Enzyme Kinetics and Detector Sensitivity Determine Limits of Detection of Amplification-Free CRISPR-Cas12 and CRISPR-Cas13 Diagnostics.

Interest in CRISPR-Cas12 and CRISPR-Cas13 detection continues to increase as these detection schemes enable the specific recognition of nucleic acids. The fundamental sensitivity limits of these schemes (and their applicability in amplification-free assays) are governed by kinetic rates. However, these kinetic rates remain poorly understood, and their reporting has been inconsistent. We quantify kinetic parameters for several enzymes (LbCas12a, AsCas12a, AapCas12b, LwaCas13a, and LbuCas13a) and their corresponding limits of detection (LoD). Collectively, we present quantification of enzyme kinetics for 14 guide RNAs (gRNAs) and nucleic acid targets for a total of 50 sets of kinetic rate parameters and 25 LoDs. We validate the self-consistency of our measurements by comparing trends and limiting behaviors with a Michaelis-Menten trans-cleavage reaction kinetics model. For our assay conditions, activated Cas12 and Cas13 enzymes exhibit trans-cleavage catalytic efficiencies between order 105 and 106 M-1 s-1. For assays that use fluorescent reporter molecules (ssDNA and ssRNA) for target detection, the kinetic rates at the current assay conditions result in an amplification-free LoD in the picomolar range. The results suggest that successful detection of target requires cleavage (by an activated CRISPR enzyme) of the order of at least 0.1% of the fluorescent reporter molecules. This fraction of reporters cleaved is required to differentiate the signal from the background, and we hypothesize that this required fraction is largely independent of the detection method (e.g., endpoint vs reaction velocity) and detector sensitivity. Our results demonstrate the fundamental nature by which kinetic rates and background signal limit LoDs and thus highlight areas of improvement for the emerging field of CRISPR diagnostics.

A Fast Experimental Scanner for Proton CT: Technical Performance and First Experience with Phantom Scans.

We report on the design, fabrication, and first tests of a tomographic scanner developed for proton computed tomography (pCT) of head-sized objects. After extensive preclinical testing, pCT is intended to be employed in support of proton therapy treatment planning and pre-treatment verification in patients undergoing particle-beam therapy. The scanner consists of two silicon-strip telescopes that track individual protons before and after the phantom, and a novel multistage scintillation detector that measures a combination of the residual energy and range of the proton, from which we derive the water equivalent path length (WEPL) of the protons in the scanned object. The set of WEPL values and the associated paths of protons passing through the object over a 360° angular scan are processed by an iterative, parallelizable reconstruction algorithm that runs on modern GP-GPU hardware. In order to assess the performance of the scanner, we have performed tests with 200 MeV protons from the synchrotron of the Loma Linda University Medical Center and the IBA cyclotron of the Northwestern Medicine Chicago Proton Center. Our first objective was calibration of the instrument, including tracker channel maps and alignment as well as the WEPL calibration. Then we performed the first CT scans on a series of phantoms. The very high sustained rate of data acquisition, exceeding one million protons per second, allowed a full 360° scan to be completed in less than 10 minutes, and reconstruction of a CATPHAN 404 phantom verified accurate reconstruction of the proton relative stopping power in a variety of materials.

A Prototype Scintillator Real-Time Beam Monitor for Ultra-high Dose Rate Radiotherapy.

