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Article ; Online: Co-Transplantation of Barcoded Lymphoid-Primed Multipotent (LMPP) and Common Lymphocyte (CLP) Progenitors Reveals a Major Contribution of LMPP to the Lymphoid Lineage.

Michaels, Victoria / Chalabi, Smahane / Legrand, Agnes / Renard, Julie / Tejerina, Emmanuel / Daouya, Marina / Fabrega, Sylvie / Megret, Jérôme / Olaso, Robert / Boland, Anne / Deleuze, Jean-François / Battail, Christophe / Tronik-Le Roux, Diana / Ezine, Sophie

International journal of molecular sciences

2023 Volume 24, Issue 5

Abstract: T cells have the potential to maintain immunological memory and self-tolerance by recognizing antigens from pathogens or tumors. In pathological situations, failure to generate de novo T cells causes immunodeficiency resulting in acute infections and ... ...

Abstract	T cells have the potential to maintain immunological memory and self-tolerance by recognizing antigens from pathogens or tumors. In pathological situations, failure to generate de novo T cells causes immunodeficiency resulting in acute infections and complications. Hematopoietic stem cells (HSC) transplantation constitutes a valuable option to restore proper immune function. However, delayed T cell reconstitution is observed compared to other lineages. To overcome this difficulty, we developed a new approach to identify populations with efficient lymphoid reconstitution properties. To this end, we use a DNA barcoding strategy based on the insertion into a cell chromosome of a lentivirus (LV) carrying a non-coding DNA fragment named barcode (BC). These will segregate through cell divisions and be present in cells' progeny. The remarkable characteristic of the method is that different cell types can be tracked simultaneously in the same mouse. Thus, we in vivo barcoded LMPP and CLP progenitors to test their ability to reconstitute the lymphoid lineage. Barcoded progenitors were co-grafted in immuno-compromised mice and their fate analyzed by evaluating the BC composition in transplanted mice. The results highlight the predominant role of LMPP progenitors for lymphoid generation and reveal valuable novel insights to be reconsidered in clinical transplantation assays.
MeSH term(s)	Animals ; Mice ; Cell Lineage/genetics ; Lymphocytes/metabolism ; Hematopoietic Stem Cells/metabolism ; T-Lymphocytes ; Hematopoietic Stem Cell Transplantation ; Cell Differentiation
Language	English
Publishing date	2023-02-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24054368
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Article: Investigation of candidate gene copy number identifies FCGR3B as a potential biomarker for rheumatoid arthritis.

Ben Kilani, Mohamed Sahbi / Cornélis, François / Olaso, Robert / Chaudru, Valerie / Petit-Teixeira, Elisabeth

Clinical and experimental rheumatology

2019 Volume 37, Issue 6, Page(s) 923–928

Abstract: Objectives: Copy number variants (CNVs) could explain a part of the missing heritability in rheumatoid arthritis (RA). Our goal is to investigate the association of RA with CNVs of three functional candidate genes, Glutathione S-transferase M1 (GSTM1), ... ...

