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Radiation mapping has attracted widespread research attention and increased public concerns on environmental monitoring. Regarding materials and their configurations, radiation detectors have been developed to identify the position and strength of the radioactive sources. However, due to the complex mechanisms of radiation-matter interaction and data limitation, high-performance and low-cost radiation mapping is still challenging. Here, we present a radiation mapping framework using Tetris-inspired detector pixels. Applying inter-pixel padding for enhancing contrast between pixels and neural networks trained with Monte Carlo (MC) simulation data, a detector with as few as four pixels can achieve high-resolution directional prediction. A moving detector with Maximum a Posteriori (MAP) further achieved radiation position localization. Field testing with a simple detector has verified the capability of the MAP method for source localization. Our framework offers an avenue for high-quality radiation mapping with simple detector configurations and is anticipated to be deployed for real-world radiation detection.

PURPOSE: Tissue factor is highly expressed in cervical carcinoma and can be targeted by tisotumab vedotin (TV), an antibody-drug conjugate. This phase Ib/II study evaluated TV in combination with bevacizumab, pembrolizumab, or carboplatin for recurrent or metastatic cervical cancer (r/mCC). METHODS: This open-label, multicenter study (ClinicalTrials.gov identifier: NCT03786081) included dose-escalation arms that assessed dose-limiting toxicities (DLTs) and identified the recommended phase II dose (RP2D) of TV in combination with bevacizumab (arm A), pembrolizumab (arm B), or carboplatin (arm C). The dose-expansion arms evaluated TV antitumor activity and safety at RP2D in combination with carboplatin as first-line (1L) treatment (arm D) or with pembrolizumab as 1L (arm E) or second-/third-line (2L/3L) treatment (arm F). The primary end point of dose expansion was objective response rate (ORR). RESULTS: A total of 142 patients were enrolled. In dose escalation (n = 41), no DLTs were observed; the RP2D was TV 2 mg/kg plus bevacizumab 15 mg/kg on day 1 once every 3 weeks, pembrolizumab 200 mg on day 1 once every 3 weeks, or carboplatin AUC 5 on day 1 once every 3 weeks. In dose expansion (n = 101), the ORR was 54.5% (n/N, 18/33; 95% CI, 36.4 to 71.9) with 1L TV + carboplatin (arm D), 40.6% (n/N, 13/32; 95% CI, 23.7 to 59.4) with 1L TV + pembrolizumab (arm E), and 35.3% (12/34; 19.7 to 53.5) with 2L/3L TV + pembrolizumab (arm F). The median duration of response was 8.6 months, not reached, and 14.1 months, in arms D, E, and F, respectively. Grade ≥3 adverse events (≥15%) were anemia, diarrhea, nausea, and thrombocytopenia in arm D and anemia in arm F (none ≥15%, arm E). CONCLUSION: TV in combination with bevacizumab, carboplatin, or pembrolizumab demonstrated manageable safety and encouraging antitumor activity in treatment-naive and previously treated r/mCC.

PEAK pseudokinases are molecular scaffolds which dimerize to regulate cell migration, morphology, and proliferation, as well as cancer progression. The mechanistic role dimerization plays in PEAK scaffolding remains unclear, as there are no structures of PEAKs in complex with their interactors. Here, we report the cryo-EM structure of dimeric PEAK3 in complex with an endogenous 14-3-3 heterodimer. Our structure reveals an asymmetric binding mode between PEAK3 and 14-3-3 stabilized by one pseudokinase domain and the SHED domain of the PEAK3 dimer. The binding interface contains a canonical phosphosite-dependent primary interaction and a unique secondary interaction not observed in previous structures of 14-3-3/client complexes. Additionally, we show that PKD regulates PEAK3/14-3-3 binding, which when prevented leads to PEAK3 nuclear enrichment and distinct protein-protein interactions. Altogether, our data demonstrate that PEAK3 dimerization forms an unusual secondary interface for 14-3-3 binding, facilitating 14-3-3 regulation of PEAK3 localization and interactome diversity.

