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Ludvikova L, Simon E, Deygas M, Panier T, Plamont MA, Ollion J, Tebo A, Piel M, Jullien L, Robert L, Le Saux T, Espagne A. Near-infrared co-illumination of fluorescent proteins reduces photobleaching and phototoxicity. Nat Biotechnol 2024; 42:872-876. [PMID: 37537501 PMCID: PMC11180605 DOI: 10.1038/s41587-023-01893-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/30/2023] [Indexed: 08/05/2023]
Abstract
Here we present a method to reduce the photobleaching of fluorescent proteins and the associated phototoxicity. It exploits a photophysical process known as reverse intersystem crossing, which we induce by near-infrared co-illumination during fluorophore excitation. This dual illumination method reduces photobleaching effects 1.5-9.2-fold, can be easily implemented on commercial microscopes and is effective in eukaryotic and prokaryotic cells with a wide range of fluorescent proteins.
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Robert L, Rousselière C, Beuscart JB, Gautier S, Delporte L, Lafci G, Gerard E, Négrier L, Mary A, Johns E, Payen A, Ducommun R, Ferret L, Voirol P, Skalafouris C, Ade M, Potier A, Dufay E, Beney J, Frery P, Drouot S, Feutry F, Corny J, Odou P, Décaudin B. [First French-speaking days of users of decision support system in clinical pharmacy: Feedback and perspectives]. ANNALES PHARMACEUTIQUES FRANÇAISES 2023; 81:1018-1030. [PMID: 37391030 DOI: 10.1016/j.pharma.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/16/2023] [Accepted: 06/26/2023] [Indexed: 07/02/2023]
Abstract
Clinical decision support systems (CDSS) are tools that have been used for several years by clinical pharmacy teams to support pharmaceutical analysis, with a perspective of contributing to the quality of care in collaboration with the other health care team members. These tools require both technical, logistical and human resources. The growing use of these systems in different establishments in France and in Europe gave birth to the idea of meeting to share our experiences. The days organized in Lille in September 2021 aimed at proposing a time of exchange and reflection on the use of these CDSS in clinical pharmacy. A first session was devoted to feedback from each establishment. These tools are essentially used to optimize pharmaceutical analysis and to secure patient medication management. This session outlined the clear advantages and common limitations of these CDSS. Two research projects were also presented to put the use of these tools into perspective. The second session of these days, in the form of workshops, addressed 4 themes that surround the implementation of CDSS: their usability, the legal aspect, the creation of rules and their possible valorization. Common problems were raised, the resolution of which requires close collaboration. This is a first step proposing a beginning of harmonization and sharing that should be deepened in order not to lose the dynamics created between the different centers. This event ended with the proposal to set up two working groups around these systems: the creation and structuring of rules for the detection of risk situations and the common valorization of the work.
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Bello Roufai D, Gonçalves A, De La Motte Rouge T, Akla S, Blonz C, Grenier J, Gligorov J, Saghatchian M, Bailleux C, Simon H, Desmoulins I, Tharin Z, Renaud E, Bertho M, Benderra MA, Delaloge S, Robert L, Cottu P, Pierga JY, Loirat D, Bertucci A, Renouf B, Bidard FC, Lerebours F. Correction: Alpelisib and fulvestrant in PIK3CA-mutated hormone receptor-positive HER2-negative advanced breast cancer included in the French early access program. Oncogene 2023; 42:1417. [PMID: 36922682 DOI: 10.1038/s41388-023-02615-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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Gampenrieder SP, Dezentjé V, Lambertini M, de Nonneville A, Marhold M, Le Du F, Cortés Salgado A, Alpuim Costa D, Vaz Batista M, Chic Ruché N, Tinchon C, Petzer A, Blondeaux E, Del Mastro L, Targato G, Bertucci F, Gonçalves A, Viret F, Bartsch R, Mannsbart C, Deleuze A, Robert L, Saavedra Serrano C, Gion Cortés M, Sampaio-Alves M, Vitorino