Gap Repair Research Articles

Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification on biology

Rad24-RFC (replication factor C) loads the 9-1-1 checkpoint clamp onto the recessed 5' ends by binding a 5' DNA at an external surface site and threading the 3' single-stranded DNA (ssDNA) into 9-1-1. We find here that Rad24-RFC loads 9-1-1 onto DNA gaps in preference to a recessed 5' end, thus presumably leaving 9-1-1 on duplex 3' ss/double-stranded DNA (dsDNA) after Rad24-RFC ejects from DNA. We captured five Rad24-RFC-9-1-1 loading intermediates using a 10-nt gap DNA. We also determined the structure of Rad24-RFC-9-1-1 using a 5-nt gap DNA. The structures reveal that Rad24-RFC is unable to melt DNA ends and that a Rad24 loop limits the dsDNA length in the chamber. These observations explain Rad24-RFC's preference for a preexisting gap of over 5-nt ssDNA and suggest a direct role of the 9-1-1 in gap repair with various TLS (trans-lesion synthesis) polymerases in addition to signaling the ATR kinase.

Thermoelectric Freeze-Casting of Biopolymer Blends: Fabrication and Characterization of Large-Size Scaffolds for Nerve Tissue Engineering Applications.

Peripheral nerve injuries (PNIs) are detrimental to the quality of life of affected individuals. Patients are often left with life-long ailments that affect them physically and psychologically. Autologous nerve transplant is still the gold standard treatment for PNIs despite limited donor site and partial recovery of nerve functions. Nerve guidance conduits are used as a nerve graft substitute and are efficient for the repair of small nerve gaps but require further improvement for repairs exceeding 30 mm. Freeze-casting is an interesting fabrication method for the conception of scaffolds meant for nerve tissue engineering since the microstructure obtained comprises highly aligned micro-channels. The present work focuses on the fabrication and characterization of large scaffolds (35 mm length, 5 mm diameter) made of collagen/chitosan blends by freeze-casting via thermoelectric effect instead of traditional freezing solvents. As a freeze-casting microstructure reference, scaffolds made from pure collagen were used for comparison. Scaffolds were covalently crosslinked for better performance under load and laminins were further added to enhance cell interactions. Microstructural features of lamellar pores display an average aspect ratio of 0.67 ± 0.2 for all compositions. Longitudinally aligned micro-channels are reported as well as enhanced mechanical properties in traction under physiological-like conditions (37 °C, pH = 7.4) resulting from crosslinking treatment. Cell viability assays using a rat Schwann cell line derived from sciatic nerve (S16) indicate that scaffold cytocompatibility is similar between scaffolds made from collagen only and scaffolds made from collagen/chitosan blend with high collagen content. These results confirm that freeze-casting via thermoelectric effect is a reliable manufacturing strategy for the fabrication of biopolymer scaffolds for future peripheral nerve repair applications.

Three Potential Elements of Developing Nerve Guidance Conduit for Peripheral Nerve Regeneration

AbstractAutograft replaced by a nerve guidance conduit (NGC) is challenging in peripheral nerve injury because current NGC is still limited by precise conductivity and excellent biocompatibility in vivo, which influences the peripheral nerve repair even for a long lesion gap repair. Several particular elements have the potential function for nerve conductivity acceleration based on the traditional three factors of neural tissue engineering. The review aims to address three questions: 1) What is the superior factor for nerve conduction in the application? 2) How can a more conductive regenerative scaffold be constructed in vivo? 3) What is the next step in nerve regeneration for NGC? The bibliometrics analysis of NGC‐related references is adopted to acquire that the conductive material, manufacturing technology of neural scaffold, and electrical stimulation (ES) play essential roles in the acceleration of nerve conduction. This review visually analyses the research status and summarizes the main types of conductive materials, the manufacturing technologies of neural scaffolds, and the characteristics of ES. The viewpoints and outlook of developing NGC are also discussed in this review. The proposed three elements are expected to improve the nerve conduction of NGC in vivo and even address the dilemma of long‐distance peripheral nerve injury.

Generation and Repair of Postreplication Gaps in Escherichia coli.

