Quantitative genetic analysis deciphers the impact of cis and trans regulation on cell-to-cell variability in protein expression levels

The authors wish to thank Dr Arianne Richard and Dr Luis Barreiro for their critical reading of the manuscript. The authors also wish to extend their gratitude to TwinsUK for sharing data. TwinsUK is funded by the Wellcome Trust, Medical Research Council, European Union, the National Institute for Health Research (NIHR)-funded BioResource, Clinical Research Facility and Biomedical Research Centre based at Guy’s and St Thomas’ NHS Foundation Trust in partnership with King’s College London.Peer reviewe

EP-1502: High resolution portal image prediction for radiotherapy treatment verification & in vivo dosimetry

International audiencePurpose/Objective: Historically designed as a control system for patient positioning for radiotherapy treatment, Electronic Portal Imaging Devices (EPIDs) are nowadays widely used for quality assurance and dosimetric verifications in new irradiation techniques. One of the main advantages of the EPID is its high resolution which can detect small details. The objective of this study is to compare the EPID image acquired during the treatment with a predicted high resolution portal image computed by Monte Carlo (MC) simulation. A new method for prediction of high resolution EPID images is tested for in vivo treatment verification. Materials and Methods: Experiments were carried out on a Siemens ARTISTETM, equipped with a 160-MLCTM, and its Siemens OptivueTM 1000 EPID. This EPID has an active detection area of 41 x 41 cm2 and a matrix of 1024 x 1024 pixels. A model of this linac and the EPID was developed with the MC code Penelope, and commissioned. We focus on a breast treatment conformational beam (6 MV) on the CIRS adult female phantom. The CT-scan of the phantom was used as input, and Hounsfield numbers were converted in density and atomic composition, so as to obtain a voxelized geometry used in the Penelope code. Particles exiting the phantom and impinging on the EPID are simulated up to the EPID in order to compute the predicted portal image by scoring the energy deposited in the phosphor layer on a 1024 x 1024 virtual grid. The simulated image was then smoothed using a denoising algorithm in order to keep the high resolution advantage. Several denoising algorithms were tested, among them IRON, LASG and a recently developed one called DPGLM. For now, we use the gamma-index technique to evaluate the accuracy of the simulated image against the experimental one. Results: Figure 1 shows the acquired image and the simulated one. The gamma-index is satisfied for 94.4 % of the pixels for 3.5 % and 3.5 mm criterion. The DPGLM gives the best result toward accuracy and computed time. Indeed, the denoising of 1024 x 1024 images takes about 1h30 mn, 2h and 5 mn using DPGLM, IRON, and LASG, respectively. The LASG algorithm is really fast but the result is too smoothed for the high resolution purpose. Conclusions: This work is the first step in the aim of in vivo dosimetry by comparing experimental portal images with high resolution predicted images obtained using MC simulations in a voxelized geometry. First results obtained on a breast treatment are encouraging, and we can expect to detect treatment errors

Search for the Production of Element 112 in the 48Ca + 238U Reaction

We have searched for the production of element 112 in the reaction of 231 MeV 48Ca with 238U. We have not observed any events with a "one event" upper limit cross section of 1.6 pb for EVR-fission events and 1.8 pb for EVR-alpha events.Comment: 6 pages, 3 figures, submitted to Phys. Rev.

Cross Section Limits for the 208^{208}Pb(86^{86}Kr,n)293^{293}118 Reaction

In April-May, 2001, the previously reported experiment to synthesize element 118 using the $^{208}$Pb($^{86}$Kr,n)$^{293}$118 reaction was repeated. No events corresponding to the synthesis of element 118 were observed with a total beam dose of 2.6 x 10$^{18}$ ions. The simple upper limit cross sections (1 event) were 0.9 and 0.6 pb for evaporation residue magnetic rigidities of 2.00 $T m$ and 2.12 $T m$, respectively. A more detailed cross section calculation, accounting for an assumed narrow excitation function, the energy loss of the beam in traversing the target and the uncertainty in the magnetic rigidity of the Z=118 recoils is also presented. Re-analysis of the primary data files from the 1999 experiment showed the reported element 118 events are not in the original data. The current results put constraints on the production cross section for synthesis of very heavy nuclei in cold fusion reactions.Comment: 7 pages, 2 figures. Submitted to EPJ

Spallation Neutron Production by 0.8, 1.2 and 1.6 GeV Protons on various Targets

Spallation neutron production in proton induced reactions on Al, Fe, Zr, W, Pb and Th targets at 1.2 GeV and on Fe and Pb at 0.8, and 1.6 GeV measured at the SATURNE accelerator in Saclay is reported. The experimental double-differential cross-sections are compared with calculations performed with different intra-nuclear cascade models implemented in high energy transport codes. The broad angular coverage also allowed the determination of average neutron multiplicities above 2 MeV. Deficiencies in some of the models commonly used for applications are pointed out.Comment: 20 pages, 32 figures, revised version, accepted fpr publication in Phys. Rev.

OX40 and 4-1BB delineate distinct immune profiles in sarcoma.

