piggyBac stem cell engineering technology offers multiple opportunities for licensing, including research uses, vector kits, iPS cell reprogramming, iPS/ES cell engineering, cell engineering, and therapeutics. piggyBac allows for highly efficient genetic modification and reprogramming of stem cells without leaving behind mutations. It can introduce transgenes, induce pluripotent reprogramming, drive differentiation, and then excise all transgenes from the genome without footprints. This overcomes limitations of viral vectors and offers advantages for stem cell engineering applications.
The document discusses several topics related to genomics and phenotypes:
1. Genome-wide genotyping and sequencing can detect common and rare genetic variants that contribute to differences between individuals.
2. Knowledge of genetic factors like variants in VKORC1 and CYP2C9 genes can help determine the appropriate drug dose of warfarin for anticoagulation therapy in patients.
3. Targeted cancer therapies like Herceptin and various tyrosine kinase inhibitors are effective for cancers with specific "driver mutations" like EGFR mutations, which can be identified through genomic analysis of each patient's tumor.
This document summarizes the expression of recombinant β-lactoglobulin (rBLG) in prokaryotic and eukaryotic cells. In Escherichia coli, rBLG was expressed with a pET26 vector and was found predominantly in a denatured form, even when expressed in the periplasm. In eukaryotic cells like COS-7 and mouse tibialis muscle, rBLG was expressed in its native conformation. The authors quantified rBLG expression using immunoassays that distinguish between native and denatured rBLG. They found higher expression levels and native folding of rBLG in eukaryotic systems compared to prokaryotic expression
This document provides an overview of VectorBase gene sets, including:
- VectorBase provides official gene sets for mosquitoes (Anopheles, Aedes, Culex) and the tick Ixodes scapularis using automated gene modeling initially, with ongoing manual curation.
- Gene sets are made using multiple approaches including aligning proteins to genomes, aligning ESTs, and ab initio gene prediction, which are then combined.
- There are limitations to automated gene sets including missed or incomplete genes due to assembly gaps/errors and lack of evidence, as well as potential merges or splits of genes. Genome assembly issues like gaps, repeats, and polymorphisms can also impact gene sets.
Comparative genome analysis requires high quality annotations of all genomic elements. Today’s sequencing projects face numerous challenges including lower coverage, more frequent assembly errors, and the lack of closely related species with well-annotated genomes. Precise elucidation of the many different biological features encoded in any genome requires careful examination and review. We need genome annotation editing tools to modify and refine the location and structure of the genome elements that predictive algorithms cannot yet resolve automatically. During the manual annotation process, curators identify elements that best represent the underlying biology and eliminate elements that reflect systemic errors of automated analyses.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, analogous to Google Docs, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Researchers from nearly one hundred institutions worldwide are currently using Apollo for distributed curation efforts in over sixty genome projects across the tree of life: from plants to arthropods, to fungi, to species of fish and other vertebrates including human, cattle (bovine), and dog.
Inferring microbial community function from taxonomic compositionMorgan Langille
1. The document describes a computational method called PI-CRUST (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) that uses 16S rRNA gene profiles to infer functional profiles of microbial communities.
2. PI-CRUST uses ancestral state reconstruction and information from sequenced genomes to determine the likely functional content of microbes based on their taxonomic identities and relationships.
3. The authors validated PI-CRUST by testing its ability to predict the functional profiles of individual genomes and by comparing its predictions to metagenomic data from human microbiome samples. PI-CRUST showed varying accuracy depending on the functional groups being predicted.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5K, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
This presentation is an introduction to Apollo for the members of the i5K Pilot Project working on species of the order Hemiptera.
Regulation of pten activity by its carboxyl terminal autoinhibitoryChau Chan Lao
Regulation of PTEN Activity by Its Carboxyl-terminal Autoinhibitory Domain.
Leticia Odriozola, Gobind Singh, Thuong Hoang, and Andrew M. Chan
From the Department of Oncological Sciences, Mount Sinai School of Medicine, New York, New York, 10029
THE JOURNAL OF BIOLOGICAL CHEMISTRY, VOL. 282, NO. 32, pp. 23306–23315, August 10, 2007
目前已知PTEN(Phosphatase and tensin homolog)是腫瘤抑制蛋白,其由403個氨基酸組成,主要分PTPase及C2 domain,C2 domain使PTEN可與細胞膜作用連結。
PTEN之C-tail(aa 350~403)被發現具有調控PTEN自身活性之功能。前人研究指出C-tail有6個可磷酸化之位置(Thr-366、Ser-370、Ser-380、Thr-382、Thr-383及Ser-385),這些位置可調控PTEN之腫瘤抑制能力、胞內之分佈及穩定性。前人產生以上位置突變之PTEN變異株,發現這些變異株具有更強的腫瘤抑制能力,但穩定性將降低,這可能是因這些變異株具有更開放結構所致。
本報告針對研究PTEN C-tail在連結細胞膜和在其本身催化活性中扮演的功能。作者先產生一系列之PTEN磷酸化位置變異株,發現S385A會促使PTEN之membrane localization in vivo及加強phosphatase活性in vitro,而且此突變會使Ser-380/Thr-382/Thr-383 cluster的磷酸化程度降低,因此知Ser-385可透過被去磷酸化以調控PTEN。而以phosphomimic residues取代Ser-380/Thr-382/Thr-383會使上述S385A所產生之PTEN催化活性反轉。之後利用免疫沉澱方法,發現C-tail之71-amino acid region會與C2 domain上之CBR3 motif作用,暗示C-tail參與連結細胞膜之調控。最後利用合成之PTEN C-tail peptide,發現其可抑制PTEN之催化活性in vitro,而在細胞表現此peptide則會抑制PTEN之membrane localization,磷酸化之Akt量亦上升。以上實驗顯示C-tail在PTEN之membrane recruitment及PTPase活性調控中扮演Autoinhibitory domain角色。
piggyBac stem cell engineering technology offers multiple opportunities for licensing, including research uses, vector kits, iPS cell reprogramming, iPS/ES cell engineering, cell engineering, and therapeutics. piggyBac allows for highly efficient genetic modification and reprogramming of stem cells without leaving behind mutations. It can introduce transgenes, induce pluripotent reprogramming, drive differentiation, and then excise all transgenes from the genome without footprints. This overcomes limitations of viral vectors and offers advantages for stem cell engineering applications.
The document discusses several topics related to genomics and phenotypes:
1. Genome-wide genotyping and sequencing can detect common and rare genetic variants that contribute to differences between individuals.
2. Knowledge of genetic factors like variants in VKORC1 and CYP2C9 genes can help determine the appropriate drug dose of warfarin for anticoagulation therapy in patients.
3. Targeted cancer therapies like Herceptin and various tyrosine kinase inhibitors are effective for cancers with specific "driver mutations" like EGFR mutations, which can be identified through genomic analysis of each patient's tumor.
This document summarizes the expression of recombinant β-lactoglobulin (rBLG) in prokaryotic and eukaryotic cells. In Escherichia coli, rBLG was expressed with a pET26 vector and was found predominantly in a denatured form, even when expressed in the periplasm. In eukaryotic cells like COS-7 and mouse tibialis muscle, rBLG was expressed in its native conformation. The authors quantified rBLG expression using immunoassays that distinguish between native and denatured rBLG. They found higher expression levels and native folding of rBLG in eukaryotic systems compared to prokaryotic expression
This document provides an overview of VectorBase gene sets, including:
- VectorBase provides official gene sets for mosquitoes (Anopheles, Aedes, Culex) and the tick Ixodes scapularis using automated gene modeling initially, with ongoing manual curation.
- Gene sets are made using multiple approaches including aligning proteins to genomes, aligning ESTs, and ab initio gene prediction, which are then combined.
- There are limitations to automated gene sets including missed or incomplete genes due to assembly gaps/errors and lack of evidence, as well as potential merges or splits of genes. Genome assembly issues like gaps, repeats, and polymorphisms can also impact gene sets.
Comparative genome analysis requires high quality annotations of all genomic elements. Today’s sequencing projects face numerous challenges including lower coverage, more frequent assembly errors, and the lack of closely related species with well-annotated genomes. Precise elucidation of the many different biological features encoded in any genome requires careful examination and review. We need genome annotation editing tools to modify and refine the location and structure of the genome elements that predictive algorithms cannot yet resolve automatically. During the manual annotation process, curators identify elements that best represent the underlying biology and eliminate elements that reflect systemic errors of automated analyses.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, analogous to Google Docs, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Researchers from nearly one hundred institutions worldwide are currently using Apollo for distributed curation efforts in over sixty genome projects across the tree of life: from plants to arthropods, to fungi, to species of fish and other vertebrates including human, cattle (bovine), and dog.
