Search

Engineered luciferase-luciferin pairs have expanded the number of cellular targets that can be visualized in tandem. While light production relies on selective processing of synthetic luciferins by mutant luciferases, little is known about the origin of selectivity. The development of new and improved pairs requires a better understanding of the structure-function relationship of bioluminescent probes. In this work, we report a biochemical approach to assessing and optimizing two popular bioluminescent pairs: Cashew/D-luc and Pecan/4'-BrLuc. Single mutants derived from Cashew and Pecan revealed key residues for selectivity and thermal stability. Stability was further improved through rational addition of beneficial residues. Additionally, adding mutations known to improve stability provided extra stability and, surprisingly, improved selectivity dramatically. The resultant improved pair of luciferases is100-fold selective for their respective substrates and highly thermally stable. Collectively, this work highlights the importance of mechanistic insight for improving bioluminescent pairs and provides significantly improved Cashew and Pecan enzymes which should be immediately suitable for multi-component imaging applications.

This study was initiated and conducted by several laboratories, 3 of the main cosmetic ingredient suppliers and 4 brands of cosmetics in France. Its objective is to show the interest and robustness of coupling chemical and genetic analyses in the identification of plant species. In this study, the Lavandula genus was used.In this study, we used two analytical methods. Chemical analysis from UHPLC (ultra-high-performance liquid chromatography) and genetic analysis from barcoding with genetic markers.Eleven lavender species were selected (botanically authenticated) and analysed. The results show that three chemical compounds (coumaric acid hexoside, ferulic acid hexoside and rosmarinic acid) and three genetic markers (RbcL, trnH-psbA and ITS) are of interest for the differentiation of species of the genus lavandula.The results show that the combination of complementary analytical methods is a relevant system to prove the botanical identification of lavender species. This first study, carried out on a plant of interest for cosmetics, demonstrates the need for authentication using a tool combining genetic and chemical analysis as an advance over traditional investigation methods used alone, in terms of identification and authentication reliability.Cette étude a été lancée et menée par plusieurs laboratoires, trois des principaux fournisseurs d’ingrédients cosmétiques et quatre marques de cosmétiques en France. Son objectif est de montrer qu’associer les analyses chimiques et génétiques dans l’identification des espèces végétales présente un intérêt et est une approche solide. Dans cette étude, c’est le genre Lavandula qui a été utilisé. MÉTHODES: Dans cette étude, nous avons fait appel à deux méthodes analytiques. L’analyse chimique, à partir de la chromatographie en phase liquide à haute performance (ultra-high-performance liquid chromatography, UHPLC), et l’analyse génétique en procédant à un codage à barres avec des marqueurs génétiques. RÉSULTATS: Onze espèces de lavande ont été sélectionnées (authentifiées du point de vue botanique) et analysées. Les résultats montrent que trois composés chimiques (acide coumarique hexoside, acide ferulique hexoside et acide rosmarinique) et trois marqueurs génétiques (RbcL, trnH-psbA et ITS) présentent un intérêt pour la différenciation des espèces du genre lavandula.Les résultats montrent que la combinaison de méthodes analytiques complémentaires est un système pertinent pour prouver l’identification végétale des espèces de lavande. Cette première étude, réalisée sur une plante qui offre un intérêt pour les cosmétiques, démontre la nécessité de procéder à une authentification à l’aide d’un outil qui conjugue analyse génétique et chimique ; elle représente une avancée par rapport aux méthodes d’investigation traditionnelles utilisées seules, en termes d’identification et de fiabilité de l’authentification.

Targeted protein degradation has recently gained widespread interest as both a novel therapeutic strategy and a useful tool in biomedical research. Targeted protein degraders are often sub-stoichiometric and do not require strong binding affinity for their targets, enabling access to previously inaccessible targets. Proteolysis-targeting chimeras (PROTACs) are one class of targeted protein degraders that promote degradation by recruiting a target protein to an E3-ligase complex via a heterobifunctional molecule. The modular nature of PROTACs allows for their rational design and systematic optimization. Here we suggest resources and methodologies for developing PROTAC degraders for researchers that may be new to the field. © 2022 Wiley Periodicals LLC.