Knowledge of the three-dimensional movement patterns of elasmobranchs is vital to understand their ecological roles and exposure to anthropogenic pressures. To date, comparative studies among species at global scales have mostly focused on horizontal movements. Our study addresses the knowledge gap of vertical movements by compiling the first global synthesis of vertical habitat use by elasmobranchs from data obtained by deployment of 989 biotelemetry tags on 38 elasmobranch species. Elasmobranchs displayed high intra- and interspecific variability in vertical movement patterns. Substantial vertical overlap was observed for many epipelagic elasmobranchs, indicating an increased likelihood to display spatial overlap, biologically interact, and share similar risk to anthropogenic threats that vary on a vertical gradient. We highlight the critical next steps toward incorporating vertical movement into global management and monitoring strategies for elasmobranchs, emphasizing the need to address geographic and taxonomic biases in deployments and to concurrently consider both horizontal and vertical movements.

Remote sensing observations from satellites and global biogeochemical models have combined to revolutionize the study of ocean biogeochemical cycling, but comparing the two data streams to each other and across time remains challenging due to the strong spatial-temporal structuring of the ocean. Here, we show that the Wasserstein distance provides a powerful metric for harnessing these structured datasets for better marine ecosystem and climate predictions. The Wasserstein distance complements commonly used point-wise difference methods such as the root-mean-squared error, by quantifying differences in terms of spatial displacement in addition to magnitude. As a test case, we consider chlorophyll (a key indicator of phytoplankton biomass) in the northeast Pacific Ocean, obtained from model simulations, in situ measurements, and satellite observations. We focus on two main applications: (i) comparing model predictions with satellite observations, and (ii) temporal evolution of chlorophyll both seasonally and over longer time frames. The Wasserstein distance successfully isolates temporal and depth variability and quantifies shifts in biogeochemical province boundaries. It also exposes relevant temporal trends in satellite chlorophyll consistent with climate change predictions. Our study shows that optimal transport vectors underlying the Wasserstein distance provide a novel visualization tool for testing models and better understanding temporal dynamics in the ocean.

Current epidemics, such as AIDS or flu, and the emergence of new threatening pathogens, such as the one causing the current coronavirus disease 2019 (COVID-19) pandemic, represent major global health challenges. While vaccination is an important part of the arsenal to counter the spread of viral diseases, it presents limitations and needs to be complemented by efficient therapeutic solutions. Intricate knowledge of host-pathogen interactions is a powerful tool to identify host-dependent vulnerabilities that can be exploited to dampen viral replication. Such host-directed antiviral therapies are promising and are less prone to the development of drug-resistant viral strains. Here, we first describe proteomics-based strategies that allow the rapid characterization of host-pathogen interactions. We then discuss how such data can be exploited to help prioritize compounds with potential host-directed antiviral activity that can be tested in preclinical models.

PurposeIn the phase III SOLAR-1 trial (NCT02437318), the PI3Kα-selective inhibitor and degrader alpelisib significantly improved median progression-free survival when added to fulvestrant in patients with phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA)-mutated, hormone receptor-positive, human epidermal growth factor receptor 2-negative advanced breast cancer. We assessed health-related quality of life using patient-reported outcome measures in these patients.Materials and methodsIn the PIK3CA-mutant cohort, 341 patients were randomly assigned 1:1 to receive alpelisib 300 mg daily or placebo plus fulvestrant 500 mg on days 1 and 15 of cycle 1 and on day 1 of subsequent 28-day cycles. Patient-reported outcomes were evaluated with the European Organisation for Research and Treatment of Cancer QoL of Cancer Patients and Brief Pain Inventory-Short Form questionnaires. Changes from baseline and time to 10% deterioration were analyzed using repeated measurement models and Cox models, respectively.ResultsGlobal Health Status/QoL and functional status were maintained from baseline (mean changes < 10 points) in the alpelisib (overall change from baseline [95% CI], -3.50 [-8.02 to 1.02]) and placebo arms (overall change from baseline [95% CI], 0.27 [-4.48 to 5.02]). Overall treatment effect in Global Health Status/QoL was not significantly different between arms (-3.77; 95% CI, -8.35 to 0.80; P = .101). Time to 10% deterioration for Global Health Status/QoL was similar between arms (hazard ratio, 1.03; 95% CI, 0.72 to 1.48). Compared with placebo, deterioration in social functioning and in diarrhea, appetite loss, nausea or vomiting, and fatigue symptom subscales occurred with alpelisib. Numerical improvement in Worst Pain was observed with alpelisib versus placebo (42% v 32%, week 24; P = .090).ConclusionIn SOLAR-1, there was no statistical difference in deterioration of Global Health Status/QoL between arms, whereas symptom subscales favored placebo for diarrhea, appetite loss, nausea or vomiting, and fatigue, known side effects of alpelisib. Treatment decisions must consider efficacy and tolerability; taken with clinical efficacy, these results support the benefit-risk profile of alpelisib in patients with hormone receptor-positive, human epidermal growth factor receptor 2-negative PIK3CA-mutated advanced breast cancer.

