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Biomolecules

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Preprints posted in the last 90 days, ranked by how well they match Biomolecules's content profile, based on 100 papers previously published here. The average preprint has a 0.09% match score for this journal, so anything above that is already an above-average fit.

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Long-Term Clinical Performance of the Tunnel Technique with Subepithelial Connective Tissue Grafting: A 16-Year Retrospective Cohort Study

Schmuecker, J.; Speer, E.; Vukovic, M.; Grimm, W.-D.

2026-08-18 dentistry and oral medicine 10.64898/2026.08.17.26360439 medRxiv
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Background: Subepithelial connective tissue grafting remains a reference treatment for predictable root coverage. Although short- and medium-term outcomes of tunnel-based procedures are well documented, evidence regarding stability beyond 10 years remains limited. This study evaluated the long-term clinical performance of a minimally invasive tunnel technique combined with subepithelial connective tissue grafting (SCTG) under routine clinical conditions. Methods: This retrospective longitudinal cohort study included 74 patients (57 women and 17 men) contributing 710 gingival recession sites treated between 2009 and 2025. All sites were treated with a tunnel approach and SCTG, with enamel matrix derivative (EMD) used in selected cases. The mean follow-up was 6.0 for 4.0 years, with a maximum observation period of 16 years. The primary outcome was recession depth reduction. Secondary outcomes included complete root coverage (CRC), mean root coverage, and long-term marginal stability. Clinically relevant relapse was defined as a 1 mm increase in recession after initial healing. Results: Mean recession reduction was 2.72 mm. Complete root coverage was achieved at 83.4% of treated sites. At the final available follow-up, no treated site showed a clinically relevant relapse of 1 mm after initial healing, and no site deteriorated beyond its baseline recession level. Treatment effects were observed across anterior and posterior regions. Conclusions: Within the limitations of a retrospective cohort design, tunnel surgery combined with SCTG was associated with high root-coverage predictability and durable marginal soft-tissue stability for observation periods extending to 16 years. These real-world data support phenotype-enhancing, minimally invasive soft-tissue augmentation as a durable therapeutic strategy for localized and multiple gingival recessions. Keywords: gingival recession; tunnel technique; subepithelial connective tissue graft; root coverage; periodontal plastic surgery; long-term stability

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PEG-Arginase 1: A Novel Therapy for Optic Nerve Injury

Yamamoto, M.; Zaidi, S. A. H.; Lemtalsi, T.; Xu, Z.; Sandow, P. V.; Caldwell, R. W.; Caldwell, R. B.; Rojas, M. A.

2026-08-27 cell biology 10.64898/2026.08.26.746813 medRxiv
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Traumatic optic neuropathy (TON) occurs due to direct or indirect injury to the optic nerve and is a significant cause of visual disability. So far, there is no effective treatment. The lack of understanding of the cellular mechanisms by which trauma induces inflammation and damage in retinal neurons is a critical knowledge gap in developing effective therapies. We have studied the role of the arginase 1 (A1) enzyme in this pathology. We have found previously that treatment with a long-acting form of human recombinant A1, pegylated A1 (PEG-A1) after optic nerve crush limits activation of retinal microglia and macrophages (M{Phi}) and reduces inflammation, thereby decreasing injury and protecting visual function. Here we report on studies designed to demonstrate the therapeutic efficacy of PEG-A1 in mouse models of direct and indirect TON and to elucidate the underlying mechanisms. We used ONC to model direct TON and sonication-induced trauma to the supraorbital rim to model indirect TON (SI-TON). At different times after injury, mice were treated with PEG-A1 which was delivered systemically by i.p. injection or locally by intravitreal injection. In order to assess the role of A1-induced activation of the ornithine/polyamine pathway in the protective effects of PEG-A1, some mice were treated with the ornithine decarboxylase (ODC) inhibitor, difluoromethylornithine (DFMO) immediately after the PEG-A1 treatment. Retinal function was determined by OptoMotry and electroretinography. Retinal injury and microglia/M{Phi} activation were assessed by immunofluorescence imaging. Expression of inflammatory cytokines was determined by Western blotting and quantitative RT PCR. Liquid chromatography mass spectrometry was used to analyze changes in arginase/ODC pathway metabolites. Results showed that PEG-A1 treatment improved neuronal survival and visual function whether delivered systemically or intravitreally. This neuroprotection was associated with decreased microglia/M{Phi} activation, decreased inflammatory cytokine expression, and increased formation of L-ornithine and putrescine. Furthermore, DFMO treatment blocked these effects, indicating that PEG-A1 limits retinal injury and preserves vision after ocular injury by activating ODC. ODC processes the arginase product L-ornithine to form polyamines which are known to promote reparative functions. Thus, PEG-A1 therapy offers a new strategy to limit trauma-induced vision loss and promote repair after TON.

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Adjacent Z-DNA contributes to the formation of homologous DNA triplex

Zhong, M.; Liu, M.; An, R.; Gao, Y.; Liang, X.