International audience; For more than a decade, high-throughput sequencing has transformed the study of marine planktonic communities and has highlighted the extent of protist diversity in these ecosystems. Nevertheless, little is known relative to their genomic diversity at the species-scale as well as their major speciation mechanisms. An increasing number of data obtained from global scale sampling campaigns is becoming publicly available, and we postulate that metagenomic data could contribute to deciphering the processes shaping protist genomic differentiation in the marine realm. As a proof of concept, we developed a findable, accessible, interoperable and reusable (FAIR) pipeline and focused on the Mediterranean Sea to study three a priori abundant protist species: Bathycoccus prasinos, Pelagomonas calceolata and Phaeocystis cordata. We compared the genomic differentiation of each species in light of geographic, environmental and oceanographic distances. We highlighted that isolation-byenvironment shapes the genomic differentiation of B. prasinos, whereas P. cordata is impacted by geographic distance (i.e. isolation-by-distance). At present time, the use of metagenomics to accurately estimate the genomic differentiation of protists remains challenging since coverages are lower compared to traditional population surveys. However, our approach sheds light on ecological and evolutionary processes occurring within natural marine populations and paves the way for future protist population metagenomic studies.

Background The COVID‐19 pandemic may induce post‐traumatic stress disorder (PTSD) symptoms among patients with cancer, who also face adaptations to their treatment. The authors assessed the occurrence of PTSD symptoms, investigated pandemic‐induced adjustments in medical oncology practice in patients with cancer, and explored risk factors for PTSD and the association between PTSD symptoms, insomnia, and quality of life (QoL). Methods This prospective French study was conducted in patients with solid/hematologic tumors who were receiving medical treatment in the day care departments of 2 cancer centers during the lockdown. Adjustments to medical oncology practice were collected from medical records. PTSD (measured using the Impact of Event Scale‐Revised), insomnia (measured using the Insomnia Severity Index), QoL (measured using the Functional Assessment of Cancer Therapy‐General instrument), and cognitive complaints (measured using the Functional Assessment of Cancer Therapy–Cognitive Function instrument) were collected through validated questionnaires. Results Clinical data and questionnaires were available for 734 and 576 patients, respectively. The median patient age was 64 years, and 69% of patients were women. Twenty‐one percent of patients had PTSD. Twenty‐seven percent (95% CI, 23%‐30%) had an adjustment in their medical oncology program, including adjournments (29%), treatment interruptions (16%), modified treatment plans (27%), or adapted monitoring (27%). Women and patients experiencing an adjustment in oncology practice had a higher odds of PTSD (odds ratio= 2.10 [95% CI, 1.07‐4.14] and 1.65 [95% CI, 1.03‐2.63]; P, Post‐traumatic stress disorder symptomatology occurred in 21% of patients with cancer during the first lockdown due to COVID‐19, was more frequent among women, and was associated with adjustment in medical oncology treatments. Caregivers should pay special attention to the psychological needs of patients with cancer to prevent or manage post‐traumatic stress disorder symptoms.

International audience; Cultivar mixtures can stabilize yield and reduce pathogen spread in plant populations. A field experiment was performed to determine (a) whether a large difference between the cultivars in the mixture (e.g., plant height or earliness) would have an impact on mixture performance, and (b) whether such differences would modify the classical rules for mixture design. Mixtures were constituted from wheat cultivars with diversity for many traits, including plant height, flowering date, disease resistance, and yield potential. The field experiment was conducted over 3 years, testing each year 72–90 mixtures of two, four, or eight cultivars, and their corresponding pure stands. Disease severity and yield of cultivar mixtures were strongly related to the mean values of the component cultivars in pure stands. Despite the considerable diversity of the mixtures tested, the classic rules (e.g., proportion of susceptible cultivars) already tested in mixtures with similar height and earliness were effective for decreasing disease severity. Agronomic heterogeneity for traits such as plant height, yield potential, or earliness of the cultivars in mixtures did not have a negative impact on disease severity and yield relative to pure stands. Increasing the number of cultivars in the mixture from two to eight had no impact on the mean disease severity and yield of the mixtures, but reduced the variability of disease severity and yield in the mixture relative to pure stands. These results suggest that it may be possible to increase within‐field wheat diversity by combining more contrasting cultivars in mixtures than was previously thought.

