Translesion and Repair DNA Polymerases: Diverse Structure and Mechanism.

The number of DNA polymerases identified in each organism has mushroomed in the past two decades. Most newly found DNA polymerases specialize in translesion synthesis and DNA repair instead of replication. Although intrinsic error rates are higher for translesion and repair polymerases than for replicative polymerases, the specialized polymerases increase genome stability and reduce tumorigenesis. Reflecting the numerous types of DNA lesions and variations of broken DNA ends, translesion and repair polymerases differ in structure, mechanism, and function. Here, we review the unique and general features of polymerases specialized in lesion bypass, as well as in gap-filling and end-joining synthesis.

Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses.

To guide the design of immunotherapy strategies for patients with early stage lung tumors, we developed a multiscale immune profiling strategy to map the immune landscape of early lung adenocarcinoma lesions to search for tumor-driven immune changes. Utilizing a barcoding method that allows a simultaneous single-cell analysis of the tumor, non-involved lung, and blood cells, we provide a detailed immune cell atlas of early lung tumors. We show that stage I lung adenocarcinoma lesions already harbor significantly altered T cell and NK cell compartments. Moreover, we identified changes in tumor-infiltrating myeloid cell (TIM) subsets that likely compromise anti-tumor T cell immunity. Paired single-cell analyses thus offer valuable knowledge of tumor-driven immune changes, providing a powerful tool for the rational design of immune therapies. VIDEO ABSTRACT.

The ubiquitin ligase RFWD3 is required for translesion DNA synthesis.

Lesions on DNA uncouple DNA synthesis from the replisome, generating stretches of unreplicated single-stranded DNA (ssDNA) behind the replication fork. These ssDNA gaps need to be filled in to complete DNA duplication. Gap-filling synthesis involves either translesion DNA synthesis (TLS) or template switching (TS). Controlling these processes, ubiquitylated PCNA recruits many proteins that dictate pathway choice, but the enzymes regulating PCNA ubiquitylation in vertebrates remain poorly defined. Here we report that the E3 ubiquitin ligase RFWD3 promotes ubiquitylation of proteins on ssDNA. The absence of RFWD3 leads to a profound defect in recruitment of key repair and signaling factors to damaged chromatin. As a result, PCNA ubiquitylation is inhibited without RFWD3, and TLS across different DNA lesions is drastically impaired. We propose that RFWD3 is an essential coordinator of the response to ssDNA gaps, where it promotes ubiquitylation to drive recruitment of effectors of PCNA ubiquitylation and DNA damage bypass.

Replication-Coupled DNA-Protein Crosslink Repair by SPRTN and the Proteasome in Xenopus Egg Extracts.

DNA-protein crosslinks (DPCs) are bulky lesions that interfere with DNA metabolism and therefore threaten genomic integrity. Recent studies implicate the metalloprotease SPRTN in S phase removal of DPCs, but how SPRTN is targeted to DPCs during DNA replication is unknown. Using Xenopus egg extracts that recapitulate replication-coupled DPC proteolysis, we show that DPCs can be degraded by SPRTN or the proteasome, which act as independent DPC proteases. Proteasome recruitment requires DPC polyubiquitylation, which is partially dependent on the ubiquitin ligase activity of TRAIP. In contrast, SPRTN-mediated DPC degradation does not require DPC polyubiquitylation but instead depends on nascent strand extension to within a few nucleotides of the lesion, implying that polymerase stalling at the DPC activates SPRTN on both leading and lagging strand templates. Our results demonstrate that SPRTN and proteasome activities are coupled to DNA replication by distinct mechanisms that promote replication across immovable protein barriers.

DNA polymerase zeta contributes to heterochromatin replication to prevent genome instability.