Background: FLASH Radiotherapy (RT) is an emergent cancer radiotherapy modality where an entire therapeutic dose is delivered at more than 1000 times higher dose rate than conventional RT. For clinical trials to be conducted safely, a precise and fast beam monitor that can generate out-of-tolerance beam interrupts is required. This paper describes the overall concept and provides results from a prototype ultra-fast, scintillator-based beam monitor for both proton and electron beam FLASH applications. Purpose: A FLASH Beam Scintillator Monitor (FBSM) is being developed that employs a novel proprietary scintillator material. The FBSM has capabilities that conventional RT detector technologies are unable to simultaneously provide: 1) large area coverage; 2) a low mass profile; 3) a linear response over a broad dynamic range; 4) radiation hardness; 5) real-time analysis to provide an IEC-compliant fast beam-interrupt signal based on true two-dimensional beam imaging, radiation do-simetry and excellent spatial resolution. Methods: The FBSM uses a proprietary low mass, less than 0.5 mm water equivalent, non-hygroscopic, radiation tolerant scintillator material (designated HM: hybrid material) that is viewed by high frame rate CMOS cameras. Folded optics using mirrors enable a thin monitor profile of ~10 cm. A field programmable gate array (FPGA) data acquisition system (DAQ) generates real-time analysis on a time scale appropriate to the FLASH RT beam modality: 100-1000 Hz for pulsed electrons and 10-20 kHz for quasi-continuous scanning proton pencil beams. An ion beam monitor served as the initial development platform for this work and was tested in low energy heavy-ion beams (86Kr+26 and protons). A prototype FBSM was fabricated and then tested in various radiation beams that included FLASH level dose per pulse electron beams, and a hospital radiotherapy clinic with electron beams. Results: Results presented in this report include image quality, response linearity, radiation hardness, spatial resolution, and real-time data processing. The HM scintillator was found to be highly radiation damage resistant. It exhibited a small 0.025%/kGy signal decrease from a 216 kGy cumulative dose resulting from continuous exposure for 15 minutes at a FLASH compatible dose rate of 237 Gy/s. Measurements of the signal amplitude vs beam fluence demonstrate linear response of the FBSM at FLASH compatible dose rates of > 40 Gy/s. Comparison with commercial Gafchromic film indicates that the FBSM produces a high resolution 2D beam image and can reproduce a nearly identical beam profile, including primary beam tails. The spatial resolution was measured at 35-40 µm. Tests of the firmware beta version show successful operation at 20,000 Hz frame rate or 50 µs/frame, where the real-time analysis of the beam parameters is achieved in less than 1 µs. Conclusions: The FBSM is designed to provide real-time beam profile monitoring over a large active area without significantly degrading the beam quality. A prototype device has been staged in particle beams at currents of single particles up to FLASH level dose rates, using both continuous ion beams and pulsed electron beams. Using a novel scintillator, beam profiling has been demonstrated for currents extending from single particles to 10 nA currents. Radiation damage is minimal and even under FLASH conditions would require ≥ 50 kGy of accumulated exposure in a single spot to result in a 1% decrease in signal output. Beam imaging is comparable to radiochromic films, and provides immediate images without hours of processing. Real-time data processing, taking less than 50 µs (combined data transfer and analysis times), has been implemented in firmware for 20 kHz frame rates for continuous proton beams.

A prototype scintillator real-time beam monitor for ultra-high dose rate radiotherapy.