M, Pecen L, Singer C, Harbeck N, Rinnerthaler G, Greil R. Influence of HER2 expression on prognosis in metastatic triple-negative breast cancer-results from an international, multicenter analysis coordinated by the AGMT Study Group. ESMO Open 2023; 8:100747. [PMID: 36563519 PMCID: PMC10024122 DOI: 10.1016/j.esmoop.2022.100747] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is associated with poor prognosis, and new treatment options are urgently needed. About 34%-39% of primary TNBCs show a low expression of human epidermal growth factor receptor 2 (HER2-low), which is a target for new anti-HER2 drugs. However, little is known about the frequency and the prognostic value of HER2-low in metastatic TNBC. PATIENTS AND METHODS We retrospectively included patients with TNBC from five European countries for this international, multicenter analysis. Triple-negativity had to be shown in a metastatic site or in the primary breast tumor diagnosed simultaneously or within 3 years before metastatic disease. HER2-low was defined as immunohistochemically (IHC) 1+ or 2+ without ERBB2 gene amplification. Survival probabilities were calculated by the Kaplan-Meier method, and multivariable hazard ratios (HRs) were estimated by Cox regression models. RESULTS In total, 691 patients, diagnosed between January 2006 and February 2021, were assessable. The incidence of HER2-low was 32.0% [95% confidence interval (CI) 28.5% to 35.5%], with similar proportions in metastases (n = 265; 29.8%) and primary tumors (n = 425; 33.4%; P = 0.324). The median overall survival (OS) in HER2-low and HER2-0 TNBC was 18.6 and 16.1 months, respectively (HR 1.00; 95% CI 0.83-1.19; P = 0.969). Similarly, in multivariable analysis, HER2-low had no significant impact on OS (HR 0.95; 95% CI 0.79-1.13; P = 0.545). No difference in prognosis was observed between HER2 IHC 0/1+ and IHC 2+ tumors (HR 0.89; 95% CI 0.69-1.17; P = 0.414). CONCLUSIONS In this large international dataset of metastatic TNBC, the frequency of HER2-low was 32.0%. Neither in univariable nor in multivariable analysis HER2-low showed any influence on OS.
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Bello Roufai D, Gonçalves A, De La Motte Rouge T, Akla S, Blonz C, Grenier J, Gligorov J, Saghatchian M, Bailleux C, Simon H, Desmoulins I, Tharin Z, Renaud E, Bertho M, Benderra MA, Delaloge S, Robert L, Cottu P, Pierga JY, Loirat D, Bertucci A, Renouf B, Bidard FC, Lerebours F. Alpelisib and fulvestrant in PIK3CA-mutated hormone receptor-positive HER2-negative advanced breast cancer included in the French early access program. Oncogene 2023:10.1038/s41388-022-02585-3. [PMID: 36611120 DOI: 10.1038/s41388-022-02585-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 01/09/2023]
Abstract
SOLAR-1 and BYLieve trials documented the efficacy of the PI3K-inhibitor alpelisib in pre-treated PIK3CA-mutant, hormone receptor-positive, HER2-negative (HR+/HER2-) advanced breast cancer (ABC) patients. We report here real-life data of patients prospectively registered in the French alpelisib early access program (EAP) opened to PIK3CA-mutant HR+/HER2- ABC patients treated with alpelisib and fulvestrant. Primary endpoint was PFS by local investigators using RECIST1.1. Eleven centers provided individual data on 233 consecutive patients. Patients had received a median number of 4 (range: 1-16) prior systemic treatments for ABC, including CDK4/6 inhibitor, chemotherapy, fulvestrant and everolimus in 227 (97.4%), 180 (77.3%), 175 (75.1%) and 131 (56.2%) patients, respectively. After a median follow-up of 7.1 months and 168 events, median PFS was 5.3 months (95% CI: 4.7-6.0). Among 186 evaluable patients, CBR at 6 months was 45.3% (95% CI: 37.8-52.8). In multivariable analysis, characteristics significantly associated with a shorter PFS were age < 60 years (HR = 1.5, 95% CI = 1.1-2.1), >5 lines of prior treatments (HR = 1.4, 95% CI = 1.0-2.0) and the C420R PI3KCA mutation (HR = 4.1, 95% CI = 1.3-13.6). N = 91 (39.1%) patients discontinued alpelisib due to adverse events. To our knowledge, this is the largest real-life assessment of alpelisib efficacy. Despite heavy pre-treatments, patients derived a clinically relevant benefit from alpelisib and fulvestrant.