The DNA polymerase zeta (Polζ) plays a critical role in bypassing DNA damage. REV3L, the catalytic subunit of Polζ, is also essential in mouse embryonic development and cell proliferation for reasons that remain incompletely understood. In this study, we reveal that REV3L protein interacts with heterochromatin components including repressive histone marks and localizes in pericentromeric regions through direct interaction with HP1 dimer. We demonstrate that Polζ/REV3L ensures progression of replication forks through difficult-to-replicate pericentromeric heterochromatin, thereby preventing spontaneous chromosome break formation. We also find that Rev3l-deficient cells are compromised in the repair of heterochromatin-associated double-stranded breaks, eliciting deletions in late-replicating regions. Lack of REV3L leads to further consequences that may be ascribed to heterochromatin replication and repair-associated functions of Polζ, with a disruption of the temporal replication program at specific loci. This is correlated with changes in epigenetic landscape and transcriptional control of developmentally regulated genes. These results reveal a new function of Polζ in preventing chromosome instability during replication of heterochromatic regions.

Host translesion polymerases are required for viral genome integrity.

Human cells encode up to 15 DNA polymerases with specialized functions in chromosomal DNA synthesis and damage repair. In contrast, complex DNA viruses, such as those of the herpesviridae family, encode a single B-family DNA polymerase. This disparity raises the possibility that DNA viruses may rely on host polymerases for synthesis through complex DNA geometries. We tested the importance of error-prone Y-family polymerases involved in translesion synthesis (TLS) to human cytomegalovirus (HCMV) infection. We find most Y-family polymerases involved in the nucleotide insertion and bypass of lesions restrict HCMV genome synthesis and replication. In contrast, other TLS polymerases, such as the polymerase ζ complex, which extends past lesions, was required for optimal genome synthesis and replication. Depletion of either the polζ complex or the suite of insertion polymerases demonstrate that TLS polymerases suppress the frequency of viral genome rearrangements, particularly at GC-rich sites and repeat sequences. Moreover, while distinct from HCMV, replication of the related herpes simplex virus type 1 is impacted by host TLS polymerases, suggesting a broader requirement for host polymerases for DNA virus replication. These findings reveal an unexpected role for host DNA polymerases in ensuring viral genome stability.

Binding of the nuclear ribonucleoprotein family member FUS to RNA prevents R-loop RNA:DNA hybrid structures.

The protein FUS (FUSed in sarcoma) is a metazoan RNA-binding protein that influences RNA production by all three nuclear polymerases. FUS also binds nascent transcripts, RNA processing factors, RNA polymerases, and transcription machinery. Here, we explored the role of FUS binding interactions for activity during transcription. In vitro run-off transcription assays revealed FUS-enhanced RNA produced by a non-eukaryote polymerase. The activity also reduced the formation of R-loops between RNA products and their DNA template. Analysis by domain mutation and deletion indicated RNA-binding was required for activity. We interpret that FUS binds and sequesters nascent transcripts to prevent R-loops from forming with nearby DNA. DRIP-seq analysis showed that a knockdown of FUS increased R-loop enrichment near expressed genes. Prevention of R-loops by FUS binding to nascent transcripts has the potential to affect transcription by any RNA polymerase, highlighting the broad impact FUS can have on RNA metabolism in cells and disease.

SCAI promotes error-free repair of DNA interstrand crosslinks via the Fanconi anemia pathway.

DNA interstrand crosslinks (ICLs) are cytotoxic lesions that threaten genome integrity. The Fanconi anemia (FA) pathway orchestrates ICL repair during DNA replication, with ubiquitylated FANCI-FANCD2 (ID2) marking the activation step that triggers incisions on DNA to unhook the ICL. Restoration of intact DNA requires the coordinated actions of polymerase ζ (Polζ)-mediated translesion synthesis (TLS) and homologous recombination (HR). While the proteins mediating FA pathway activation have been well characterized, the effectors regulating repair pathway choice to promote error-free ICL resolution remain poorly defined. Here, we uncover an indispensable role of SCAI in ensuring error-free ICL repair upon activation of the FA pathway. We show that SCAI forms a complex with Polζ and localizes to ICLs during DNA replication. SCAI-deficient cells are exquisitely sensitive to ICL-inducing drugs and display major hallmarks of FA gene inactivation. In the absence of SCAI, HR-mediated ICL repair is defective, and breaks are instead re-ligated by polymerase θ-dependent microhomology-mediated end-joining, generating deletions spanning the ICL site and radial chromosomes. Our work establishes SCAI as an integral FA pathway component, acting at the interface between TLS and HR to promote error-free ICL repair.