BACKGROUND: FLASH Radiotherapy (RT) is an emergent cancer RT modality where an entire therapeutic dose is delivered at more than 1000 times higher dose rate than conventional RT. For clinical trials to be conducted safely, a precise and fast beam monitor that can generate out-of-tolerance beam interrupts is required. This paper describes the overall concept and provides results from a prototype ultra-fast, scintillator-based beam monitor for both proton and electron beam FLASH applications. PURPOSE: A FLASH Beam Scintillator Monitor (FBSM) is being developed that employs a novel proprietary scintillator material. The FBSM has capabilities that conventional RT detector technologies are unable to simultaneously provide: (1) large area coverage; (2) a low mass profile; (3) a linear response over a broad dynamic range; (4) radiation hardness; (5) real-time analysis to provide an IEC-compliant fast beam-interrupt signal based on true two-dimensional beam imaging, radiation dosimetry and excellent spatial resolution. METHODS: The FBSM uses a proprietary low mass, less than 0.5 mm water equivalent, non-hygroscopic, radiation tolerant scintillator material (designated HM: hybrid material) that is viewed by high frame rate CMOS cameras. Folded optics using mirrors enable a thin monitor profile of ∼10 cm. A field programmable gate array (FPGA) data acquisition system generates real-time analysis on a time scale appropriate to the FLASH RT beam modality: 100-1000 Hz for pulsed electrons and 10-20 kHz for quasi-continuous scanning proton pencil beams. An ion beam monitor served as the initial development platform for this work and was tested in low energy heavy-ion beams (86Kr+26 and protons). A prototype FBSM was fabricated and then tested in various radiation beams that included FLASH level dose per pulse electron beams, and a hospital RT clinic with electron beams. RESULTS: Results presented in this report include image quality, response linearity, radiation hardness, spatial resolution, and real-time data processing. The HM scintillator was found to be highly radiation damage resistant. It exhibited a small 0.025%/kGy signal decrease from a 216 kGy cumulative dose resulting from continuous exposure for 15 min at a FLASH compatible dose rate of 237 Gy/s. Measurements of the signal amplitude versus beam fluence demonstrate linear response of the FBSM at FLASH compatible dose rates of >40 Gy/s. Comparison with commercial Gafchromic film indicates that the FBSM produces a high resolution 2D beam image and can reproduce a nearly identical beam profile, including primary beam tails. The spatial resolution was measured at 35-40 µm. Tests of the firmware beta version show successful operation at 20 000 Hz frame rate or 50 µs/frame, where the real-time analysis of the beam parameters is achieved in less than 1 µs. CONCLUSIONS: The FBSM is designed to provide real-time beam profile monitoring over a large active area without significantly degrading the beam quality. A prototype device has been staged in particle beams at currents of single particles up to FLASH level dose rates, using both continuous ion beams and pulsed electron beams. Using a novel scintillator, beam profiling has been demonstrated for currents extending from single particles to 10 nA currents. Radiation damage is minimal and even under FLASH conditions would require ≥50 kGy of accumulated exposure in a single spot to result in a 1% decrease in signal output. Beam imaging is comparable to radiochromic films, and provides immediate images without hours of processing. Real-time data processing, taking less than 50 µs (combined data transfer and analysis times), has been implemented in firmware for 20 kHz frame rates for continuous proton beams.

Current status of the preclinical evaluation of alternating electric fields as a form of cancer therapy.

Exposing cancer cells to alternating electric fields of 100-300 kHz frequency and 1-4 V/cm strength has been shown to significantly reduce cancer growth in cell culture and in human patients. This form of anti-cancer therapy is more commonly referred to as tumor treating fields (TTFields), a novel treatment modality that has been approved by the U.S. Food and Drug Administration for use in patients with glioblastoma and malignant pleural mesothelioma. Pivotal trials in other solid organ cancer trials are underway. In regards to overall survival, TTFields alone is comparable to chemotherapy alone in recurrent glioblastoma. However, when combined with adjuvant chemotherapy, TTFields prolong median survival by 4.9 months in newly-diagnosed glioblastoma. TTFields hold promise as a therapeutic approach to numerous solid organ cancers. This review summarizes the current status of TTFields research at the preclinical level, highlighting recent aspects of a relatively complex working hypothesis. In addition, we point out the gaps between limited preclinical in vivo studies and the available clinical data. To date, no customized system for TTFields delivery in rodent models of glioblastoma has been presented. We aim to motivate the expansion of TTFields preclinical research and facilitate the availability of suitable hardware, to ultimately improve outcomes in patients with cancer.

A truncated DNA-damage-signaling response is activated after DSB formation in the G1 phase of Saccharomyces cerevisiae.

In Saccharomyces cerevisiae, the DNA damage response (DDR) is activated by the spatio-temporal colocalization of Mec1-Ddc2 kinase and the 9-1-1 clamp. In the absence of direct means to monitor Mec1 kinase activation in vivo, activation of the checkpoint kinase Rad53 has been taken as a proxy for DDR activation. Here, we identify serine 378 of the Rad55 recombination protein as a direct target site of Mec1. Rad55-S378 phosphorylation leads to an electrophoretic mobility shift of the protein and acts as a sentinel for Mec1 activation in vivo. A single double-stranded break (DSB) in G1-arrested cells causes phosphorylation of Rad55-S378, indicating activation of Mec1 kinase. However, Rad53 kinase is not detectably activated under these conditions. This response required Mec1-Ddc2 and loading of the 9-1-1 clamp by Rad24-RFC, but not Rad9 or Mrc1. In addition to Rad55-S378, two additional direct Mec1 kinase targets are phosphorylated, the middle subunit of the ssDNA-binding protein RPA, RPA2 and histone H2A (H2AX). These data suggest the existence of a truncated signaling pathway in response to a single DSB in G1-arrested cells that activates Mec1 without eliciting a full DDR involving the entire signaling pathway including the effector kinases.

