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Thoracic aortic aneurysms (TAA) represent a critical health issue for which computational models can significantly contribute to better understand the physiopathology. Among different computational frameworks, the Homogenized Constrained Mixture Theory has shown to be a computationally efficient option, allowing the inclusion of several mechanically significant constituents into a layer-specific mixture. Different patient-specific Growth and Remodeling (G&R) models correctly predicted TAA progression, although simplifications such as the inclusion of a limited number of collagen fibers and imposed boundary conditions might limit extensive analyses. The current study aims to enhance existing models by incorporating several discrete collagen fibers and to remove restrictive boundary conditions of the previous models. The implementation of discretized fiber dispersion presents a more realistic description of the vessel, while the removal of boundary conditions was addressed by including cross-links in the model to provide a supplemental stiffness against through-thickness shearing, a feature that was previously absent, and by the development of a non-local framework that ensures the stable deposition and degradation of collagen fibers. With these improvements, the current model represents a step forward towards more robust and comprehensive simulations of TAA growth.

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The highly blistering sulfur mustard analogue agent T (bis(2-chloroethylthioethyl) ether), also known as O-mustard or oxy-mustard, is a common impurity in military grade sulfur mustard (SM) and a component of mixtures such as "HT" that are still found in old munitions. Together with sesquimustard (Q), it is the most important SM analogue and tightly regulated as a Schedule 1 chemical under the Chemical Weapons Convention. We report the adducts of T with nucleophilic Cys34 and other residues in human serum albumin (HSA) formed in vitro. A micro liquid chromatography electrospray ionization high-resolution tandem-mass spectrometry method (µLC-ESI MS/HR MS) was developed for the detection and identification of biomarker peptides alkylated by a T-derived hydroxyethylthioethyloxyethylthioethyl (HETEOETE)-moiety (as indicated by an asterisk below). Following proteolysis of T-exposed human plasma with pronase, the dipeptide Cys34*Pro and the single amino acid residue His* were produced. The use of proteinase K yielded Cys34*ProPhe and the use of pepsin generated ValThrGlu48*Phe, AlaGlu230*ValSerLysLeu, and LeuGlyMet329*Phe. Corresponding peptide-adducts of SM and Q were detected in a common workflow that in principle allowed the estimation of the mustard or mustard composition encountered during exposure. Novel adducts of Q at the Glu230 and Met239 residues were detected and are reported accordingly. Based on molecular dynamics simulations, we identified regular interactions of the Cys34(-HETEOETE)-moiety with several glutamic acid residues in HSA including Glu86, which is not an obvious interaction partner by visual inspection of the HSA crystal structure. The existence of this and other intramolecular cross-links was experimentally proven for the first time.

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Vitrimers are a new class of heterogeneous polymers that combine the best features of thermosets with those of thermoplastics. The introduction of cross-links strongly changes the viscoelastic behavior of vitrimer materials. However, the characterization and understanding of the nanostructures and interfaces in vitrimers resulting from dynamic cross-linking formation remain a major challenge. Here, using dynamic modes of atomic force microscopy (AFM), namely intermodulation AFM (ImAFM) and AFM-based dynamic mechanical analysis (AFM-nDMA), local viscoelastic properties and interfaces at the nanoscale length of high-density polyethylene (HDPE) vitrimer materials are reported. ImAFM imaging in combination with the k-means clustering algorithm clearly reveals two distinct phases in the vitrimer system with highly different viscoelastic properties. AFM-nDMA further provides quantitative nanoviscoelastic properties at the nanoscale to confirm that there is a cross-linking-rich aggregation area forming a nanosize network structure in the cross-linking-poor matrix phase. The cross-linking-rich region shows a similar elastic modulus but much higher adhesion force measured by AFM compared to the cross-linking-poor HDPE matrix. Furthermore, the frequency influence on the local viscoelastic properties of HDPE vitrimer at the nanoscale was initially screened. The observed HDPE vitrimer nanostructures and viscoelastic properties at the nanoscale also provide explanations on the observed bulk HDPE vitrimer crystallinity decrease and dimensional stability increase compared to HDPE. Therefore, probing the viscoelastic properties and interfaces of HDPE vitrimer provides important insights into understanding of the correlations between the vitrimer nanostructure and the bulk mechanical and rheological behaviors.