PrimPol Is Required for Replicative Tolerance of G Quadruplexes in Vertebrate Cells.

G quadruplexes (G4s) can present potent blocks to DNA replication. Accurate and timely replication of G4s in vertebrates requires multiple specialized DNA helicases and polymerases to prevent genetic and epigenetic instability. Here we report that PrimPol, a recently described primase-polymerase (PrimPol), plays a crucial role in the bypass of leading strand G4 structures. While PrimPol is unable to directly replicate G4s, it can bind and reprime downstream of these structures. Disruption of either the catalytic activity or zinc-finger of PrimPol results in extreme G4-dependent epigenetic instability at the BU-1 locus in avian DT40 cells, indicative of extensive uncoupling of the replicative helicase and polymerase. Together, these observations implicate PrimPol in promoting restart of DNA synthesis downstream of, but closely coupled to, G4 replication impediments.

Extraction of Moso Bamboo Parameters Based on the Combination of ALS and TLS Point Cloud Data.

Extracting moso bamboo parameters from single-source point cloud data has limitations. In this article, a new approach for extracting moso bamboo parameters using airborne laser scanning (ALS) and terrestrial laser scanning (TLS) point cloud data is proposed. Using the field-surveyed coordinates of plot corner points and the Iterative Closest Point (ICP) algorithm, the ALS and TLS point clouds were aligned. Considering the difference in point distribution of ALS, TLS, and the merged point cloud, individual bamboo plants were segmented from the ALS point cloud using the point cloud segmentation (PCS) algorithm, and individual bamboo plants were segmented from the TLS and the merged point cloud using the comparative shortest-path (CSP) method. The cylinder fitting method was used to estimate the diameter at breast height (DBH) of the segmented bamboo plants. The accuracy was calculated by comparing the bamboo parameter values extracted by the above methods with reference data in three sample plots. The comparison results showed that by using the merged data, the detection rate of moso bamboo plants could reach up to 97.30%; the R2 of the estimated bamboo height was increased to above 0.96, and the root mean square error (RMSE) decreased from 1.14 m at most to a range of 0.35-0.48 m, while the R2 of the DBH fit was increased to a range of 0.97-0.99, and the RMSE decreased from 0.004 m at most to a range of 0.001-0.003 m. The accuracy of moso bamboo parameter extraction was significantly improved by using the merged point cloud data.

Automated Phenotypic Trait Extraction for Rice Plant Using Terrestrial Laser Scanning Data.

To quickly obtain rice plant phenotypic traits, this study put forward the computational process of six rice phenotype features (e.g., crown diameter, perimeter of stem, plant height, surface area, volume, and projected leaf area) using terrestrial laser scanning (TLS) data, and proposed the extraction method for the tiller number of rice plants. Specifically, for the first time, we designed and developed an automated phenotype extraction tool for rice plants with a three-layer architecture based on the PyQt5 framework and Open3D library. The results show that the linear coefficients of determination (R2) between the measured values and the extracted values marked a better reliability among the selected four verification features. The root mean square error (RMSE) of crown diameter, perimeter of stem, and plant height is stable at the centimeter level, and that of the tiller number is as low as 1.63. The relative root mean squared error (RRMSE) of crown diameter, plant height, and tiller number stays within 10%, and that of perimeter of stem is 18.29%. In addition, the user-friendly automatic extraction tool can efficiently extract the phenotypic features of rice plant, and provide a convenient tool for quickly gaining phenotypic trait features of rice plant point clouds. However, the comparison and verification of phenotype feature extraction results supported by more rice plant sample data, as well as the improvement of accuracy algorithms, remain as the focus of our future research. The study can offer a reference for crop phenotype extraction using 3D point clouds.

Assessment of Panorama Photogrammetry as a Tool for Long-Range Deformation Monitoring.