The role of Monte Carlo simulation in understanding the performance of proton computed tomography.

Proton computed tomography (pCT) is a promising tomographic imaging modality allowing direct reconstruction of proton relative stopping power (RSP) required for proton therapy dose calculation. In this review article, we aim at highlighting the role of Monte Carlo (MC) simulation in pCT studies. After describing the requirements for performing proton computed tomography and the various pCT scanners actively used in recent research projects, we present an overview of available MC simulation platforms. The use of MC simulations in the scope of investigations of image reconstruction, and for the evaluation of optimal RSP accuracy, precision and spatial resolution omitting detector effects is then described. In the final sections of the review article, we present specific applications of realistic MC simulations of an existing pCT scanner prototype, which we describe in detail.

Comparative accuracy and resolution assessment of two prototype proton computed tomography scanners.

BACKGROUND: Improving the accuracy of relative stopping power (RSP) in proton therapy may allow reducing range margins. Proton computed tomography (pCT) has been shown to provide state-of-the-art RSP accuracy estimation, and various scanner prototypes have recently been built. The different approaches used in scanner design are expected to impact spatial resolution and RSP accuracy. PURPOSE: The goal of this study was to perform the first direct comparison, in terms of spatial resolution and RSP accuracy, of two pCT prototype scanners installed at the same facility and by using the same image reconstruction algorithm. METHODS: A phantom containing cylindrical inserts of known RSP was scanned at the phase-II pCT prototype of the U.S. pCT collaboration and at the commercially oriented ProtonVDA scanner. Following distance-driven binning filtered backprojection reconstruction, the radial edge spread function of high-density inserts was used to estimate the spatial resolution. RSP accuracy was evaluated by the mean absolute percent error (MAPE) over the inserts. No direct imaging dose estimation was possible, which prevented a comparison of the two scanners in terms of RSP noise. RESULTS: In terms of RSP accuracy, both scanners achieved the same MAPE of 0.72% when excluding the porous sinus insert from the evaluation. The ProtonVDA scanner reached a better overall MAPE when all inserts and the body of the phantom were accounted for (0.81%), compared to the phase-II scanner (1.14%). The spatial resolution with the phase-II scanner was found to be 0.61 lp/mm, while for the ProtonVDA scanner somewhat lower at 0.46 lp/mm. CONCLUSIONS: The comparison between two prototype pCT scanners operated in the same clinical facility showed that they both fulfill the requirement of an RSP accuracy of about 1%. Their spatial resolution performance reflects the different design choices of either a scanner with full tracking capabilities (phase-II) or of a more compact tracker system, which only provides the positions of protons but not their directions (ProtonVDA).

Proof of concept image artifact reduction by energy-modulated proton computed tomography (EMpCT).

PURPOSE: To reduce imaging artifacts and improve image quality of a specific proton computed tomography (pCT) prototype scanner by combining pCT data acquired at two different incident proton energies to avoid protons stopping in sub-optimal detector sections. METHODS: Image artifacts of a prototype pCT scanner are linked to protons stopping close to internal structures of the scanner's multi-stage energy detector. We aimed at avoiding such protons by acquiring pCT data at two different incident energies and combining the data in post-processing from which artifact-reduced images of the relative stopping power (RSP) were calculated. Energy-modulated pCT (EMpCT) images were assessed visually and quantitatively and compared to the original mono-energetic images in terms of RSP accuracy and noise. Data were acquired for a homogeneous water phantom. RESULTS: RSP images reconstructed from the mono-energetic datasets displayed local image artifacts which were ring-shaped due to the homogeneity of the phantom. The merged EMpCT dataset achieved a superior visual image quality with reduced artifacts and only minor remaining rings. The inter-quartile range (25/75) of RSP values was reduced from 0.7% with the current standard acquisition to 0.2% with EMpCT due to the reduction of ring artifacts. In this study, dose was doubled compared to a standard scan, but we discuss strategies to reduce excess dose. CONCLUSIONS: EMpCT allows to effectively avoid regions of the energy detector that cause image artifacts. Thereby, image quality is improved.

