This document discusses the structural studies of bacterial TIR-domain containing proteins from Paracoccus denitrificans. It summarizes that the TIR domain plays a role in interfering with the host's innate immune responses. It describes the crystallization and X-ray diffraction of the TIR domain from P. denitrificans, showing it binds to TLR4 and MyD88 domains. Future work is proposed to determine additional bacterial and plant TIR domain structures and interactions.
Regulation of KDM5 by multiple cofactors regulates cancer and stem cellsChristopher Wynder
Presentation of data regarding proteins that regulate the activity of KDM5b.
The studies use multiple disciplines including in vitro enzymology, ES cell studies of differentiation, Mass spectrometry to detect protein protein interactions.
These studies resulted in a comprehensive view of KDM5b function. It required development of at least three novel assays that are focused on moving epigenetic research from yeast and HeLa cell types to primary, clinically relevant cell types.
The techniques have been successfully used in Embryonic stem cells (human and mouse), Neural stem cells (mouse and patient derived as well as iPSCs.
KDM5 epigenetic modifiers as a focus for drug discoveryChristopher Wynder
A summary presentation of my scientific work.
My laboratory focused on an enzyme KDM5b (aka PLU-1, JARID1b) that was widely expressed during development and played a key role in progression of breast cancer through HER-2.
My lab focused on understanding the key biochemical activity of the enzyme through dissecting the proteomic and genomic interactors.
Our results were confirmed through the use of ES cells, adult stem cells and mouse models.
Much of this work remains unpublished, please contact me for more information and/or access to any reagents that I still have as part of this work.
crwynder@gmail.com
Regulation of KDM5 by multiple cofactors regulates cancer and stem cellsChristopher Wynder
Presentation of data regarding proteins that regulate the activity of KDM5b.
The studies use multiple disciplines including in vitro enzymology, ES cell studies of differentiation, Mass spectrometry to detect protein protein interactions.
These studies resulted in a comprehensive view of KDM5b function. It required development of at least three novel assays that are focused on moving epigenetic research from yeast and HeLa cell types to primary, clinically relevant cell types.
The techniques have been successfully used in Embryonic stem cells (human and mouse), Neural stem cells (mouse and patient derived as well as iPSCs.
KDM5 epigenetic modifiers as a focus for drug discoveryChristopher Wynder
A summary presentation of my scientific work.
My laboratory focused on an enzyme KDM5b (aka PLU-1, JARID1b) that was widely expressed during development and played a key role in progression of breast cancer through HER-2.
My lab focused on understanding the key biochemical activity of the enzyme through dissecting the proteomic and genomic interactors.
Our results were confirmed through the use of ES cells, adult stem cells and mouse models.
Much of this work remains unpublished, please contact me for more information and/or access to any reagents that I still have as part of this work.
crwynder@gmail.com
Dr. Jesús Jiménez Barbero - Simposio Internacional 'Química: respuestas para ...Fundación Ramón Areces
Los días 8 y 9 de octubre de 2014, la Fundación Ramón Areces acogió el Simposio Internacional 'Química: respuestas para una vida mejor', organizado en colaboración con la Fundación General CSIC. Su finalidad fue ofrecer a los participantes una visión atractiva de la química moderna que sirva de base al desarrollo de nuevas respuestas para una sociedad en rápida evolución.
Characterization of the phi29 Bacteriophage Nanomotorpcpchic
The purpose is to present the evolution of our understanding to the Bacillus subtilis phi29 bacteriophage viral motor\'s structure based on the work of a prominent scientist, Peixuan Guo.
Plant epigenetic memory in plant growth behavior and stress response. Sally M...CIAT
Speaker: Sally Mackenzie, Lloyd and Dottie Huck Chair for Functional Genomics, Department of Biology, Pennsylvania State University. Fellow in the American Society of Plant Biologists and the American Association for the Advancement of Science (AAAS).
Event: Robert D. Havener Seminar on “Innovations for Crop Productivity”.
http://ciat.cgiar.org/event/robert-d-havener-seminar-on-innovations-for-crop-productivity/
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Abberant hypomethylation in DNA regions with noncanonical folding potential (ncDNA motifs) is believed to predetermine tumor development - presumably, by facilitating G-quadruplex (G4) and/or i-motif (IM) formation via altering nucleosome positioning (stable G4s induce subsequent genomic rearrangements). We questioned whether CpG methylation per se affects the dsDNA-ncDNA equilibrium. Thermodynamic studies of genomic and model oligonucleotides with methylated CpG sites at different positions are reported. The genomic oligonucleotides analyzed in this work are DNA fragments with reportedly different methylation statuses in colorectal cancer and normal cells. Free energies of duplex, ncDNA formation from single strands were calculated based on melting curve analyses. Polyethylenglycole was used to imitate crowding effect. Our results suggest that CpG methylation may alter the energetic barrier for dsDNA-IM transitions.