Inferring microbial community function from taxonomic compositionMorgan Langille
1. The document describes a computational method called PI-CRUST (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) that uses 16S rRNA gene profiles to infer functional profiles of microbial communities.
2. PI-CRUST uses ancestral state reconstruction and information from sequenced genomes to determine the likely functional content of microbes based on their taxonomic identities and relationships.
3. The authors validated PI-CRUST by testing its ability to predict the functional profiles of individual genomes and by comparing its predictions to metagenomic data from human microbiome samples. PI-CRUST showed varying accuracy depending on the functional groups being predicted.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5K, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
This presentation is an introduction to Apollo for the members of the i5K Pilot Project working on species of the order Hemiptera.
Regulation of pten activity by its carboxyl terminal autoinhibitoryChau Chan Lao
Regulation of PTEN Activity by Its Carboxyl-terminal Autoinhibitory Domain.
Leticia Odriozola, Gobind Singh, Thuong Hoang, and Andrew M. Chan
From the Department of Oncological Sciences, Mount Sinai School of Medicine, New York, New York, 10029
THE JOURNAL OF BIOLOGICAL CHEMISTRY, VOL. 282, NO. 32, pp. 23306–23315, August 10, 2007
目前已知PTEN(Phosphatase and tensin homolog)是腫瘤抑制蛋白,其由403個氨基酸組成,主要分PTPase及C2 domain,C2 domain使PTEN可與細胞膜作用連結。
PTEN之C-tail(aa 350~403)被發現具有調控PTEN自身活性之功能。前人研究指出C-tail有6個可磷酸化之位置(Thr-366、Ser-370、Ser-380、Thr-382、Thr-383及Ser-385),這些位置可調控PTEN之腫瘤抑制能力、胞內之分佈及穩定性。前人產生以上位置突變之PTEN變異株,發現這些變異株具有更強的腫瘤抑制能力,但穩定性將降低,這可能是因這些變異株具有更開放結構所致。
本報告針對研究PTEN C-tail在連結細胞膜和在其本身催化活性中扮演的功能。作者先產生一系列之PTEN磷酸化位置變異株,發現S385A會促使PTEN之membrane localization in vivo及加強phosphatase活性in vitro,而且此突變會使Ser-380/Thr-382/Thr-383 cluster的磷酸化程度降低,因此知Ser-385可透過被去磷酸化以調控PTEN。而以phosphomimic residues取代Ser-380/Thr-382/Thr-383會使上述S385A所產生之PTEN催化活性反轉。之後利用免疫沉澱方法,發現C-tail之71-amino acid region會與C2 domain上之CBR3 motif作用,暗示C-tail參與連結細胞膜之調控。最後利用合成之PTEN C-tail peptide,發現其可抑制PTEN之催化活性in vitro,而在細胞表現此peptide則會抑制PTEN之membrane localization,磷酸化之Akt量亦上升。以上實驗顯示C-tail在PTEN之membrane recruitment及PTPase活性調控中扮演Autoinhibitory domain角色。
This document describes engineering a novel secretion signal (SS) that is capable of directing the secretion of recombinant proteins from both prokaryotes and eukaryotes. The researchers demonstrated secretion of fusion reporter proteins containing the SS in Escherichia coli, Saccharomyces cerevisiae and six different eukaryotic cell lines. They also showed estrogen-inducible secretion of fusion reporter proteins in six common eukaryotic cell lines. The SS allows flexible strategy for production and secretion of recombinant proteins in numerous hosts and rapid study of protein expression.
Comparative genome analysis requires high quality annotations of all genomic elements. Today’s sequencing projects face numerous challenges including lower coverage, more frequent assembly errors, and the lack of closely related species with well-annotated genomes. Precise elucidation of the many different biological features encoded in any genome requires careful examination and review. We need genome annotation editing tools to modify and refine the location and structure of the genome elements that predictive algorithms cannot yet resolve automatically. During the manual annotation process, curators identify elements that best represent the underlying biology and eliminate elements that reflect systemic errors of automated analyses.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, analogous to Google Docs, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Researchers from nearly one hundred institutions worldwide are currently using Apollo for distributed curation efforts in over sixty genome projects across the tree of life: from plants to arthropods, to fungi, to species of fish and other vertebrates including human, cattle (bovine), and dog.
Introduction to Apollo: A webinar for the i5K Research CommunityMonica Munoz-Torres
This document provides an introduction and outline for a webinar on using the Apollo genome annotation editing tool. It was presented by Monica Munoz-Torres of BBOP to the i5K Research Community. The webinar aimed to help participants better understand genome curation in the context of automated and manual annotation. It also aimed to familiarize participants with Apollo's functionality and how to identify homologs of known genes, corroborate gene models using evidence, and modify automated annotations in Apollo. The document includes sections on genome sequencing projects, the objectives and uses of genome annotation, and a biological refresher on concepts relevant to manual annotation like genes, transcription, translation, and genome curation steps.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5K, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
This presentation is an introduction to Apollo for the members of the i5K Pilot Project on Eurytemora affinis
This document provides an introduction and overview of manual genome annotation using the Apollo genome annotation tool. It begins with an outline of the webinar topics, which include an introduction to manual annotation and its necessity, an overview of the Apollo tool and its functionality for collaborative curation, and examples and demonstrations. The document then covers key concepts for manual annotation such as the definition of a gene, genome curation steps, transcription and translation including reading frames, splice sites, and phase. The goal of the webinar is to help participants better understand genome curation and manual annotation using Apollo to identify and modify gene models.
This study aims to clone and analyze GAPDH genes from various plant species to compare amino acid sequences related to catalytic function. Previous work successfully cloned GAPDH from Oxalis corniculata and Plectranthus amboinicus but not Myrtaceae psidium. The current study will continue work on the cloned samples through midipreps, restriction enzyme digestion and sequencing. Sequence data will undergo bioinformatics analysis to compare conserved amino acids of the GAPDH protein between plant species. Results could provide new genetic information published in GenBank and further the understanding of energy production pathways in plants.
Single molecule real time (SMRT) RNA sequencing was used to analyze transcriptomes of human bone marrow progenitor and differentiated cell subpopulations. This revealed over 10 times more transcript isoforms than previous methods and distinct isoform compositions between cell types. Mass spectrometry validated novel protein variants predicted from isoforms, including one for EEF1A1 only in progenitors. Distinct isoforms also distinguished cell types from paralogous gene loci not detectable before by full length sequencing.
This document describes a proposed method to map neural circuits in the Drosophila olfactory system using chemical control of flp-frt recombination. The researchers plan to fuse the flippase gene to a destabilizing domain, allowing chemical control of flippase activity and recombination through the stabilizing ligand trimethoprim. This would enable sparse labeling of individual neurons using a GFP reporter to trace their projections, avoiding issues with current heat shock methods. The proposed method involves cloning a UAS-flp-DD construct, transfecting Drosophila, and predicting the system would allow mapping neuronal projections by varying ligand levels to control the number of labeled neurons.
Mdm2 oncoprotein. Cell Mol Life Sci 55:96–107
1) Researchers identified a novel oncogene, ribosomal protein L10a (RPL10a), using a cDNA library from Daudi cells to transform p53 knockout mouse embryonic fibroblast cells.
2) Western blot analysis of tumors from myc mice showed different levels of p53 and ARF expression, indicating deregulation of the myc-ARF-p53 pathway.
3) Sequencing of DNA from foci identified RPL10a as a potential oncogene, and its interaction with Mdm2 may imitate effects of myc overexpression, contributing to tumor progression in the absence of p53
Phages can adapt to changes in host cell receptors by evolving new receptor-binding proteins (RBPs) that recognize different receptors. For example, mutations in the gene encoding protein J of phage λ allow it to recognize the new receptor OmpF in E. coli when the cognate receptor LamB is reduced. Phages may also evolve to access masked receptors by producing enzymes to degrade capsules or biofilms covering receptors. To evade host restriction systems, phages can lack restriction sites, encode DNA modifying enzymes, or produce proteins that inhibit restriction enzyme activity. CRISPR-Cas systems provide immunity by incorporating phage DNA into CRISPR loci, producing CRISPR RNAs that target invading phage
The document describes the Gateway cloning system, a molecular biology technique for efficiently transferring DNA fragments between plasmids. It involves site-specific recombination mediated by bacteriophage lambda enzymes and proprietary enzyme mixes. DNA fragments flanked by att sites can be shuttled between donor, entry, and destination vectors for functional analysis and protein expression. The process is based on two recombination reactions - BP reaction inserts DNA into an entry vector, while LR reaction transfers it to an expression vector. This technique provides a rapid and accurate method for cloning genes into multiple vectors.