Particle-Tracking Proton Computed Tomography-Data Acquisition, Preprocessing, and Preconditioning.

Proton CT (pCT) is a promising new imaging technique that can reconstruct relative stopping power (RSP) more accurately than x-ray CT in each cubic millimeter voxel of the patient. This, in turn, will result in better proton range accuracy and, therefore, smaller planned tumor volumes (PTV). The hardware description and some reconstructed images have previously been reported. In a series of two contributions, we focus on presenting the software algorithms that convert pCT detector data to the final reconstructed pCT images for application in proton treatment planning. There were several options on how to accomplish this, and we will describe our solutions at each stage of the data processing chain. In the first paper of this series, we present the data acquisition with the pCT tracking and energy-range detectors and how the data are preprocessed, including the conversion to the well-formatted track information from tracking data and water-equivalent path length from the data of a calibrated multi-stage energy-range detector. These preprocessed data are then used for the initial image formation with an FDK cone-beam CT algorithm. The output of data acquisition, preprocessing, and FDK reconstruction is presented along with illustrative imaging results for two phantoms, including a pediatric head phantom. The second paper in this series will demonstrate the use of iterative solvers in conjunction with the superiorization methodology to further improve the images resulting from the upfront FDK image reconstruction and the implementation of these algorithms on a hybrid CPU/GPU computer cluster.

Phosphorylation of Rad55 on serines 2, 8, and 14 is required for efficient homologous recombination in the recovery of stalled replication forks.

DNA damage checkpoints coordinate the cellular response to genotoxic stress and arrest the cell cycle in response to DNA damage and replication fork stalling. Homologous recombination is a ubiquitous pathway for the repair of DNA double-stranded breaks and other checkpoint-inducing lesions. Moreover, homologous recombination is involved in postreplicative tolerance of DNA damage and the recovery of DNA replication after replication fork stalling. Here, we show that the phosphorylation on serines 2, 8, and 14 (S2,8,14) of the Rad55 protein is specifically required for survival as well as for normal growth under genome-wide genotoxic stress. Rad55 is a Rad51 paralog in Saccharomyces cerevisiae and functions in the assembly of the Rad51 filament, a central intermediate in recombinational DNA repair. Phosphorylation-defective rad55-S2,8,14A mutants display a very slow traversal of S phase under DNA-damaging conditions, which is likely due to the slower recovery of stalled replication forks or the slower repair of replication-associated DNA damage. These results suggest that Rad55-S2,8,14 phosphorylation activates recombinational repair, allowing for faster recovery after genotoxic stress.

Robust Iterative Methods: Convergence and Applications to Proton Computed Tomography.

Robust methods, such as Tikhonov regularization and Bounded data uncertainty, have been used extensively in relatively small problems involving dense matrices for many decades, but have not been used in large-scale iterative methods for image reconstruction in particle imaging until recently. In this case, robust methods may allow more accurate reconstruction of images in the presence of errors of both the energy measurement of the protons and ions but also in the estimated path taken by the proton or ion through the object. Robust systems may also be used when entire blocks of data are missing, or in low-dose reconstructions using a very small number of particles without substantial loss of image quality. In this contribution, we demonstrate that robust methods show great promise in proton/ion (particle) computed tomography (pCT), and, for the first time, that they can be proven to converge. Thus, the convergence of robust methods as well as benefits for reconstruction in uncertain systems is shown to constitute the main advantage for pCT reconstruction.

Improving single-event proton CT by removing nuclear interaction events within the energy/range detector.

