Application of Pulsed Field Gel Electrophoresis to Determine γ-ray-induced Double-strand Breaks in Yeast Chromosomal Molecules

The frequency of DNA double-strand breaks (dsb) was determined in yeast cells exposed to γ-rays under anoxic conditions. Genomic DNA of treated cells was separated by pulsed field gel electrophoresis, and two different approaches for the evaluation of the gels were employed: (1) The DNA mass distribution profile obtained by electrophoresis was compared to computed profiles, and the number of DSB per unit length was then derived in terms of a fitting procedure; (2) hybridization of selected chromosomes was performed, and a comparison of the hybridization signals in treated and untreated samples was then used to derive the frequency of dsb

Modelling intra-beam scattering in the LHC for longitudinal beam loss studies

In the Large Hadron Collider (LHC), intra-beam scattering (IBS) is one of the main drivers of longitudinal emittance growth during the long injection plateau. With the halo of the longitudinal bunch distribution being close to the separatrix, IBS consequently drives beam losses by pushing particles outside the RF bucket at the flat-bottom. As IBS and beam losses impose a requirement on the minimum RF bucket size, this mechanism has an important impact on the RF power requirements for the High Luminosity (HL-) LHC. In this contribution, the effect of IBS is introduced in the Beam Longitudinal Dynamics (BLonD) tracking code. This numerical model is then benchmarked against analytical estimates, as well as against beam measurements performed in the LHC. The impact of IBS-driven losses on the RF power requirements is discussed through the correlation between the time spent at flat-bottom and the average bunch length, which translates into start-of-ramp losses

Cellular Radiosensitivity: How much better do we understand it?

Purpose: Ionizing radiation exposure gives rise to a variety of lesions in DNA that result in genetic instability and potentially tumorigenesis or cell death. Radiation extends its effects on DNA by direct interaction or by radiolysis of H2O that generates free radicals or aqueous electrons capable of interacting with and causing indirect damage to DNA. While the various lesions arising in DNA after radiation exposure can contribute to the mutagenising effects of this agent, the potentially most damaging lesion is the DNA double strand break (DSB) that contributes to genome instability and/or cell death. Thus in many cases failure to recognise and/or repair this lesion determines the radiosensitivity status of the cell. DNA repair mechanisms including homologous recombination (HR) and non-homologous end-joining (NHEJ) have evolved to protect cells against DNA DSB. Mutations in proteins that constitute these repair pathways are characterised by radiosensitivity and genome instability. Defects in a number of these proteins also give rise to genetic disorders that feature not only genetic instability but also immunodeficiency, cancer predisposition, neurodegeneration and other pathologies. Conclusions: In the past fifty years our understanding of the cellular response to radiation damage has advanced enormously with insight being gained from a wide range of approaches extending from more basic early studies to the sophisticated approaches used today. In this review we discuss our current understanding of the impact of radiation on the cell and the organism gained from the array of past and present studies and attempt to provide an explanation for what it is that determines the response to radiation

Machine learning-based extraction of longitudinal beam parameters in the LHC

Accurate knowledge of beam parameters is essential for optimizing the performance of particle accelerators like the Large Hadron Collider (LHC). An initial machine-learning (ML) model for the reconstruction of the longitudinal distribution has been extended to extract the main parameters of multiple bunches at LHC injection. The extended model utilizes an encoder-decoder architecture to analyze sets of longitudinal profile measurements. Its development was partially driven by the need of a real-time beam energy error estimate, which was not directly available in the past. The derived beam parameters moreover include injection phase error, bunch length and intensity in the LHC, as well as the RF voltages at extraction from the Super Proton Synchrotron (SPS) and at capture in the LHC. In this paper, we compare the results of the ML model with conventional measurements of bunch length and energy error, from the beam quality monitor (BQM) and the orbit acquisition system, respectively. These benchmarks demonstrate the potential of applying the ML model for operational exploitation in LHC

Complex Reorganization and Predominant Non-Homologous Repair Following Chromosomal Breakage in Karyotypically Balanced Germline Rearrangements and Transgenic Integration

We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically-interpreted translocations and inversions. We confirm that the recently described phenomenon of “chromothripsis” (massive chromosomal shattering and reorganization) is not unique to cancer cells but also occurs in the germline where it can resolve to a karyotypically balanced state with frequent inversions. We detected a high incidence of complex rearrangements (19.2%) and substantially less reliance on microhomology (31%) than previously observed in benign CNVs. We compared these results to experimentally-generated DNA breakage-repair by sequencing seven transgenic animals, and revealed extensive rearrangement of the transgene and host genome with similar complexity to human germline alterations. Inversion is the most common rearrangement, suggesting that a combined mechanism involving template switching and non-homologous repair mediates the formation of balanced complex rearrangements that are viable, stably replicated and transmitted unaltered to subsequent generations