Parallel mechanisms of epigenetic reprogramming in the germlineLoki Stormbringer
Germ cells possess the extraordinary and unique capacity to give rise to a new organism and create an enduring link between all generations. To acquire this property, primordial germ cells (PGCs) transit through an unprecedented programme of sequential epigenetic events that culminates in an epigenomic basal state that is the foundation of totipotency. This process is underpinned by genome-wide DNA demethylation, which may occur through several overlapping pathways, including conversion to 5-hydroxymethylcytosine. We propose that the epigenetic programme in PGCs operates through multiple parallel mechanisms to ensure robustness at the level of individual cells while also being flexible through functional redundancy to guarantee high fidelity of the process. Gaining a better understanding of the molecular mechanisms that direct epigenetic reprogramming in PGCs will enhance our ability to manipulate epigenetic memory, cell-fate decisions and applications in regenerative medicine.
The GeneArt® Gene Synthesis service consists of chemical synthesis, cloning, and sequence verification of virtually any desired genetic sequence. You will receive a bacterial stab and/or purified plasmid containing your synthesized gene—ready for downstream applications.
Whether you have limited cloning experience or simply want to save time, the GeneArt® Gene Synthesis service helps you move your ideas from the planning stage to the laboratory more quickly. Benefit from our experience in successfully producing over 180,000 constructs for customers as diverse as large pharmaceutical companies, biotechnology start-ups, and basic research institutions. The comparison shown in the figure below highlights the time and effort saved compared to traditional cloning. For more information visit:
https://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Cloning/gene-synthesis.html?CID=genesynthesis-SS-12312
The document describes the genome of the nematode C. elegans, noting that it has two sexes, hermaphrodites and males, with sex determined chromosomally. Classical genetic techniques can be used to study C. elegans, mapping mutant genes to chromosomes. The genome project involved sequencing over 2500 cosmids and other clones to assemble the physical map and fully sequence the genome.
This document discusses epigenomics and bioinformatics approaches for profiling the epigenome. It notes that the lab has over 100 people working in areas like hardware engineering, mathematics, and molecular biology. It then summarizes different techniques for profiling the epigenome using next generation sequencing, including MBD-Seq to identify methylated regions and directional RNA-seq to study non-coding RNA and alternative splicing. Integrating these diverse datasets requires normalization methods and reference databases that are still being developed.
This document discusses functional annotation and the Gene Ontology. It describes how functional annotation attaches biological information to sequences through searches of databases for homology, domains, and pathways as well as manual curation. Searches include BLAST for homology, Pfam and InterPro for domains, and KEGG and Reactome for pathways. Assignments include EC numbers for metabolic pathways and Gene Ontology terms from automated and manual annotation. Manual annotation combines all evidence and allows incorporation of experimental data but requires more time.
The document discusses functional annotation of differentially expressed genes using various bioinformatics tools. It describes using g:Profiler and DAVID to identify gene ontology terms enriched in differentially expressed genes. Specific steps are outlined, including uploading gene lists to the tools, selecting appropriate organisms, downloading results tables containing significantly enriched terms and associated genes. Functional networks can also be generated using the ClueGO app in Cytoscape. The purpose is to understand the biological processes, molecular functions and cellular components that may be perturbed based on changes in gene expression.
this is a presentation on gene expression vector that includes what is expression vector, how many types of expression vector and difference between cloning and expression vector
Plasmids are extrachromosomal DNA molecules found in bacteria that can replicate independently of the bacterial chromosome. They contain an origin of replication and may have genes for antibiotic resistance, virulence factors, or degradation of molecules. Plasmids can be classified based on their ability to integrate into chromosomes, copy number, ability to conjugate, and compatibility with other plasmids. Common plasmids used for cloning include pBR322, pUC, and pGEM3Z. These vectors contain antibiotic resistance genes and can be used to select for recombinant plasmids using antibiotic selection or blue/white screening of beta-galactosidase activity. pGEM3Z also allows for in vitro transcription of cloned genes.
Directly e-mailing authors of newly published papers encourages community curation, by Stephanie Bunt, Gary Grumbling, Helen Field, Steven Marygold, Thom Kaufman, Kathy Matthews, Nick Brown and Gillian Millburn.
Presented at the 5th International Biocuration Conference, hosted by PIR in Washington, DC, April 2-4, 2012.
Viralzone: a web resource dedicated to viruses, by Patrick Masson, Chantal Hulo, Edouard De Castro, Lydie Bougueleret, Philippe Le Mercier and Ioannis Xenarios.
Presented at the 5th International Biocuration Conference, hosted by PIR in Washington, DC, April 2-4, 2012.
This document describes engineering a novel secretion signal (SS) that is capable of directing the secretion of recombinant proteins from both prokaryotes and eukaryotes. The researchers demonstrated secretion of fusion reporter proteins containing the SS in Escherichia coli, Saccharomyces cerevisiae and six different eukaryotic cell lines. They also showed estrogen-inducible secretion of fusion reporter proteins in six common eukaryotic cell lines. The SS allows flexible strategy for production and secretion of recombinant proteins in numerous hosts and rapid study of protein expression.
Comparative genome analysis requires high quality annotations of all genomic elements. Today’s sequencing projects face numerous challenges including lower coverage, more frequent assembly errors, and the lack of closely related species with well-annotated genomes. Precise elucidation of the many different biological features encoded in any genome requires careful examination and review. We need genome annotation editing tools to modify and refine the location and structure of the genome elements that predictive algorithms cannot yet resolve automatically. During the manual annotation process, curators identify elements that best represent the underlying biology and eliminate elements that reflect systemic errors of automated analyses.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, analogous to Google Docs, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Researchers from nearly one hundred institutions worldwide are currently using Apollo for distributed curation efforts in over sixty genome projects across the tree of life: from plants to arthropods, to fungi, to species of fish and other vertebrates including human, cattle (bovine), and dog.
Introduction to Apollo: A webinar for the i5K Research CommunityMonica Munoz-Torres
This document provides an introduction and outline for a webinar on using the Apollo genome annotation editing tool. It was presented by Monica Munoz-Torres of BBOP to the i5K Research Community. The webinar aimed to help participants better understand genome curation in the context of automated and manual annotation. It also aimed to familiarize participants with Apollo's functionality and how to identify homologs of known genes, corroborate gene models using evidence, and modify automated annotations in Apollo. The document includes sections on genome sequencing projects, the objectives and uses of genome annotation, and a biological refresher on concepts relevant to manual annotation like genes, transcription, translation, and genome curation steps.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5K, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
This presentation is an introduction to Apollo for the members of the i5K Pilot Project on Eurytemora affinis
This document provides an introduction and overview of manual genome annotation using the Apollo genome annotation tool. It begins with an outline of the webinar topics, which include an introduction to manual annotation and its necessity, an overview of the Apollo tool and its functionality for collaborative curation, and examples and demonstrations. The document then covers key concepts for manual annotation such as the definition of a gene, genome curation steps, transcription and translation including reading frames, splice sites, and phase. The goal of the webinar is to help participants better understand genome curation and manual annotation using Apollo to identify and modify gene models.
This study aims to clone and analyze GAPDH genes from various plant species to compare amino acid sequences related to catalytic function. Previous work successfully cloned GAPDH from Oxalis corniculata and Plectranthus amboinicus but not Myrtaceae psidium. The current study will continue work on the cloned samples through midipreps, restriction enzyme digestion and sequencing. Sequence data will undergo bioinformatics analysis to compare conserved amino acids of the GAPDH protein between plant species. Results could provide new genetic information published in GenBank and further the understanding of energy production pathways in plants.
Single molecule real time (SMRT) RNA sequencing was used to analyze transcriptomes of human bone marrow progenitor and differentiated cell subpopulations. This revealed over 10 times more transcript isoforms than previous methods and distinct isoform compositions between cell types. Mass spectrometry validated novel protein variants predicted from isoforms, including one for EEF1A1 only in progenitors. Distinct isoforms also distinguished cell types from paralogous gene loci not detectable before by full length sequencing.
This document describes a proposed method to map neural circuits in the Drosophila olfactory system using chemical control of flp-frt recombination. The researchers plan to fuse the flippase gene to a destabilizing domain, allowing chemical control of flippase activity and recombination through the stabilizing ligand trimethoprim. This would enable sparse labeling of individual neurons using a GFP reporter to trace their projections, avoiding issues with current heat shock methods. The proposed method involves cloning a UAS-flp-DD construct, transfecting Drosophila, and predicting the system would allow mapping neuronal projections by varying ligand levels to control the number of labeled neurons.
Mdm2 oncoprotein. Cell Mol Life Sci 55:96–107
1) Researchers identified a novel oncogene, ribosomal protein L10a (RPL10a), using a cDNA library from Daudi cells to transform p53 knockout mouse embryonic fibroblast cells.
2) Western blot analysis of tumors from myc mice showed different levels of p53 and ARF expression, indicating deregulation of the myc-ARF-p53 pathway.