When replication forks encounter template lesions, one result is lesion skipping, where the stalled DNA polymerase transiently stalls, disengages, and then reinitiates downstream to leave the lesion behind in a postreplication gap. Despite considerable attention in the 6 decades since postreplication gaps were discovered, the mechanisms by which postreplication gaps are generated and repaired remain highly enigmatic. This review focuses on postreplication gap generation and repair in the bacterium Escherichia coli. New information to address the frequency and mechanism of gap generation and new mechanisms for their resolution are described. There are a few instances where the formation of postreplication gaps appears to be programmed into particular genomic locations, where they are triggered by novel genomic elements.

The effect of ultrasound on bone healing across a bone gap, an experimental study of a delayed union model

The aim of the study is to determine whether ultrasound accelerates bone repair across a bone gap. To replicate the clinical situation of bone repair in a severe tibial fracture, such as Gustilo grade three, we designed an experimental model to determine whether ultrasound can promote bone healing in the presence of a bone gap. The effect of ultrasound on bone healing of a tibial bone gap held in an external fixator was studied. 60 New Zealand White rabbits were divided into four groups. In one group of 6 animals, a tibial osteotomy was closed or compressed and studied at six weeks (Comparative Group). In 3 groups of 18 animals each, a tibial bone gap was maintained and was untreated, treated with ultrasound or mock ultrasound (Control Group). The repair of the bone gaps was studied in 3 animals each at 2,4,6,8,10 and 12 weeks. Investigation was by histology, angiography, radiography and densitometry. Three of the 18 untreated group progressed to delayed union, compared with 4 in the ultrasound and 3 in the mock ultrasound group (Control Group). Statistical analysis showed no difference between the three groups. 5 of the 6 closed/compressed osteotomies (Comparative Group) united faster at 6 weeks. The healing pattern of the bone gap groups were similar. We recommend this as a delayed union model. We found no evidence that ultrasound accelerated bone healing, reduced the rate of delayed union or increased callus formation in this model of delayed union. This study simulates delayed union following a compound tibial fracture and has clinical relevance concerning treatment of a delay in union with ultrasound.

RecF protein targeting to postreplication (daughter strand) gaps I: DNA binding by RecF and RecFR.

In bacteria, the repair of post-replication gaps by homologous recombination requires the action of the recombination mediator proteins RecF, RecO and RecR. Whereas the role of the RecOR proteins to displace the single strand binding protein (SSB) and facilitate RecA loading is clear, how RecF mediates targeting of the system to appropriate sites remains enigmatic. The most prominent hypothesis relies on specific RecF binding to gap ends. To test this idea, we present a detailed examination of RecF and RecFR binding to more than 40 DNA substrates of varying length and structure. Neither RecF nor the RecFR complex exhibited specific DNA binding that can explain the targeting of RecF(R) to post-replication gaps. RecF(R) bound to dsDNA and ssDNA of sufficient length with similar facility. DNA binding was highly ATP-dependent. Most measured Kd values fell into a range of 60-180 nM. The addition of ssDNA extensions on duplex substrates to mimic gap ends or CPD lesions produces only subtle increases or decreases in RecF(R) affinity. Significant RecFR binding cooperativity was evident with many DNA substrates. The results indicate that RecF or RecFR targeting to post-replication gaps must rely on factors not yet identified, perhaps involving interactions with additional proteins.

Structure-forming CAG/CTG repeats interfere with gap repair to cause repeat expansions and chromosome breaks

Expanded CAG/CTG repeats are sites of DNA damage, leading to repeat length changes. Homologous recombination (HR) is one cause of repeat instability and we hypothesized that gap filling was a driver of repeat instability during HR. To test this, we developed an assay such that resection and ssDNA gap fill-in would occur across a (CAG)70 or (CTG)70 repeat tract. When the ssDNA template was a CTG sequence, there were increased repeat contractions and a fragile site was created leading to large-scale deletions. When the CTG sequence was on the resected strand, resection was inhibited, resulting in repeat expansions. Increased nucleolytic processing by deletion of Rad9, the ortholog of 53BP1, rescued repeat instability and chromosome breakage. Loss of Rad51 increased contractions implicating a protective role for Rad51 on ssDNA. Together, our work implicates structure-forming repeats as an impediment to resection and gap-filling which can lead to mutations and large-scale deletions.