Data filtering is crucial for accurate relative stopping power (RSP) reconstruction in proton CT (pCT). In this work, we assess different filters and their performance for the US pCT collaboration prototype pCT system in Monte Carlo (MC) simulations. The potential of using the recently proposed [Formula: see text]-E filter for removing nuclear interactions that occurred in the energy/range detector of the pCT system is investigated. Full pCT scans were acquired with the TOPAS MC simulated version of the prototype scanner that comprises two tracking detectors and a five stage energy/range detector. An ideal water cylinder and a water cylinder with five tissue inserts were investigated. Before image reconstruction, a [Formula: see text] WEPL filter was applied as the only filter, or in addition to filters acting on the energy deposit in each of the energy detector stages, as done currently with the prototype. The potential of the [Formula: see text]-E filter that was recently proposed for helium imaging was assessed. The results were compared to simulations for which nuclear interactions were disabled representing ground truth. The [Formula: see text] WEPL filter alone was not sufficient to filter out all nuclear interaction events and systematic fluctuations in the form of ring artifacts were present in the pCT reconstructed images. Applying energy filters currently used with the device prior to the [Formula: see text] WEPL filter only slightly improved the image quality. A [Formula: see text] WEPL filter improved the mean RSP accuracy, but could not fully remove the systematic fluctuations. The [Formula: see text]-E filter in addition to the current reconstruction procedure efficiently removed the systematic fluctuations and the achieved RSP accuracy closely matched the simulation without nuclear interactions. This study demonstrates the dependence of the accuracy of the usual [Formula: see text] WEPL filter on uncertainties arising within the energy detector. By enabling to remove such uncertainties, the [Formula: see text]-E method proved to yield some potential for improving the accuracy of pCT.

Experimental comparison of proton CT and dual energy x-ray CT for relative stopping power estimation in proton therapy.

Proton computed tomography (pCT) has been proposed as an alternative to x-ray computed tomography (CT) for acquiring relative to water stopping power (RSP) maps used for proton treatment planning dose calculations. In parallel, it has been shown that dual energy x-ray CT (DECT) improves RSP accuracy when compared to conventional single energy x-ray CT. This study aimed at directly comparing the RSP accuracy of both modalities using phantoms scanned at an advanced prototype pCT scanner and a state-of-the-art DECT scanner. Two phantoms containing 13 tissue-mimicking inserts of known RSP were scanned at the pCT phase II prototype and a latest generation dual-source DECT scanner (Siemens SOMATOM Definition FORCE). RSP accuracy was compared by mean absolute percent error (MAPE) over all inserts. A highly realistic Monte Carlo (MC) simulation was used to gain insight on pCT image artifacts which degraded MAPE. MAPE was 0.55% for pCT and 0.67% for DECT. The realistic MC simulation agreed well with pCT measurements ([Formula: see text]). Both simulation and experimental results showed ring artifacts in pCT images which degraded the MAPE compared to an ideal pCT simulation ([Formula: see text]). Using the realistic simulation, we could identify sources of artifacts, which are attributed to the interfaces in the five-stage plastic scintillator energy detector and calibration curve interpolation regions. Secondary artifacts stemming from the proton tracker geometry were also identified. The pCT prototype scanner outperformed a state-of-the-art DECT scanner in terms of RSP accuracy (MAPE) for plastic tissue mimicking inserts. Since artifacts tended to concentrate in the inserts, their mitigation may lead to further improvements in the reported pCT accuracy.

Nanodosimetry-based quality factors for radiation protection in space.

Evaluation and monitoring of the cancer risk from space radiation exposure is a crucial requirement for the success of long-term space missions. One important task in the risk calculation is to properly weigh the various components of space radiation dose according to their assumed contribution to the cancer risk relative to the risk associated with radiation of low ionization density. Currently, quality factors of radiation both on the ground and in space are defined by national and international commissions based on existing radiobiological data and presumed knowledge of the ionization density distribution of the radiation field at a given point of interest. This approach makes the determination of the average quality factor ofa given radiation field a rather complex task. In this contribution, we investigate the possibility to define quality factors of space radiation exposure based on nanodosimetric data. The underlying formalism of the determination of quality factors on the basis of nanodosimetric data is described, and quality factors for protons and ions (helium and carbon) of different energies based on simulated nanodosimetric data are presented. The value and limitations of this approach are discussed.