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Hydrogels are soft materials engineered to suit a multitude of applications that exploit their tunable mechanochemical properties. Dynamic hydrogels employing noncovalent, physically cross-linked networks dominated by either enthalpic or entropic interactions enable unique rheological and stimuli-responsive characteristics. In contrast to enthalpy-driven interactions that soften with increasing temperature, entropic interactions result in largely temperature-independent mechanical properties. By engineering interfacial polymer-particle interactions, we can induce a dynamic-to-covalent transition in entropic hydrogels that leads to biomimetic non-ergodic aging in the microstructure without altering the network mesh size. This transition is tuned by varying temperature and formulation conditions such as pH, which allows for multivalent tunability in properties. These hydrogels can thus be designed to exhibit either temperature-independent metastable dynamic cross-linking or time-dependent stiffening based on formulation and storage conditions, all while maintaining structural features critical for controlling mass transport, akin to many biological tissues. Such robust materials with versatile and adaptable properties can be utilized in applications such as wildfire suppression, surgical adhesives, and depot-forming injectable drug delivery systems.

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Increased fracture risk in type 1 diabetes (T1D) patients is not fully captured by bone mineral density (BMD) by DXA. Advanced glycation end-products (AGEs) have been implicated in the increased fracture risk in T1D, yet recent publications question this. To test the hypothesis that enzymatic collagen cross-links rather than AGEs correlate with fracture incidence in T1D, we analyzed iliac crest biopsies from sex-matched, fracturing T1D patients (N = 5; T1DFx), 6 non-fracturing T1D patients (T1DNoFx), and 6 healthy subjects, by Raman microspectroscopy as a function of tissue age (based on double fluorescent labels), in intracortical and trabecular bone, to determine pyridinoline (Pyd), ε-N-Carboxymethyl-L-lysine, and pentosidine (PEN)). There were no differences in the clinical characteristics between the T1DFx and T1DNoFx groups. At trabecular forming surfaces, T1DFx patients had higher PEN and Pyd content compared to T1DNoFx ones. Previous studies have shown that elevated PEN does not necessarily correlate with fracture incidence in postmenopausal, long-term T1D patients. On the other hand, the elevated Pyd content in the T1DFx patients would be consistent with published studies showing a significant correlation between elevated trivalent enzymatic collagen cross-links and fracture occurrence independent of BMD. Collagen fibers with high Pyd content are more brittle. Thus, a plausible suggestion is that it is the enzymatic collagen cross-links that either by themselves or in combination with the adverse effects of increased AGE accumulation that result in fragility fracture in T1D.

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Acrylic adhesive sheets have been used for many applications, from popular seal materials to high-end electrical devices. One of the basic and critical design features of adhesives is effective covalent cross-linking for superior adhesive properties. On the other hand, covalent cross-linking prevents reuse or recycling of the adhesive. This makes the adhesive sheets insoluble and poorly workable. For development of sustainable adhesives, we investigated the adhesive sheets based on acrylic elastomers with "Movable Cross-links" (M-PEA-CD (0.5)) copolymerized with 0.5 mol % cyclodextrin monomers. The peel strength and creep resistance of M-PEA-CD (0.5) were greater than those of adhesives (N-PEA) without any cross-links. M-PEA-CD (0.5) was recyclable via dissolution in ethyl acetate. Furthermore, the recycled M-PEA-CD (0.5) from solution exhibited the same adhesion properties as virgin M-PEA-CD (0.5). Spectroscopic and mechanical measurements indicated that topological cross-linking with Cyclodextrin (CD) moieties generated novel recyclable adhesive sheets without restricting the polymer main chains, unlike covalent cross-linking (CC-PEA). The movable cross-links were maintained in both the solid state and in solution, which allowed recycling of the elastomer via simple methods.

