypes, providing model-organism, not direct human-cell, evidence. (lange2021interpretingthepathogenicity pages 1-4, he2026ciliopathyrelatedb9protein pages 7-9, he2026ciliopathyrelatedb9protein pages 5-7, he2026ciliopathyrelatedb9protein pages 9-11)
Real-world use is currently principally molecular diagnosis and interpretation of suspected ciliopathies, including evaluating recessive B9D2 variants alongside clinical features and family segregation. The cell and animal assays above provide experimental ways to assess variant effects; they do not constitute a validated B9D2-targeted treatment. Accordingly, the most defensible concise annotation is: human B9D2/MKSR2 is a B9-domain scaffold in the MKS1–B9D2–B9D1 complex, acting at the ciliary TZ to organize TMEM67 and preserve ciliary protein compartmentalization; it also promotes early mother-centriole ciliogenesis and contributes to axonemal homeostasis. A tight-junction role is supported in rat epithelial models but remains less firmly established for human physiology. (okazaki2020formationofthe pages 7-11, caenenbraz2024newfunctionsof pages 10-12, he2026ciliopathyrelatedb9protein pages 4-5, he2026ciliopathyrelatedb9protein pages 5-7)
References
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(he2026ciliopathyrelatedb9protein pages 1-2): Ruida He, Yan Li, Minjun Jin, Hui-Ke Jiao, Yue Shen, Qize Han, Xilang Pan, S. Wang, Zaisheng Lin, Jing-Shi Li, Chao Lu, Dan Meng, Zong-Fu Cao, Qing Shang, Nan Lv, Kai Wan, Huafang Gao, Xu Ma, Hai-Yan Yin, Haishuang Chang, Liang Wang, Min-Na Luo, Junmin Pan, Chengtian Zhao, and Muqing Cao. Ciliopathy-related b9 protein complex regulates ciliary axonemal microtubule posttranslational modifications and initiation of ciliogenesis. Journal of Clinical Investigation, Oct 2026. URL: https://doi.org/10.1172/jci196365, doi:10.1172/jci196365. This article has 1 citations and is from a highest quality peer-reviewed journal.
(he2026ciliopathyrelatedb9protein pages 5-7): Ruida He, Yan Li, Minjun Jin, Hui-Ke Jiao, Yue Shen, Qize Han, Xilang Pan, S. Wang, Zaisheng Lin, Jing-Shi Li, Chao Lu, Dan Meng, Zong-Fu Cao, Qing Shang, Nan Lv, Kai Wan, Huafang Gao, Xu Ma, Hai-Yan Yin, Haishuang Chang, Liang Wang, Min-Na Luo, Junmin Pan, Chengtian Zhao, and Muqing Cao. Ciliopathy-related b9 protein complex regulates ciliary axonemal microtubule posttranslational modifications and initiation of ciliogenesis. Journal of Clinical Investigation, Oct 2026. URL: https://doi.org/10.1172/jci196365, doi:10.1172/jci196365. This article has 1 citations and is from a highest quality peer-reviewed journal.
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(caenenbraz2024newfunctionsof pages 8-10): Chloe Caenen-Braz, Latifa Bouzhir, and Pascale Dupuis-Williams. New functions of b9d2 in tight junctions and epithelial polarity. Scientific Reports, Oct 2024. URL: https://doi.org/10.1038/s41598-024-75577-w, doi:10.1038/s41598-024-75577-w. This article has 5 citations and is from a peer-reviewed journal.
(caenenbraz2024newfunctionsof pages 10-12): Chloe Caenen-Braz, Latifa Bouzhir, and Pascale Dupuis-Williams. New functions of b9d2 in tight junctions and epithelial polarity. Scientific Reports, Oct 2024. URL: https://doi.org/10.1038/s41598-024-75577-w, doi:10.1038/s41598-024-75577-w. This article has 5 citations and is from a peer-reviewed journal.
(caenenbraz2024newfunctionsof pages 2-3): Chloe Caenen-Braz, Latifa Bouzhir, and Pascale Dupuis-Williams. New functions of b9d2 in tight junctions and epithelial polarity. Scientific Reports, Oct 2024. URL: https://doi.org/10.1038/s41598-024-75577-w, doi:10.1038/s41598-024-75577-w. This article has 5 citations and is from a peer-reviewed journal.