The impact of secondary fragments on the image quality of helium ion imaging.

Single-event ion imaging enables the direct reconstruction of the relative stopping power (RSP) information required for ion-beam therapy. Helium ions were recently hypothesized to be the optimal species for such technique. The purpose of this work is to investigate the effect of secondary fragments on the image quality of helium CT (HeCT) and to assess the performance of a prototype proton CT (pCT) scanner when operated with helium beams in Monte Carlo simulations and experiment. Experiments were conducted installing the U.S. pCT consortium prototype scanner at the Heidelberg Ion-Beam Therapy Center (HIT). Simulations were performed with the scanner using the TOPAS toolkit. HeCT images were reconstructed for a cylindrical water phantom, the CTP404 (sensitometry), and the CTP528 (line-pair) [Formula: see text] ® modules. To identify and remove individual events caused by fragmentation, the multistage energy detector of the scanner was adapted to function as a [Formula: see text] telescope. The use of the developed filter eliminated the otherwise arising ring artifacts in the HeCT reconstructed images. For the HeCT reconstructed images of a water phantom, the maximum RSP error was improved by almost a factor 8 with respect to unfiltered images in the simulation and a factor 10 in the experiment. Similarly, for the CTP404 module, the mean RSP accuracy improved by a factor 6 in both the simulation and the experiment when the filter was applied (mean relative error 0.40% in simulation, 0.45% in experiment). In the evaluation of the spatial resolution through the CTP528 module, the main effect of the filter was noise reduction. For both simulated and experimental images the spatial resolution was ∼4 lp cm-1. In conclusion, the novel filter developed for secondary fragments proved to be effective in improving the visual quality and RSP accuracy of the reconstructed images. With the filter, the pCT scanner is capable of accurate HeCT imaging.

Esc4/Rtt107 and the control of recombination during replication.

When replication forks stall during DNA synthesis, cells respond by assembling multi-protein complexes to control the various pathways that stabilize the replication machinery, repair the replication fork, and facilitate the reinitiation of processive DNA synthesis. Increasing evidence suggests that cells have evolved scaffolding proteins to orchestrate and control the assembly of these repair complexes, typified in mammalian cells by several BRCT-motif containing proteins, such as Brca1, Xrcc1, and 53BP1. In Saccharomyces cerevisiae, Esc4 contains six such BRCT domains and is required for the most efficient response to a variety of agents that damage DNA. We show that Esc4 interacts with several proteins involved in the repair and processing of stalled or collapsed replication forks, including the recombination protein Rad55. However, the function of Esc4 does not appear to be restricted to a Rad55-dependent process, as we observed an increase in sensitivity to the DNA alkylating agent methane methylsulfonate (MMS) in a esc4Deltarad55Delta mutant, as well as in double mutants of esc4Delta and other recombination genes, compared to the corresponding single mutants. In addition, we show that Esc4 forms multiple nuclear foci in response to treatment with MMS. Similar behavior is also observed in the absence of damage when either of the S-phase checkpoint proteins, Tof1 or Mrc1, is deleted. Thus, we propose that Esc4 associates with ssDNA of stalled forks and acts as a scaffolding protein to recruit and/or modulate the function of other proteins required to reinitiate DNA synthesis.

Direct kinase-to-kinase signaling mediated by the FHA phosphoprotein recognition domain of the Dun1 DNA damage checkpoint kinase.

