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Artikel von 🤖 🧠 Thibault GEOUI 🧬 💊
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These vials on the table are our experimental drugs in human clinical trials discovered using AI faster, cheaper, and with the higher probability of…
These vials on the table are our experimental drugs in human clinical trials discovered using AI faster, cheaper, and with the higher probability of…
Beliebt bei 🤖 🧠 Thibault GEOUI 🧬 💊
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At ReInvent we shared some exciting work with Genentech about implementing agents in research. Want to learn more about where and how these can be…
At ReInvent we shared some exciting work with Genentech about implementing agents in research. Want to learn more about where and how these can be…
Beliebt bei 🤖 🧠 Thibault GEOUI 🧬 💊
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Building a New Golden Age of Innovation in Drug Development
Drug Discovery & Development
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The Making of Reaxys—Towards Unobstructed Access to Relevant Chemistry Information
American Chemical Society
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Extraction of proteins from formalin-fixed, paraffin-embedded tissue using the Qproteome extraction technique and preparation of tryptic peptides for liquid chromatography/mass spectrometry analysis.
Curr Protoc Mol Biol.
This unit provides a robust, reliable, and easy-to-use kit-based method for extraction of intact, non-degraded proteins from formalin-fixed, paraffin-embedded (FFPE) tissue, and their subsequent use for analysis by liquid chromatography/mass spectrometry (LC/MS). After deparaffinization, proteins are extracted from unstained sections of FFPE rat liver tissue. After a simple cleanup step using organic extraction, the sample is transferred into a buffer optimized for trypsin digestion of the…
This unit provides a robust, reliable, and easy-to-use kit-based method for extraction of intact, non-degraded proteins from formalin-fixed, paraffin-embedded (FFPE) tissue, and their subsequent use for analysis by liquid chromatography/mass spectrometry (LC/MS). After deparaffinization, proteins are extracted from unstained sections of FFPE rat liver tissue. After a simple cleanup step using organic extraction, the sample is transferred into a buffer optimized for trypsin digestion of the extracted proteins. Subsequently, LC/MS is used to identify the proteins that gave rise to the tryptic peptides. Comparing formalin-fixed and frozen tissues, good correlation is observed in the mass spectrometric pattern attributable to the tryptic peptides and number of identified proteins. Since FFPE tissues are generally available in clinical practice, this method can be used to analyze biomarkers in different pathological situations (e.g., healthy vs. diseased). The method can also be used for protein extraction from fresh-frozen tissue.
Andere Autor:innen -
A bridge crosses the active-site canyon of the Epstein-Barr virus nuclease with DNase and RNase activities.
J. Mol. Biol.
Epstein-Barr virus, a double-stranded DNA (dsDNA) virus, is a major human pathogen from the herpesvirus family. The nuclease is one of the lytic cycle proteins required for successful viral replication. In addition to the previously described endonuclease and exonuclease activities on single-stranded DNA and dsDNA substrates, we observed an RNase activity for Epstein-Barr virus nuclease in the presence of Mn(2+), giving a possible explanation for its role in host mRNA degradation. Its crystal…
Epstein-Barr virus, a double-stranded DNA (dsDNA) virus, is a major human pathogen from the herpesvirus family. The nuclease is one of the lytic cycle proteins required for successful viral replication. In addition to the previously described endonuclease and exonuclease activities on single-stranded DNA and dsDNA substrates, we observed an RNase activity for Epstein-Barr virus nuclease in the presence of Mn(2+), giving a possible explanation for its role in host mRNA degradation. Its crystal structure shows a catalytic core of the D-(D/E)XK nuclease superfamily closely related to the exonuclease from bacteriophage lambda with a bridge across the active-site canyon. This bridge may reduce endonuclease activity, ensure processivity or play a role in strand separation of dsDNA substrates. As the DNA strand that is subject to cleavage is likely to make a sharp turn in front of the bridge, endonuclease activity on single-stranded DNA stretches appears to be possible, explaining the cleavage of circular substrates.
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New insights on the role of the gamma-herpesvirus uracil-DNA glycosylase leucine loop revealed by the structure of the Epstein-Barr virus enzyme in complex with an inhibitor protein.
J Mol Biol.