International audience; Yellow rust is the major wheat disease in central West Asia and North Africa. Recently, severe epidemics have occurred, with major yield losses in 2010–2011 in Lebanon and Syria. We conducted an extensive field survey, with a collection of 273 samples of Puccinia striiformis f. sp. tritici , to explore the origin of these epidemics. All samples were genotyped with 20 microsatellite markers, and 54 isolates were pathotyped. The population was dominated by the PstS2 lineage, which has spread worldwide since 2000 and displays considerable pathotype diversity (10 pathotypes). The 22 multilocus genotypes (MLGs) detected corresponded to variants of the clonal lineage PstS2, but they differed from the common PstS2 genotype found in the worldwide study conducted between 1981 and 2010. No strong differentiation was observed between Lebanon and Syria. The dominant MLG in Syria was common to both countries. Nine MLGs were found exclusively in the Syrian population and four were restricted to the Lebanese population, including the dominant MLG in Lebanon. The predominant MLG‐11 was found in nine pathotypes, at high frequency. The dominant pathotype in Syria was virulent against widely deployed resistance genes (Yr2 , Yr6 , Yr7 , Yr9 , Yr25 , and Yr27 ); virulence against Yr3 , Yr8 , Yr17 , and YrSP occurred at various frequencies, but Yr1 , Yr4 , Yr5 , Yr10 , Yr15 , and Yr32 were effective against all isolates. No host effect was detected. The presence of diverse host populations consisting of landraces and elite varieties, and diverse climatic conditions may account for the unexpectedly high diversity of this clonal population.

OBJECTIVE To determine whether ileocaecal endometriosis (ICE) is a marker for low rectal endometriosis (LRE) severity. DESIGN Retrospective cohort study. SETTING France. POPULATION AND SAMPLE Analysis of 375 colorectal resections performed in women undergoing complete surgery for LRE from January 1995 to December 2015 in a university centre for endometriosis. METHODS Univariate and multivariate analysis of anatomical, postoperative clinical, and long-term outcomes according to presence of ICE. MAIN OUTCOMES AND MEASURES Mean number and type of deep infiltrating endometriosis (DIE) lesions, the existence of an associated endometrioma, and mean total American Society for Reproductive Medicine (ASRM) score. RESULTS The prevalence of ICE was 25.6%. Primary end-point data showed that women with ICE had a significantly higher adjusted number of DIE lesions (OR = 1.43, 95% CI 1.02-3.03; P = 0.048), higher prevalence of endometriomas (OR = 1.91, 95% CI 1.04-3.51; P = 0.044), more associated DIE sigmoid lesions (OR = 2.12, 95% CI 1.07-3.91; P = 0.025), and a higher mean total ASRM score (OR = 2.07, 95% CI 1.12-4.14; P = 0.025). Women with ICE resected during the surgical procedure for LRE did not have more adverse postoperative clinical outcomes than ICE-negative patients. CONCLUSION Ileocaecal endometriosis was significantly associated with greater LRE severity. In a complete surgical resection strategy, combining resection of ICE and LRE did not appear to increase postoperative rates of complications, morbidity or recurrence, nor did it seem to impair long-term clinical outcomes. TWEETABLE ABSTRACT In women with low rectal endometriosis, 25% have an associated ileocaecal location that is a marker for severity.

Chemical modifications can enhance the properties of DNA by imparting nuclease resistance and generating more-diverse physical structures. However, native DNA polymerases generally cannot synthesize significant lengths of DNA with modified nucleotide triphosphates. Previous efforts have identified a mutant of DNA polymerase I from Thermus aquaticus DNA (SFM19) as capable of synthesizing a range of short, 2'-modified DNAs; however, it is limited in the length of the products it can synthesize. Here, we rationally designed and characterized ten mutants of SFM19. From this, we identified enzymes with substantially improved activity for the synthesis of 2'F-, 2'OH-, 2'OMe-, and 3'OMe-modified DNA as well as for reverse transcription of 2'OMe DNA. We also evaluated mutant DNA polymerases previously only tested for synthesis for 2'OMe DNA and showed that they are capable of an expanded range of modified DNA synthesis. This work significantly expands the known combinations of modified DNA and Taq DNA polymerase mutants.