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Osteopontin (OPN) and Bone Sialoprotein (BSP), abundantly expressed by osteoblasts and osteoclasts, appear to have important, partly overlapping functions in bone. In gene-knockout (KO, -/-) models of either protein and their double (D)KO in the same CD1/129sv genetic background, we analyzed the morphology, matrix characteristics, and biomechanical properties of femur bone in 2 and 4 month old, male and female mice. OPN-/- mice display inconsistent, perhaps localized hypermineralization, while the BSP-/- are hypomineralized throughout ages and sexes, and the low mineralization of young DKO mice recovers with age. The higher contribution of primary bone remnants in OPN-/- shafts suggests a slow turnover, while their lower percentage in BSP-/- indicates rapid remodeling, despite FTIR-based evidence in this genotype of a high maturity of the mineralized matrix. In 3-point bending assays, OPN-/- bones consistently display higher Maximal Load, Work to Max. Load and in young mice Ultimate Stress, an intrinsic characteristic of the matrix. Young male and old female BSP-/- also display high Work to Max. Load along with low Ultimate Stress. Principal Component Analysis confirms the major role of morphological traits in mechanical competence, and evidences a grouping of the WT phenotype with the OPN-/- and of BSP-/- with DKO, driven by both structural and matrix parameters, suggesting that the presence or absence of BSP has the most profound effects on skeletal properties. Single or double gene KO of OPN and BSP thus have multiple distinct effects on skeletal phenotypes, confirming their importance in bone biology and their interplay in its regulation.

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Mitochondrial DNA (mtDNA) plays a key role in mitochondrial and cellular functions. mtDNA is maintained by active DNA turnover and base excision repair (BER). In BER, one of the toxic repair intermediates is 5'-deoxyribose phosphate (5'dRp). Human mitochondrial DNA polymerase γ has weak dRp lyase activities, and another known dRp lyase in the nucleus, human DNA polymerase ß, can also localize to mitochondria in certain cell and tissue types. Nonetheless, whether additional proteins have the ability to remove 5'dRp in mitochondria remains unknown. Our prior work on the AP lyase activity of mitochondrial transcription factor A (TFAM) has prompted us to examine its ability to remove 5'dRp residues in vitro. TFAM is the primary DNA-packaging factor in human mitochondria and interacts with mitochondrial DNA extensively. Our data demonstrate that TFAM has the dRp lyase activity with different DNA substrates. Under single-turnover conditions, TFAM removes 5'dRp residues at a rate comparable to that of DNA polymerase (pol) ß, albeit slower than that of pol λ. Among the three proteins examined, pol λ shows the highest single-turnover rates in dRp lyase reactions. The catalytic effect of TFAM is facilitated by lysine residues of TFAM via Schiff base chemistry, as evidenced by the observation of dRp-lysine adducts in mass spectrometry experiments. The catalytic effect of TFAM observed here is analogous to the AP lyase activity of TFAM reported previously. Together, these results suggest a potential role of TFAM in preventing the accumulation of toxic DNA repair intermediates.

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Zwitterions (ZIs), which are molecules bearing an equal number of positive and negative charges and typically possessing large dipole moments, can play an important role in improving the characteristics of a wide variety of novel battery electrolytes. Significant Coulombic interactions among ZI charged groups and any mobile ions present can lead to several beneficial phenomena within electrolytes, such as increased salt dissociation, the formation of ordered pathways for ion transport, and enhanced mechanical robustness. In some cases, ZI additives can also boost electrochemical stability at the electrolyte/electrode interface and enable longer battery cycling. Here, a brief summary of selected key historical and recent advances in the use of ZI materials to enrich the performance of three distinct classes of battery electrolytes is presented. These include: ionic liquid-based, conventional solvent-based, and solid matrix-based (non-ceramic) electrolytes. Exploring a greater chemical diversity of ZI types and electrolyte pairings will likely lead to more discoveries that can empower next-generation battery designs in the years to come.