3) Sequencing of DNA from foci identified RPL10a as a potential oncogene, and its interaction with Mdm2 may imitate effects of myc overexpression, contributing to tumor progression in the absence of p53
Phages can adapt to changes in host cell receptors by evolving new receptor-binding proteins (RBPs) that recognize different receptors. For example, mutations in the gene encoding protein J of phage λ allow it to recognize the new receptor OmpF in E. coli when the cognate receptor LamB is reduced. Phages may also evolve to access masked receptors by producing enzymes to degrade capsules or biofilms covering receptors. To evade host restriction systems, phages can lack restriction sites, encode DNA modifying enzymes, or produce proteins that inhibit restriction enzyme activity. CRISPR-Cas systems provide immunity by incorporating phage DNA into CRISPR loci, producing CRISPR RNAs that target invading phage
The document describes the Gateway cloning system, a molecular biology technique for efficiently transferring DNA fragments between plasmids. It involves site-specific recombination mediated by bacteriophage lambda enzymes and proprietary enzyme mixes. DNA fragments flanked by att sites can be shuttled between donor, entry, and destination vectors for functional analysis and protein expression. The process is based on two recombination reactions - BP reaction inserts DNA into an entry vector, while LR reaction transfers it to an expression vector. This technique provides a rapid and accurate method for cloning genes into multiple vectors.
Parallel mechanisms of epigenetic reprogramming in the germlineLoki Stormbringer
Germ cells possess the extraordinary and unique capacity to give rise to a new organism and create an enduring link between all generations. To acquire this property, primordial germ cells (PGCs) transit through an unprecedented programme of sequential epigenetic events that culminates in an epigenomic basal state that is the foundation of totipotency. This process is underpinned by genome-wide DNA demethylation, which may occur through several overlapping pathways, including conversion to 5-hydroxymethylcytosine. We propose that the epigenetic programme in PGCs operates through multiple parallel mechanisms to ensure robustness at the level of individual cells while also being flexible through functional redundancy to guarantee high fidelity of the process. Gaining a better understanding of the molecular mechanisms that direct epigenetic reprogramming in PGCs will enhance our ability to manipulate epigenetic memory, cell-fate decisions and applications in regenerative medicine.
The GeneArt® Gene Synthesis service consists of chemical synthesis, cloning, and sequence verification of virtually any desired genetic sequence. You will receive a bacterial stab and/or purified plasmid containing your synthesized gene—ready for downstream applications.
Whether you have limited cloning experience or simply want to save time, the GeneArt® Gene Synthesis service helps you move your ideas from the planning stage to the laboratory more quickly. Benefit from our experience in successfully producing over 180,000 constructs for customers as diverse as large pharmaceutical companies, biotechnology start-ups, and basic research institutions. The comparison shown in the figure below highlights the time and effort saved compared to traditional cloning. For more information visit:
https://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Cloning/gene-synthesis.html?CID=genesynthesis-SS-12312
The document describes the genome of the nematode C. elegans, noting that it has two sexes, hermaphrodites and males, with sex determined chromosomally. Classical genetic techniques can be used to study C. elegans, mapping mutant genes to chromosomes. The genome project involved sequencing over 2500 cosmids and other clones to assemble the physical map and fully sequence the genome.
This document discusses epigenomics and bioinformatics approaches for profiling the epigenome. It notes that the lab has over 100 people working in areas like hardware engineering, mathematics, and molecular biology. It then summarizes different techniques for profiling the epigenome using next generation sequencing, including MBD-Seq to identify methylated regions and directional RNA-seq to study non-coding RNA and alternative splicing. Integrating these diverse datasets requires normalization methods and reference databases that are still being developed.
This document discusses functional annotation and the Gene Ontology. It describes how functional annotation attaches biological information to sequences through searches of databases for homology, domains, and pathways as well as manual curation. Searches include BLAST for homology, Pfam and InterPro for domains, and KEGG and Reactome for pathways. Assignments include EC numbers for metabolic pathways and Gene Ontology terms from automated and manual annotation. Manual annotation combines all evidence and allows incorporation of experimental data but requires more time.
The document discusses functional annotation of differentially expressed genes using various bioinformatics tools. It describes using g:Profiler and DAVID to identify gene ontology terms enriched in differentially expressed genes. Specific steps are outlined, including uploading gene lists to the tools, selecting appropriate organisms, downloading results tables containing significantly enriched terms and associated genes. Functional networks can also be generated using the ClueGO app in Cytoscape. The purpose is to understand the biological processes, molecular functions and cellular components that may be perturbed based on changes in gene expression.
this is a presentation on gene expression vector that includes what is expression vector, how many types of expression vector and difference between cloning and expression vector
Plasmids are extrachromosomal DNA molecules found in bacteria that can replicate independently of the bacterial chromosome. They contain an origin of replication and may have genes for antibiotic resistance, virulence factors, or degradation of molecules. Plasmids can be classified based on their ability to integrate into chromosomes, copy number, ability to conjugate, and compatibility with other plasmids. Common plasmids used for cloning include pBR322, pUC, and pGEM3Z. These vectors contain antibiotic resistance genes and can be used to select for recombinant plasmids using antibiotic selection or blue/white screening of beta-galactosidase activity. pGEM3Z also allows for in vitro transcription of cloned genes.
Directly e-mailing authors of newly published papers encourages community curation, by Stephanie Bunt, Gary Grumbling, Helen Field, Steven Marygold, Thom Kaufman, Kathy Matthews, Nick Brown and Gillian Millburn.
Presented at the 5th International Biocuration Conference, hosted by PIR in Washington, DC, April 2-4, 2012.
Viralzone: a web resource dedicated to viruses, by Patrick Masson, Chantal Hulo, Edouard De Castro, Lydie Bougueleret, Philippe Le Mercier and Ioannis Xenarios.
Presented at the 5th International Biocuration Conference, hosted by PIR in Washington, DC, April 2-4, 2012.
This document describes a study using the ODIN text mining system to extract relationships between genes, drugs, and diseases from biomedical literature and validate those relationships against the PharmGKB knowledge base. The researchers developed methods to improve relationship ranking and conducted a revalidation experiment with curators from Stanford evaluating a sample of automatically extracted relationships. The curators provided feedback that led to improvements in the interactive curation interface to better suit their needs. Lessons were learned about obtaining user requirements and rapidly implementing and testing prototypes to develop usable curation tools.
Aptamer Base: A collaborative knowledge base to describe aptamers and SELEX experiments, by Cruz-Toledo, Jose; McKeague, Maureen; Zhang, Xueru; Giamberardino, Amanda; McConnell, Erin; Francis, Tariq; DeRosa, Maria; Dumontier, Michel.
Presented at the 5th International Biocuration Conference, hosted by PIR in Washington, DC, April 2-4, 2012.
Using computational predictions to improve literature-based Gene Ontology ann...Pascale Gaudet
Using computational predictions to improve literature-based Gene Ontology annotations
The document discusses using computational gene ontology (GO) predictions to identify potential errors or areas for improvement in manually curated, literature-based GO annotations. Discrepancies between manual and computational annotations are analyzed to flag genes for review. Several attributes of flagged genes are examined to help prioritize curation efforts, including type of discrepancy, GO aspect, literature support, and source of computational prediction. While most current literature-based GO annotations are accurate, comparing to computational predictions provides an approach to continually improve annotation quality over time. Additional work is still needed to develop predictive models to better target genes most likely to need annotation updates.
BioDBCore: Current Status and Next DevelopmentsPascale Gaudet
The document discusses BioDBCore, a collaborative project aimed at gathering and standardizing metadata about biological databases. It provides an overview of BioDBCore's goals of improving data integration, encouraging standards, and maximizing resources. BioDBCore is led by Pascale Gaudet and Philippe Rocca-Serra and implemented on the BioSharing website. The document outlines the BioDBCore descriptors for databases and provides an example entry for the dictyBase database. It discusses maintaining and expanding BioDBCore records with the help of database providers and journals.
PomBase Community Curation: A Fast Track to Capture Expert Knowledge, Antonia Lock, Kim Rutherford, Midori Harris, Mark Mcdowall, Paul Kersey, Stephen Oliver, Jurg Bahler and Valerie Wood.
Presented at the 5th International Biocuration Conference, hosted by PIR in Washington, DC, April 2-4, 2012.
This document discusses protein microarrays and their development and applications. It describes some key differences between protein and DNA microarrays, such as the challenges of amplifying and predicting protein activity and interactions due to their 3D structures. Various methods for capturing proteins on chips are presented, including different oriented immobilization techniques. Applications of protein microarrays include analyzing protein interactions, screening for drug targets, and developing techniques like self-assembly and covalent mRNA-protein fusion protein microarrays. Detection methods like fluorescence, enzymatic reactions, and mass spectrometry are also summarized.