We study a Reaction-Diffusion model describing the nonlinear oscillations of a transport barrier in a finite shear-layer (width dE ≪ a), where a is the plasma minor radius, based on a 1D reduced model derived to explain nonlinear barrier oscillations in 3D turbulence simulations [P. Beyer, S. Benkadda, G. Fuhr-Chaudier et al., Phys. Rev. Lett. 94, 105001 (2005)]. We show that this single nonlinear equation encompasses most of the physics of these barrier relaxations. The nonlinear oscillations have common characteristics with type-III edge localized modes (ELMs), such as a repetition frequency which decreases with increasing power. In addition to the flow shear, the shear-layer width is also shown to control the nature of the oscillations. (© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Objective To evaluate the overall benefits of non-taxane chemotherapies in a non-selected population including unfit patients presenting with symptoms and pain. Patients and Methods This randomized phase II study reports data from 92 patients (52% >70 years old; 40% with a performance score of 2) previously treated with taxane-based chemotherapy, collected from 15 centres in France. Patients received i.v. mitoxantrone (MTX), oral vinorelbine, or oral etoposide, together with oral prednisone. Palliative benefit (pain response without progression of the disease), biological and tumoural responses, and toxicity profile as well as geriatric assessment (in elderly population) were analysed on an intention-to-treat basis. Results The palliative response rate was 17% for the whole population, and reached 29% when considering the MTX arm. Pain control was achieved in 40% of the patients. The median overall survival was 10.4 months, and was longer in palliative responders. Few grade 3–4 toxicities were observed. The subgroup analysis of elderly patients showed similar results regarding the number and dose intensity of treatments, efficacy and safety. Conclusion In a population including frail and/or elderly patients, who are poorly represented in most clinical studies, non-taxane chemotherapy may remain a relevant option for metastatic prostate cancer having relapsed after a docetaxel-based regimen. Although new treatment options are now approved, the decision-making process should take into account their expected benefit/risk ratio based on the patient status.

This paper assesses linear regression-based methods in downscaling daily precipitation from the general circulation model (GCM) scale to a regional climate model (RCM) scale (45- and 15-km grids) and down to a station scale across North America. Traditional downscaling experiments (linking reanalysis/dynamical model predictors to station precipitation) as well as nontraditional experiments such as predicting dynamic model precipitation from larger-scale dynamic model predictors or downscaling dynamic model precipitation from predictors at the same scale are conducted. The latter experiments were performed to address predictability limit and scale issues. The results showed that the downscaling of daily precipitation occurrence was rarely successful at all scales, although results did constantly improve with the increased resolution of climate models. The explained variances for downscaled precipitation amounts at the station scales were low, and they became progressively better when using predictors from a higher-resolution climate model, thus showing a clear advantage in using predictors from RCMs driven by reanalysis at its boundaries, instead of directly using reanalysis data. The low percentage of explained variances resulted in considerable underestimation of daily precipitation mean and standard deviation. Although downscaling GCM precipitation from GCM predictors (or RCM precipitation from RCM predictors) cannot really be considered downscaling, as there is no change in scale, the exercise yields interesting information as to the limit in predictive ability at the station scale. This was especially clear at the GCM scale, where the inability of downscaling GCM precipitation from GCM predictors demonstrates that GCM precipitation-generating processes are largely at the subgrid scale (especially so for convective events), thus indicating that downscaling precipitation at the station scale from GCM scale is unlikely to be successful. Although results became better at the RCM scale, the results indicate that, overall, regression-based approaches did not perform well in downscaling precipitation over North America. Copyright © 2013 John Wiley & Sons, Ltd.