The serine-threonine kinase Dun1 contains a forkhead-associated (FHA) domain and functions in the DNA damage checkpoint pathway of Saccharomyces cerevisiae. It belongs to the Chk2 family of checkpoint kinases, which includes S. cerevisiae Rad53 and Mek1, Schizosaccharomyces pombe Cds1, and human Chk2. Dun1 is required for DNA damage-induced transcription of certain target genes, transient G(2)/M arrest after DNA damage, and DNA damage-induced phosphorylation of the DNA repair protein Rad55. Here we report that the FHA phosphoprotein recognition domain of Dun1 is required for direct phosphorylation of Dun1 by Rad53 kinase in vitro and in vivo. trans phosphorylation by Rad53 does not require the Dun1 kinase activity and is likely to involve only a transient interaction between the two kinases. The checkpoint functions of Dun1 kinase in DNA damage-induced transcription, G(2)/M cell cycle arrest, and Rad55 phosphorylation are severely compromised in an FHA domain mutant of Dun1. As a consequence, the Dun1 FHA domain mutant displays enhanced sensitivity to genotoxic stress induced by UV, methyl methanesulfonate, and the replication inhibitor hydroxyurea. We show that the Dun1 FHA domain is critical for direct kinase-to-kinase signaling from Rad53 to Dun1 in the DNA damage checkpoint pathway.

Stopping power accuracy and achievable spatial resolution of helium ion imaging using a prototype particle CT detector system.

A precise relative stopping power map of the patient is crucial for accurate particle therapy. Charged particle imaging determines the stopping power either tomographically - particle computed tomography (pCT) - or by combining prior knowledge from particle radiography (pRad) and x-ray CT. Generally, multiple Coulomb scattering limits the spatial resolution. Compared to protons, heavier particles scatter less due to their lower charge/mass ratio. A theoretical framework to predict the most likely trajectory of particles in matter was developed for light ions up to carbon and was found to be the most accurate for helium comparing for fixed initial velocity. To further investigate the potential of helium in particle imaging, helium computed tomography (HeCT) and radiography (HeRad) were studied at the Heidelberg Ion-Beam Therapy Centre (HIT) using a prototype pCT detector system registering individual particles, originally developed by the U.S. pCT collaboration. Several phantoms were investigated: modules of the Catphan QA phantom for analysis of spatial resolution and achievable stopping power accuracy, a paediatric head phantom (CIRS) and a custommade phantom comprised of animal meat enclosed in a 2 % agarose mixture representing human tissue. The pCT images were reconstructed applying the CARP iterative reconstruction algorithm. The MTF10% was investigated using a sharp edge gradient technique. HeRad provides a spatial resolution above that of protons (MTF1010%=6.07 lp/cm for HeRad versus MTF10%=3.35 lp/cm for proton radiography). For HeCT, the spatial resolution was limited by the number of projections acquired (90 projections for a full scan). The RSP accuracy for all inserts of the Catphan CTP404 module was found to be 2.5% or better and is subject to further optimisation. In conclusion, helium imaging appears to offer higher spatial resolution compared to proton imaging. In future studies, the advantage of helium imaging compared to other imaging modalities in clinical applications will be further explored.

Software platform for simulation of a prototype proton CT scanner.

PURPOSE: Proton computed tomography (pCT) is a promising imaging technique to substitute or at least complement x-ray CT for more accurate proton therapy treatment planning as it allows calculating directly proton relative stopping power from proton energy loss measurements. A proton CT scanner with a silicon-based particle tracking system and a five-stage scintillating energy detector has been completed. In parallel a modular software platform was developed to characterize the performance of the proposed pCT. METHOD: The modular pCT software platform consists of (1) a Geant4-based simulation modeling the Loma Linda proton therapy beam line and the prototype proton CT scanner, (2) water equivalent path length (WEPL) calibration of the scintillating energy detector, and (3) image reconstruction algorithm for the reconstruction of the relative stopping power (RSP) of the scanned object. In this work, each component of the modular pCT software platform is described and validated with respect to experimental data and benchmarked against theoretical predictions. In particular, the RSP reconstruction was validated with both experimental scans, water column measurements, and theoretical calculations. RESULTS: The results show that the pCT software platform accurately reproduces the performance of the existing prototype pCT scanner with a RSP agreement between experimental and simulated values to better than 1.5%. CONCLUSIONS: The validated platform is a versatile tool for clinical proton CT performance and application studies in a virtual setting. The platform is flexible and can be modified to simulate not yet existing versions of pCT scanners and higher proton energies than those currently clinically available.