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Barbier A, Rousselière C, Robert L, Cousein E, Décaudin B. [Development of a methodological guide on the implementation of a pharmaceutical decision support system: Feedback from a French university hospital]. ANNALES PHARMACEUTIQUES FRANÇAISES 2023; 81:163-172. [PMID: 35792150 DOI: 10.1016/j.pharma.2022.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/25/2022] [Accepted: 06/29/2022] [Indexed: 01/07/2023]
Abstract
OBJECTIVE Develop a methodological guide on the implementation of a PDSS (pharmaceutical decision support system). METHOD Observational study, retrospective conducted at Lille University Hospital from May 2017 to December 2020, corresponding to the period of implementation and then use of the software. The different phases of the project are described as well as the methodology at each stage. RESULTS Four stages seem necessary for the establishment of the PDSS: reflection and preparation of the project, contracting, implementation, use and evaluation. Based on these results and our experience, in particular the difficulties encountered, a methodological diagram of the various steps necessary for the implementation of a PDSS is proposed. CONCLUSION The establishment of a PDSS, especially in the field of clinical pharmacy, is a long multidisciplinary process. Several steps, from project preparation to production start-up are necessary. Planning the different stages is essential for the proper implementation of the SADP so that the installation is as efficient as possible.
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Corné J, Quillien V, Godey F, Le Du F, Robert L, Bourien H, Brunot A, Crouzet L, Perrin C, Lefeuvre-Plesse C, Dieras V, De La Motte Rouge T. 144P Development of a 6-color multiplex crystal digital PCR assay for the simultaneous detection of ESR1 and PIK3CA mutations in the plasma of metastatic breast cancer patients. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.09.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Barry F, Benart L, Robert L, Gala A, Ferrières-Hoa A, Loup V, Anahory T, Brouillet S, Hamamah S. [HLA-C KIR interactions and placental defects: Implications in ART pregnancy issues]. GYNECOLOGIE, OBSTETRIQUE, FERTILITE & SENOLOGIE 2022; 50:600-609. [PMID: 35724923 DOI: 10.1016/j.gofs.2022.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 06/05/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVE The aim of this review is to update data concerning the impact of HLA-C KIR system on placental disorders and assess the involvement on ART clinical outcomes. METHOD Ensuring the maintenance of human pregnancy requires the set up of immunological tolerance to prevent foetus rejection. This phenomenon involves different actors of the immune system: among them, uterine NK cells (uNK) hold specific KIR (killer-cell immunoglobulin-like) receptors linking to HLA molecules on the surface of trophoblastic cells at implantation. Many studies provided evidence that the specific interaction between maternal KIR and foetal HLA-C could influence the process of placentation; according to the KIR haplotype and the type of HLA-C, the interaction could be detrimental for placental function. We reviewed the latest data available regarding HLA-C KIR interactions and ART outcomes. RESULTS The available results highlight a significant increase of preeclampsia risk and recurrent miscarriages when the maternal inhibitory haplotype KIR AA is present, this risk is all the more enhanced when the interaction occurs with foetal HLA-C2. Recent data suggest the consequences of this detrimental interaction in case of DET (double embryo transfer) or use of donor's oocytes in ART practice. On the other hand, maternal KIR AB or BB haplotypes haven't been related to an additional obstetrical risk, as well as the foetal HLA-C1 homozygous allotype. CONCLUSION Despite the existence of many confoundings in current literature on the subject, interaction between maternal KIR and foetal HLA-C represent a promising target lead to broaden the spectrum of placental defects etiologies, especially in the reproductive health area.
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Penverne Y, Delelis-Fanien H, Robert L, Berthier F, Jenvrin J, Montassier E. Le numéro commun santé : enjeux et impacts. ANNALES FRANCAISES DE MEDECINE D URGENCE 2021. [DOI: 10.3166/afmu-2021-0355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Les questions relatives aux numéros d’urgence concernent en premier lieu nos concitoyens. Elles relèvent également d’enjeux de société au travers de l’impératif de maintien du fonctionnement du système dans son ensemble. Souvent réduites aux désaccords entre professionnels de l’urgence, il apparaît nécessaire de considérer les constats portés sur le territoire national et d’objectiver les impératifs opérationnels afin d’œuvrer à la mise en place d’un système lisible, simplifié et efficient. La singularité et la complexité des demandes de soins urgents, non programmés, relève d’une prise en charge spécifique. L’instauration d’un numéro commun santé, articulé et interopéré avec les services de secours et de sécurité, répond à un modèle organisationnel cible en lien avec la réalité du besoin en France, principalement constitué par la demande sanitaire. Ainsi, le service d’accès aux soins (SAS), désormais inscrit dans la loi, constitue un objectif central d’amélioration de la prise en charge des patients en situation d’urgence ou nécessitant des soins non programmés ambulatoires. Il répond à la volonté de convergence des professionnels de santé de la ville et de l’hôpital dans un objectif d’efficience grâce à l’adaptation de la réponse sanitaire au besoin de soins réels du patient. Accéder au SAS par le numéro commun santé contribue à la mise en œuvre globale d’un dispositif pertinent au regard des contraintes opérationnelles et médicoéconomiques actuelles.