Epstein-Barr virus (EBV) is a human gamma-herpesvirus. Within its 86 open reading frame containing genome, two enzymes avoiding uracil incorporation into DNA can be found: uracil triphosphate hydrolase and uracil-DNA glycosylase (UNG). The latter one excises uracil bases that are due to cytosine deamination or uracil misincorporation from double-stranded DNA substrates. The EBV enzyme belongs to family 1 UNGs. We solved the three-dimensional structure of EBV UNG in complex with the uracil-DNA…
Epstein-Barr virus (EBV) is a human gamma-herpesvirus. Within its 86 open reading frame containing genome, two enzymes avoiding uracil incorporation into DNA can be found: uracil triphosphate hydrolase and uracil-DNA glycosylase (UNG). The latter one excises uracil bases that are due to cytosine deamination or uracil misincorporation from double-stranded DNA substrates. The EBV enzyme belongs to family 1 UNGs. We solved the three-dimensional structure of EBV UNG in complex with the uracil-DNA glycosylase inhibitor protein (Ugi) from bacteriophage PBS-2 at a resolution of 2.3 A by X-ray crystallography. The structure of EBV UNG encoded by the BKRF3 reading frame shows the excellent global structural conservation within the solved examples of family 1 enzymes. Four out of the five catalytic motifs are completely conserved, whereas the fifth one, the leucine loop, carries a seven residue insertion. Despite this insertion, catalytic constants of EBV UNG are similar to those of other UNGs. Modelling of the EBV UNG-DNA complex shows that the longer leucine loop still contacts DNA and is likely to fulfil its role of DNA binding and deformation differently than the enzymes with previously solved structures. We could show that despite the evolutionary distance of EBV UNG from the natural host protein, bacteriophage Ugi binds with an inhibitory constant of 8 nM to UNG. This is due to an excellent specificity of Ugi for conserved elements of UNG, four of them corresponding to catalytic motifs and a fifth one corresponding to an important beta-turn structuring the catalytic site.
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Contribution to the Epstein-Barr virus Structural Genomic Project: The Uracil-DNA Glycosylase and the Nucleic-Acid Metabolism Enzyme
PhD Thesis / Tel Archive
Epstein-Barr Virus (EBV) is a Human γ –herpesvirus. It is the causative agent of
diseases such as Infectious Mononucleosis and it is associated with several
immunoproliferative syndromes. Unlike other herpesviruses such as herpes-simplex,
there is no treatment against EBV. EBV genome features 86 open-reading frames
which are potential targets for a structural genomics approach and for the rational
design of new drugs. The first round of selected targets encode for 23 proteins…Epstein-Barr Virus (EBV) is a Human γ –herpesvirus. It is the causative agent of
diseases such as Infectious Mononucleosis and it is associated with several
immunoproliferative syndromes. Unlike other herpesviruses such as herpes-simplex,
there is no treatment against EBV. EBV genome features 86 open-reading frames
which are potential targets for a structural genomics approach and for the rational
design of new drugs. The first round of selected targets encode for 23 proteins. The
main problem we encountered was, unexpectedly, the poor expression and solubility
of the majority of the selected targets. Among the 8 soluble proteins we obtained, 5
were crystallized and 4 structures were solved. The main success factor was an
individual treatment of each target rather than the use of standard protocols. The
Uracil-DNA Glycosylase (UNG) is a DNA repair enzyme. It was impossible to obtain
crystals of the protein alone, but crystals diffracting to 2.3 Å grew upon the formation
of a complex with a phage-encoded inhibitory protein. The analysis of the structure of
this complex shows that the « leucin-loop », a major domain of the active site,
features a 7 residue insertion which is common to all γ –herpesvirus. Despite this
difference, catalytic constants are similar to other organisms UNGs, suggesting a
similar interaction with DNA. Current work and problems associated with other
targets is also reported (in particular on the Alkaline Exonuclease). -
Structural genomics of the Epstein-Barr virus.
Acta Crystallogr D Biol Crystallogr.