2026-09-30 molecular biology 10.64898/2026.09.29.755329 medRxiv
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Whether the homologous parallel triplex (HP-triplex, formed by dsDNA and a homologous ssDNA) acts as an intermediate prior to DNA recombination remains controversy, owing to the intrinsic instability and lake of experimental data. Here, we report a HP-triplex that is stable at least at 35 oC under protein-free conditions. Two complementary circular ssDNAs were first hybridized at a 1:1 ratio to form an LR-chimera containing both Z-DNA and B-DNA. Then the circular homologous ssDNA (T-rich) was found to easily hybridize with this LR-chimera to form the HP-triplex (strand ratio of 2:1), involving both left- and right-handed triplex parts under the topological constraint. The third strand locates in the major groove and forms hydrogen bonds with both bases in each base pair of dsDNA without obvious strand exchange. Our data indicate that the third-strand ssDNA may first bind to the B-DNA region, followed by association with the Z-DNA region to assemble the full triplex structure. Structural simulations and analyses reveal that topological constraint imposed by the circular architecture raises the energy barrier for strand displacement, thereby stabilizing this triplex. In summary, the dynamic HP triplex can be stabilized via a Z B junction structure that mimics the in vivo one formed by negative supercoiling. These findings demonstrate that HP-triplex may act as an intermediate for DNA recombination, anti-gene strategy, and other interactions between dsDNA and homologous ssDNA or RNA.

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ALDH3A2 acts as a metabolic safeguard that regulates sphingolipid metabolism to suppress DNA damage and cell death

Hotani, T.; Sasano, M.; Okada, T.; Kajimoto, T.; Shinohara, M.; Ninagawa, S.; Iwasaki, T.; Yokoi, M.; Sugasawa, K.; Sakai, W.

2026-07-31 molecular biology 10.64898/2026.07.31.741968 medRxiv
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Highly reactive aldehydes are generated during metabolic processes in the body, and their detoxification is essential for maintaining cellular homeostasis. Hexadecenal, a long-chain fatty aldehyde, is formed during the sphingolipid degradation pathway from the lipid mediator sphingosine-1-phosphate (S1P). However, the cytotoxicity resulting from dysregulation of hexadecenal metabolism is still unclear. To elucidate the effects of impaired hexadecenal metabolism, we analyzed the function of ALDH3A2, an aldehyde dehydrogenase in humans. Our results revealed that ALDH3A2 enzymatic activity is crucial for the suppression of DNA damage, particularly interstrand DNA crosslinks, upon S1P exposure. Furthermore, we demonstrated that hexadecenal accumulation promotes cell death accompanied by the activation of cellular stress responses and morphological abnormalities in the endoplasmic reticulum. These findings suggest that ALDH3A2 functions as a metabolic safeguard to suppress DNA damage and cell death in response to the enhanced metabolic flux of hexadecenal.

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Exploring the molecular function of metabolites identified in Elite Controllers and their role in epithelial integrity and immune regulation

Chapartegui-Gonzalez, I.; Narayanan, A.; Cena Diez, R.; Sonnerborg, A.; Ray, S.

2026-07-30 molecular biology 10.64898/2026.07.29.741523 medRxiv
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Despite advances in treatment, HIV-1 infection continues to remain a major global health challenge, prompting ongoing efforts to understand the mechanisms that enable natural viral suppression and immune control. Elite controllers (ECs), a rare subset of PLWH individuals, naturally suppress HIV-1 replication without antiretroviral therapy, highlighting the importance of host-related factors in viral control. Understanding the mechanisms underlying this unique phenotype is crucial for developing novel therapeutic strategies. Previous studies from our group identified certain EC-specific metabolites, called dipeptides (DPs), and investigated their antiviral properties. We hypothesize that these dipeptides may potentially affect epithelial barrier integrity by modulating the expression of tight junction proteins, which in turn influences the mucosal barrier function, a key factor in HIV-1 pathogenesis. Therefore, in this study we investigated the impact of ten EC-specific DPs on tight junction (TJ) gene and protein expression in epithelial models derived from the female reproductive and gastrointestinal tracts, where we observed enhanced expression of different TJ genes (CLDN1, CLDN3, CLDN4, CLDN7, CLDN14, TJP1, TJP2, OCLN) and proteins (CLDN1, CLDN7, and CLDN14), suggesting the potential influence of these dipeptides on epithelial barrier function. Furthermore, we also examined different proteomic profiles between dipeptide (WG)-treated HeLa CD4+ CCR5+ cells compared with the untreated ones, and observed significantly reduced abundance of pro-inflammatory proteins, such as RELB Proto-Oncogene (RELB), TNF--induced protein 1 (TNFAIP1), TNF receptor superfamily member 1A (TNFRSF1A), and IL-32, in dipeptide-treated cells; and increased expression of proteins associated with tissue homeostasis (SMAD family member 5 [SMAD5]), cellular proliferation (transforming growth factor {beta} receptor 3 [TGFBR3]), and epithelial integrity, like CD81. Interestingly, KEGG analysis revealed possible attenuation of NF-{kappa}B, MAPK, TNF, and JAK-STAT signaling pathways, along with the enrichment of mTOR and PI3K-AKT pathways in treated HeLa CD4+ CCR5+ cells. Overall, this study investigated the potential interplay between tight junction proteins and key signaling pathways involved in maintaining epithelial barrier integrity and modulating immune activation, potentially contributing to both HIV-1 control and to the chronic inflammation associated with infection.