Clinical Significance of Optic Disc Progression by Topographic Change Analysis Maps in Glaucoma: An 8-Year Follow-Up Study

Aim. To investigate the ability of Heidelberg Retina Tomograph (HRT3) Topographic Change Analysis (TCA) map to predict the subsequent development of clinical change, in patients with glaucoma. Materials. 61 eyes of 61 patients, which, from a retrospective review were defined as stable on optic nerve head (ONH) stereophotographs and visual field (VF), were enrolled in a prospective study. Eyes were classified as TCA-stable or TCA-progressed based on the TCA map. All patients underwent HRT3, VF, and ONH stereophotography at 9–12 months intervals. Clinical glaucoma progression was determined by masked assessment of ONH stereophotographs and VF Guided Progression Analysis. Results. The median (IQR) total HRT follow-up period was 8.1 (7.3, 9.1) years, which included a median retrospective and prospective follow-up time of 3.9 (3.1, 5.0) and 4.0 (3.5, 4.7) years, respectively. In the TCA-stable eyes, VF and/or photographic progression occurred in 5/13 (38.4%) eyes compared to 11/48 (22.9%) of the TCA-progressed eyes. There was no statistically significant association between TCA progression and clinically relevant (photographic and/or VF) progression (hazard ratio, 1.18; P=0.762). The observed median time to clinical progression from enrollment was significantly shorter in the TCA-progressed group compared to the TCA-stable group (P=0.04). Conclusion. Our results indicate that the commercially available TCA progression criteria do not adequately predict subsequent photographic and/or VF progression

Beam longitudinal dynamics simulation studies

The beam longitudinal dynamics code blond, utilized tool, has been developed at CERN since 2014. It has emerged as a central tool for conducting longitudinal beam dynamics simulations. In this paper, we present this modular simulation suite and the various physics models that can be included and combined by the user. We detail the reference frame, the equations of motion, the plethora of options for radio-frequency parameters such as phase noise, fixed-field acceleration, and feedback models for the CERN accelerators, as well as the modeling of collective effects and synchrotron radiation. We also present various methods of generating multibunch distributions matched to a given impedance model. blond is furthermore a well tested and optimized simulation suite, which is demonstrated through examples, too

Tumor-Infiltrating Clonal Hematopoiesis

BACKGROUND: Clonal hematopoiesis of indeterminate potential (CHIP) is an age-related condition associated with increased mortality among patients with cancer. CHIP mutations with high variant-allele frequencies can be detected in tumors, a phenomenon we term tumor-infiltrating clonal hematopoiesis (TI-CH). The frequency of TI-CH and its effect on tumor evolution are unclear. METHODS: We characterized CHIP and TI-CH in 421 patients with early-stage non-small-cell lung cancer (NSCLC) from the TRACERx study and in 49,351 patients from the MSK-IMPACT pan-cancer cohort. We studied the association of TI-CH with survival and disease recurrence and evaluated the functional effect of TET2-mutant CHIP on the biologic features of lung tumors. RESULTS: Among patients with NSCLC, 42% of those with CHIP had TI-CH. TI-CH independently predicted an increased risk of death or recurrence, with an adjusted hazard ratio of 1.80 (95% confidence interval [CI], 1.23 to 2.63) as compared with the absence of CHIP and an adjusted hazard ratio of 1.62 (95% CI, 1.02 to 2.56) as compared with CHIP in the absence of TI-CH. Among patients with solid tumors, 26% of those with CHIP had TI-CH. TI-CH conferred a risk of death from any cause that was 1.17 times (95% CI, 1.06 to 1.29) as high as the risk with CHIP in the absence of TI-CH. TET2 mutations were the strongest genetic predictor of TI-CH; such mutations enhanced monocyte migration to lung tumor cells, fueled a myeloid-rich tumor microenvironment in mice, and resulted in the promotion of tumor organoid growth. CONCLUSIONS: TI-CH increased the risk of disease recurrence or death among patients with NSCLC and the risk of death from any cause among patients with solid tumors. TI-CH remodeled the tumor immune microenvironment and accelerated tumor organoid growth, findings that support a role for an aging-related hematologic clonal proliferation in cancer evolution. (Funded by the Royal Society and others.)