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Cuvelier E, Robert L, Musy E, Rousselière C, Marcilly R, Gautier S, Odou P, Beuscart JB, Décaudin B. The clinical pharmacist's role in enhancing the relevance of a clinical decision support system. Int J Med Inform 2021; 155:104568. [PMID: 34537687 DOI: 10.1016/j.ijmedinf.2021.104568] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 08/18/2021] [Accepted: 08/31/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Clinical decision support systems (CDSSs) can improve the quality of patient care by helping physicians to review their prescriptions and thus to optimize drug treatments. Nevertheless, the "alert fatigue" brought on by a large number of irrelevant alerts can decrease a CDSS's effectiveness and thus clinical value. Involving a clinical pharmacist in the development and management of a CDSS can reduce the number of irrelevant alerts presented to physicians. Clinical pharmacists screen alerts and suggest PIs for physicians, corresponding to any proposed therapeutic change about health products, only for relevant alerts could improve the relevance and the acceptance of the information given to physicians about the risks faced by their patients. OBJECTIVE To assess the value of involving clinical pharmacists in the development and maintenance of decision support rules for generating alerts and pharmaceutical interventions (PIs) and to describe the level of acceptance of these PIs by the physicians. METHOD In a retrospective, single-centre study, we evaluated the number of PIs accepted from alerts generated by the CDSS when a clinical pharmacist had developed and managed this tool. During the first 7 months of development of the CDSS, a clinical pharmacist analyzed alerts triggered by the CDSS according to its technical validity and pharmaceutical relevance. Lastly, for alerts that led to a PI, the level of acceptance by physicians was documented. RESULTS During the study, 1430 alerts were analysed: 186 (13%) were considered to be technically invalid - mainly due to the characteristics of the interface. Of the 1244 (87.0%) technically valid alerts, 353 (24.6%) were pharmaceutically relevant and led to a PI. The three main causes of pharmaceutical irrelevance were a lack of specificity in the CDSS (70.8%), lack of relevance with regard to the ward's habits (15.6%), and the pharmacist's decision to recommend monitoring for the patient rather than sending a PI immediately (10.8%). 64.6% of the submitted PIs were accepted by the physicians. CONCLUSION The standardized analysis of alerts by a clinical pharmacist appears to be a good way of improving the development of CDSS by limiting the generation of irrelevant alerts and the latter's transmission to physicians. The involvement of a clinical pharmacist in the development and implementation of a CDSS appears to be novel and may help to optimize drug treatment.
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Deloupy A, Sauveplane V, Robert J, Aymerich S, Jules M, Robert L. Extrinsic noise prevents the independent tuning of gene expression noise and protein mean abundance in bacteria. SCIENCE ADVANCES 2020; 6:eabc3478. [PMID: 33028528 PMCID: PMC7541070 DOI: 10.1126/sciadv.abc3478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/25/2020] [Indexed: 05/03/2023]
Abstract
It is generally accepted that prokaryotes can tune gene expression noise independently of protein mean abundance by varying the relative levels of transcription and translation. Here, we address this question quantitatively, using a custom-made library of 40 Bacillus subtilis strains expressing a fluorescent protein under the control of different transcription and translation control elements. We quantify noise and mean protein abundance by fluorescence microscopy and show that for most of the natural transcription range of B. subtilis, expression noise is equally sensitive to variations in the transcription or translation rate because of the prevalence of extrinsic noise. In agreement, analysis of whole-genome transcriptomic and proteomic datasets suggests that noise optimization through transcription and translation tuning during evolution may only occur in a regime of weak transcription. Therefore, independent control of mean abundance and noise can rarely be achieved, which has strong implications for both genome evolution and biological engineering.