Dr. Jesús Jiménez Barbero - Simposio Internacional 'Química: respuestas para ...Fundación Ramón Areces
Los días 8 y 9 de octubre de 2014, la Fundación Ramón Areces acogió el Simposio Internacional 'Química: respuestas para una vida mejor', organizado en colaboración con la Fundación General CSIC. Su finalidad fue ofrecer a los participantes una visión atractiva de la química moderna que sirva de base al desarrollo de nuevas respuestas para una sociedad en rápida evolución.
Characterization of the phi29 Bacteriophage Nanomotorpcpchic
The purpose is to present the evolution of our understanding to the Bacillus subtilis phi29 bacteriophage viral motor\'s structure based on the work of a prominent scientist, Peixuan Guo.
Plant epigenetic memory in plant growth behavior and stress response. Sally M...CIAT
Speaker: Sally Mackenzie, Lloyd and Dottie Huck Chair for Functional Genomics, Department of Biology, Pennsylvania State University. Fellow in the American Society of Plant Biologists and the American Association for the Advancement of Science (AAAS).
Event: Robert D. Havener Seminar on “Innovations for Crop Productivity”.
http://ciat.cgiar.org/event/robert-d-havener-seminar-on-innovations-for-crop-productivity/
Crimson Publishers- CPG Methylation in G-Quadruplex and IMotif DNA StructuresCrimsonPublishers-SBB
Abberant hypomethylation in DNA regions with noncanonical folding potential (ncDNA motifs) is believed to predetermine tumor development - presumably, by facilitating G-quadruplex (G4) and/or i-motif (IM) formation via altering nucleosome positioning (stable G4s induce subsequent genomic rearrangements). We questioned whether CpG methylation per se affects the dsDNA-ncDNA equilibrium. Thermodynamic studies of genomic and model oligonucleotides with methylated CpG sites at different positions are reported. The genomic oligonucleotides analyzed in this work are DNA fragments with reportedly different methylation statuses in colorectal cancer and normal cells. Free energies of duplex, ncDNA formation from single strands were calculated based on melting curve analyses. Polyethylenglycole was used to imitate crowding effect. Our results suggest that CpG methylation may alter the energetic barrier for dsDNA-IM transitions.
Presentació en power point de l'evolució de la figura de Jesús des de l'art paleocristià fins a l'art figuratiu. Dedicat a les alumnes de l'INS de la Pobla de Segur.,
The RET proto-oncogene encodes a receptor tyrosine kinase for members of the glial cell line-derived neurotrophic factor family of extracellular signalling molecules. RET loss of function mutations are associated with the development of Hirschsprung's disease, while gain of function mutations are associated with the development of various types of human cancer, including medullary thyroid carcinoma, multiple endocrine neoplasias type 2A and 2B, pheochromocytoma and parathyroid hyperplasia.
RET is an abbreviation for "rearranged during transfection", as the DNA sequence of this gene was originally found to be rearranged within a 3T3 fibroblast cell line following its transfection with DNA taken from human lymphoma cells. The human gene RET is localized to chromosome 10 (10q11.2) and contains 21 exons.
The natural alternative splicing of the RET gene results in the production of 3 different isoforms of the protein RET. RET51, RET43 and RET9 contain 51, 43 and 9 amino acids in their C-terminal tail respectively. The biological roles of isoforms RET51 and RET9 are the most well studied in-vivo as these are the most common isoforms in which RET occurs.
Common to each isoform is a domain structure. Each protein is divided into three domains: an N-terminal extracellular domain with four cadherin-like repeats and a cysteine-rich region, a hydrophobic transmembrane domain and a cytoplasmic tyrosine kinase domain, which is split by an insertion of 27 amino acids. Within the cytoplasmic tyrosine kinase domain, there are 16 tyrosines (Tyrs) in RET9 and 18 in RET51. Tyr1090 and Tyr1096 are present only in the RET51 isoform.
The extracellular domain of RET contains nine N-glycosylation sites. The fully glycosylated RET protein is reported to have a molecular weight of 170 kDa although it is not clear to which isoform this molecular weight relates.