The origins of the upper branch of the Atlantic meridional overturning circulation (AMOC) are traced with backward-in-time Lagrangian trajectories, quantifying the partition of volume transport between different routes of entry from the Indo-Pacific into the Atlantic. Particles are advected by the velocity field from a recent release of "Estimating the Circulation and Climate of the Ocean" (ECCOv4). This global time-variable velocity field is a dynamically consistent interpolation of over 1 billion oceanographic observations collected between 1992 and 2015. Of the 13.6 Sverdrups (1 Sv = 106 m3/s) flowing northward across 6°S, 15% enters the Atlantic from Drake Passage, 35% enters from the straits between Asia and Australia (Indonesian Throughflow), and 49% comes from the region south of Australia (Tasman Leakage). Because of blending in the Agulhas region, water mass properties in the South Atlantic are not a good indicator of origin.

The origins of the upper branch of the Atlantic meridional overturning circulation (AMOC) are traced with backward-in-time Lagrangian trajectories, quantifying the partition of volume transport between different routes of entry from the Indo-Pacific into the Atlantic. Particles are advected by the velocity field from a recent release of "Estimating the Circulation and Climate of the Ocean" (ECCOv4). This global time-variable velocity field is a dynamically consistent interpolation of over 1 billion oceanographic observations collected between 1992 and 2015. Of the 13.6 Sverdrups (1 Sv = 106 m3/s) flowing northward across 6°S, 15% enters the Atlantic from Drake Passage, 35% enters from the straits between Asia and Australia (Indonesian Throughflow), and 49% comes from the region south of Australia (Tasman Leakage). Because of blending in the Agulhas region, water mass properties in the South Atlantic are not a good indicator of origin.

An unsupervised learning method is presented for determining global marine ecological provinces (eco-provinces) from plankton community structure and nutrient flux data. The systematic aggregated eco-province (SAGE) method identifies eco-provinces within a highly nonlinear ecosystem model. To accommodate the non-Gaussian covariance of the data, SAGE uses t-stochastic neighbor embedding (t-SNE) to reduce dimensionality. Over a hundred eco-provinces are identified with the density-based spatial clustering of applications with noise (DBSCAN) algorithm. Using a connectivity graph with ecological dissimilarity as the distance metric, robust aggregated eco-provinces (AEPs) are objectively defined by nesting the eco-provinces. Using the AEPs, the control of nutrient supply rates on community structure is explored. Eco-provinces and AEPs are unique and aid model interpretation. They could facilitate model intercomparison and potentially improve understanding and monitoring of marine ecosystems.