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A strong, tough, and stable adhesion system used in various environments must be developed. A long-lasting adhesion system should effectively perform in the following five aspects: adhesion strength, toughness, energy dissipation property, self-restoration property, and creep resistance property. However, these properties are difficult to balance using conventional adhesives. Here, a new topological adhesion system using single-movable cross-network (SC) materials [SC(DMAAm) Adh] was designed. 3-(Trimethoxysilyl) propyl acrylate was used as the anchor, N,N-dimethyl acrylamide (DMAAm) was used as the main chain monomer, and γ-cyclodextrin (γ-CD) units acted as movable cross-links. The movable cross-links provided SC(DMAAm) Adh with energy dissipation properties, thereby improving its toughness. The γ-CD units also acted as bulky stoppers that provided a high adhesion strength and self-restoration properties. Moreover, the combination of the movable cross-links and bulky stoppers provided creep resistance to SC(DMAAm) Adh. The performance of the adhesion systems under different mobilities of the polymer chains was examined by adjusting the water content. In proper water-containing states, all mechanical properties of SC(DMAAm) Adh were better than those of the adhesion systems using homopolymers [P(DMAAm) Adh] and polymers with covalent cross-linking points [CP(DMAAm) Adh].

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Myosin heavy chain (MHC) isoforms and meat quality characteristics of different muscles were investigated to explore their potential relationships in yaks. Results showed that semitendinosus (ST), longissimus thoracis (LT), and infraspinatus (IS) have a greater ratio of MHC IIb (47.84%), MHC IIa (73.27%), and MHC I (24.26%), respectively, than the other two muscles. Compared with LT or ST, IS exhibited more intense color, greater water-holding capacity, and initial tenderness with higher intermuscular fat (IMF) and collagen (of lower cross-linking level), presenting overall better quality. Variations in MHC isoforms accounted for the muscle-specific meat quality. Specifically, MHC I was positively associated with redness, myoglobin, IMF, collagen, pH, and thermal stability and negatively associated with myofibril fragmentation index, fiber thickness, collagen cross-linking, and drip loss. These results provide insights into the relationships between MHC isoforms and meat quality in yaks and the MHC I isoform has an extensive influence on meat quality.

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Recently, many tough synthetic hydrogels have been created as promising candidates in fields such as smart electronic devices. In this paper, we propose a simple strategy to construct tough and robust hydrogels. Two-dimensional Ti3C2Tx MXene nanosheets and metal ions were introduced into poly(acrylamide-co-acrylic acid) hydrogels, the MXene nanosheets acted as multifunctional cross-linkers and effective stress-transfer centers, and physical cross-links were formed between Fe3+ and carboxylic acid. Under deformation, the coordination interactions exhibit reversible dissociation and reorganization properties, suggesting a novel mechanism of energy dissipation and stress redistribution. The design enabled the hydrogel to exhibit outstanding and balanced mechanical properties (tensile strength of up to 5.67 MPa and elongation at break of up to 508%). This study will facilitate the diverse applications of metallosupramolecular hydrogels.

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Collagen as the main protein in Extra Cellular Matrix (ECM) is the main load-bearing component of fibrous tissues. Nanostructure and architecture of collagen fibrils play an important role in mechanical behavior of these tissues. Extensive experimental and theoretical studies have so far been performed to capture these properties, but none of the current models realistically represent the complexity of network mechanics because still less is known about the collagen's inner structure and its effect on the mechanical properties of tissues. The goal of this review article is to emphasize the significance of cross-links in computational modeling of different collagen-based tissues, and to reveal the need for continuum models to consider cross-links properties to better reflect the mechanical behavior observed in experiments. In addition, this study outlines the limitations of current investigations and provides potential suggestions for the future work.

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PURPOSE: This study aimed to investigate the effect of collagen cross-link deficiency on collagen fiber formation around an implant and its effect on the osseointegration process. METHODS: Wistar rats were fed 0.1% beta-aminopropionitrile (BAPN) dissolved in water to induce collagen cross-link deficiency. Custom-made mini-implants with machined surfaces were placed proximal to the tibia. At 1, 2, and 4 weeks postoperatively, the bone area around the implant, bone-implant contact ratio, osteoclast/osteocyte activity, and osseointegration strength were evaluated using histological and immunohistochemical analyses and biomechanical tests. RESULTS: Long-term disturbance of collagen cross-link formation in the BAPN group resulted in faster collagen fiber maturation than that in controls, with a defective collagen structure, low bone formation quantity, and low bone-implant contact values. Deficiency of collagen cross-links resulted in increased bone resorption and decreased osteocyte activity. CONCLUSIONS: Collagen cross-linking is important for the formation of the collagen matrix, and their deficiency may impair bone activity around implants, affecting the osseointegration process.