Genetic Dna And Bioinformatics ( Accession No. Xp EssayJessica Deakin
This document discusses natural language processing (NLP) for Sanskrit and different part-of-speech (POS) tagging methods. It introduces NLP and POS tagging, noting that POS tagging is the first step in developing NLP applications. It then discusses different tagsets and POS tagging approaches for Sanskrit like hidden Markov models and conditional random fields.
Stephen Friend Fanconi Anemia Research Fund 2012-01-21Sage Base
This document summarizes Stephen Friend's presentation on using data intensive science and bionetworks to build better maps of human diseases. It discusses how collecting and integrating massive amounts of molecular and clinical data using open information systems and computing could enable the development of more comprehensive and probabilistic causal models of diseases. These evolving disease maps may help identify causal genes and pathways involved in various conditions. The presentation outlines Sage Bionetworks' mission to create a commons for scientists to collaborate on building and refining such integrative bionetworks to accelerate the elimination of human disease.
Proteomics in VSC for crop improvement programmeSumanthBT1
Proteomics techniques such as gel electrophoresis and mass spectrometry are used to separate and identify proteins. Two-dimensional gel electrophoresis separates proteins by size and charge, while MALDI-TOF mass spectrometry relies on mass spectrometry to analyze proteins and peptides. Protein-protein interactions can be studied using techniques like yeast two-hybrid systems and co-immunoprecipitation. Databases such as UniProt, PDB, and KEGG provide information on protein sequences, structures, and pathways.
PROKARYOTIC TRANSCRIPTOMICS AND METAGENOMICSLubna MRL
After billions of years of evolution, prokaryotes have developed a huge diversity of regulatory mechanisms, many of which are probably uncharacterized. Now that the powerful tool of whole-transcriptome analysis can be used to study the RNA of bacteria and archaea, a new set of un expected RNA-based regulatory strategies might be revealed.
Metagenomics, together with in vitro evolution and high-throughput screening technologies, provides industry with an unprecedented chance to bring biomolecules into industrial application.
Microarrays allow researchers to examine gene expression patterns across thousands of genes simultaneously. A microarray contains probes for known genes that are used to detect complementary mRNA in a biological sample. Microarrays can be used to study gene expression differences between normal and diseased tissues, classify tumor subtypes, and diagnose cancers. They also show promise for personalized cancer treatment by predicting patient prognosis and response to therapy.
Nuclear Transport And Its Effect On Breast Cancer Tumor CellsStephanie Clark
The document discusses nuclear transport and its role in breast cancer tumor cells. It explains that nuclear transport involves the movement of large molecules in and out of the cell nucleus through nuclear pore complexes. It notes that various nuclear transport pathways play an important role in the progression and suppression of breast cancer tumor cells. Disrupting nuclear transport sequences can alter protein localization and functionality, as seen with spleen tyrosine kinase, which is a candidate tumor suppressor for breast cancer.
1) AbstractDB & ProteinComplexDB are databases that contain protein complexes extracted from PubMed abstracts along with the abstracts themselves.
2) The databases were developed using a Bayesian classifier to rank abstracts by their relevance to protein complexes based on the frequency of discriminatory words.
3) The databases allow users to validate extracted protein complexes by searching against known complex databases and enable scientists to evaluate and revise the data.
The document provides an overview of genomics and proteomics. It defines genomics as the study of an organism's complete set of genes and discusses structural, functional and comparative genomics. It also defines proteomics as the study of the complete set of proteins and discusses structural, functional and expression proteomics. The key techniques discussed for both include sequencing, 2D gel electrophoresis, mass spectrometry and database searching.
The document discusses exploring disease networks and how science is performed through networked approaches. It describes how understanding disease requires integrating DNA, RNA, protein and molecular networks. It highlights the EGFR pathway example to show biomarkers can predict treatment response complexity. CETP inhibition example shows causal relationships are not always correlative. Networked approaches are needed to generate, analyze and support new models through data sharing to help understand disease mechanisms and save costs. Synapse is proposed as a platform to enable open sharing of clinical and genomic data as well as model building, similar to how software development occurs through tools like GitHub.
This document outlines a talk on protein function and bioinformatics. It discusses why bioinformatics is needed due to the rapid increase in genomic data. It introduces various bioinformatics tools for tasks like sequence analysis, database searches, and structure prediction. As a case study, it examines the genome of the psychrophilic archaeon Methanococcoides burtonii, identifying cold-adaptation features like CSP-like proteins and modified tRNAs. It emphasizes that bioinformatics provides useful predictions but must be integrated with experimental data.
This document discusses the complexity of the transcriptome and the many sources of technical noise in RNA-Seq experiments. It notes that the transcriptome includes different combinations of exons from genes and that RNA-Seq experiments can be affected by over a dozen technical factors related to sample preparation and sequencing. Accurately analyzing results requires controlling for these sources of variability.
DNA Markers Techniques for Plant Varietal Identification Senthil Natesan
This document discusses DNA marker techniques for plant varietal identification. It provides background information on the importance of identifying crop varieties at different stages of seed production. While morphological traits can identify varieties, they are influenced by the environment and require a full growing season. The document then discusses various molecular marker techniques like RFLP, PCR, AFLP, SSR, and ISSR that can help with rapid and reliable varietal identification. It also covers the relative importance of markers, the skills and costs required for molecular marker analysis, and considerations for selecting the appropriate marker type.
The document discusses several techniques for studying protein-protein interactions, including the yeast two-hybrid system. It describes the basic procedure of the yeast two-hybrid system and some advantages, such as its ability to detect weak and transient interactions in vivo. The document also summarizes several modifications to the original yeast two-hybrid system, including the use of three proteins, dual bait systems, and recruitment systems to address some of the limitations and disadvantages of the classical yeast two-hybrid approach.
BioSmalltalk is a library for bioinformatics implemented in Pharo and part of the Open Bioinformatics Foundation. It provides basic operations on biological sequences like DNA, RNA, and proteins such as transcription, translation, complement, and reverse complement. It also includes utilities for sequence alignment, statistics, plotting, and accessing databases. The library is used in applications like analyzing positive selection in cattle breeds and using dog feces DNA profiling to solve a homicide case.
The document describes a microarray study to analyze gene expression in atherosclerotic plaques and correlate it with factors related to plaque vulnerability. Specimens will be obtained from human carotid/coronary arteries and atherosclerotic plaques in mouse models. Gene expression will be profiled using microarrays and correlated with histopathology, pH, temperature, spectroscopy and other variables. The goal is to identify genes associated with vulnerable plaques and rupture. Plaques from influenza-infected and drug-treated mice will also be analyzed to study effects on gene expression and plaque structure.
132 gene expression in atherosclerotic plaquesSHAPE Society
This document discusses microarray studies to analyze gene expression in atherosclerotic plaques and correlate it with factors related to plaque vulnerability. It begins with background on the history and applications of DNA microarrays. Key steps discussed include probe design, sample preparation including tissue collection, labeling RNA samples, hybridizing samples to a microarray chip, scanning and analyzing image data. The document outlines creating a custom microarray based on selected genes and correlating gene expression with temperature, pH, spectroscopy and histopathology of plaques. It will also analyze gene expression in influenza-infected mice and mice where plaques are induced to rupture with drugs. Human carotid artery specimens from surgery will be analyzed from symptomatic and asymptomatic patients.
The document describes a microarray study to analyze gene expression in atherosclerotic plaques and correlate it with factors related to plaque vulnerability. Specimens will be obtained from human carotid/coronary arteries and atherosclerotic plaques in mouse models. Gene expression will be profiled using microarrays and correlated with histopathology, pH, temperature, spectroscopy and other variables. Plaques from influenza-infected and drug-treated mice will also be analyzed to identify genes associated with plaque rupture. The goal is to better understand plaque vulnerability and identify potential drug targets.
Freshworks Rethinks NoSQL for Rapid Scaling & Cost-EfficiencyScyllaDB
Freshworks creates AI-boosted business software that helps employees work more efficiently and effectively. Managing data across multiple RDBMS and NoSQL databases was already a challenge at their current scale. To prepare for 10X growth, they knew it was time to rethink their database strategy. Learn how they architected a solution that would simplify scaling while keeping costs under control.
Main news related to the CCS TSI 2023 (2023/1695)Jakub Marek
An English 🇬🇧 translation of a presentation to the speech I gave about the main changes brought by CCS TSI 2023 at the biggest Czech conference on Communications and signalling systems on Railways, which was held in Clarion Hotel Olomouc from 7th to 9th November 2023 (konferenceszt.cz). Attended by around 500 participants and 200 on-line followers.