Abstract	Objectives: Copy number variants (CNVs) could explain a part of the missing heritability in rheumatoid arthritis (RA). Our goal is to investigate the association of RA with CNVs of three functional candidate genes, Glutathione S-transferase M1 (GSTM1), Glutathione S-transferase T1 (GSTT1) and Fcγ receptor type IIIAB (FCGR3B). Methods: We quantified the absolute copy number of GSTM1, GSTT1 and FCGR3B genes using droplet digital PCR. Transmission of copy number alleles was investigated in trio families with RA using family-based association tests (Transmission Disequilibrium Test and Genotype Haplotype Relative Risk). Clinical, environmental and biological data on RA patients were also used to stratify patients sample in analysis. Results: Copy numbers from zero to three were identified. Genotype combinations characterised in 182 trios allowed testing the association with RA. Genotypes without null allele of FCGR3B gene were significantly associated with RA (3.41x10-7). Three copy numbers of this gene is observed only in cases of RA (n=14) and a protective effect of null allele was characterised (OR=0.3 (0.17-0.53)). Conclusions: CNVs in FCGR3B are associated with RA in our set of samples. This gene may play a role in physiopathology of this disease.
MeSH term(s)	Arthritis, Rheumatoid/genetics ; Biomarkers ; DNA Copy Number Variations/genetics ; GPI-Linked Proteins/genetics ; Gene Dosage ; Genetic Predisposition to Disease/genetics ; Genotype ; Glutathione Transferase ; Humans ; Polymerase Chain Reaction/methods ; Receptors, IgG
Chemical Substances	Biomarkers ; FCGR3B protein, human ; GPI-Linked Proteins ; Receptors, IgG ; Glutathione Transferase (EC 2.5.1.18)
Language	English
Publishing date	2019-03-07
Publishing country	Italy
Document type	Journal Article
ZDB-ID	605886-3
ISSN	1593-098X ; 0392-856X
ISSN (online)	1593-098X
ISSN	0392-856X
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Article ; Online: Genome-wide association study of a semicontinuous trait: illustration of the impact of the modeling strategy through the study of Neutrophil Extracellular Traps levels.

Munsch, Gaëlle / Proust, Carole / Labrouche-Colomer, Sylvie / Aïssi, Dylan / Boland, Anne / Morange, Pierre-Emmanuel / Roche, Anne / de Chaisemartin, Luc / Harroche, Annie / Olaso, Robert / Deleuze, Jean-François / James, Chloé / Emmerich, Joseph / Smadja, David M / Jacqmin-Gadda, Hélène / Trégouët, David-Alexandre

NAR genomics and bioinformatics

2023 Volume 5, Issue 2, Page(s) lqad062

Abstract: Over the last years, there has been a considerable expansion of genome-wide association studies (GWAS) for discovering biological pathways underlying pathological conditions or disease biomarkers. These GWAS are often limited to binary or quantitative ... ...

Abstract	Over the last years, there has been a considerable expansion of genome-wide association studies (GWAS) for discovering biological pathways underlying pathological conditions or disease biomarkers. These GWAS are often limited to binary or quantitative traits analyzed through linear or logistic models, respectively. In some situations, the distribution of the outcome may require more complex modeling, such as when the outcome exhibits a semicontinuous distribution characterized by an excess of zero values followed by a non-negative and right-skewed distribution. We here investigate three different modeling for semicontinuous data: Tobit, Negative Binomial and Compound Poisson-Gamma. Using both simulated data and a real GWAS on Neutrophil Extracellular Traps (NETs), an emerging biomarker in immuno-thrombosis, we demonstrate that Compound Poisson-Gamma was the most robust model with respect to low allele frequencies and outliers. This model further identified the MIR155HG locus as significantly (
Language	English
Publishing date	2023-06-28
Publishing country	England
Document type	Journal Article
ISSN	2631-9268
ISSN (online)	2631-9268
DOI	10.1093/nargab/lqad062
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Article ; Online: High diagnostic potential of short and long read genome sequencing with transcriptome analysis in exome-negative developmental disorders.

Lecoquierre, François / Quenez, Olivier / Fourneaux, Steeve / Coutant, Sophie / Vezain, Myriam / Rolain, Marion / Drouot, Nathalie / Boland, Anne / Olaso, Robert / Meyer, Vincent / Deleuze, Jean-François / Dabbagh, Dana / Gilles, Isabelle / Gayet, Claire / Saugier-Veber, Pascale / Goldenberg, Alice / Guerrot, Anne-Marie / Nicolas, Gaël

Human genetics

2023 Volume 142, Issue 6, Page(s) 773–783

Abstract: Exome sequencing (ES) has become the method of choice for diagnosing rare diseases, while the availability of short-read genome sequencing (SR-GS) in a medical setting is increasing. In addition, new sequencing technologies, such as long-read genome ... ...