PC36. Peripheral and Trigeminal Nerve Stimulation Improve Functional Outcomes of Nerve Recovery in a Rodent Forelimb Gap Repair Model

PC36. Peripheral and Trigeminal Nerve Stimulation Improve Functional Outcomes of Nerve Recovery in a Rodent Forelimb Gap Repair Model

Parental histone distribution and location of the replication obstacle at nascent strands control homologous recombination

The advance and stability of replication forks rely on a tight co-regulation of DNA synthesis and nucleosome assembly. We show that mutants affected in parental histone recycling are impaired in the recombinational repair of the single-stranded DNA gaps generated in response to DNA adducts that hamper replication, which are then filled in by translesion synthesis. These recombination defects are in part due to an excess of parental nucleosomes at the invaded strand that destabilizes the sister chromatid junction formed after strand invasion through a Srs2-dependent mechanism. In addition, we show that a dCas9∗/R-loop is more recombinogenic when the dCas9∗/DNA-RNA hybrid interferes with the lagging than with the leading strand, and this recombination is particularly sensitive to problems in the deposition of parental histones at the strand that contains the hindrance. Therefore, parental histone distribution and location of the replication obstacle at the lagging or leading strand regulate homologous recombination.

Effects of Altering Magnesium Metal Surfaces on Degradation In Vitro and In Vivo during Peripheral Nerve Regeneration.

In vivo use of biodegradable magnesium (Mg) metal can be plagued by too rapid a degradation rate that removes metal support before physiological function is repaired. To advance the use of Mg biomedical implants, the degradation rate may need to be adjusted. We previously demonstrated that pure Mg filaments used in a nerve repair scaffold were compatible with regenerating peripheral nerve tissues, reduced inflammation, and improved axonal numbers across a short-but not long-gap in sciatic nerves in rats. To determine if the repair of longer gaps would be improved by a slower Mg degradation rate, we tested, in vitro and in vivo, the effects of Mg filament polishing followed by anodization using plasma electrolytic oxidation (PEO) with non-toxic electrolytes. Polishing removed oxidation products from the surface of as-received (unpolished) filaments, exposed more Mg on the surface, produced a smoother surface, slowed in vitro Mg degradation over four weeks after immersion in a physiological solution, and improved attachment of cultured epithelial cells. In vivo, treated Mg filaments were used to repair longer (15 mm) injury gaps in adult rat sciatic nerves after placement inside hollow poly (caprolactone) nerve conduits. The addition of single Mg or control titanium filaments was compared to empty conduits (negative control) and isografts (nerves from donor rats, positive control). After six weeks in vivo, live animal imaging with micro computed tomography (micro-CT) showed that Mg metal degradation rates were slowed by polishing vs. as-received Mg, but not by anodization, which introduced greater variability. After 14 weeks in vivo, functional return was seen only with isograft controls. However, within Mg filament groups, the amount of axonal growth across the injury site was improved with slower Mg degradation rates. Thus, anodization slowed degradation in vitro but not in vivo, and degradation rates do affect nerve regeneration.

Chitosan conduits enriched with fibrin-collagen hydrogel with or without adipose-derived mesenchymal stem cells for the repair of 15-mm-long sciatic nerve defect.

Hollow conduits of natural or synthetic origins have shown acceptable regeneration results in short nerve gap repair; however, results are still not comparable with the current gold standard technique "autografts". Hollow conduits do not provide a successful regeneration outcome when it comes to critical nerve gap repair. Enriching the lumen of conduits with different extracellular materials and cells could provide a better biomimicry of the natural nerve regenerating environment and is expected to ameliorate the conduit performance. In this study, we evaluated nerve regeneration in vivo using hollow chitosan conduits or conduits enriched with fibrin-collagen hydrogels alone or with the further addition of adipose-derived mesenchymal stem cells in a 15 mm rat sciatic nerve transection model. Unexpected changes in the hydrogel consistency and structural stability in vivo led to a failure of nerve regeneration after 15 weeks. Nevertheless, the molecular assessment in the early regeneration phase (7, 14, and 28 days) has shown an upregulation of useful regenerative genes in hydrogel enriched conduits compared with the hollow ones. Hydrogels composed of fibrin-collagen were able to upregulate the expression of soluble NRG1, a growth factor that plays an important role in Schwann cell transdifferentiation. The further enrichment with adipose-derived mesenchymal stem cells has led to the upregulation of other important genes such as ErbB2, VEGF-A, BDNF, c-Jun, and ATF3.