This study investigates panorama photogrammetry (PPh) as a potential method to collect massive 3D information for long-range deformation monitoring. Particularly, this study focuses on areas with measuring restrictions, i.e., inaccessible objects and distances above 0.6 km. Under these particular conditions, geodetic techniques based on Electromagnetic Distance Meters (EDMs) or Total Stations (TSs) can provide coordinates with a precision better than 1 cm, but only for a limited number of discrete points. For mass capture, Terrestrial Laser Scanning (TLS) is normally the preferred solution, but long-range instruments are expensive, and drawbacks such as weak return signals and non-automatic target recognition appear. As an alternative, PPh is investigated in the well-controlled area of La Muela in Cortes de Pallas, where images are automatically captured from geodetic pillars using a GigaPan device, processed, and then rigorously compared to TLS point clouds. The results obtained after integrating both techniques into a high-accuracy geodetic reference frame show that PPh and TLS provide similar precision to within approximately 4 cm in the range of 0.6-1.0 km. Therefore, considering cost-effectiveness and ease of use, the proposed method can be considered a low-cost alternative to TLS for long-range deformation monitoring.

Prognostic value of tertiary lymphoid structures (TLS) in digestive system cancers: a systematic review and meta-analysis.

BACKGROUND: Existing literature suggests that tertiary lymphatic structure (TLS) is associated with the progression of cancer. However, the prognostic role of TLS in digestive system cancers remains controversial. This meta-analysis aims to synthesize currently available evidence in the association between TLS and the survival of digestive system cancers. METHODS: We systematically searched three digital databases (PubMed, Embase, Web of Science) for articles published from database inception to December 23, 2022. Study selection criteria are based on PECO framework: P (population: patients with digestive system cancers), E (exposure: presence of TLS), C (comparator: absence of TLS), O (outcome: overall survival, OS; recurrence-free survival, RFS; disease-free survival, DFS). The Quality in Prognostic Studies (QUIPS) tool was used to assess risk of bias for included studies. The study protocol was registered with PROSPERO (CRD42023416307). RESULTS: A total of 25 studies with 6910 patients were included into the final meta-analysis. Random-effects models revealed that the absence of TLS was associated with compromised OS, RFS, and DFS of digestive system cancers, with pooled hazard ratios (HRs) of 1.74 (95% CI: 1.50-2.03), 1.96 (95% CI: 1.58-2.44), and 1.81 (95% CI: 1.49-2.19), respectively. Subgroup analyses disclosed a stronger TLS-survival association for pancreatic cancer, compared with other digestive system cancers. CONCLUSION: TLS may be of prognostic significance for digestive system cancers. More original studies are needed to further corroborate this finding.

Does surgeon sex and anthropometry matter for tool usability in traditional laparoscopic surgery? A systematic review and meta-analysis.

INTRODUCTION: Hand size, strength, and stature all impact a surgeon's ability to perform Traditional Laparoscopic Surgery (TLS) comfortably and effectively. This is due to limitations in instrument and operating room design. This article aims to review performance, pain, and tool usability data based on biological sex and anthropometry. METHODS: PubMed, Embase, and Cochrane databases were searched in May 2023. Retrieved articles were screened based on whether a full-text, English article was available in which original results were stratified by biological sex or physical proportions. Article quality was discussed using the Mixed Methods Appraisal Tool (MMAT). Data were summarized in three main themes: task performance, physical discomfort, and tool usability and fit. Task completion times, pain prevalence, and grip style results between male and female surgeons formed three meta-analyses. RESULTS: A total of 1354 articles were sourced, and 54 were deemed suitable for inclusion. The collated results showed that female participants, predominantly novices, took 2.6-30.1 s longer to perform standardized laparoscopic tasks. Female surgeons reported pain at double the frequency of their male colleagues. Female surgeons and those with a smaller glove size were consistently more likely to report difficulty and require modified (potentially suboptimal) grip techniques with standard laparoscopic tools. CONCLUSIONS: The pain and stress reported by female or small-handed surgeons when using laparoscopic tools demonstrates the need for currently available instrument handles, including robotic hand controls, to become more size-inclusive. However, this study is limited by reporting bias and inconsistencies; furthermore, most data was collected in a simulated environment. Additional research into how anthropometric tool design impacts the live operating performance of experienced female surgeons would further inform this area of investigation.