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Meta-analyses of the NEPTUNE dataset related to high and low risk FSGS and cellular APOL1 models identifies Calcium signalling, mTOR signaling and inflammation-associated pathways as operative in APOL1-mediated kidney disease.

Wruck, W.; Thimm, C.; Adjaye, J.

2026-07-31 molecular biology 10.64898/2026.07.30.741742 medRxiv
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BackgroundThe variants G1 and G2 within the APOL1 gene confer a higher risk of APOL1-mediated kidney disease (AMKD) whilst associated with an evolutionary advantage against trypanosome-mediated sleeping sickness. MethodsIn this study, we analysed transcriptome data of kidney biopsies from FSGS patients with the APOL1 high-risk (HR) and low-risk (LR) variants and compared it to cellular models based on patient-specific podocytes, HEK cells with engineered over-expressing HR variants and HR variant single-cell-RNA-seq data from kidney organoids. ResultsWe identified a signature of up- and down-regulated genes between biopsies from FSGS patients with APOL1 HR and LR variants. The up-regulated genes are functionally annotated to be associated with Calcium and mTOR signaling, whilst the down-regulated genes with inflammatory and immune response pathways. These pathways were confirmed by comparing with cellular models. Analysis of small molecules reverting the IFN-{gamma} stimulated gene expression to the non-stimulated gene expression in genome-edited APOL-G1 kidney organoids revealed several putative candidates such as the mTOR inhibitor AZD-2014. ConclusionWe have unveiled a signature of up- and down-regulated genes between APOL1 HR and LR kidney biopsies which could be assigned as associated with Calcium and mTOR signaling and down-regulated immune response.

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Investigating the oral and dental effects of nicotine pouches: findings from a patient and professional survey with in-person assessment.

Holliday, R.; Currie, C.; Jackson, J.; Allison, J.; Ash, E.; Lansdowne, N.; Basta, P.; Tapon, R.; Atkinson, N.; Fucile, A.; Padgett, E.; Warner, S.; Miluna-Meldere, S.; Crombie, L.; Toma, Z.; Nile, C.; Jakubovics, N.; Kist, R.; Robinson, M.

2026-10-05 dentistry and oral medicine 10.64898/2026.09.29.26364219 medRxiv
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Background: Nicotine pouches (NPs) are increasingly popular tobacco-free nicotine products, particularly among young people. Despite growing use, evidence regarding their oral health effects remains limited. Methods: We employed a mixed-methods approach comprising: (1) a national cross-sectional survey of NP users, (2) a survey of UK dental professionals, and (3) in-person clinical assessments of NP users. Survey data explored patterns of NP use, oral and dental side effects, and perceptions of risk. Clinical assessments included comprehensive oral examinations, periodontal assessments, and histopathological investigation of lesions where indicated. Results: A total of 3,659 NP users completed the public survey. Participants were predominantly male (89%) and aged 16-22 years (78%). Overall, 45% reported at least one oral or dental side effect. The most commonly reported effects were gingival recession (60%), burning sensations (41%), white patches (30%), and dry mouth (29%). Higher nicotine exposure was associated with increasing numbers of reported side effects. Among 126 dental professionals, oral lesions associated with NP use were commonly observed clinically, while only 17% reported seeing no oral or dental effects. Thirty-three NP users underwent in-person assessment. Ten lesions were biopsied; six demonstrated hyperkeratosis and four showed oral epithelial dysplasia (three mild, one moderate). All dysplastic lesions occurred at pouch placement sites. In two cases, clinical follow-up demonstrated partial or complete resolution of lesions following cessation of NP use. Periodontal assessments demonstrated generally low levels of periodontal disease and gingival recession across the cohort. Conclusions: Oral and dental side effects associated with NP use were commonly reported by users and observed by dental professionals. Histopathological assessment identified biopsy-confirmed oral epithelial dysplasia in lesions occurring at pouch placement sites, representing, to our knowledge, the first such report associated with NP use. Evidence of lesion improvement following discontinuation of use suggests that at least some NP-associated oral changes may be reversible. Although causality cannot be established, these findings highlight the need for vigilance among dental professionals and urgent longitudinal research to determine the incidence, progression, and reversibility of NP-associated oral lesions.

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Repeated intermittent clenbuterol administration induces exposure history-dependent proteomic remodeling in mouse skeletal muscle

Hitachi, K.; Yamaguchi, H.; Kiyofuji, Y.; Tsuchida, K.