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Robert L, Ollion J, Elez M. Real-time visualization of mutations and their fitness effects in single bacteria. Nat Protoc 2019; 14:3126-3143. [PMID: 31554956 DOI: 10.1038/s41596-019-0215-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 06/21/2019] [Indexed: 11/09/2022]
Abstract
Mutations are the driving force of evolution and the source of important pathologies. The characterization of the dynamics and effects of mutations on fitness is therefore central to our understanding of evolution and to human health. This protocol describes how to implement two methods that we recently developed: mutation visualization (MV) and microfluidic mutation accumulation (µMA), which allow the occurrence of mutations created by DNA replication errors (MV) and the evolution of cell fitness during MA (µMA) to be followed directly in individual cells of Escherichia coli. MV provides a quantitative characterization of the dynamics of mutation occurrences, and µMA allows precise estimation of the distribution of fitness effects (DFEs) of mutations. Both methods use microfluidics and time-lapse microscopy, and a fluorescent mismatch repair (MMR) MutL protein is used as a marker for nascent mutations. Here, we present a single protocol describing how to implement the MV and µMA methods, including detailed procedures for microfluidic setup installation, data acquisition and data analysis and interpretation. Using this procedure, the microfluidic setup installation can be completed within 1 d, and automated data acquisition takes 2-4 d.
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Ollion J, Elez M, Robert L. High-throughput detection and tracking of cells and intracellular spots in mother machine experiments. Nat Protoc 2019; 14:3144-3161. [PMID: 31554957 DOI: 10.1038/s41596-019-0216-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 06/21/2019] [Indexed: 01/06/2023]
Abstract
The analysis of bacteria at the single-cell level is essential to characterization of processes in which cellular heterogeneity plays an important role. BACMMAN (bacteria mother machine analysis) is a software allowing fast and reliable automated image analysis of high-throughput 2D or 3D time-series images from experiments using the 'mother machine', a very popular microfluidic device allowing biological processes in bacteria to be investigated at the single-cell level. Here, we describe how to use some of the BACMMAN features, including (i) segmentation and tracking of bacteria and intracellular fluorescent spots, (ii) visualization and editing of the results, (iii) configuration of the image-processing pipeline for different datasets and (iv) BACMMAN coupling to data analysis software for visualization and analysis of data subsets with specific properties. Among software specifically dedicated to the analysis of mother machine data, only BACMMAN allows segmentation and tracking of both bacteria and intracellular spots. For a single position, single channel with 1,000 frames (2-GB dataset), image processing takes ~6 min on a regular computer. Numerous implemented algorithms, easy configuration and high modularity ensure wide applicability of the BACMMAN software.
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Hornebeck W, Starkey PM, Gordon JL, Legrand Y, Pignaud G, Robert L, Caen JP, Ehrlich HP, Barrett AJ. The Elastase-Like Enzyme of Platelets. Thromb Haemost 2019; 42:1681-1683. [DOI: 10.1055/s-0038-1657076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Legrand Y, Caen J, Robert L. Substrate Specificity of Leukocyte and Platelet Elastases. Thromb Haemost 2018. [DOI: 10.1055/s-0038-1646760] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Legrand Y, Caen JP, Robert L, Wautier JL. Platelet Elastase and Leukocyte Elastase are two Different Entities. Thromb Haemost 2018. [DOI: 10.1055/s-0038-1649273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Robert L, Ollion J, Robert J, Song X, Matic I, Elez M. Mutation dynamics and fitness effects followed in single cells. Science 2018; 359:1283-1286. [DOI: 10.1126/science.aan0797] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 10/19/2017] [Accepted: 01/30/2018] [Indexed: 12/12/2022]
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Elez M, Robert L, Matic I. Method for Detecting and Studying Genome-Wide Mutations in Single Living Cells in Real Time. Methods Mol Biol 2018; 1736:29-39. [PMID: 29322456 DOI: 10.1007/978-1-4939-7638-6_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
DNA sequencing and fluctuation test have been choice methods for studying DNA mutations for decades. Although invaluable tools allowing many important discoveries on mutations, they are both highly influenced by fitness effects of mutations, and therefore suffer several limits. Fluctuation test is for example limited to mutations that produce an identifiable phenotype, which is the minority of all generated mutations. Genome-wide extrapolations using this method are therefore difficult. DNA sequencing detects almost all DNA mutations in population of cells. However, the obtained population mutation spectrum is biased because of the fitness effects of newly generated mutations. For example, mutations that affect fitness strongly and negatively are underrepresented, while those with a strong positive effect are overrepresented. Single-cell genome sequencing can solve this problem. However, sufficient amount of DNA for this approach is obtained by massive whole-genome amplification, which produces many artifacts.We describe the first direct method for monitoring genome-wide mutations in living cells independently of their effect on fitness. This method is based on the following three facts. First, DNA replication errors are the major source of DNA mutations. Second, these errors are the target for an evolutionarily conserved mismatch repair (MMR) system, which repairs the vast majority of replication errors. Third, we recently showed that the fluorescently labeled MMR protein MutL forms fluorescent foci on unrepaired replication errors. If not repaired, the new round of DNA synthesis fixes these errors in the genome permanently, i.e., they become mutations. Therefore, visualizing foci of the fluorescently tagged MutL in individual living cells allows detecting mutations as they appear, before the expression of the phenotype.