BRT: An Efficient and Scalable Blockchain-Based Revocation Transparency System for TLS Connections.

Log-based public key infrastructure(PKI) refers to a robust class of CA-attack-resilient PKI that enhance transparency and accountability in the certificate revocation and issuance process by compelling certificate authorities (CAs) to submit revocations to publicly and verifiably accessible logs. However, log-based PKIs suffer from a reliance on centralized and consistent sources of information, rendering them susceptible to split-world attacks, and they regrettably fail to provide adequate incentives for recording or monitoring CA behavior. Blockchain-based PKIs address these limitations by enabling decentralized log audits through automated financial incentives. However, they continue to face challenges in developing a scalable revocation mechanism suited for lightweight clients. In this paper, we introduce BRT, a scalable blockchain-based system for certificate and revocation transparency. It serves to log, audit, and validate the status of certificates within the transport layer security (TLS)/secure sockets layer(SSL) PKI domain. We designed an audit-on-chain framework, coupled with an off-chain storage/computation system, to enhance the efficiency of BRT when operating in a blockchain environment. By implementing a blockchain-based prototype, we demonstrate that BRT achieves storage-efficient log recording with a peak compression rate reaching 8%, cost-effective log updates for large-scale certificates, and near-instantaneous revocation checks for users.

Non-Destructive Measurements for 3D Modeling and Monitoring of Large Buildings Using Terrestrial Laser Scanning and Unmanned Aerial Systems.

Along with the development and improvement of measuring technologies and techniques in recent times, new methods have appeared to model and monitor the behavior of land and constructions over time. The main purpose of this research was to develop a new methodology to model and monitor large buildings in a non-invasive way. The methods proposed in this research are non-destructive and can be used to monitor the behavior of buildings over time. A method of comparing point clouds obtained using terrestrial laser scanning combined with aerial photogrammetric methods was used in this study. The advantages and disadvantages of using non-destructive measurement techniques over the classic methods were also analyzed. With a building located in the University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca campus as a case study and with the help of the proposed methods, the deformations over time of the facades of that building were determined. As one of the main conclusions of this case study, it can be stated that the proposed methods are adequate to model and monitor the behavior of constructions over time, ensuring a satisfactory degree of precision and accuracy. The methodology can be successfully applied to other similar projects.

TLS Protocol Analysis Using IoTST-An IoT Benchmark Based on Scheduler Traces.

The Internet of Things (IoT) envisions billions of everyday objects sharing information. As new devices, applications and communication protocols are proposed for the IoT context, their evaluation, comparison, tuning and optimization become crucial and raise the need for a proper benchmark. While edge computing aims to provide network efficiency by distributed computing, this article moves towards sensor nodes in order to explore efficiency in the local processing performed by IoT devices. We present IoTST, a benchmark based on per-processor synchronized stack traces with the isolation and precise determination of the introduced overhead. It produces comparable detailed results and assists in determining the configuration that has the best processing operating point so that energy efficiency can also be considered. On benchmarking applications which involve network communication, the results can be influenced by the constant changes that occur in the state of the network. In order to circumvent such problems, different considerations or assumptions were used in the generalization experiments and the comparison to similar studies. To present IoTST usage on a real problem, we implemented it on a commercial off the-shelf (COTS) device and benchmarked a communication protocol, producing comparable results that are unaffected by the current network state. We evaluated different Transport-Layer Security (TLS) 1.3 handshake cipher suites at different frequencies and with various numbers of cores. Among other results, we could determine that the selection of a specific suite (Curve25519 and RSA) can improve the computation latency by up to four times over the worst suite candidate (P-256 and ECDSA), while both providing the same security level (128 bits).

Multisensor and Multiscale Data Integration Method of TLS and GPR for Three-Dimensional Detailed Virtual Reconstruction.