(moran2024transportandbarrier pages 5-6): Ailis L. Moran, Laura Louzao-Martinez, Dominic P. Norris, Dorien J. M. Peters, and Oliver E. Blacque. Transport and barrier mechanisms that regulate ciliary compartmentalization and ciliopathies. Nature Reviews Nephrology, 20:83-100, Oct 2024. URL: https://doi.org/10.1038/s41581-023-00773-2, doi:10.1038/s41581-023-00773-2. This article has 48 citations and is from a domain leading peer-reviewed journal.
(dowdle2011disruptionofa pages 9-11): William E. Dowdle, Jon F. Robinson, Andreas Kneist, M. Salomé Sirerol-Piquer, Suzanna G.M. Frints, Kevin C. Corbit, Norann A. Zaghloul, Gesina van Lijnschoten, Leon Mulders, Dideke E. Verver, Klaus Zerres, Randall R. Reed, Tania Attié-Bitach, Colin A. Johnson, José Manuel García-Verdugo, Nicholas Katsanis, Carsten Bergmann, and Jeremy F. Reiter. Disruption of a ciliary b9 protein complex causes meckel syndrome. Oct 2011. URL: https://doi.org/10.1016/j.ajhg.2011.09.013, doi:10.1016/j.ajhg.2011.09.013. This article has 194 citations.
(dowdle2011disruptionofa pages 8-9): William E. Dowdle, Jon F. Robinson, Andreas Kneist, M. Salomé Sirerol-Piquer, Suzanna G.M. Frints, Kevin C. Corbit, Norann A. Zaghloul, Gesina van Lijnschoten, Leon Mulders, Dideke E. Verver, Klaus Zerres, Randall R. Reed, Tania Attié-Bitach, Colin A. Johnson, José Manuel García-Verdugo, Nicholas Katsanis, Carsten Bergmann, and Jeremy F. Reiter. Disruption of a ciliary b9 protein complex causes meckel syndrome. Oct 2011. URL: https://doi.org/10.1016/j.ajhg.2011.09.013, doi:10.1016/j.ajhg.2011.09.013. This article has 194 citations.
(he2026ciliopathyrelatedb9protein pages 7-9): Ruida He, Yan Li, Minjun Jin, Hui-Ke Jiao, Yue Shen, Qize Han, Xilang Pan, S. Wang, Zaisheng Lin, Jing-Shi Li, Chao Lu, Dan Meng, Zong-Fu Cao, Qing Shang, Nan Lv, Kai Wan, Huafang Gao, Xu Ma, Hai-Yan Yin, Haishuang Chang, Liang Wang, Min-Na Luo, Junmin Pan, Chengtian Zhao, and Muqing Cao. Ciliopathy-related b9 protein complex regulates ciliary axonemal microtubule posttranslational modifications and initiation of ciliogenesis. Journal of Clinical Investigation, Oct 2026. URL: https://doi.org/10.1172/jci196365, doi:10.1172/jci196365. This article has 1 citations and is from a highest quality peer-reviewed journal.
(he2026ciliopathyrelatedb9protein pages 9-11): Ruida He, Yan Li, Minjun Jin, Hui-Ke Jiao, Yue Shen, Qize Han, Xilang Pan, S. Wang, Zaisheng Lin, Jing-Shi Li, Chao Lu, Dan Meng, Zong-Fu Cao, Qing Shang, Nan Lv, Kai Wan, Huafang Gao, Xu Ma, Hai-Yan Yin, Haishuang Chang, Liang Wang, Min-Na Luo, Junmin Pan, Chengtian Zhao, and Muqing Cao. Ciliopathy-related b9 protein complex regulates ciliary axonemal microtubule posttranslational modifications and initiation of ciliogenesis. Journal of Clinical Investigation, Oct 2026. URL: https://doi.org/10.1172/jci196365, doi:10.1172/jci196365. This article has 1 citations and is from a highest quality peer-reviewed journal.
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