Cancer genomics has revealed many genes and core molecular processes that contribute to human malignancies, but the genetic and molecular bases of many rare cancers remains unclear. Genetic predisposition accounts for 5 to 10% of cancer diagnoses in children1,2, and genetic events that cooperate with known somatic driver events are poorly understood. Pathogenic germline variants in established cancer predisposition genes have been recently identified in 5% of patients with the malignant brain tumour medulloblastoma3. Here, by analysing all protein-coding genes, we identify and replicate rare germline loss-of-function variants across ELP1 in 14% of paediatric patients with the medulloblastoma subgroup Sonic Hedgehog (MBSHH). ELP1 was the most common medulloblastoma predisposition gene and increased the prevalence of genetic predisposition to 40% among paediatric patients with MBSHH. Parent-offspring and pedigree analyses identified two families with a history of paediatric medulloblastoma. ELP1-associated medulloblastomas were restricted to the molecular SHHα subtype4 and characterized by universal biallelic inactivation of ELP1 owing to somatic loss of chromosome arm 9q. Most ELP1-associated medulloblastomas also exhibited somatic alterations in PTCH1, which suggests that germline ELP1 loss-of-function variants predispose individuals to tumour development in combination with constitutive activation of SHH signalling. ELP1 is the largest subunit of the evolutionarily conserved Elongator complex, which catalyses translational elongation through tRNA modifications at the wobble (U34) position5,6. Tumours from patients with ELP1-associated MBSHH were characterized by a destabilized Elongator complex, loss of Elongator-dependent tRNA modifications, codon-dependent translational reprogramming, and induction of the unfolded protein response, consistent with loss of protein homeostasis due to Elongator deficiency in model systems7-9. Thus, genetic predisposition to proteome instability may be a determinant in the pathogenesis of paediatric brain cancers. These results support investigation of the role of protein homeostasis in other cancer types and potential for therapeutic interference.

Recent measurements of methane (CH4) by the Mars Science Laboratory (MSL) now confront us with robust data that demand interpretation. Thus far, the MSL data have revealed a baseline level of CH4 (∼0.4 parts per billion by volume [ppbv]), with seasonal variations, as well as greatly enhanced spikes of CH4 with peak abundances of ∼7 ppbv. What do these CH4 revelations with drastically different abundances and temporal signatures represent in terms of interior geochemical processes, or is martian CH4 a biosignature? Discerning how CH4 generation occurs on Mars may shed light on the potential habitability of Mars. There is no evidence of life on the surface of Mars today, but microbes might reside beneath the surface. In this case, the carbon flux represented by CH4 would serve as a link between a putative subterranean biosphere on Mars and what we can measure above the surface. Alternatively, CH4 records modern geochemical activity. Here we ask the fundamental question: how active is Mars, geochemically and/or biologically? In this article, we examine geological, geochemical, and biogeochemical processes related to our overarching question. The martian atmosphere and surface are an overwhelmingly oxidizing environment, and life requires pairing of electron donors and electron acceptors, that is, redox gradients, as an essential source of energy. Therefore, a fundamental and critical question regarding the possibility of life on Mars is, "Where can we find redox gradients as energy sources for life on Mars?" Hence, regardless of the pathway that generates CH4 on Mars, the presence of CH4, a reduced species in an oxidant-rich environment, suggests the possibility of redox gradients supporting life and habitability on Mars. Recent missions such as ExoMars Trace Gas Orbiter may provide mapping of the global distribution of CH4. To discriminate between abiotic and biotic sources of CH4 on Mars, future studies should use a series of diagnostic geochemical analyses, preferably performed below the ground or at the ground/atmosphere interface, including measurements of CH4 isotopes, methane/ethane ratios, H2 gas concentration, and species such as acetic acid. Advances in the fields of Mars exploration and instrumentation will be driven, augmented, and supported by an improved understanding of atmospheric chemistry and dynamics, deep subsurface biogeochemistry, astrobiology, planetary geology, and geophysics. Future Mars exploration programs will have to expand the integration of complementary areas of expertise to generate synergistic and innovative ideas to realize breakthroughs in advancing our understanding of the potential of life and habitable conditions having existed on Mars. In this spirit, we conducted a set of interdisciplinary workshops. From this series has emerged a vision of technological, theoretical, and methodological innovations to explore the martian subsurface and to enhance spatial tracking of key volatiles, such as CH4.