2026-07-24 molecular biology 10.64898/2026.07.24.740506 medRxiv
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Clenbuterol (CB), a {beta}2-adrenergic receptor agonist, is known to increase skeletal muscle mass. However, because its effects are influenced by treatment duration, dose, and {beta}-adrenergic receptor responsiveness, it remains unclear how extended intermittent CB exposure alters the skeletal muscle proteome. In this study, we established a repeated intermittent CB administration model in mice and compared the effects of single and repeated CB exposure on plantaris muscle using label-free quantitative proteomics. Repeated CB exposure produced a more evident muscle-weight response than single exposure under the same long-term experimental timeline. Proteomic profiling revealed that repeated CB exposure was not a simple reproduction or amplification of the single CB response, but was associated with distinct changes in sarcomere-associated, tissue-remodeling-related, membrane-trafficking-related, and metabolic proteins. Integrated response-class analysis further identified multiple patterns of protein regulation, including shared CB-responsive proteins and proteins preferentially identified as changed under repeated CB conditions. Immunoblotting validated representative proteins from these response classes: Klhl40 and Napa as shared CB-responsive proteins, Galectin-3 as a strongly CB-responsive remodeling-related protein, and Rab18 as a protein change more clearly detected under repeated CB conditions. Together, these findings indicate that repeated intermittent CB exposure induces exposure history-dependent proteomic remodeling in skeletal muscle. This study provides a resource for understanding the molecular consequences of repeated CB exposure and for future mechanistic studies of {beta}2-adrenergic stimulation-induced skeletal muscle adaptation.

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A progressive reduction in basal phosphorylation of glutamate receptors along postweaning development accompanies maturation of hippocampal theta-burst-induced LTP.

Bento, M.; Guerreiro-Pinto, V.; Gil, M.; Rodrigues, N. C.; Cunha-reis, D.

2026-07-31 neuroscience 10.64898/2026.07.30.741885 medRxiv
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Tackling developmental changes in long-term potentiation (LTP) expression during adolescence is crucial to understand disease susceptibility in neurodevelopmental disorders, epileptogenesis or drug abuse. This paper investigated the alterations in the resting phosphorylation state of synaptic proteins essential for synaptic transmission and hippocampal LTP expression from weaning (3 weeks) to adulthood (12 weeks). Synaptic AMPA GluA1 and GluA2 subunit levels increased, yet to different extents, as the GluA1/GluA2 ratio also increased. Conversely, GluA1 phosphorylation in both Ser831 and Ser845 progressively decreased from weaning to adulthood, suggesting an enhanced availability of these sites for activity-dependent phosphorylation. In accordance, LTP induced by different theta-burst stimulation (TBS) intensities in the CA1 area of rat hippocampal slices enhanced gradually in this developmental period. In contrast, basal phosphorylation of GluN1, GluN2B and CaMKII increased during adolescence. Altogether, these findings suggest that alterations in AMPA receptor subunit composition and basal phosphorylation are crucial for the maturation of hippocampal LTP during adolescence, while a mild enhancement in synaptic CaMKII levels may further provide the necessary structural support to LTP expression and stability. Given the reported involvement of GluA1 phosphorylation changes in epileptogenesis and neurodevelopmental disorders, these findings provide important insights into hippocampal synaptic plasticity in normal and altered brain development and epileptogenesis.

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VCP inhibition preserves photoreceptor integrity under hydroquinone-induced oxidative stress in a human iPSC-RPE/porcine neuroretina co-culture model

Almansa-Garcia, A.-C.; Armento, A.; Antony, S.; Jarboui, M.-A.; Fernandez-Godino, R.; Cossio, E.; Cao, B.; Petremann-Dume, A.-S.; Vollert, A.; Kilger, E.; Bolz, S.; Ueffing, M.; Arango-Gonzalez, B.

2026-08-21 cell biology 10.64898/2026.08.18.745423 medRxiv
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Age-related macular degeneration (AMD) is the leading cause of irreversible vision loss in older adults. It is characterised by early retinal pigment epithelium (RPE) dysfunction followed by progressive photoreceptor degeneration. Cigarette smoking is a major environmental risk factor for AMD, and hydroquinone (HQ), a redox-active cigarette smoke component, induces oxidative stress and apoptosis in RPE cells. To analyse how RPE stress contributes to photoreceptor degeneration, we employed a retinal co-culture model composed of human induced pluripotent stem cell-derived RPE (iPSC-RPE) cells in conjunction with porcine neuroretina explants. Exposure to HQ induced oxidative stress in iPSC-RPE cells as well as retinal photoreceptors (RPR), resulting in apoptosis, executed at least in part by caspase activation. Concomitantly, HQ caused endoplasmic reticulum (ER) stress (ERAD) in RPR followed by their degeneration, evidenced by reduced outer nuclear layer (ONL) rows and shortened RPR outer segments (OS). Based on earlier results, which suggest a perturbation of proteostasis due to HQ, we tested whether ML240, a bona fide inhibitor of valosin-containing protein (VCP), would influence the degree of degenerative activities. ML240 did not prevent HQ-induced apoptosis in iPSC-RPE cells. However, it significantly preserved photoreceptor integrity, retaining OS length and cone density in HQ-stressed co-cultures. Proteomic analysis suggested that ML240 reshapes stress response patterns of the HQ-exposed neuroretina, as evidenced by a reduction in ERAD-associated markers, increased levels of antioxidant response proteins, and the preservation of cytochrome c enrichment in photoreceptor inner segments, which indicates improved mitochondrial integrity consistent with the observed preservation of photoreceptor structure. Together, these findings establish the iPSC-RPE/neuroretina co-culture as a platform to analyse pathophysiological features of AMD, dissect cell type-specific retinal responses to environmental stress and test neuroprotective pharmacological approaches to protect photoreceptors in oxidative stress-associated retinal degeneration.