Novel PVAMA/GelMA aerogels prepared by liquid-phase collection of photoinitiated polymerisation: injectable and flowable low-density 3D scaffolds for bone regeneration.

Nanofibrous scaffolds, which are morphologically/structurally similar to native extracellular matrix, are ideal biomaterials for tissue engineering and regenerative medicine. However, the use of traditional electrospinning techniques to produce three-dimensional (3D) nanofibrous scaffolds with desired structural properties presents difficulty. To address this challenge, we prepared a novel liquid-phase-collected photoinitiated polymerised aerogel 3D scaffold (LPPI-AG) using the thermally induced (nanofiber) self-aggregation method after liquid-phase electrospinning of the hydroxyapatite-doped methacrylated polyvinyl alcohol/methacrylated gelatine solution obtained by photoinitiated polymerisation. The fabricated aerogel scaffolds had a high porosity of approximately 99.01% ± 0.40% and an interconnected network structure with pore sizes ranging from submicron to ∼300 μm. The new aerogel rapidly became flowable when exposed to a solution, and it can fill gaps and repair gap edges effectively and be loaded with nutrients and growth factors that promote bone growth for bone tissue engineering. LPPI-AG scaffolds can considerably promote osteogenic differentiation of bone marrow mesenchymal stem cells in vitro. Furthermore, in vivo studies showed that the LPPI-AG scaffold significantly promoted bone formation in a mouse model of critical-size calvarial defects.

A Systematic Review and Meta-Analysis of Nerve Gap Repair: Comparative Effectiveness of Allografts, Autografts, and Conduits.

Ideal nerve repair involves tensionless direct repair, which may not be possible after resection. Bridging materials include nerve autograft, allograft, or conduit. This study aimed to perform a systematic literature review and meta-analysis to compare the meaningful recovery (MR) rates and postoperative complications following autograft, allograft, and conduit repairs in nerve gaps greater than 5 mm and less than 70 mm. A secondary aim was to perform a comparison of procedure costs. The search was conducted in MEDLINE from January of 1980 to March of 2020, following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Studies were included whether they reported nerve injury type, repair type, gap length, and outcomes for MR rates. Thirty-five studies with 1559 nerve repairs were identified. Overall MR for sensory and motor function was not significantly different between autograft ( n = 670) and allograft ( n = 711) across both short and long gaps. However, MR rates for autograft (81.6%) and allograft (87.1%) repairs were significantly higher compared with conduits (62.2%) ( P < 0.05) in sensory short gap repairs. Complication rates were comparable for autograft and allograft but higher for conduit with regard to pain. Analysis of costs showed that total costs for allograft repair were less than autograft in the inpatient setting and were comparable in the outpatient setting. Literature showed comparable rates of MR between autograft and allograft, regardless of gap length or nerve type. Furthermore, the rates of MR were lower in conduit repairs. In addition, the economic analysis performed demonstrates that allograft does not represent an increased economic burden compared with autograft.