Systemic relapse after radiotherapy and surgery is the major cause of disease-related mortality in sarcoma patients. Combining radiotherapy and immunotherapy is under investigation as a means to improve response rates. However, the immune contexture of sarcoma is understudied. Here, we use a retrospective cohort of sarcoma patients, treated with neoadjuvant radiotherapy, and TCGA data. We explore therapeutic targets of relevance to sarcoma, using genomics and multispectral immunohistochemistry to provide insights into the tumor immune microenvironment across sarcoma subtypes. Differential gene expression between radioresponsive myxoid liposarcoma (MLPS) and more radioresistant undifferentiated pleomorphic sarcoma (UPS) indicated UPS contained higher transcript levels of a number of immunotherapy targets (CD73/NT5E, CD39/ENTPD1, CD25/IL2RA, and 4-1BB/TNFRSF9). We focused on 4-1BB/TNFRSF9 and other costimulatory molecules. In TCGA data, 4-1BB correlated to an inflamed and exhausted phenotype. OX40/TNFRSF4 and 4-1BB/TNFRSF9 were highly expressed in sarcoma subtypes versus other cancers. Despite OX40 and 4-1BB being described as Treg markers, we identified that they delineate distinct tumor immune profiles. This was true for sarcoma and other cancers. While only a limited number of samples could be analyzed, spatial analysis of OX40 expression identified two diverse phenotypes of OX40+ Tregs, one associated with and one independent of tertiary lymphoid structures (TLSs). Patient stratification is of intense interest for immunotherapies. We provide data supporting the viewpoint that a cohort of sarcoma patients, appropriately selected, are promising candidates for immunotherapies. Spatial profiling of OX40+ Tregs, in relation to TLSs, could be an additional metric to improve future patient stratification

Inhibition of the Staphylococcus aureus c-di-AMP cyclase DacA by direct interaction with the phosphoglucosamine mutase GlmM

c-di-AMP is an important second messenger molecule that plays a pivotal role in regulating fundamental cellular processes, including osmotic and cell wall homeostasis in many Gram-positive organisms. In the opportunistic human pathogen Staphylococcus aureus, c-di-AMP is produced by the membrane-anchored DacA enzyme. Inactivation of this enzyme leads to a growth arrest under standard laboratory growth conditions and a re-sensitization of methicillin-resistant S. aureus (MRSA) strains to ß-lactam antibiotics. The gene coding for DacA is part of the conserved three-gene dacA/ybbR/glmM operon that also encodes the proposed DacA regulator YbbR and the essential phosphoglucosamine mutase GlmM, which is required for the production of glucosamine-1-phosphate, an early intermediate of peptidoglycan synthesis. These three proteins are thought to form a complex in vivo and, in this manner, help to fine-tune the cellular c-di-AMP levels. To further characterize this important regulatory complex, we conducted a comprehensive structural and functional analysis of the S. aureus DacA and GlmM enzymes by determining the structures of the S. aureus GlmM enzyme and the catalytic domain of DacA. Both proteins were found to be dimers in solution as well as in the crystal structures. Further site-directed mutagenesis, structural and enzymatic studies showed that multiple DacA dimers need to interact for enzymatic activity. We also show that DacA and GlmM form a stable complex in vitro and that S. aureus GlmM, but not Escherichia coli or Pseudomonas aeruginosa GlmM, acts as a strong inhibitor of DacA function without the requirement of any additional cellular factor. Based on Small Angle X-ray Scattering (SAXS) data, a model of the complex revealed that GlmM likely inhibits DacA by masking the active site of the cyclase and preventing higher oligomer formation. Together these results provide an important mechanistic insight into how c-di-AMP production can be regulated in the cell

EVIDENCE OF PRIMARY EVENTS IN 20Ne, 22Ne FRAGMENTATION FROM COINCIDENCE MEASUREMENTS IN 20, 22Ne + 93Nb REACTION AT 30 MeV/A

Evidence that primary ejectiles formation strongly depends on the projectile structure is given by comparison of 20Ne + 93Nb and 22Ne + 93Nb reactions at 30 MeV/A. Pick-up, stripping, break-up mechanism are identified using light particles-projectile fragments coïncidence measurements

Recent acquisition of Helicobacter pylori by Baka Pygmies

Both anatomically modern humans and the gastric pathogen Helicobacter pylori originated in Africa, and both species have been associated for at least 100,000 years. Seven geographically distinct H. pylori populations exist, three of which are indigenous to Africa: hpAfrica1, hpAfrica2, and hpNEAfrica. The oldest and most divergent population, hpAfrica2, evolved within San hunter-gatherers, who represent one of the deepest branches of the human population tree. Anticipating the presence of ancient H. pylori lineages within all hunter-gatherer populations, we investigated the prevalence and population structure of H. pylori within Baka Pygmies in Cameroon. Gastric biopsies were obtained by esophagogastroduodenoscopy from 77 Baka from two geographically separated populations, and from 101 non-Baka individuals from neighboring agriculturalist populations, and subsequently cultured for H. pylori. Unexpectedly, Baka Pygmies showed a significantly lower H. pylori infection rate (20.8%) than non-Baka (80.2%). We generated multilocus haplotypes for each H. pylori isolate by DNA sequencing, but were not able to identify Baka-specific lineages, and most isolates in our sample were assigned to hpNEAfrica or hpAfrica1. The population hpNEAfrica, a marker for the expansion of the Nilo-Saharan language family, was divided into East African and Central West African subpopulations. Similarly, a new hpAfrica1 subpopulation, identified mainly among Cameroonians, supports eastern and western expansions of Bantu languages. An age-structured transmission model shows that the low H. pylori prevalence among Baka Pygmies is achievable within the timeframe of a few hundred years and suggests that demographic factors such as small population size and unusually low life expectancy can lead to the eradication of H. pylori from individual human populations. The Baka were thus either H. pylori-free or lost their ancient lineages during past demographic fluctuations. Using coalescent simulations and phylogenetic inference, we show that Baka almost certainly acquired their extant H. pylori through secondary contact with their agriculturalist neighbors