Recent measurements of methane (CH4) by the Mars Science Laboratory (MSL) now confront us with robust data that demand interpretation. Thus far, the MSL data have revealed a baseline level of CH4 (∼0.4 parts per billion by volume [ppbv]), with seasonal variations, as well as greatly enhanced spikes of CH4 with peak abundances of ∼7 ppbv. What do these CH4 revelations with drastically different abundances and temporal signatures represent in terms of interior geochemical processes, or is martian CH4 a biosignature? Discerning how CH4 generation occurs on Mars may shed light on the potential habitability of Mars. There is no evidence of life on the surface of Mars today, but microbes might reside beneath the surface. In this case, the carbon flux represented by CH4 would serve as a link between a putative subterranean biosphere on Mars and what we can measure above the surface. Alternatively, CH4 records modern geochemical activity. Here we ask the fundamental question: how active is Mars, geochemically and/or biologically? In this article, we examine geological, geochemical, and biogeochemical processes related to our overarching question. The martian atmosphere and surface are an overwhelmingly oxidizing environment, and life requires pairing of electron donors and electron acceptors, that is, redox gradients, as an essential source of energy. Therefore, a fundamental and critical question regarding the possibility of life on Mars is, "Where can we find redox gradients as energy sources for life on Mars?" Hence, regardless of the pathway that generates CH4 on Mars, the presence of CH4, a reduced species in an oxidant-rich environment, suggests the possibility of redox gradients supporting life and habitability on Mars. Recent missions such as ExoMars Trace Gas Orbiter may provide mapping of the global distribution of CH4. To discriminate between abiotic and biotic sources of CH4 on Mars, future studies should use a series of diagnostic geochemical analyses, preferably performed below the ground or at the ground/atmosphere interface, including measurements of CH4 isotopes, methane/ethane ratios, H2 gas concentration, and species such as acetic acid. Advances in the fields of Mars exploration and instrumentation will be driven, augmented, and supported by an improved understanding of atmospheric chemistry and dynamics, deep subsurface biogeochemistry, astrobiology, planetary geology, and geophysics. Future Mars exploration programs will have to expand the integration of complementary areas of expertise to generate synergistic and innovative ideas to realize breakthroughs in advancing our understanding of the potential of life and habitable conditions having existed on Mars. In this spirit, we conducted a set of interdisciplinary workshops. From this series has emerged a vision of technological, theoretical, and methodological innovations to explore the martian subsurface and to enhance spatial tracking of key volatiles, such as CH4.

Introduction: Although the fascia iliaca compartment block (FICB) seems to be an ideal technique for femoral neck and shaft fractures occurring in resource-poor settings, it has been unclear how effective it is when used by emergency physicians (EP) with little training in the technique, using equipment, medications and methods that differ from those commonly available in developed countries. This series was designed to demonstrate that EPs in a resource-poor setting can provide effective analgesia for femur fractures with anatomic landmark-guided FICBs, clinician-compounded lidocaine-epinephrine (1:100,000), and a standard injection needle.Methods: Over a three-month period, patients ≥12 years old presenting to the emergency department with hip or femur fractures and a Likert visual analogue scale >4 had an EP-administered FICB. EPs used a standard intramuscular needle and a lidocaine-epinephrine solution they compounded at the bedside and located the injection site using only anatomic landmarks. EPs evaluated the patient’s pain level at 30 minutes and at two hours post-FICB. We also reviewed articles since 2016 that describe the FICB.Results: We enrolled a non-consecutive sample of 10 patients in the case series. Five had femoral neck (hip) fractures and five had femoral shaft fractures. All patients had a reduction in their pain levels after the FICB. On average, the block took effect about three minutes after injection. At 30 minutes all patients reported clinically meaningful pain reduction. The analgesic effect of the compounded agent lasted approximately 200 minutes. No adverse effects were reported. No published journal articles about FICB since 2016 were from resource-poor settings, and only one was from a developing country.Conclusion: This series suggests that the FICB is effective even when performed with the minimal materials that are usually available in resource-poor settings. Methods such as this, which use simplified clinical tests and techniques applicable in resource-poor settings, can assist global emergency medicine (EM). We can assist global EM by similarly finding methods to simplify useful clinical tests and techniques that can be used in resource-poor settings.