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Cell-surface proteins known as adhesins enable bacteria to colonize particular environments, and in Gram-positive bacteria often contain autocatalytically formed covalent intramolecular cross-links. While investigating the prevalence of such cross-links, a remarkable example was discovered in Mobiluncus mulieris, a pathogen associated with bacterial vaginosis. This organism encodes a putative adhesin of 7651 residues. Crystallography and mass spectrometry of two selected domains, and AlphaFold structure prediction of the remainder of the protein, were used to show that this adhesin belongs to the family of thioester, isopeptide and ester-bond-containing proteins (TIE proteins). It has an N-terminal domain homologous to thioester adhesion domains, followed by 51 immunoglobulin (Ig)-like domains containing ester- or isopeptide-bond cross-links. The energetic cost to the M. mulieris bacterium in retaining such a large adhesin as a single gene or protein construct suggests a critical role in pathogenicity and/or persistence.

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PURPOSE: Biophysical and biochemical attributes of the extracellular matrix are major determinants of cell fate in homeostasis and disease. Ocular hypertension and glaucoma are diseases where the trabecular meshwork tissue responsible for aqueous humor egress becomes stiffer accompanied by changes in its matrisome in a segmental manner with regions of high or low flow. Prior studies demonstrate these alterations in the matrix are dynamic in response to age and pressure changes. The underlying reason for segmentation or differential response to pressure and stiffening are unknown. This is largely due to a lack of appropriate models (in vitro or ex vivo) to study this phenomena. METHODS: Primary trabecular meshwork cells were isolated from segmental flow regions, and cells were cultured for 4 weeks in the presence or absence or dexamethasone to obtain cell derived matrices (CDM). The biomechanical attributes of the CDM, composition of the matrisome, and incidence of crosslinks were determined by atomic force microscopy and mass spectrometry. RESULTS: Data demonstrate that matrix deposited by cells from low flow regions are stiffer and exhibit a greater number of immature and mature crosslinks, and that these are exacerbated in the presence of steroid. We also show a differential response of high or low flow cells to steroid via changes observed in the matrix composition. However, no correlations were observed between elastic moduli and presence or absence of mature and immature crosslinks in the CDMs. CONCLUSION: Regardless of a direct correlation between matrix stiffness and crosslinks, we observed distinct differences in the composition and mechanics of the matrices deposited by segmental flow cells. These results suggest distinct differences in cellular identify and likely a basis for mechanical memory post isolation and culture. Nevertheless, we conclude that although a mechanistic basis for matrix stiffness was undetermined in this study, it is a viable tool to study cell-matrix interactions and further our understanding of trabecular meshwork pathobiology.

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DNA-protein cross-links remain the least-studied type of DNA damage. Recently, their repair was shown to involve proteolysis; however, the fate of the peptide remnant attached to DNA is unclear. Particularly, peptide cross-links could interfere with DNA polymerases. Apurinuic/apyrimidinic (AP) sites, abundant and spontaneously arising DNA lesions, readily form cross-links with proteins. Their degradation products (AP site-peptide cross-links, APPXLs) are non-instructive and should be even more problematic for polymerases. Here, we address the ability of human DNA polymerases involved in DNA repair and translesion synthesis (POLß, POLλ, POLη, POLκ and PrimPOL) to carry out synthesis on templates containing AP sites cross-linked to the N-terminus of a 10-mer peptide (APPXL-I) or to an internal lysine of a 23-mer peptide (APPXL-Y). Generally, APPXLs strongly blocked processive DNA synthesis. The blocking properties of APPXL-I were comparable with those of an AP site, while APPXL-Y constituted a much stronger obstruction. POLη and POLκ demonstrated the highest bypass ability. DNA polymerases mostly used dNTP-stabilized template misalignment to incorporate nucleotides when encountering an APPXL. We conclude that APPXLs are likely highly cytotoxic and mutagenic intermediates of AP site-protein cross-link repair and must be quickly eliminated before replication.