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Eun YJ, Ho PY, Kim M, LaRussa S, Robert L, Renner LD, Schmid A, Garner E, Amir A. Archaeal cells share common size control with bacteria despite noisier growth and division. Nat Microbiol 2017; 3:148-154. [PMID: 29255255 DOI: 10.1038/s41564-017-0082-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 11/21/2017] [Indexed: 01/23/2023]
Abstract
In nature, microorganisms exhibit different volumes spanning six orders of magnitude 1 . Despite their capability to create different sizes, a clonal population in a given environment maintains a uniform size across individual cells. Recent studies in eukaryotic and bacterial organisms showed that this homogeneity in cell size can be accomplished by growing a constant size between two cell cycle events (that is, the adder model 2-6 ). Demonstration of the adder model led to the hypothesis that this phenomenon is a consequence of convergent evolution. Given that archaeal cells share characteristics with both bacteria and eukaryotes, we investigated whether and how archaeal cells exhibit control over cell size. To this end, we developed a soft-lithography method of growing the archaeal cells to enable quantitative time-lapse imaging and single-cell analysis, which would be useful for other microorganisms. Using this method, we demonstrated that Halobacterium salinarum, a hypersaline-adapted archaeal organism, grows exponentially at the single-cell level and maintains a narrow-size distribution by adding a constant length between cell division events. Interestingly, the archaeal cells exhibited greater variability in cell division placement and exponential growth rate across individual cells in a population relative to those observed in Escherichia coli 6-9 . Here, we present a theoretical framework that explains how these larger fluctuations in archaeal cell cycle events contribute to cell size variability and control.
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Perney P, Nalpas B, Alarcon R, Vial B, Robert L, Rouch J, Legrand T, Ewert V, Simon N, Donnadieu-Rigole H, Pelletier S. PO2-6EVALUATION OF A COGNITIVE REHABILITATION PROGRAM IN 491 PATIENTS. Alcohol Alcohol 2017. [DOI: 10.1093/alcalc/agx074.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Robert L, Labat-Robert J. Comments on the history of medical-biological studies of aging, the birth of scientific gerontology. Curr Res Transl Med 2017; 65:44-47. [PMID: 28340696 DOI: 10.1016/j.retram.2016.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 08/19/2016] [Indexed: 10/20/2022]
Abstract
Recent books (Immunity. How Elie Metchnikoff changed the course of modern medicine and Expectations of Life) reviewed the important contribution of Metchnikoff to the emergence of gerontology as a new branch of biomedical sciences. Here, we insist on Metchnikoff's contribution and pivotal role in the emergence of nutrition as a science and its importance for health and longevity. The discovery of phagocytosis by Metchnikoff and of its evolutionary ancestry are at the origin of the emergence of cellular immunity as an independent science besides humoral immunity. The longevity of Metchnikoff (71years) at a time when average life expectancy of men did hardly pass 50years certainly contributed to the acceptance of his teachings. The recent increase of the senior population in most advanced countries is a good opportunity to review the contributions of nutrition to longevity.
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Robert L, Labat-Robert J. Platelets, Micro-Particles and Elastase. A Review with Extrapolation to the Mechanism of Generation and Bio-Pathology of Platelet Fragments. Pathol Oncol Res 2017; 23:455-458. [DOI: 10.1007/s12253-017-0199-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 01/16/2017] [Indexed: 11/29/2022]
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Robert L. Tribute to Prof. Ines Mandl. Curr Res Transl Med 2016; 65:S2452-3186(16)30032-0. [PMID: 28466823 DOI: 10.1016/j.retram.2016.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 08/19/2016] [Indexed: 11/26/2022]
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