BACKGROUND: T cells expressing antigen-specific chimeric antigen receptors (CARs) improve outcomes for CD19-expressing B cell malignancies. We evaluated a human application of T cells that were genetically modified using the Sleeping Beauty (SB) transposon/transposase system to express a CD19-specific CAR. METHODS: T cells were genetically modified using DNA plasmids from the SB platform to stably express a second-generation CD19-specific CAR and selectively propagated ex vivo with activating and propagating cells (AaPCs) and cytokines. Twenty-six patients with advanced non-Hodgkin lymphoma and acute lymphoblastic leukemia safely underwent hematopoietic stem cell transplantation (HSCT) and infusion of CAR T cells as adjuvant therapy in the autologous (n = 7) or allogeneic settings (n = 19). RESULTS: SB-mediated genetic transposition and stimulation resulted in 2,200- to 2,500-fold ex vivo expansion of genetically modified T cells, with 84% CAR expression, and without integration hotspots. Following autologous HSCT, the 30-month progression-free and overall survivals were 83% and 100%, respectively. After allogeneic HSCT, the respective 12-month rates were 53% and 63%. No acute or late toxicities and no exacerbation of graft-versus-host disease were observed. Despite a low antigen burden and unsupportive recipient cytokine environment, CAR T cells persisted for an average of 201 days for autologous recipients and 51 days for allogeneic recipients. CONCLUSIONS: CD19-specific CAR T cells generated with SB and AaPC platforms were safe, and may provide additional cancer control as planned infusions after HSCT. These results support further clinical development of this nonviral gene therapy approach. TRIAL REGISTRATION: Autologous, NCT00968760; allogeneic, NCT01497184; long-term follow-up, NCT01492036. FUNDING: National Cancer Institute, private foundations, and institutional funds. Please see Acknowledgments for details.

DNA helicases are motor proteins that unwind double-stranded DNA (dsDNA) to reveal single-stranded DNA (ssDNA) needed for many biological processes. The RecQ helicase is involved in repairing damage caused by DNA breaks and stalled replication forks via homologous recombination. Here, the helicase activity of RecQ was visualized on single molecules of DNA using a fluorescent sensor that directly detects ssDNA. By monitoring the formation and progression of individual unwinding forks, we observed that both the frequency of initiation and the rate of unwinding are highly dependent on RecQ concentration. We establish that unwinding forks can initiate internally by melting dsDNA and can proceed in both directions at up to 40-60 bp/s. The findings suggest that initiation requires a RecQ dimer, and that continued processive unwinding of several kilobases involves multiple monomers at the DNA unwinding fork. We propose a distinctive model wherein RecQ melts dsDNA internally to initiate unwinding and subsequently assembles at the fork into a distribution of multimeric species, each encompassing a broad distribution of rates, to unwind DNA. These studies define the species that promote resection of DNA, proofreading of homologous pairing, and migration of Holliday junctions, and they suggest that various functional forms of RecQ can be assembled that unwind at rates tailored to the diverse biological functions of RecQ helicase.

Microgrids are an increasingly common component of the evolving electricity grids with the potential to improve local reliability, reduce costs, and increase penetration rates for distributed renewable generation. The additional complexity of microgrids often leads to increased investment costs, creating a barrier for widespread adoption. These costs may result directly from specific needs for islanding detection, protection systems and power quality assurance that would otherwise be avoided in simpler system configurations. However, microgrids also facilitate additional value streams that may make up for their increased costs and improve the economic viability of microgrid deployment. This paper analyses the literature currently available on research relevant to value streams occurring in microgrids that may contribute to offset the increased investment costs. A review on research related to specific microgrid requirements is also presented.