Models of Human Diseases Conference (2010) Tetrahymena model by Dr. R. Pearl...Medical Education Advising
The Ciliate Protozoan Tetrahymena thermophila as an important animal model organism
Dr. R.E. Pearlman, York University
Models of Human Diseases Conference
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TELOMERE, TELOMERE STRUCTURE, ITS FUNCTION AND USE IN PLANT BREEDING. Telomere in plant breeding perspective. Case studies related to telomere in case of plant breeding. telomeres can be made use as markers in plant breeding.
This course required us to present an article which prof gave us randomly. And my article is a review paper related to TLR signaling! I upload here just hope that it can be useful for someone who is interested in this approach for studyding TLR signaling dynamics based on Synthetic ligands!
Many thanks for your look at my presentation and leave some comments if I got mistakes inside!
SmartScreen Technology for Building a Better AssayKristin Rider
A lipid derived nanoparticle the recreates the cellular membrane in solution based assays. See increased enzymatic activity, identify more relevant biological substrates, find novel hits from the compound library.
Dev Dives: Train smarter, not harder – active learning and UiPath LLMs for do...UiPathCommunity
💥 Speed, accuracy, and scaling – discover the superpowers of GenAI in action with UiPath Document Understanding and Communications Mining™:
See how to accelerate model training and optimize model performance with active learning
Learn about the latest enhancements to out-of-the-box document processing – with little to no training required
Get an exclusive demo of the new family of UiPath LLMs – GenAI models specialized for processing different types of documents and messages
This is a hands-on session specifically designed for automation developers and AI enthusiasts seeking to enhance their knowledge in leveraging the latest intelligent document processing capabilities offered by UiPath.
Speakers:
👨🏫 Andras Palfi, Senior Product Manager, UiPath
👩🏫 Lenka Dulovicova, Product Program Manager, UiPath
Neuro-symbolic is not enough, we need neuro-*semantic*Frank van Harmelen
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All of this illustrated with link prediction over knowledge graphs, but the argument is general.
Connector Corner: Automate dynamic content and events by pushing a buttonDianaGray10
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Create a campaign using Mailchimp with merge tags/fields
Send an interactive Slack channel message (using buttons)
Have the message received by managers and peers along with a test email for review
But there’s more:
In a second workflow supporting the same use case, you’ll see:
Your campaign sent to target colleagues for approval
If the “Approve” button is clicked, a Jira/Zendesk ticket is created for the marketing design team
But—if the “Reject” button is pushed, colleagues will be alerted via Slack message
Join us to learn more about this new, human-in-the-loop capability, brought to you by Integration Service connectors.
And...
Speakers:
Akshay Agnihotri, Product Manager
Charlie Greenberg, Host
Kubernetes & AI - Beauty and the Beast !?! @KCD Istanbul 2024Tobias Schneck
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Let me take this questions and provide you a short journey through existing deployment models and use cases for AI software. On practical examples, we discuss what cloud/on-premise strategy we may need for applying it to our own infrastructure to get it to work from an enterprise perspective. I want to give an overview about infrastructure requirements and technologies, what could be beneficial or limiting your AI use cases in an enterprise environment. An interactive Demo will give you some insides, what approaches I got already working for real.
The Art of the Pitch: WordPress Relationships and SalesLaura Byrne
Clients don’t know what they don’t know. What web solutions are right for them? How does WordPress come into the picture? How do you make sure you understand scope and timeline? What do you do if sometime changes?
All these questions and more will be explored as we talk about matching clients’ needs with what your agency offers without pulling teeth or pulling your hair out. Practical tips, and strategies for successful relationship building that leads to closing the deal.
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Cheryl Hung, ochery.com
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https://alandix.com/academic/papers/synergy2024-epistemic/
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To Graph or Not to Graph Knowledge Graph Architectures and LLMs
STP seminar 04/08
1. Structural studies of bacterial TIR-
domain containing proteins:
Paracoccus denitrificans
Chan Siew Leong
Pascual’s Lab
Burnham Institute for Medical Research
2. Innate immunity
First line of defense
Innate immunity is the common mode of defense
against microorganisms, using limited set of pattern-
recognition molecules.
Rely on receptors to recognize microbial signatures
such as LPS, CpG DNA, peptidoglycan and dsRNA
from viruses.
Toll-like receptors (TLR): Signal Transduction
through the TIR (Toll/IL-1 receptor) domain
3. Signaling of Toll-like Receptor
Trinchieri, G. and A. Sher (2007). Nat. Rev. Immunol. 7: 179
4. Models of Ligand-Induced TLR Activation
Leucine-Rich Repeats (LRR)
Toll/IL-1 Receptor (TIR) domain
Jin, M. S. et al. (2007). Cell 130: 1071
Kim, H. M. et al. (2007). Cell 130: 906
Brodsky, I. and R. Medzhitov (2007). Cell 130: 979
5. Protein and non-protein ligands bind to different surfaces of
TLR’s Leucine Rich-Region
Jin, M. S. et al. (2007). Cell 130: 1071
Kim, H. M. et al. (2007). Cell 130: 906
11. • What role does TIR domain play in bacteria?