The original Czech 🇨🇿 version of the presentation can be found here: https://www.slideshare.net/slideshow/hlavni-novinky-souvisejici-s-ccs-tsi-2023-2023-1695/269688092 .
The videorecording (in Czech) from the presentation is available here: https://youtu.be/WzjJWm4IyPk?si=SImb06tuXGb30BEH .
zkStudyClub - LatticeFold: A Lattice-based Folding Scheme and its Application...Alex Pruden
Folding is a recent technique for building efficient recursive SNARKs. Several elegant folding protocols have been proposed, such as Nova, Supernova, Hypernova, Protostar, and others. However, all of them rely on an additively homomorphic commitment scheme based on discrete log, and are therefore not post-quantum secure. In this work we present LatticeFold, the first lattice-based folding protocol based on the Module SIS problem. This folding protocol naturally leads to an efficient recursive lattice-based SNARK and an efficient PCD scheme. LatticeFold supports folding low-degree relations, such as R1CS, as well as high-degree relations, such as CCS. The key challenge is to construct a secure folding protocol that works with the Ajtai commitment scheme. The difficulty, is ensuring that extracted witnesses are low norm through many rounds of folding. We present a novel technique using the sumcheck protocol to ensure that extracted witnesses are always low norm no matter how many rounds of folding are used. Our evaluation of the final proof system suggests that it is as performant as Hypernova, while providing post-quantum security.
Paper Link: https://eprint.iacr.org/2024/257
Let's Integrate MuleSoft RPA, COMPOSER, APM with AWS IDP along with Slackshyamraj55
Discover the seamless integration of RPA (Robotic Process Automation), COMPOSER, and APM with AWS IDP enhanced with Slack notifications. Explore how these technologies converge to streamline workflows, optimize performance, and ensure secure access, all while leveraging the power of AWS IDP and real-time communication via Slack notifications.
Fueling AI with Great Data with Airbyte WebinarZilliz
This talk will focus on how to collect data from a variety of sources, leveraging this data for RAG and other GenAI use cases, and finally charting your course to productionalization.
Skybuffer AI: Advanced Conversational and Generative AI Solution on SAP Busin...Tatiana Kojar
Skybuffer AI, built on the robust SAP Business Technology Platform (SAP BTP), is the latest and most advanced version of our AI development, reaffirming our commitment to delivering top-tier AI solutions. Skybuffer AI harnesses all the innovative capabilities of the SAP BTP in the AI domain, from Conversational AI to cutting-edge Generative AI and Retrieval-Augmented Generation (RAG). It also helps SAP customers safeguard their investments into SAP Conversational AI and ensure a seamless, one-click transition to SAP Business AI.
With Skybuffer AI, various AI models can be integrated into a single communication channel such as Microsoft Teams. This integration empowers business users with insights drawn from SAP backend systems, enterprise documents, and the expansive knowledge of Generative AI. And the best part of it is that it is all managed through our intuitive no-code Action Server interface, requiring no extensive coding knowledge and making the advanced AI accessible to more users.
FREE A4 Cyber Security Awareness Posters-Social Engineering part 3Data Hops
Free A4 downloadable and printable Cyber Security, Social Engineering Safety and security Training Posters . Promote security awareness in the home or workplace. Lock them Out From training providers datahops.com
Introduction of Cybersecurity with OSS at Code Europe 2024Hiroshi SHIBATA
I develop the Ruby programming language, RubyGems, and Bundler, which are package managers for Ruby. Today, I will introduce how to enhance the security of your application using open-source software (OSS) examples from Ruby and RubyGems.
The first topic is CVE (Common Vulnerabilities and Exposures). I have published CVEs many times. But what exactly is a CVE? I'll provide a basic understanding of CVEs and explain how to detect and handle vulnerabilities in OSS.
Next, let's discuss package managers. Package managers play a critical role in the OSS ecosystem. I'll explain how to manage library dependencies in your application.
I'll share insights into how the Ruby and RubyGems core team works to keep our ecosystem safe. By the end of this talk, you'll have a better understanding of how to safeguard your code.
Taking AI to the Next Level in Manufacturing.pdfssuserfac0301
Read Taking AI to the Next Level in Manufacturing to gain insights on AI adoption in the manufacturing industry, such as:
1. How quickly AI is being implemented in manufacturing.
2. Which barriers stand in the way of AI adoption.
3. How data quality and governance form the backbone of AI.
4. Organizational processes and structures that may inhibit effective AI adoption.
6. Ideas and approaches to help build your organization's AI strategy.
Your One-Stop Shop for Python Success: Top 10 US Python Development Providersakankshawande
Simplify your search for a reliable Python development partner! This list presents the top 10 trusted US providers offering comprehensive Python development services, ensuring your project's success from conception to completion.
TrustArc Webinar - 2024 Global Privacy SurveyTrustArc
How does your privacy program stack up against your peers? What challenges are privacy teams tackling and prioritizing in 2024?
In the fifth annual Global Privacy Benchmarks Survey, we asked over 1,800 global privacy professionals and business executives to share their perspectives on the current state of privacy inside and outside of their organizations. This year’s report focused on emerging areas of importance for privacy and compliance professionals, including considerations and implications of Artificial Intelligence (AI) technologies, building brand trust, and different approaches for achieving higher privacy competence scores.
See how organizational priorities and strategic approaches to data security and privacy are evolving around the globe.
This webinar will review:
- The top 10 privacy insights from the fifth annual Global Privacy Benchmarks Survey
- The top challenges for privacy leaders, practitioners, and organizations in 2024
- Key themes to consider in developing and maintaining your privacy program
A Comprehensive Guide to DeFi Development Services in 2024Intelisync
DeFi represents a paradigm shift in the financial industry. Instead of relying on traditional, centralized institutions like banks, DeFi leverages blockchain technology to create a decentralized network of financial services. This means that financial transactions can occur directly between parties, without intermediaries, using smart contracts on platforms like Ethereum.
In 2024, we are witnessing an explosion of new DeFi projects and protocols, each pushing the boundaries of what’s possible in finance.
In summary, DeFi in 2024 is not just a trend; it’s a revolution that democratizes finance, enhances security and transparency, and fosters continuous innovation. As we proceed through this presentation, we'll explore the various components and services of DeFi in detail, shedding light on how they are transforming the financial landscape.
At Intelisync, we specialize in providing comprehensive DeFi development services tailored to meet the unique needs of our clients. From smart contract development to dApp creation and security audits, we ensure that your DeFi project is built with innovation, security, and scalability in mind. Trust Intelisync to guide you through the intricate landscape of decentralized finance and unlock the full potential of blockchain technology.
Ready to take your DeFi project to the next level? Partner with Intelisync for expert DeFi development services today!
Skybuffer SAM4U tool for SAP license adoptionTatiana Kojar
Manage and optimize your license adoption and consumption with SAM4U, an SAP free customer software asset management tool.
SAM4U, an SAP complimentary software asset management tool for customers, delivers a detailed and well-structured overview of license inventory and usage with a user-friendly interface. We offer a hosted, cost-effective, and performance-optimized SAM4U setup in the Skybuffer Cloud environment. You retain ownership of the system and data, while we manage the ABAP 7.58 infrastructure, ensuring fixed Total Cost of Ownership (TCO) and exceptional services through the SAP Fiori interface.
HCL Notes and Domino License Cost Reduction in the World of DLAUpanagenda
Webinar Recording: https://www.panagenda.com/webinars/hcl-notes-and-domino-license-cost-reduction-in-the-world-of-dlau/
The introduction of DLAU and the CCB & CCX licensing model caused quite a stir in the HCL community. As a Notes and Domino customer, you may have faced challenges with unexpected user counts and license costs. You probably have questions on how this new licensing approach works and how to benefit from it. Most importantly, you likely have budget constraints and want to save money where possible. Don’t worry, we can help with all of this!
We’ll show you how to fix common misconfigurations that cause higher-than-expected user counts, and how to identify accounts which you can deactivate to save money. There are also frequent patterns that can cause unnecessary cost, like using a person document instead of a mail-in for shared mailboxes. We’ll provide examples and solutions for those as well. And naturally we’ll explain the new licensing model.
Join HCL Ambassador Marc Thomas in this webinar with a special guest appearance from Franz Walder. It will give you the tools and know-how to stay on top of what is going on with Domino licensing. You will be able lower your cost through an optimized configuration and keep it low going forward.
These topics will be covered
- Reducing license cost by finding and fixing misconfigurations and superfluous accounts
- How do CCB and CCX licenses really work?