Abstract	Exome sequencing (ES) has become the method of choice for diagnosing rare diseases, while the availability of short-read genome sequencing (SR-GS) in a medical setting is increasing. In addition, new sequencing technologies, such as long-read genome sequencing (LR-GS) and transcriptome sequencing, are being increasingly used. However, the contribution of these techniques compared to widely used ES is not well established, particularly in regards to the analysis of non-coding regions. In a pilot study of five probands affected by an undiagnosed neurodevelopmental disorder, we performed trio-based short-read GS and long-read GS as well as case-only peripheral blood transcriptome sequencing. We identified three new genetic diagnoses, none of which affected the coding regions. More specifically, LR-GS identified a balanced inversion in NSD1, highlighting a rare mechanism of Sotos syndrome. SR-GS identified a homozygous deep intronic variant of KLHL7 resulting in a neoexon inclusion, and a de novo mosaic intronic 22-bp deletion in KMT2D, leading to the diagnosis of Perching and Kabuki syndromes, respectively. All three variants had a significant effect on the transcriptome, which showed decreased gene expression, mono-allelic expression and splicing defects, respectively, further validating the effect of these variants. Overall, in undiagnosed patients, the combination of short and long read GS allowed the detection of cryptic variations not or barely detectable by ES, making it a highly sensitive method at the cost of more complex bioinformatics approaches. Transcriptome sequencing is a valuable complement for the functional validation of variations, particularly in the non-coding genome.
MeSH term(s)	Child ; Humans ; Exome/genetics ; Developmental Disabilities/diagnosis ; Developmental Disabilities/genetics ; Pilot Projects ; Chromosome Mapping ; Gene Expression Profiling/methods
Language	English
Publishing date	2023-04-19
Publishing country	Germany
Document type	Journal Article
ZDB-ID	223009-4
ISSN	1432-1203 ; 0340-6717
ISSN (online)	1432-1203
ISSN	0340-6717
DOI	10.1007/s00439-023-02553-1
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Article ; Online: A comparison of high-throughput SARS-CoV-2 sequencing methods from nasopharyngeal samples.

Gerber, Zuzana / Daviaud, Christian / Delafoy, Damien / Sandron, Florian / Alidjinou, Enagnon Kazali / Mercier, Jonathan / Gerber, Sylvain / Meyer, Vincent / Boland, Anne / Bocket, Laurence / Olaso, Robert / Deleuze, Jean-François

Scientific reports

2022 Volume 12, Issue 1, Page(s) 12561

Abstract: The COVID-19 pandemic caused by the new Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to threaten public health and burden healthcare systems worldwide. Whole SARS-CoV-2 genome sequencing has become essential for epidemiological ... ...

Abstract	The COVID-19 pandemic caused by the new Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to threaten public health and burden healthcare systems worldwide. Whole SARS-CoV-2 genome sequencing has become essential for epidemiological monitoring and identification of new variants, which could represent a risk of increased transmissibility, virulence, or resistance to vaccines or treatment. Different next-generation sequencing approaches are used in SARS-CoV-2 sequencing, although with different ability to provide whole genome coverage without gaps and to reliably detect new variants. In this study, we compared the performance of three target enrichment methods (two multiplex amplification methods and one hybridization capture) using nasopharyngeal swabs from infected individuals. We applied these target enrichment methods to the same set of nasopharyngeal samples (N = 93) in high-throughput mode. SARS-CoV-2 genome was obtained using short-read next-generation sequencing. We observed that each method has some advantages, such as high mapping rate (CleanPlex and COVIDSeq) or absence of systematic variant calling error (SureSelect) as well as their limitations such as suboptimal uniformity of coverage (CleanPlex), high cost (SureSelect) or supply shortages (COVIDSeq). Nevertheless, each of the three target enrichment kits tested in this study yielded acceptable results of whole SARS-CoV-2 genome sequencing and either of them can therefore be used in prospective programs of genomic surveillance of SARS-CoV-2. Genomic surveillance will be crucial to overcoming the ongoing pandemic of COVID-19, despite its successive waves and continually emerging variants.
MeSH term(s)	COVID-19/diagnosis ; Genome, Viral ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Pandemics ; Prospective Studies ; RNA, Viral/genetics ; SARS-CoV-2/genetics
Chemical Substances	RNA, Viral
Language	English
Publishing date	2022-07-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-16549-w
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Article ; Online: Temporal Gene Expression Profiles Reflect the Dynamics of Lymphoid Differentiation.