POLQ seals post-replicative ssDNA gaps to maintain genome stability in BRCA-deficient cancer cells

POLQ is a key effector of DSB repair by microhomology-mediated end-joining (MMEJ) and is overexpressed in many cancers. POLQ inhibitors confer synthetic lethality in HR and Shieldin-deficient cancer cells, which has been proposed to reflect a critical dependence on the DSB repair pathway by MMEJ. Whether POLQ also operates independent of MMEJ remains unexplored. Here, we show that POLQ-deficient cells accumulate post-replicative ssDNA gaps upon BRCA1/2 loss or PARP inhibitor treatment. Biochemically, cooperation between POLQ helicase and polymerase activities promotes RPA displacement and ssDNA-gap fill-in, respectively. POLQ is also capable of microhomology-mediated gap skipping (MMGS), which generates deletions during gap repair that resemble the genomic scars prevalent in POLQ overexpressing cancers. Our findings implicate POLQ in mutagenic post-replicative gap sealing, which could drive genome evolution in cancer and whose loss places a critical dependency on HR for gap protection and repair and cellular viability.

Assessment of Human Epineural Conduit of Different Size Diameters on Efficacy of Nerve Regeneration and Functional Outcomes.

Different types of nerve conduits are used to bridge peripheral nerve gaps when a tension-free repair is unattainable. To best support nerve regeneration, naturally occurring conduits have been tested. Since allografts offer an unlimited source of epineurium, we have developed human epineural conduit (hEC) as a novel technology to bridge nerve gaps. Considering acellular properties, and lack of immunogenic response, epineurium-derived conduits represent an attractive material, when compared with nerve allografts that require systemic immunosuppression. In this study, we introduce the hEC as a novel naturally occurring material applied for repair of nerve gaps after trauma. We tested the application of hEC created from human sciatic nerve in the restoration of 20 mm sciatic nerve defects in the nude rat model. Four experimental groups were studied: group 1: no repair control (n = 6), group 2: autograft control (n = 6), group 3: matched diameter hEC (n = 6), and group 4: large diameter hEC (n = 6). Functional tests of toe-spread and pin prick were performed at 1, 3, 6, 9, 12 weeks after repair. At 12 weeks, nerve samples were collected for immunostaining of Laminin B, S-100, glial fibrillary acidic protein (GFAP), nerve growth factor (NGF), vascular endothelial growth factor (VEGF), von Willebrand factor, and histomorphometric analysis of myelin thickness, axonal density, fiber diameter, and percentage of the myelinated nerve fibers. Muscle samples were gathered for gastrocnemius muscle index (GMI) and muscle fiber area ratio measurements. Best functional recovery, as well as GMI, was revealed for the autograft group, and was comparable to the matched hEC group. Significant differences were revealed between matched and large hEC groups in expression of S100 (p = 0.0423), NGF (p = 0.269), VEGF (p = 0.0003) as well as in percentage of myelinated fibers (p < 0.001) and axonal density (p = 0.0003). We established the feasibility of hEC creation. The innovative method introduces an alternative technique to autograft repair of nerve defects.

Multifaceted polymeric nerve guidance conduits with distinctive double-layered architecture and plasma-induced inner chemistry gradient for the repair of critical-sized defects

Despite tissue engineering advances, current nerve guidance conduits (NGCs) are still failing in repairing critical-sized defects. This study aims, therefore, at tackling large nerve gaps (2 cm) by designing NGCs possessing refined physicochemical properties enhancing the activity of Schwann cells (SCs) that support nerve regeneration over long distances. As such, a combinatorial strategy adopting novel plasma-induced surface chemistry and architectural heterogeneity was considered. A mechanically suitable copolymer (Polyactive®) was electrospun to produce nanofibrous NGCs mimicking the extracellular matrix. An innovative seamless double-layered architecture consisting of an inner wall comprised of bundles of aligned fibers with intercalated random fibers and an outer wall fully composed of random fibers was conceived to synergistically provide cell guidance cues and sufficient nutrient inflow. NGCs were subjected to argon plasma treatments using a dielectric barrier discharge (DBD) and a plasma jet (PJ). Surface chemical changes were examined by advanced X-ray photoelectron spectroscopy (XPS) micro-mappings. The DBD homogeneously increased the surface oxygen content from 17 % to 28 % on the inner wall. The PJ created a gradient chemistry throughout the inner wall with an oxygen content gradually increasing from 21 % to 30 %. In vitro studies revealed enhanced primary SC adhesion, elongation and proliferation on plasma-treated NGCs. A cell gradient was observed on the PJ-treated NGCs thus underlining the favorable oxygen gradient in promoting cell chemotaxis. A gradual change from circular to highly elongated SC morphologies mimicking the bands of Büngner was visualized along the gradient. Overall, plasma-treated NGCs are promising candidates paving the way towards critical nerve gap repair.