• An evolved mechanism to interfere with host’s innate
immune responses?
12. TIR-Containing Proteins (E. coli and B. melitensis) reduce cytokine
secretion and increases accumulation of intracellular bacteria
Cirl, C. et al. (2008). Nat. Med. published online 9 March 2008; doi:10.1038/nm1734
13. TIR-Containing Proteins (E. coli and B. melitensis) impair TLR
signaling and interact with MyD88
Cirl, C. et al. (2008). Nat. Med. published online 9 March 2008; doi:10.1038/nm1734
14. Objectives:
Determine 3D Structure of prokaryote TIR domain
Prokaryote TIR vs. Eukaryote TIR
Interaction between Prokaryote TIR and Eukaryote TIR
Plant TIR domains
15. TIR-Like Proteins from Paracoccus denitrificans (PdTLP)
>PdTLP(Paracoccus denitrificans)
MSANDRAIETLRREIAKLQTDGAAIARKDAGIRAKLASAMAAQAKAKTAPALRLKQAEASRLEKELMATSKSQADIATKIAKKQSSLSAKLVVQ
ANEAKKADAKAKKNQERVSKTQEEATRKLEAGYRKLTLENQSLEQRLQRELSAMKPTAGPTTNADLTSAPPHDIFISHAWEDKADFVEALAHTL
RAAGAEVWYDDFSLRPGDSLRRSIDKGLGSSRFGIVVLSTHFFKKEWPQKELDGLFQLESSGRSRILPIWHKVSKDEVASFSPTMADKLAFNTS
TKSVDEIVADLMAIIRD
16.9kDa; 154 a.a; 3M; ! = 23490
1 2 3 4 5 6
Lane 1: MW Marker
Lane 2: Cell Lysate
Lane 3: After IPTG induction
Lane 4: Full Length PdTLP (after His-
Trap and S200 Gel Filtration)
Lane 5: After Chymotripsin Digestion
Lane 6: After final S-200 Gel
Filtration
Chymotrypsin cleavage
Coiled-coil domain TIR
16. PdTLP is composed of two independent folded domains
Low, L. Y. et al. (2007). Biochem. Biophy. Res. Comm. 356: 481
18. Crystallization PdTIR
PdTIR on Native Gel
• Protein concentration 5.3 mg/ml in buffer 10 mM Tris pH 8.0
• Room temperature and 4°C
• Screening: Classics, PEGS, Hampton I & II, Wizard I & II,
MPD, PACT, Cryos, JCSG+ Screening Suites.
• 0.1 M Sodium cacodylate pH 6.5, 0.2 M Ammonium sulfate
and 30% PEG 8000
19. X-ray diffraction of Pd TIR-domain crystals: 2.4 Å
• 0.1 M Sodium cacodylate pH 6.5, 0.2 M Ammonium sulfate and 30% PEG 8000
• Sitting drop, 4°C, 7 days
• Orthorhombic crystal system; P212121 space group; a=80.78, b=85.61; c=89.62
20.
21. PdTLP!s TIR domain binds to TLR4 and MyD88 TIR domains
Low, L. Y. et al. (2007). Biochem. Biophy. Res. Comm. 356: 481
24. Plant TIR Domains
• p50 effector associates with TIR
domain (LRR?)
• Mechanism of signaling is not
known
Burch-Smith, T. M. and S. P. Dinesh-Kumar (2007). Science 401: pe46
25. Arabidopsis TIR-Containing Protein exists as monomer and dimer
Dynamic Light Scattering (DLS) Native Gel
8.6 5.0 2.5 mg/ml
•Two species, non homogenous
•Poor Polyindex ~ 0.6
26. Arabidopsis TIR-Containing Protein exists as monomer under
reducing conditions
Dynamic Light Scattering (DLS) Native Gel
1.0 5.0 7.5 10.6
mg/ml
•Homogenous
•PolyIndex = 0.26
27. Future work
Determine crystal structure of TIR-Like Protein from
Paracoccus denitrificans
Structures of TLP from other organisms (E. coli, Brucella,
Yersinia, Agrobacterium, Arabidopsis)
Do bacterial TIR domains use BB-loop to bind to MyD88
and other adaptors?
Interactions between TIR domains and in-complex with
other adaptors