Chalabi, Smahane / Legrand, Agnes / Michaels, Victoria / Palomares, Marie-Ange / Olaso, Robert / Boland, Anne / Deleuze, Jean-François / Ezine, Sophie / Battail, Christophe / Tronik-Le Roux, Diana

International journal of molecular sciences

2022 Volume 23, Issue 3

Abstract: Understanding the emergence of lymphoid committed cells from multipotent progenitors (MPP) is a great challenge in hematopoiesis. To gain deeper insight into the dynamic expression changes associated with these transitions, we report the quantitative ... ...

Abstract	Understanding the emergence of lymphoid committed cells from multipotent progenitors (MPP) is a great challenge in hematopoiesis. To gain deeper insight into the dynamic expression changes associated with these transitions, we report the quantitative transcriptome of two MPP subsets and the common lymphoid progenitor (CLP). While the transcriptome is rather stable between MPP2 and MPP3, expression changes increase with differentiation. Among those, we found that pioneer lymphoid genes such as
MeSH term(s)	Animals ; Cells, Cultured ; Female ; Gene Expression Profiling/methods ; Gene Expression Regulation ; Gene Regulatory Networks ; Genetic Markers ; Hematopoiesis ; High-Throughput Nucleotide Sequencing ; Lymphoid Progenitor Cells/chemistry ; Lymphoid Progenitor Cells/cytology ; Male ; Mice ; RNA, Long Noncoding/genetics ; Sequence Analysis, RNA
Chemical Substances	Genetic Markers ; RNA, Long Noncoding
Language	English
Publishing date	2022-01-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23031115
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Article ; Online: Penetrance estimation of Alzheimer disease in SORL1 loss-of-function variant carriers using a family-based strategy and stratification by APOE genotypes.

Schramm, Catherine / Charbonnier, Camille / Zaréa, Aline / Lacour, Morgane / Wallon, David / Boland, Anne / Deleuze, Jean-François / Olaso, Robert / Alarcon, Flora / Campion, Dominique / Nuel, Grégory / Nicolas, Gaël

Genome medicine

2022 Volume 14, Issue 1, Page(s) 69

Abstract: Background: Alzheimer disease (AD) is a common complex disorder with a high genetic component. Loss-of-function (LoF) SORL1 variants are one of the strongest AD genetic risk factors. Estimating their age-related penetrance is essential before putative ... ...