Introduction: Academic departments of emergency medicine are becoming increasingly involved in assisting with the development of long-term emergency medicine training programs in low and middle-income countries. This article presents our 10-year experience working with local partners to improve emergency medical care education in Guyana.Methods: The Vanderbilt Department of Emergency Medicine has collaborated with the Georgetown Public Hospital Corporation on the development of Emergency Medicine skills followed by the implementation of an emergency medicine residency training program. Residency development included a needs assessment, proposed curriculum, internal and external partnerships, University of Guyana and Ministry of Health approval, and funding.Results: In our experience, we have found that our successful program initiation was due in large part to the pre-existing interest of several local partners and followed by long-term involvement within the country. As a newer specialty without significant local expertise, resident educational needs mandated a locally present full time EM trained attending to serve as the program director. Both external and internal funding was required to achieve this goal. Local educational efforts were best supplemented by robust distance learning. The program was developed to conform to local academic standards and to train the residents to the level of consultant physicians. Despite the best preparations, future challenges remain.Conclusion: While every program has unique challenges, it is likely many of the issues we havefaced are generalizable to other settings and will be useful to other programs considering or currentlyconducting this type of collaborative project. [West J Emerg Med. 2013;14(5):477–481.]

DNA breaks can be repaired with high fidelity by homologous recombination. A ubiquitous protein that is essential for this DNA template-directed repair is RecA. After resection of broken DNA to produce single-stranded DNA (ssDNA), RecA assembles on this ssDNA into a filament with the unique capacity to search and find DNA sequences in double-stranded DNA (dsDNA) that are homologous to the ssDNA. This homology search is vital to recombinational DNA repair, and results in homologous pairing and exchange of DNA strands. Homologous pairing involves DNA sequence-specific target location by the RecA-ssDNA complex. Despite decades of study, the mechanism of this enigmatic search process remains unknown. RecA is a DNA-dependent ATPase, but ATP hydrolysis is not required for DNA pairing and strand exchange, eliminating active search processes. Using dual optical trapping to manipulate DNA, and single-molecule fluorescence microscopy to image DNA pairing, we demonstrate that both the three-dimensional conformational state of the dsDNA target and the length of the homologous RecA-ssDNA filament have important roles in the homology search. We discovered that as the end-to-end distance of the target dsDNA molecule is increased, constraining the available three-dimensional (3D) conformations of the molecule, the rate of homologous pairing decreases. Conversely, when the length of the ssDNA in the nucleoprotein filament is increased, homology is found faster. We propose a model for the DNA homology search process termed 'intersegmental contact sampling', in which the intrinsic multivalent nature of the RecA nucleoprotein filament is used to search DNA sequence space within 3D domains of DNA, exploiting multiple weak contacts to rapidly search for homology. Our findings highlight the importance of the 3D conformational dynamics of DNA, reveal a previously unknown facet of the homology search, and provide insight into the mechanism of DNA target location by this member of a universal family of proteins.

DNA breaks can be repaired with high fidelity by homologous recombination. A ubiquitous protein that is essential for this DNA template-directed repair is RecA. After resection of broken DNA to produce single-stranded DNA (ssDNA), RecA assembles on this ssDNA into a filament with the unique capacity to search and find DNA sequences in double-stranded DNA (dsDNA) that are homologous to the ssDNA. This homology search is vital to recombinational DNA repair, and results in homologous pairing and exchange of DNA strands. Homologous pairing involves DNA sequence-specific target location by the RecA-ssDNA complex. Despite decades of study, the mechanism of this enigmatic search process remains unknown. RecA is a DNA-dependent ATPase, but ATP hydrolysis is not required for DNA pairing and strand exchange, eliminating active search processes. Using dual optical trapping to manipulate DNA, and single-molecule fluorescence microscopy to image DNA pairing, we demonstrate that both the three-dimensional conformational state of the dsDNA target and the length of the homologous RecA-ssDNA filament have important roles in the homology search. We discovered that as the end-to-end distance of the target dsDNA molecule is increased, constraining the available three-dimensional (3D) conformations of the molecule, the rate of homologous pairing decreases. Conversely, when the length of the ssDNA in the nucleoprotein filament is increased, homology is found faster. We propose a model for the DNA homology search process termed 'intersegmental contact sampling', in which the intrinsic multivalent nature of the RecA nucleoprotein filament is used to search DNA sequence space within 3D domains of DNA, exploiting multiple weak contacts to rapidly search for homology. Our findings highlight the importance of the 3D conformational dynamics of DNA, reveal a previously unknown facet of the homology search, and provide insight into the mechanism of DNA target location by this member of a universal family of proteins.