The success of biomaterial-based tissue engineering strategies for peripheral nerve regeneration.

Peripheral nerve injury is a clinically common injury that causes sensory dysfunction and locomotor system degeneration, which seriously affects the quality of the patients' daily life. Long gapped defects in large nerve are difficult to repair via surgery and limited donor source of autologous nerve greatly challenges the successful nerve repair by transplantation. Significantly, remarkable progress has been made in repairing the peripheral nerve injury using artificial nerve grafts and a variety of products for peripheral nerve repair have emerged been approved globally in recent years. The raw materials of these commercial products includes natural/synthetic polymers, extracellular matrix. Despite a lot of effort, the desirable functional recovery still remains great challenges in long gapped nerve defects. Thus this review discusses the recent development of tissue engineering products for peripheral nerve repair and the design of bionic grafts improving the local microenvironment for accelerating nerve regeneration against locomotor disorder, which may provide potential strategies for the repair of long gaps or thick nerve defects by multifunctional biomaterials.

Preparation and Characterization of Nickel-Based Brazing Powder and Paste for Wide Gap Repair on IN738 Alloy

Preparation and Characterization of Nickel-Based Brazing Powder and Paste for Wide Gap Repair on IN738 Alloy

Unexpected new insights into DNA clamp loaders: Eukaryotic clamp loaders contain a second DNA site for recessed 5' ends that facilitates repair and signals DNA damage: Eukaryotic clamp loaders contain a second DNA site for recessed 5' ends that facilitates repair and signals DNA damage.

Clamp loaders are pentameric AAA+ assemblies that use ATP to open and close circular DNA sliding clamps around DNA. Clamp loaders show homology in all organisms, from bacteria to human. The eukaryotic PCNA clamp is loaded onto 3' primed DNA by the replication factor C (RFC) hetero-pentameric clamp loader. Eukaryotes also have three alternative RFC-like clamp loaders (RLCs) in which the Rfc1 subunit is substituted by another protein. One of these is the yeast Rad24-RFC (Rad17-RFC in human) that loads a 9-1-1 heterotrimer clamp onto a recessed 5' end of DNA. Recent structural studies of Rad24-RFC have discovered an unexpected 5' DNA binding site on the outside of the clamp loader and reveal how a 5' end can be utilized for loading the 9-1-1 clamp onto DNA. In light of these results, new studies reveal that RFC also contains a 5' DNA binding site, which functions in gap repair. These studies also reveal many new features of clamp loaders. As reviewed herein, these recent studies together have transformed our view of the clamp loader mechanism.

Changes in the architecture and abundance of replication intermediates delineate the chronology of DNA damage tolerance pathways at UV-stalled replication forks in human cells.

DNA lesions in S phase threaten genome stability. The DNA damage tolerance (DDT) pathways overcome these obstacles and allow completion of DNA synthesis by the use of specialised translesion (TLS) DNA polymerases or through recombination-related processes. However, how these mechanisms coordinate with each other and with bulk replication remains elusive. To address these issues, we monitored the variation of replication intermediate architecture in response to ultraviolet irradiation using transmission electron microscopy. We show that the TLS polymerase η, able to accurately bypass the major UV lesion and mutated in the skin cancer-prone xeroderma pigmentosum variant (XPV) syndrome, acts at the replication fork to resolve uncoupling and prevent post-replicative gap accumulation. Repriming occurs as a compensatory mechanism when this on-the-fly mechanism cannot operate, and is therefore predominant in XPV cells. Interestingly, our data support a recombination-independent function of RAD51 at the replication fork to sustain repriming. Finally, we provide evidence for the post-replicative commitment of recombination in gap repair and for pioneering observations of in vivo recombination intermediates. Altogether, we propose a chronology of UV damage tolerance in human cells that highlights the key role of polη in shaping this response and ensuring the continuity of DNA synthesis.