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Reverse DTNB assay: a novel in vitrobiochemical approach to detect oxidized thiol modifications

Choudhuri, A.; Chakraborty, S.; Mishra, A.; Sengupta, R.

2026-08-06 biochemistry 10.64898/2026.08.02.742231 medRxiv
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The participation of sulfhydryl or thiol functions in a multitude of protein posttranslational modifications, although reflects on the redox versatility of cysteine residues, but their assessment in a dynamic cellular milieu involving the facile inter-conversion of SH to SSG, S-S, SNO, and S-R has been overwhelmingly difficult despite theirimplications in protein folding, enzyme structure and function, signalling and detoxification pathways, and pathophysiological ramifications.The current methodology, in contrast to a wide variety of cumbersome and prolonged techniques,repurposes the conventional DTNB assay for a hassle-free qualitative and quantitative analysisof redox-modified single or multiple susceptible thiol residues of cysteines in pure proteins as well as in a complex mixture of proteins.In this study, we document the thiol content, bearing the susceptibility to undergo reversible, oxidative thiol modifications, utilizing reverse DTNB assay in cell-free lysates and purified proteins that might provide a possible framework for dissecting the physiological phenomena behind the concealment of the susceptible cysteines through their redox-modified forms.

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Complex Modulation of IL-6 Signaling by Apelin and Elabela in HTR-8/SVneo Cells Under Cobalt Chloride Induced Chemical Hypoxia

Soloshenko, A. J.; Brown, C.; Sun, X.; Roy, A. N.; Ray, J.; Elsangeedy, E.; Chappell, M.; Yamaleyeva, L. M.

2026-08-21 molecular biology 10.64898/2026.08.20.746041 medRxiv
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Preeclampsia is a pregnancy complication characterized by hypertension, proteinuria, and end-organ dysfunction. Abnormal placentation leading to reduced placental perfusion may contribute to its development. Previous studies demonstrated that the activation of the apelin receptor (APJ) system has hypotensive, renoprotective, and antioxidant effects in preeclamptic rat models. Apelin and elabela (ELA) can stimulate the proliferation of trophoblast cells, suggesting a role in embryonic development. However, the mechanisms underlying the actions of apelin or ELA in trophoblast cells are not well understood, particularly in hypoxic settings. The immortalized HTR-8/SVneo trophoblastic cells were treated with cobalt chloride (CoCl2) at 0.2 mM for 24 hours to mimic hypoxic conditions. RT-qPCR, ELISA or Western blotting was used to measure mRNA or protein levels of apelin, elabela, and the components of IL-6 signaling in cell lysates or conditioned media. The exposure to CoCl2 increased total apelin and elabela content approximately 2-fold in the conditioned media but did not affect APJ levels. CoCl2 upregulated proinflammatory cytokine concentrations: soluble fms-like tyrosine kinase 1 (sFlt-1), soluble gp130 (sgp130), interleukin-6 (IL-6), and sIL-6 receptor (IL-s6R). Both apelin and elabela downregulated IL-6 mRNA but had no effect on sFlt-1 mRNA. Apelin attenuated sgp130, while ELA decreased the membrane form of IL-s6R. Apelin also decreased the pSTAT3/STAT3 ratio. CoCl2-induced hypoxia upregulated the pro-inflammatory milieu in HTR-8/SVneo cells. Local activation of this peptidergic system may be a compensatory response of the trophoblast cells to hypoxia as exogenous apelin and elabela treatment ameliorated the hypoxia-induced pro-inflammatory milieu.

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Within-mouth spillover of dental restorations on periodontal status

Baumeister, S.-E.; Hagenfeld, D.; Nolde, M.; Samietz, S.; Kanzow, P.; Völzke, H.; Kocher, T.; Holtfreter, B.

2026-08-14 dentistry and oral medicine 10.64898/2026.08.13.26360345 medRxiv
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Abstract Aim: To test whether neighbouring-tooth restorations affect a focal tooths periodontal status (within-mouth spillover), and whether accounting for them alters the established association at the restored surface. Materials and methods: Prospective tooth-surface data from the Study of Health in Pomerania (SHIP): SHIP-START (N=2,715/1,982/1,397, follow-ups 1-3) and SHIP-TREND (N=2,123). Own and neighbouring-tooth restoration were defined at baseline; probing depth (PD), clinical attachment level (CAL), bleeding on probing (BOP) and deep pockets (PD >=4 mm) at follow-up. A neighbourhood-exposure mixed model with generalized propensity-score adjustment estimated both effects, with two corroborating estimators. Results: Own restoration was associated with worse periodontal status at that surface (crown PD exp(beta) up to 1.10). Neighbouring-tooth restorations raised focal-tooth PD (spillover exp(beta) 1.03-1.05) and deep-pocket risk (risk ratio up to 1.25); CAL and BOP showed none consistently. It attenuated with tooth-lag, nearing the null by two to three teeth in most estimators. Ignoring interference modestly inflated the direct effect; an opposing-tooth negative control showed none; untreated caries reproduced it. Conclusions: Dental restorations exert a within-mouth spillover on neighbouring-tooth PD: their periodontal footprint extends beyond the restored tooth. The direct association persists, modestly attenuated, after accounting for the neighbourhood.