Integrated TLS and GPR data can provide multisensor and multiscale spatial data for the comprehensive identification and analysis of surficial and subsurface information, but a reliable systematic methodology associated with data integration of TLS and GPR is still scarce. The aim of this research is to develop a methodology for the data integration of TLS and GPR for detailed, three-dimensional (3D) virtual reconstruction. GPR data and high-precision geographical coordinates at the centimeter level were simultaneously gathered using the GPR system and the Global Navigation Satellite System (GNSS) signal receiver. A time synchronization algorithm was proposed to combine each trace of the GPR data with its position information. In view of the improved propagation model of electromagnetic waves, the GPR data were transformed into dense point clouds in the geodetic coordinate system. Finally, the TLS-based and GPR-derived point clouds were merged into a single point cloud dataset using coordinate transformation. In addition, TLS and GPR (250 MHz and 500 MHz antenna) surveys were conducted in the Litang fault to assess the feasibility and overall accuracy of the proposed methodology. The 3D realistic surface and subsurface geometry of the fault scarp were displayed using the integration data of TLS and GPR. A total of 40 common points between the TLS-based and GPR-derived point clouds were implemented to assess the data fusion accuracy. The difference values in the x and y directions were relatively stable within 2 cm, while the difference values in the z direction had an abrupt fluctuation and the maximum values could be up to 5 cm. The standard deviations (STD) of the common points between the TLS-based and GPR-derived point clouds were 0.9 cm, 0.8 cm, and 2.9 cm. Based on the difference values and the STD in the x, y, and z directions, the field experimental results demonstrate that the GPR-derived point clouds exhibit good consistency with the TLS-based point clouds. Furthermore, this study offers a good future prospect for the integration method of TLS and GPR for comprehensive interpretation and analysis of the surficial and subsurface information in many fields, such as archaeology, urban infrastructure detection, geological investigation, and other fields.

Remarks on Geomatics Measurement Methods Focused on Forestry Inventory.

This contribution focuses on a comparison of modern geomatics technologies for the derivation of growth parameters in forest management. The present text summarizes the results of our measurements over the last five years. As a case project, a mountain spruce forest with planned forest logging was selected. In this locality, terrestrial laser scanning (TLS) and terrestrial and drone close-range photogrammetry were experimentally used, as was the use of PLS mobile technology (personal laser scanning) and ALS (aerial laser scanning). Results from the data joining, usability, and economics of all technologies for forest management and ecology were discussed. ALS is expensive for small areas and the results were not suitable for a detailed parameter derivation. The RPAS (remotely piloted aircraft systems, known as "drones") method of data acquisition combines the benefits of close-range and aerial photogrammetry. If the approximate height and number of the trees are known, one can approximately calculate the extracted cubage of wood mass before forest logging. The use of conventional terrestrial close-range photogrammetry and TLS proved to be inappropriate and practically unusable in our case, and also in standard forestry practice after consultation with forestry workers. On the other hand, the use of PLS is very simple and allows you to quickly define ordered parameters and further calculate, for example, the cubic volume of wood stockpiles. The results from our research into forestry show that drones can be used to estimate quantities (wood cubature) and inspect the health status of spruce forests, However, PLS seems, nowadays, to be the best solution in forest management for deriving forest parameters. Our results are mainly oriented to practice and in no way diminish the general research in this area.

ALS mutations in TLS/FUS disrupt target gene expression.

Amyotrophic lateral sclerosis (ALS) is caused by mutations in a number of genes, including the gene encoding the RNA/DNA-binding protein translocated in liposarcoma or fused in sarcoma (TLS/FUS or FUS). Previously, we identified a number of FUS target genes, among them MECP2. To investigate how ALS mutations in FUS might impact target gene expression, we examined the effects of several FUS derivatives harboring ALS mutations, such as R521C (FUS(C)), on MECP2 expression in transfected human U87 cells. Strikingly, FUS(C) and other mutants not only altered MECP2 alternative splicing but also markedly increased mRNA abundance, which we show resulted from sharply elevated stability. Paradoxically, however, MeCP2 protein levels were significantly reduced in cells expressing ALS mutant derivatives. Providing a parsimonious explanation for these results, biochemical fractionation and in vivo localization studies revealed that MECP2 mRNA colocalized with cytoplasmic FUS(C) in insoluble aggregates, which are characteristic of ALS mutant proteins. Together, our results establish that ALS mutations in FUS can strongly impact target gene expression, reflecting a dominant effect of FUS-containing aggregates.