- Understanding the DLAU tool and how to best utilize it
- Tips for common problem areas, like team mailboxes, functional/test users, etc
- Practical examples and best practices to implement right away
WeTestAthens: Postman's AI & Automation Techniques
Bairoch ISB closing-talk: CALIPHO
1. CALIPHO: two missions for one goal:
increasing our knowledge on human
proteins
Amos
Bairoch
April
4,
2012
2. Computer
Analysis
and
Laboratory
Inves6ga6on
of
Proteins
of
Human
Origin
Its
two
missions:
Carry
out
laboratory
experiments
on
selected
sets
of
uncharacterized
human
proteins
to
discover
their
func6on
Develop
neXtProt,
an
ambi6ous
new
knowledge
resource
centered
around
human
proteins
3. ‘The’
human
genome
• Sequencing
a
human
genome
is
no
longer
a
technological
challenge;
• Making
sense
of
what
it
tells
us
is
s6ll
much
more
problema6c
then
anyone
ever
expected.
4. Almost 12 years ago, at the 4th
Siena meeting, we proposed to
annotate in Swiss-Prot all the
human proteins
5. Some
stats
on
human
proteins
from
UniProtKB/Swiss-‐Prot
• 20’244
reviewed
entries
(~protein-‐coding
genes);
• 16’000
addi6onal
isoforms
in
about
8’100
entries
(40%
but
will
probably
rise
to
>60%):
50’000
different
protein
sequences;
• 65’000
variants;
22’500
linked
to
diseases;
the
rest
are
SNPs
that
are
SAPs
(2
per
proteins).
This
is
the
6p
of
the
iceberg;
• 80’000
PTMs
(50%
of
which
are
experimental).
This
is
the
6p
of
the
6p
of
the
iceberg!
6. Some
issues
about
protein-‐coding
genes
• We
completely
agree
with
what
was
shown
earlier
in
this
mee6ng
by
the
HAVANA
group:
that
there
are
slightly
less
then
20K
protein-‐coding
genes;
• Many
weirdos
in
the
genome:
bicistronic
mRNAs,
genes
that
produce
through
splicing
proteins
with
no
sequence
rela6onship,
mul6ple
genes
for
the
same
protein,
etc;
• Varia6on
in
term
not
only
of
SNPs
but
of
copy
number.
And
some
segrega6ng
pseudogenes
(olfactory
receptors);
• How
many
have
been
proven
at
protein
level?
– Using
the
protein
evidence
“metric”
used
at
UniProt
and
neXtProt,
we
are
now
at
about
70%;
– But
if
we
were
hun6ng
everywhere
in
good-‐quality
MS
data,
it
would
rise
to
about
85%.
The
big
issue
in
proteomics
is
how
to
hunt
for
the
last
15%
8. From
genome
to
proteome
~ 20’000 protein ~ 5'000'000
coding-genes different
proteins
post-translational
modifications of proteins
alternative splicing
(PTMs)
of mRNA
50-100 fold increase
2-5 fold increase
~ 50 to 100’000
transcripts
(mRNAs)
Protein
complexity
10. Many
human
proteins
for
which
we
lack
func6onal
knowledge
1. Similar
to
characterized
proteins
in
distant
organisms
(bacteria,
plants,
yeast),
but
no
valida6on
in
mammals;
2. Presence
of
domains
that
help
predict
a
‘general’
func6on
but
not
a
precise
one
(examples:
hydrolase
fold,
GPCR);
3. Presence
of
domains
or
sequence
features
that
help
define
some
proper6es
(examples:
PDZ
-‐>
PPI,
many
TMs
-‐>
integral
membrane
protein);
4. “Orphan”.
With
no
similarity
to
any
characterized
proteins
but
that
can
be
conserved
across
a
more
or
less
wide
taxonomic
space.
About
5’000
human
proteins
are
in
one
of
the
above
four
categories
11. Overview
of
the
CALIPHO
wet
lab
strategy
In
silico
selecCon
:
sequence
analysis,
phylogeny,
data
mining
Tissue/cell
line
expression
(RT-‐PCR)
Cloning
of
cDNA
in
the
Gateway
system
Yeast
two
hybrid
Subcellular
locaCon
in
HeLa
cells
Recombinant
protein
(confocal
imaging)
producCon
in
E.Coli
ValidaCon
of
protein-‐protein
interacCons
(GST
pull
down,
co-‐IP)
3D
structure
by
NMR
Data
mining,
Modelling
Hypothesis
generaCon
FuncConal
assays
on
cell
lines
(RNAi)
In
vivo
validaCon
(animal
models
eg
zebrafish)
CALIPHO@UniGe
collaborators
CALIPHO@SIB
12. Aner
2.5
years…
• A
protein
involved
in
ciliogenesis;
• An
enzyme
involved
in
a
salvage
pathway
not
yet
characterized
in
vertebrates;
• A
myristoylated
and
palmitoylated
protein
that
could
be
involved
in
membrane
blebbing;
• A
mitochondrial
protein
that
may
play
a
role
in
a
Mt
import
mechanism.
13. Personal
view
• Cons:
– It
takes
much
longer
than
what
you
expect
or
want!
And
magic
and
luck
seem
to
be
the
most
important
factors
in
successful
experiments!
– The
low
ra6o
of
quality/cost
for
many
lab
reagents
(defec6ve
an6bodies
for
example!);
– You
can’t
freely
share
preliminary
results
with
everyone
because
you
may
(will!)
be
scooped.
• Pros:
– Fun
to
see
bioinforma6cs
predic6ons
confirmed
in
the
lab;
– Nice
collabora6ons;
– Great
lab
atmosphere.
14. • What:
a
comprehensive
resource
that
complements
SIB/
EBI
Swiss-‐Prot
human
protein
annota6on
efforts.
We
expect
neXtProt
to
become
a
central
resource
for
human
protein-‐centric
informa6on;
• How:
– by
mining,
in
the
most
appropriate
way
and
with
stringent
quality
criteria,
many
high-‐throughput
data
resources.
We
plan
to
add
addi6onal
protein/protein
and
protein/small
molecules
interac6ons,
proteomics
data,
pathways/networks
informa6on,
varia6on
data
(such
as
SNP
frequencies),
siRNA
screen
data,
phylogene6c
profiling,
etc.;
– by
integra6ng
experimental
results
from
an
extensive
network
of
collabora6ng
laboratories.
15. Sequence databases Enzyme and pathway
Proteomics EMBL databases
HPA IPI BioCyc
PeptideAtlas PIR BRENDA
PRIDE RefSeq Pathway_Interaction_DB Family and domain
UniGene Reactome
databases
Gene3D
InterPro
2D-gel databases PANTHER
PIRSF
ANU-2DPAGE
Aarhus/Ghent-2DPAGE In Swiss-Prot users always need to navigate Pfam
PRINTS
Cornea-2DPAGE toward many external resources so as to ProDom
DOSAC-COBS-2DPAGE
PROSITE
HSC-2DPAGE consolidate data into knowledge
SMART
OGP
TIGRFAMs
PMMA-2DPAGE
REPRODUCTION-2DPAGE
SWISS-2DPAGE
World-2DPAGE UniProtKB/Swiss-Prot
Human entries links Miscellaneous
ArrayExpress
Organism-specific Bgee
databases BindingDB
CleanEx
GeneCards
dbSNP
H-InvDB
HGNC
In neXtProt the most pertinent data will be DIP
DrugBank
MIM integrated so as to enable complex queries
GO
Orphanet
HOGENOM
PharmGKB
HOVERGEN
IntAct
LinkHub
NextBio
Genome annotation
databases 3D structure Protein family/group
databases databases
Ensembl
GeneID PTM databases DisProt GermOnline
KEGG GlycoSuiteDB HSSP MEROPS
NMPDR PhosphoSite PDB PeroxiBase
PDBsum REBASE
SMR TCDB
16. What
is
not
neXtProt?
• No,
neXtProt
is
not
a
replacement
for
UniProtKB/Swiss-‐Prot;
• No,
neXtProt
is
not
universal
in
coverage,
it
is
intended
to
provide
knowledge
per6nent
to
human
proteins;
• No,
neXtProt
is
not
a
sequence
resource:
it
uses
the
sequence
data
curated
in
Swiss-‐Prot.
17. When
and
what?
• In
early
2011
we
released
a
first
public
version
that
contained
in
terms
of
data:
– All
of
Swiss-‐Prot
human
data:
sequences
and
annota6ons;
– Human
Protein
Atlas
(HPA)
organ
and
6ssue
expression
informa6on
from
IHC
(an6bodies);
– Metadata
on
mRNA
expression
from
microarrays
and
ESTs
from
Bgee
(analyzed
from
ArrayExpress
and
UniGene);
– Addi6onal
SNPs
from
dbSNP
and
Ensembl;
– Chromosomal
loca6on
and
exons
mapping
from
Ensembl;
– Affymetrix
and
Illumina
chip
sets
iden6fiers.
• In
terms
of
interface,
it
offers:
– An
intui6ve
query
interface;
– Many
specialized
views
(func6on,
medical,
expression,
etc);
– The
possibility
to
tag
and
label
proteins.