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Structural conservation of the gabapentinoid binding site in human and Caenorhabditis elegans α2δ subunits: a docking and molecular dynamics perspective

Sultana, J.; Mkrtchyan, L.; Castano, J. D.; Castillo, J. d.; Beaudry, F.

2026-09-17 molecular biology 10.64898/2026.09.15.751774 medRxiv
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Pain is a global health burden, highlighting the need for effective therapeutic strategies. Gabapentin (GBP) and pregabalin (PGB), used for neuropathic pain, act primarily through 2{delta} auxiliary subunits of voltage-gated calcium channels. Caenorhabditis elegans expresses UNC-36, an ortholog of mammalian 2{delta} proteins involved in calcium-channel function and nocifensive behavior. However, whether UNC-36 preserves the molecular features required for gabapentinoid recognition remains unclear. We compared human 2{delta}-1 and UNC-36 using sequence and structural analyses, molecular docking, 500-ns molecular dynamics simulations, interaction profiling, principal component and free-energy landscape analyses, and MM/GBSA calculations. UNC-36 preserved the overall architecture of the mammalian gabapentinoid-binding region despite substantial sequence divergence, and both ligands remained associated with the modeled pockets. However, residue-level interaction networks differed between species. Human 2{delta}-1 showed greater contributions from aromatic interactions, whereas UNC-36 relied more prominently on cationic and hydrogen-bond donor interactions mediated by Arg501 and Arg503. The human 2{delta}-1-PGB complex maintained the most stable ligand pose, whereas 2{delta}-1-GBP showed greater positional variation. In UNC-36, PGB exhibited greater deviation from its initial binding pose than GBP. The first two principal components accounted for more conformational variance in UNC-36 complexes than in human complexes. MM/GBSA estimates showed that PGB was energetically favored over GBP in human 2{delta}-1, whereas GBP was favored over PGB in UNC-36. These findings show that conservation of the gabapentinoid-binding architecture is accompanied by species-specific differences in interaction chemistry, conformational dynamics, and estimated binding energetics, providing a molecular basis for interpreting C. elegans gabapentinoid responses in a translational context.

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Assessing the physiological S nitrosoproteome reveals nitric oxide mediated regulatory networks in rice

Chakraborty, S.; Roy, S.; Choudhuri, A.; Poddar, S.; Bhattacharya, S.; Sengupta, R.

2026-07-31 biochemistry 10.64898/2026.07.30.741409 medRxiv
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Nitric oxide metabolism-based protein post-translational modifications, such as reversible S- nitrosylation, have been at the pinnacle of plant redox research owing to their significant correlation with seed dormancy, interaction with other signaling molecules, plant development and metabolism, biotic and abiotic plant stress responses, immune defense responses against plant pathogens, and senescence. The rapid interconversion of reactive nitrogen species, the abrogation of nitric oxide homeostasis by exogenous supplementation of NO donors and scavengers, the lack of spatio-temporal specificity of NO signaling, and the limited bioavailability or assay sensitivity for detection often limit the effectiveness of identifying and characterizing S-nitrosothiols in plants. Hitherto unknown, we report the first experimental evidence of the total in vivo S-nitrosoproteome in Oryza sativa L. subsp. indica, comprising 134 PSNOs, enriched with 169 putative sites susceptible to S-nitrosylation, without any exogenous supplementation of NO donors. In the present study, mercuric salt- driven facile decomposition of S-nitrosoproteins in the presence of nitrone spin trap 5,5- dimethyl-1-pyrroline N-oxide, resulting in the synthesis of DMPO-nitrone adducts with PSNO-derived protein thiyl radicals in O. sativa, has been demonstrated as an efficient and novel strategy for characterizing the PSNOs using mass spectrometry analysis. The evidence of physiological levels of PSNOs was further re-examined in a bi-directional qualitative and quantitative approach involving the 2,3-diaminonaphthalene assay in tandem with fluorescence-based visualization and fluorometric quantification. In silico analyses, involving both functional enrichment and pathway prediction analyses, have furthermore revealed unique protein-protein interaction networks and signaling pathways among the S- nitrosoproteome candidates and their predictable physiological roles in O. sativa indica, awaiting further in vitro validation for their functional correlation in response to S- nitrosylation. In conclusion, the present study provides novel evidence of nitric oxide signaling in rice cultivars under physiological conditions, bringing new insights into the potential in vivo transnitrosylation of regulatory or active-site cysteine thiols.

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Midbody inheritance predicts re-entry into quiescence, but not lineage potential, in mouse hematopoietic stem cells

Fukushima, T.; Wehling, A.; Shimamoto, R.; Asada, S.; Kawamura, S.; Fukuyama, T.; Goyama, S.; Schroeder, T.; Kitamura, T.; Tanaka, Y.