Abstract	Background: Alzheimer disease (AD) is a common complex disorder with a high genetic component. Loss-of-function (LoF) SORL1 variants are one of the strongest AD genetic risk factors. Estimating their age-related penetrance is essential before putative use for genetic counseling or preventive trials. However, relative rarity and co-occurrence with the main AD risk factor, APOE-ε4, make such estimations difficult. Methods: We proposed to estimate the age-related penetrance of SORL1-LoF variants through a survival framework by estimating the conditional instantaneous risk combining (i) a baseline for non-carriers of SORL1-LoF variants, stratified by APOE-ε4, derived from the Rotterdam study (N = 12,255), and (ii) an age-dependent proportional hazard effect for SORL1-LoF variants estimated from 27 extended pedigrees (including 307 relatives ≥ 40 years old, 45 of them having genotyping information) recruited from the French reference center for young Alzheimer patients. We embedded this model into an expectation-maximization algorithm to accommodate for missing genotypes. To correct for ascertainment bias, proband phenotypes were omitted. Then, we assessed if our penetrance curves were concordant with age distributions of APOE-ε4-stratified SORL1-LoF variant carriers detected among sequencing data of 13,007 cases and 10,182 controls from European and American case-control study consortia. Results: SORL1-LoF variants penetrance curves reached 100% (95% confidence interval [99-100%]) by age 70 among APOE-ε4ε4 carriers only, compared with 56% [40-72%] and 37% [26-51%] in ε4 heterozygous carriers and ε4 non-carriers, respectively. These estimates were fully consistent with observed age distributions of SORL1-LoF variant carriers in case-control study data. Conclusions: We conclude that SORL1-LoF variants should be interpreted in light of APOE genotypes for future clinical applications.
MeSH term(s)	Alzheimer Disease/genetics ; Apolipoproteins E/genetics ; Case-Control Studies ; Genotype ; Humans ; LDL-Receptor Related Proteins/genetics ; Membrane Transport Proteins/genetics ; Penetrance
Chemical Substances	ApoE protein, human ; Apolipoproteins E ; LDL-Receptor Related Proteins ; Membrane Transport Proteins ; SORL1 protein, human
Language	English
Publishing date	2022-06-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2484394-5
ISSN	1756-994X ; 1756-994X
ISSN (online)	1756-994X
ISSN	1756-994X
DOI	10.1186/s13073-022-01070-6
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Article ; Online: Publisher Correction: Penetrance estimation of Alzheimer disease in SORL1 loss-of-function variant carriers using a family-based strategy and stratification by APOE genotypes.

Genome medicine

2022 Volume 14, Issue 1, Page(s) 83

Language	English
Publishing date	2022-08-03
Publishing country	England
Document type	Published Erratum
ZDB-ID	2484394-5
ISSN	1756-994X ; 1756-994X
ISSN (online)	1756-994X
ISSN	1756-994X
DOI	10.1186/s13073-022-01091-1
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Article ; Online: Relationship between genetic polymorphisms of cytokines and self-reported sleep complaints and habitual caffeine consumption.

Drogou, Catherine / Erblang, Mégane / Metlaine, Arnaud / Berot, Stéphanie / Derbois, Céline / Olaso, Robert / Boland, Anne / Deleuze, Jean-François / Thomas, Claire / Léger, Damien / Chennaoui, Mounir / Sauvet, Fabien / Gomez-Merino, Danielle

Sleep medicine

2022 Volume 101, Page(s) 66–76

Abstract: Pro-inflammatory cytokines are involved in sleep-wake regulation and are associated with caffeine consumption. This is a cross-sectional study in 1023 active French workers investigating associations between self-reported sleep complaints (>3months) and ... ...