18. Bronze,
silver
and
gold
• We
have
a
three-‐6ered
approach
as
to
data
quality:
– Bronze:
noisy
or
low
quality
data
that
is
not
imported
in
the
plarorm;
– Silver:
good
data,
but…..
– Gold:
data
that
we
believe
to
be
of
a
swiss-‐(prot)-‐level
quality.
• By
default
searches
in
neXtProt
are
carried
out
on
gold
data;
• Quality
classifica6on
is
a
dynamic
process.
26. PTMs
We
are
loading
high-‐quality
sets
of
PTMs,
star6ng
with
N-‐glycosyla6on
and
phosphoryla6on
27. Pep6de
iden6fica6ons
• HUPO
brain
and
plasma
project
pep6des
from
Pep6deAtlas;
• Sets
linked
with
PTMs;
• Carapito
et
al
mitochondrial
N-‐terminome
project.
And
to
be
loaded
soon:
• Other
HUPO
data
sets;
• Data
from
various
labs
(Vienna,
Geneva,
Roche
(Basel),
Montpellier,
etc.).
28. New
subcellular
localiza6on
data
• From
two
projects:
DKFZ
GFP-‐cDNA@EMBL
and
WIS
Kahn
Dynamic
Proteomics
db
29. Data
export
• Export
of
data
both
in
XML
and
in
PEFF
formats;
• neXtProt
is
the
first
resource
to
offer
support
to
the
PSI
PEFF
format;
• This
enriched
FASTA
format
allows
search
engines
and
other
tools
to
easily
and
consistently
access
data
essen6al
to
the
success
of
HPP,
namely
sequence
varia6ons
and
PTMs.
30. Download
by
FTP
• At
np.nextprot.org
• To
obtain
downloads
in
XML
or
PEFF;
• These
files
are
also
available
per
chromosome
as
well
as
‘report’
files
31. What’s
next
in
term
of
tools
• A
tool
for
the
the
analysis
of
lists
of
proteins
so
as
to
explore
their
enrichment
in
various
types
of
annota6ons,
including
Gene
Ontology
(GO)
terms.
32. Programma6c
access
• We
will
build
an
API
to
allow
third
party
sonware
tools
to
make
use
of
the
data
in
neXtProt;
• Together
with
BIONEXT,
we
have
obtained
a
grant
to
develop
this
API
and
integrate
a
version
of
their
3D
structure
visualisa6on
tool
in
neXtProt.
33. A
note
about
variants
• There
are
now
over
420’000
variants
loaded
in
neXtProt;
• The
65’000
from
Swiss-‐Prot,
the
others
have
been
loaded
from
dbSNP
through
Ensembl;
• We
will
also
load
the
Cosmic
variants
as
well
as
other
sources.
34. We
also
want
to
do
many
other
things
as
quickly
as
possible
but…
35. The
road
map:
principles
• Our
vision
is
to
gradually
build
up
neXtProt,
not
only
by
adding
new
data
resources
but:
– By
integra6ng
state
of
the
art
data
mining
tools;
– By
integra6ng
some
forms
of
“social
networking”
func6onali6es
allowing
researchers
to
share
ideas
and
data;
– By
enabling
the
modeling
of
hypothesis
inside
the
framework
of
the
plarorm.
• To
work
closely
with
collaborators
and
users
to
define
how
the
data
and
tools
that
we
will
incorporate
into
neXtProt
will
be
useful
for
their
research.
36. A
new
resource
for
cell
lines
• There
are
three
ontologies
catering
for
cell
lines
(MCCL
CLO,
Brenda);
• A
large
number
of
on-‐line
catalogs:
ATCC,
CBA,
CCRID,
Coriell,
DSMZ,
ECACC,
ICLC,
IFO,
IZSLER,
JCRB,
RCB,
Riken;
• There
are
informa6on
resources:
CABRI,
CCLE,
COPE,
HyperCLDB,
Lonza;
• Databases
storing
cell
lines
as
“samples”:
Cosmic
• Topical
reviews
on
‘categories’
of
cell
lines;
• Various
lists
of
contaminated
cell
lines….
But
there
were
so
far
no
single
resource
pooling
together
all
this
informa6on
in
an
awempt
to
create
a
cell
line
thesaurus..
37.
• Not
an
ontology,
but
a
thesaurus;
• Links
to
all
the
ontologies,
catalogs,
resources,
publica6ons,
web
sites,
etc.
(over
20’000
Xref);
• Current
version:
8766
cell
lines.
The
next
version
(May)
will
have
over
10’000
lines,
5’000
synonyms;
• Scope:
vertebrates
(80%
human,
15%
mouse
and
rat,
the
reminder
are
associated
with
about
100
species;
• Currently
available
in
a
Swiss-‐Prot
like
text-‐based
format
at:
np://np.nextprot.org/
• But
it
will
soon
also
be
available
in
OBO
format
as
it
has
a
number
of
rela6onships
(derives_from,
etc.);
• Currently:
no
links
to
6ssues
and
diseases,
but
this
will
be
added
later.
38. ID 22Rv1!
AC CVCL_1045!
SY 22RV1; 22Rv-1; CWR22-Rv1; CWR22R-V1; CWR22Rv1!
DR CLO; CLO_0001199!
DR CLO; CLO_0001200!
DR Brenda; BTO:0002999!
DR CLDB; cl7072!
DR ATCC; CRL-2505!
DR CCLE; 22RV1_PROSTATE!
DR CCRID; 3131C0001000700100!
DR Cosmic; 924100!
DR DSMZ; ACC-438!
DR ECACC; 05092802!
DR PubMed; 14518029!
WW http://capcelllines.ca/details.asp?id=53!
WW http://bio.lonza.com/extras/cell-transfection-database/..!
OX NCBI_TaxID=9606; ! Homo sapiens!
HI CVCL_3967 ! CWR22!
//!
39.
40. The
ISB
• A
young
society
but
already
very
ac6ve:
• Pros:
– Over
310
ac6ve
members
from
15
countries;
– The
interna6onal
mee6ng
(now
yearly);
– Good
links
to
journals
such
as
Database
and
NAR;
– Common
projects
such
as
BioDBCore
• Cons:
– Not
enough
grass
root
involvements
of
the
members;
– Not
yet
enough
awareness
of
the
existence
of
the
society
by
would-‐be
members
in
many
countries
(Eastern
Europe,
South
America,
etc.)
but
also
closer
to
‘home’
(in
the
US).
Be
more
proacCve!
41. Biocura6on
is
an
expanding
field
• Good
news:
– Increasing
number
of
biocurators
in
academia
and
industry;
– More
and
more
knowledge
resources
incorporate
some
amount
of
manual
biocura6on.
• Bad
news:
– The
usual
problem
of
long-‐term
funding
and
sustainability
of
key
resources;
– A
lot
of
re-‐inven6ng
the
wheel
as
annota6on
SOPs
are
generally
not
easily
available.
42. The
data
flood
• Yes
it
exists
but…..
• A
big
propor6on
of
the
data
that
accumulates
today
is
not
going
to
be
useful
in
a
few
years;
• For
example:
if
we
have
clean
full
length
genome
sequence
of
“all”
representa6ve
species
on
earth
this
is
only
10
petabytes
of
informa6on
(10
million
species
with
1
billion
bp
each);
• The
genome
of
a
human
being
stored
as
variant
file
is
only
60
Mb
(compressed).
So
storing
the
varia6on
informa6on
for
10
billion
individuals
is
slightly
less
than
1
exabyte
–
not
a
big
challenge
in
term
of
technology
and
price
in
2020;
• In
the
meanwhile
we
are
s6ll
encapsula6ng
our
most
important
knowledge
using
a
16th
century
technology:
free
43. CALIPHO@UniGe_and_SIB
• neXtProt
content:
– Coordinator:
Pascale
Gaudet
– Biocurators:
Guislaine
Argoud-‐Puy,
Aurore
Britan,
Jonas
Cicenas,
Isabelle
Cusin,
Paula
Duek,
Nevila,
Nouspikel
– QA:
Monique
Zahn
• neXtProt
sobware
developers:
– Olivier
Evalet,
Alain
Gateau,
Anne
Gleizes,
Mario
Pereira,
Catherine
Zwahlen
(and
for
two
years:
Alexandre
Masselot)
• Laboratory
research:
– Franck
Bontems,
Marjorie
Desmurs,
Camille
Mary,
Rachel
Porcelli,
Irene
Rossito,
Lisa
Salleron,
Fabiana
Tirone
• Directed
by:
– Amos
Bairoch
and
Lydie
Lane
And
we
have
a
posi6on
open
for
a
Java
developer
(will
soon
be
announced
on
the
ISB
web)