2026-07-29 cell biology 10.64898/2026.07.28.739739 medRxiv
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Hematopoietic stem cells (HSCs) give rise to all blood cell lineages and possess long-term self-renewal potential. HSCs undergo symmetric division for their expansion and asymmetric division to generate one HSCs and one progenitor cells which contribute to production of mature blood cells. The midbody is a structure which is formed in the center of the intercellular bridge during cytokinesis. However, the midbody is either asymmetrically inherited by one daughter cell or symmetrically released after cell division, whether these distinct patterns of midbody inheritance influence HSC fate remain poorly understood. In this study, we designed a fusion protein hmKO2 and MgcRacGAP which is a component of midbody. We then traced the midbody inheritance during cell division and the future cell fates of HSC daughters after division by time-lapse imaging. As a result, we found that the midbody release correlated with the delay of the time to the next division but not to the lineage potential of HSCs, indicating the possibility that midbody remnant plays some roles in cell cycle progression. HighlightHematopoietic stem cells exhibit a low frequency of midbody inheritance. Midbody inheritance does not affect the lineage potential of daughter cells. Midbody loss is associated with delayed entry into the next cell cycle.

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Extracellular matrix stiffness in oral squamous cell carcinoma: a systematic review and meta-analysis of associations with tumor progression and prognosis

Lima, I. F. P.; Toebe Silva, A. C.; Engler, A. J.; Bittencourt, L. d. S.; Lamers, M. L.

2026-10-05 dentistry and oral medicine 10.64898/2026.09.28.26363990 medRxiv
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Objective: To critically evaluate the influence of extracellular matrix stiffness on tumor progression, prognosis, and clinical implications in patients with oral squamous cell carcinoma. Design: This systematic review followed the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines, and the protocol was registered in PROSPERO (CRD420251156429). Five databases (PubMed, Scopus, Embase, Web of Science, and OATD) were searched without restrictions on publication year or language. Human studies that evaluated extracellular matrix stiffness in oral squamous cell carcinoma, either as an assessment method or as a prognostic factor, were included; in vitro and animal studies were excluded. Results: Eight human studies involving 436 patients were included. Elastography was the most frequent measurement method, employed in four studies. Mean tumor thickness was reported in three studies and ranged from 3.0 to 4.4 mm. Extracellular matrix stiffness was expressed in various units (e.g., 37.7 gf, 23.5 kPa) and was consistently higher in tumor tissue than in normal mucosa in all studies. Three studies demonstrated a significant positive correlation between stiffness and tumor thickness. One study identified predictive cut-off values for lymph node metastasis and reported that high matrix stiffness was an independent predictor of worse overall survival (HR = 4.022; 95% CI: 1.294-12.495; p = 0.016) and recurrence-free survival (HR = 5.680; 95% CI: 1.146-28.143; p = 0.033). A meta-analysis of five studies (307 patients) showed a significantly higher standardized stiffness in oral squamous cell carcinoma compared with normal oral mucosa (standardized mean difference = 5.28; 95% CI: 2.61-7.94; p < 0.001), with substantial heterogeneity (I2= 98.6%). Conclusions: Extracellular matrix stiffness is elevated in oral squamous cell carcinoma and is associated with greater tumor thickness, lymph node metastasis and, in one study, worse survival. These findings support extracellular matrix stiffness as a potential biomechanical marker, pending further validation in standardized prospective studies.

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Performance of Contemporary Large Language Models on the National Prosthodontic Resident Examination: A Multi-Year Comparative Study

Chen, Y.-w.; Bhunyanaphakul, V.; Kosago, P.; Finkelman, M.; Lee, D. J.

2026-10-21 dentistry and oral medicine 10.64898/2026.10.19.26365937 medRxiv
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Purpose: To compare the performance of three large language models (LLMs), ChatGPT-o1, Grok 3, and Gemini 2.0 Pro, on the American College of Prosthodontists' National Prosthodontic Resident Examination (NPRE). Materials and Methods: Official NPRE examinations from years 2015-2024 were retrieved from the American College of Prosthodontists website and used to prompt each LLM. Paid access tiers and advanced reasoning were enabled. Responses from LLMs were recorded and compared against the official answer keys for accuracy, variability across years, and consistency of responses. Duplicate questions were retained for the primary analysis and removed in a sensitivity analysis. Accuracy (percent correct) was compared using generalized estimating equations binary logistic regression (primary); Cochran's Q with Bonferroni-adjusted McNemar tests (sensitivity). Year-to-year variability (SD of annual accuracy) was compared using weighted Levene tests. Consistency across duplicate items was quantified as the percentage of perfect matches and compared using Cochran's Q with Bonferroni-adjusted McNemar tests. Results: Across 1,487 questions, overall accuracy differed among models (global P < 0.001). ChatGPT-o1 achieved 78.4% correct, Grok 3 76.4%, and Gemini 2.0 Pro 73.2%; ChatGPT-o1 and Grok 3's accuracy significantly exceeded Gemini 2.0 Pro (both P [&le;] 0.016), with no significant difference between ChatGPT-o1 and Grok 3 (P = 0.099). After removing duplicates (n = 1,200), results were similar: ChatGPT-o1, Grok 3, and Gemini 2.0 Pro were 77.1%, 76.6%, and 71.5% correct, respectively; ChatGPT-o1 and Grok 3's accuracy was significantly higher than Gemini 2.0 Pro (both P < 0.001). Variability across years did not differ significantly (P [&ge;] 0.097). Grok 3 showed significantly higher perfect-match consistency (79.2%) than ChatGPT-o1 (69.4%) and Gemini 2.0 Pro (64.5%) (P [&le;] 0.010). Conclusions: Contemporary LLMs showed 70-80% accuracy on postgraduate prosthodontic multiple-choice content. While promising for educational support, residual error and inconsistency warrant human oversight and transparent methods reporting before curricular adoption.