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In this study, we subjected 5,5-diethoxy-4-oxopent-2-enal (DOPE), a model amino acids cross-linking reagent, to reactions with N-acetylcysteine (Ac-Cys) and Nα-acetyllysine (Ac-Lys), and identified three pyrrole cross-links. The compounds were isolated and their structures were rigorously determined by spectrometric and spectroscopic methods, including 2D NMR experiments. The use of 2D NMR spectroscopy was crucial to determine the position of the substituents in the pyrrole rings. The products were identified as 2,4-, 2,3-, and 2,5-substituted pyrroles. The data obtained from their structural characterisation can help similar studies on amino acids modifications induced by analogous bifunctional carbonyl compounds. Our results show that the study of pathways in which model electrophiles modify amino acids may be helpful for similar studies dealing with identification of structural changes in cysteine- and lysine-containing proteins associated with oxidative stress.

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DNA interstrand cross-links, such as those formed by psoralen-UVA irradiation, are highly toxic lesions in both humans and bacteria, with a single lesion being lethal in Escherichia coli. Despite the lack of effective repair, human cancers and bacteria can develop resistance to cross-linking treatments, although the mechanisms of resistance remain poorly defined. Here, we subjected E. coli to repeated psoralen-UVA exposure to isolate three independently derived strains that were >10,000-fold more resistant to this treatment than the parental strain. Analysis of these strains identified gain-of-function mutations in the transcriptional regulator AcrR and the alpha subunit of RNA polymerase that together could account for the resistance of these strains. Resistance conferred by the AcrR mutation is mediated at least in part through the regulation of the AcrAB-TolC efflux pump. Resistance via mutations in the alpha subunit of RNA polymerase occurs through a still-uncharacterized mechanism that has an additive effect with mutations in AcrR. Both acrR and rpoA mutations reduced cross-link formation in vivo. We discuss potential mechanisms in relation to the ability to repair and survive interstrand DNA cross-links. IMPORTANCE Psoralen DNA interstrand cross-links are highly toxic lesions with antimicrobial and anticancer properties. Despite the lack of effective mechanisms for repair, cells can become resistant to cross-linking agents through mechanisms that remain poorly defined. We derived resistant mutants and identified that two gain-of-function mutations in AcrR and the alpha subunit of RNA polymerase confer high levels of resistance to E. coli treated with psoralen-UVA. Resistance conferred by AcrR mutations occurs through regulation of the AcrAB-TolC efflux pump, has an additive effect with RNA polymerase mutations, acts by reducing the formation of cross-links in vivo, and reveals a novel mechanism by which these environmentally and clinically important agents are processed by the cell.

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BACKGROUND: DNA-protein cross-links (DPCs) are one of the most deleterious DNA lesions, originating from various sources, including enzymatic activity. For instance, topoisomerases, which play a fundamental role in DNA metabolic processes such as replication and transcription, can be trapped and remain covalently bound to DNA in the presence of poisons or nearby DNA damage. Given the complexity of individual DPCs, numerous repair pathways have been described. The protein tyrosyl-DNA phosphodiesterase 1 (Tdp1) has been demonstrated to be responsible for removing topoisomerase 1 (Top1). Nevertheless, studies in budding yeast have indicated that alternative pathways involving Mus81, a structure-specific DNA endonuclease, could also remove Top1 and other DPCs. RESULTS: This study shows that MUS81 can efficiently cleave various DNA substrates modified by fluorescein, streptavidin or proteolytically processed topoisomerase. Furthermore, the inability of MUS81 to cleave substrates bearing native TOP1 suggests that TOP1 must be either dislodged or partially degraded prior to MUS81 cleavage. We demonstrated that MUS81 could cleave a model DPC in nuclear extracts and that depletion of TDP1 in MUS81-KO cells induces sensitivity to the TOP1 poison camptothecin (CPT) and affects cell proliferation. This sensitivity is only partially suppressed by TOP1 depletion, indicating that other DPCs might require the MUS81 activity for cell proliferation. CONCLUSIONS: Our data indicate that MUS81 and TDP1 play independent roles in the repair of CPT-induced lesions, thus representing new therapeutic targets for cancer cell sensitisation in combination with TOP1 inhibitors.

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