Abstract	Pro-inflammatory cytokines are involved in sleep-wake regulation and are associated with caffeine consumption. This is a cross-sectional study in 1023 active French workers investigating associations between self-reported sleep complaints (>3months) and total sleep time (TST) with nine single-nucleotide-polymorphisms (SNPs) including pro-inflammatory cytokines, according to caffeine consumption. Participants were characterized as low, moderate and high (0-50, 51-300, and >300 mg/day) caffeine consumers. After adjusting the odd ratios (OR) for age, gender, and smoking, the risk of sleep complaints was higher in subjects with genetic mutations in tumor necrosis factor alpha (TNF-α, rs 1800629) (ORa [95%CI] = 1.43 [1.07-1.92] for both G/A and A/A aggregate genotypes) or interleukin-1 beta (IL-1β, rs1143627) (ORa = 1.61 [1.08-2.44] for homozygous A/A genotype), and the risk was higher when subjects carry the mutations in TNF-α plus IL-1β regardless of caffeine consumption. When stratified with caffeine consumption, the risk of sleep complaints was higher in TNF-α A allele carriers in high caffeine consumers, and in homozygous A/A genotype of IL-1β in moderate and high consumers. None of the nine SNPs influence TST, with the exception of the mutation on CYP1A2 and only when stratified with caffeine consumption. Our results also indicated more caffeine side-effects when carrying mutation on IL1β. This study showed that polymorphisms in TNF-α and/or IL-1β influenced sleep complaints but did not influence total sleep time. This suggests that management of sleep complaints, which can be addressed by clinical interventions, should consider the influence of the genetic profile of pro-inflammatory cytokines.
MeSH term(s)	Humans ; Cytokines/genetics ; Caffeine/adverse effects ; Tumor Necrosis Factor-alpha/genetics ; Self Report ; Cross-Sectional Studies ; Sleep/genetics ; Polymorphism, Single Nucleotide/genetics ; Genotype ; Genetic Predisposition to Disease
Chemical Substances	Cytokines ; Caffeine (3G6A5W338E) ; Tumor Necrosis Factor-alpha
Language	English
Publishing date	2022-10-23
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2012041-2
ISSN	1878-5506 ; 1389-9457
ISSN (online)	1878-5506
ISSN	1389-9457
DOI	10.1016/j.sleep.2022.10.013
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Article ; Online: Heterogeneity of SARS-CoV-2 virus produced in cell culture revealed by shotgun proteomics and supported by genome sequencing.

Gallais, Fabrice / Pible, Olivier / Gaillard, Jean-Charles / Debroas, Stéphanie / Batina, Hélène / Ruat, Sylvie / Sandron, Florian / Delafoy, Damien / Gerber, Zuzana / Olaso, Robert / Gas, Fabienne / Bellanger, Laurent / Deleuze, Jean-François / Grenga, Lucia / Armengaud, Jean

Analytical and bioanalytical chemistry

2021 Volume 413, Issue 29, Page(s) 7265–7275

Abstract: COVID-19 is the most disturbing pandemic of the past hundred years. Its causative agent, the SARS-CoV-2 virus, has been the subject of an unprecedented investigation to characterize its molecular structure and intimate functioning. While markers for its ... ...

Abstract	COVID-19 is the most disturbing pandemic of the past hundred years. Its causative agent, the SARS-CoV-2 virus, has been the subject of an unprecedented investigation to characterize its molecular structure and intimate functioning. While markers for its detection have been proposed and several diagnostic methodologies developed, its propensity to evolve and evade diagnostic tools and the immune response is of great concern. The recent spread of new variants with increased infectivity requires even more attention. Here, we document how shotgun proteomics can be useful for rapidly monitoring the evolution of the SARS-CoV-2 virus. We evaluated the heterogeneity of purified SARS-CoV-2 virus obtained after culturing in the Vero E6 cell line. We found that cell culture induces significant changes that are translated at the protein level, such changes being detectable by tandem mass spectrometry. Production of viral particles requires careful quality control which can be easily performed by shotgun proteomics. Although considered relatively stable so far, the SARS-CoV-2 genome turns out to be prone to frequent variations. Therefore, the sequencing of SARS-CoV-2 variants from patients reporting only the consensus genome after its amplification would deserve more attention and could benefit from more in-depth analysis of low level but crystal-clear signals, as well as complementary and rapid analysis by shotgun proteomics.
MeSH term(s)	Amino Acid Sequence ; Cell Culture Techniques ; Genome, Viral ; Humans ; Proteomics/methods ; Real-Time Polymerase Chain Reaction/methods ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; SARS-CoV-2/pathogenicity ; Tandem Mass Spectrometry/methods ; Viral Proteins/chemistry ; Virulence
Chemical Substances	Viral Proteins
Language	English
Publishing date	2021-05-20
Publishing country	Germany
Document type	Journal Article
ZDB-ID	201093-8
ISSN	1618-2650 ; 0016-1152 ; 0372-7920
ISSN (online)	1618-2650
ISSN	0016-1152 ; 0372-7920
DOI	10.1007/s00216-021-03401-9
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