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Dental Anxiety in Oral-Systemic Health: Empirical Evaluation of a Published Conceptual Model

Kajita, M.; Yada, A.; Ylostalo, P.; Pohjola, V.; Sipila, K.; Humphris, G.; Auvinen, J.; Lahti, S.

2026-09-28 dentistry and oral medicine 10.64898/2026.09.25.26364045 medRxiv
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Objectives: A previously published conceptual mapping review integrated fragmented evidence on dental anxiety (DA) into a broader conceptual model of potential causes and consequences. This study focused on consequences, extending from oral health-related behaviours through oral disease to systemic health, and empirically evaluated these hypothesized relationships on the population level. Methods: Cross-sectional data from the 46-year follow-up of the Northern Finland Birth Cohort 1966 (n = 1,859) were analysed using structural equation modelling. DA was modelled as a latent construct; delayed/problem-oriented dental attendance and home oral care as behavioural proxies; periodontal disease burden as the percentage of sites with probing pocket depth >=4 mm; and cardiovascular risk as a Framingham-based risk score. Generalized anxiety, sex, and education were covariates. Smoking-stratified multigroup analyses assessed model robustness. Results: The prespecified associations were observed across behavioural, periodontal, and systemic-risk domains. Higher DA was associated with more delayed/problem-oriented attendance and poorer home care; both were associated with greater periodontal disease burden, which in turn was associated with higher cardiovascular risk. Model fit was good (chi-square(119) = 529.98, CFI = 0.962, TLI = 0.951, RMSEA = 0.043, SRMR = 0.051). The overall association between DA and cardiovascular risk was small (beta = 0.066, p = .004), with a small decomposed indirect association (beta = 0.013, p = .006) and a remaining direct association (beta = 0.053, p = .022). Smoking-stratified multigroup comparisons found no differences in the structural associations by smoking status. Conclusions: This population-based evaluation provides preliminary empirical support for the conceptual model. Findings extend the relevance of DA beyond dental attendance and oral health outcomes to a broader oral-systemic public-health context. Cross-sectional data cannot establish temporal or causal ordering; longitudinal replication is needed.

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Functional and molecular profiles of the neuroretina and retinal pigmented epithelium-choroid in response to aging and Nrf2 deletion

Wells, B. L.; Filiberti, A. J.; Stanford, D. R.; Pham, K. D.; Walton, D. A.; Plafker, S. M.; Freeman, W. M.; Chucair-Elliott, A. J.

2026-10-09 molecular biology 10.64898/2026.10.08.757667 medRxiv
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Purpose: Age is the leading factor for age-related macular degeneration (AMD), in which retinal pigmented epithelium (RPE) atrophy is a hallmark. The nuclear factor-erythroid 2-related factor 2 (Nrf2), a major anti-stress transcription factor, decreases in AMD, suggesting bioenergetic stress interacts with age during AMD pathogenesis. We profiled visual function and gene expression of the retina and RPE-choroid with Nrf2 deletion and aging. Methods: We tested 3mo and 14mo Nrf2 null (Nrf2 KO) and Nrf2 WT mice for optokinetic tracking (OKT) and dark-adapted electroretinography (ERG) responses. Eyes were harvested for retina outer nuclear layer (ONL) thickness analysis and retina and RPE-choroid cup RNA isolation for RNAseq profiling. Results: Visual acuity was reduced with aging with lower values in the Nrf2 KO vs Nrf2 WT comparison at 14mo. We observed aged-related reduction of a-, b-, and c-wave ERG amplitudes in both WT and KO mice. Age-related c-wave decline was exacerbated by Nrf2 loss. By RNAseq, two-way ANOVA of RPE-choroid samples revealed differentially expressed genes (DEGs) with age and genotype main effects, as well as DEGs with age and genotype interaction effects. Age DEGs were over-represented in pathways related to inflammation and phagocytosis. Genotype DEGs were associated with alterations in antioxidant and inflammatory processes. Retina RNAseq showed age and genotype DEGs. Conclusions: Ablation of Nrf2 exacerbates age-related declines suggesting that decrease in Nrf2 with aging has functional consequences for inflammation/resiliency. We provide retina and RPE-choroid bulk-RNAseq datasets from the same cohort of mice that can be interrogated to better understand degeneration of retina/RPE-choroid.