Epstein-Barr virus is a herpesvirus that causes infectious mononucleosis, carcinomas and immunoproliferative disease. Its genome encodes 86 proteins, which provided targets for a structural genomics project. After updating the annotation of the genome, 23 open reading frames were chosen for expression in Escherichia coli, initially selecting for those with known enzyme activity and then supplementing this set based on a series of predicted properties, in particular secondary structure. The…
Epstein-Barr virus is a herpesvirus that causes infectious mononucleosis, carcinomas and immunoproliferative disease. Its genome encodes 86 proteins, which provided targets for a structural genomics project. After updating the annotation of the genome, 23 open reading frames were chosen for expression in Escherichia coli, initially selecting for those with known enzyme activity and then supplementing this set based on a series of predicted properties, in particular secondary structure. The major obstacle turned out to be poor expression and low solubility. Surprisingly, this could not be overcome by modifications of the constructs, changes of expression temperature or strain or renaturation. Of the eight soluble proteins, five were crystallized using robotic nanolitre-drop crystallization trials, which led to four solved structures. Although these results depended on individual treatment rather than standardized protocols, a high-throughput miniaturized crystallization screening protocol was a key component of success with these difficult proteins.
Andere Autor:innen
Projekte
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ChemSearch Challenge 2016
Elsevier Opens Second Reaxys ChemSearch Challenge, Inviting Entrants to Compete in Solving Chemistry Conundrums
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Reaxys 2016 Launch
Elsevier Launches New Release of Reaxys to Enable Chemists to Find the Shortest Path From Question to Answer
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New Go to Market Framework, including public-beta process for online product
–Heute
Auszeichnungen/Preise
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Innovation award
Elsevier
For the development and launch of Embiology
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Lead the Way award
Elsevier
"Lead the Way award" for the category Engage and understand the people we serve.
#1 out of 180 submissions, selected by Elsevier's CEO.
Challenged to redefine the market position of Reaxys, we partnered with a best-in-class scientific marketing agency to develop the “ChemSearchChallenge.” The mission was to engage chemists worldwide to help solve their real world problems. Based on market research and community engagement, we understood that if chemists cannot get their answers fast…"Lead the Way award" for the category Engage and understand the people we serve.
#1 out of 180 submissions, selected by Elsevier's CEO.
Challenged to redefine the market position of Reaxys, we partnered with a best-in-class scientific marketing agency to develop the “ChemSearchChallenge.” The mission was to engage chemists worldwide to help solve their real world problems. Based on market research and community engagement, we understood that if chemists cannot get their answers fast, it’s as if the information does not exist. In the first 3 weeks, 900+ participants registered and 1000+ new followers were added to Twitter. It has proven to be an innovative and customer-centric approach to community engagement.
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Customer Focus Award
Elsevier
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MENRT (French Research Ministry) PhD Scholarship
French Research Ministry
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Study abroad scholarship
Région Rhône-Alpes
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French
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Jetzt anmelden und ansehenWeitere Aktivitäten von 🤖 🧠 Thibault GEOUI 🧬 💊
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The End of Pre-Training Scaling Laws: A Wake-Up Call for Data Readiness? … … … Ilya Sutskever recently made a bold point: the scaling era of…
The End of Pre-Training Scaling Laws: A Wake-Up Call for Data Readiness? … … … Ilya Sutskever recently made a bold point: the scaling era of…
Geteilt von 🤖 🧠 Thibault GEOUI 🧬 💊
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Ilya Sutskever just confirmed at NeurIPS that pre-training scaling laws for LLMs have ended 👇 The compute is scaling but data isn’t (new or…
Ilya Sutskever just confirmed at NeurIPS that pre-training scaling laws for LLMs have ended 👇 The compute is scaling but data isn’t (new or…
Beliebt bei 🤖 🧠 Thibault GEOUI 🧬 💊
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San Francisco, Boston, Munich,.. Christmas all over the world. With 2 laughing eyes and 1 crying eye. Where was the best party? Everywhere. Every…
San Francisco, Boston, Munich,.. Christmas all over the world. With 2 laughing eyes and 1 crying eye. Where was the best party? Everywhere. Every…
Beliebt bei 🤖 🧠 Thibault GEOUI 🧬 💊
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The Return-to-Office Trap: Driving Out the Best 🤩 , Keeping the Rest 🤪 … … … During COVID, companies discovered the power of WFH (work from…
The Return-to-Office Trap: Driving Out the Best 🤩 , Keeping the Rest 🤪 … … … During COVID, companies discovered the power of WFH (work from…
Geteilt von 🤖 🧠 Thibault GEOUI 🧬 💊
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