Refining Gene Ontology to Include Terms and Relationships Relevant to exRNA Communications
•
1 like•1,461 views
The document discusses efforts to standardize terminology related to extracellular vesicles (EVs) and exRNA-containing particles through developing new terms and relationships within the Gene Ontology (GO). It describes work with domain experts to propose additions to GO's Cellular Component branch to accurately describe and classify EVs and exRNA communications. The goal is to strike a balance between overgeneralizing and being too specific when defining terms in this emerging research area.
Report
Share
Report
Share
Download to read offline
![An ontology is used to represent domain knowledge in a standard
machine-readable way to enable data annotation, discovery, and
integration. The Extracellular RNA Communication Consortium has
established an ontology group to work towards standardization and
classification of the terms used to describe extracellular vesicles
(EVs).
As part of this ontology effort, we have worked with domain experts
and ontology experts to propose new terms and relationships that
can be added to the widely-used Gene Ontology (GO) for describing
EVs and other exRNA-containing particles. Our proposal reflects
broad community consensus, as it was reviewed and approved by:
• International Society for Extracellular Vesicles
• American Society for Exosomes and Microvesicles.
In this attempt to standardize exRNA-related terminology, we strive to
strike a balance between the “lumper” and “splitter” approaches in
this new and incompletely understood domain. We are currently
working closely with the GO Consortium to incorporate the proposed
terms and relationships into the GO Cellular Component branch.
Extension of GO Cellular Component branch to include terms
and relationships relevant to exRNA communications
Refining Gene Ontology to Include Terms and Relationships Relevant to exRNA Communications
Cheung KH1, Laurent LC2, Roncaglia P3, Gould S4, Mathivanan S5, Hill AF6, Lotvall J6, Subramanian S7, Roth M7, Alexander R8, Kitchen R1, Rozowsky J1,
Wauben M9, Quesenberry P10, Patel T11, Breakefield X12, Thery C13, Ezrin A14, Su A15, Galas D8, Gerstein MB1, Milosavljevic A7
1Yale University, New Haven, CT, USA; 2UC San Diego, La Jolla, CA, USA; 3European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, UK and The Gene Ontology Consortium; 4Johns Hopkins
University School of Medicine, Baltimore, MD, USA; 5La Trobe University, Bundoora, Victoria, Australia; 6University of Gothenburg, Gothenburg, Sweden; 7Baylor College of Medicine, Houston, TX, USA; 8Pacific Northwest Diabetes
Research Institute, Seattle, WA, USA; 9Universiteit Utrecht, Utrecht, Netherlands; 10University Medicine Comprehensive Cancer Center, Providence, RI, USA; 11Mayo Clinic, Jacksonville, FL, USA; 12Harvard Medical School, Boston,
MA, USA;13Institut Curie, INSERM U932, Paris, France; 14NX PharmaGen, Louisville, KY, USA; 15The Scripps Research Institute, La Jolla, CA, USA
Abstract
• Add more terms and relationships that are relevant
to exRNA communications
• Annotate metadata (metadata working group)
• Link to other ontologies
• Develop use cases for ontological data integration
Future Directions
GO Browser
GO:1990684 protein-lipid-RNA complex
definition: "A macromolecular complex containing separate
protein, lipid and RNA molecules. Separate in this context means
not covalently bound to each other." [GOC:vesicles,
PMID:21423178, PMID:22028337, PMID:23559634]
comment: Examples of protein-lipid-RNA complexes are
described in PMID:21423178 and PMID:23559634, both showing
evidence that high-density lipoprotein (HDL) and, to a lesser
extent, low-density lipoprotein (HDL) transport endogenous
microRNAs (miRNAs) and deliver them to recipient cells with
functional targeting capabilities. Also see fig. 1 in the review
PMID:22028337. Not to be confused with GO:0034364 'high-
density lipoprotein particle' or GO:0034362 'low-density lipoprotein
particle', which describe complexes of proteins and lipids only,
without RNAs.
synonym: "miRNA-lipoprotein complex" RELATED []
is_a: GO:0032991 ! macromolecular complex
relationship: has_part CHEBI:18059 ! lipid
relationship: has_part CHEBI:33697 ! ribonucleic acid
relationship: has_part PR:000000001 ! protein
Acknowledgements
• Extracellular RNA Communications Consortium
• External RNA Controls Consortium
• International Society for Extracellular Vesicles
• American Society for Exosomes and Microvesicles
• Gene Ontology Consortium
• This work was supported in part by NIH Common Fund
Legend:
• Rectangles represent GO terms.
• Ovals represent synonyms.
• Arrows represent is_a relationships.
• Dashed lines represent synonymous relationships.
• White rectangles represent existing GO terms.
• Black arrows represent existing is_a relationships.
• Red markings represent either new terms/synonyms or
existing terms/synonyms with new relationships.](https://image.slidesharecdn.com/erccgoposter2015-04-16-150803161443-lva1-app6892/85/Refining-Gene-Ontology-to-Include-Terms-and-Relationships-Relevant-to-exRNA-Communications-1-320.jpg)
Recommended
Extracellular RNA Communication: Mechanisms, Biomarkers, and Therapies
The document summarizes work from the Extracellular RNA Communication Consortium (ERCC) on extracellular RNA (exRNA). It describes how exRNA profiles differ between biofluids like plasma, urine, saliva and cerebrospinal fluid (CSF). For example, over 60% of RNA in plasma is YRNA. It also highlights studies from the ERCC on the biogenesis of exRNAs, their potential as biomarkers for diseases like glioblastoma, and therapies using exosomes from stem cells which rescued mice from lethal liver failure.
Third Natural Eukaryotic Epigenetic Mark Found.pdf
A group at the Marine Biology Laboratory (MBL) now found a third epigenetic mark in this freshwater invertebrate, Adineta vaga, which has previously been found only in bacteria. For the first time, a horizontally transferred gene has been shown to remodel gene regulatory systems in eukaryotes.
Undergraduate Research Grant
This grant proposal aims to analyze protein-protein interactions within the type-III secretion system (T3SS) of the pathogenic bacterium Chromobacterium violaceum. The researchers will use molecular techniques like PCR and the yeast two-hybrid system to study interactions between 11 proteins that are thought to be involved in Cpi-2, one of two T3SSs found in C. violaceum. Understanding these interactions could help identify new drug targets and vaccine components to treat infections caused by this antibiotic-resistant bacterium. The proposal outlines experiments to clone the genes of interest, test protein interactions using yeast two-hybrid screens, and build an interaction map of the Cpi-2 T3SS apparatus.
Testing for Food Authenticity
This document discusses food authenticity testing and the issues with current testing methods. It introduces next generation sequencing (NGS) as a new method for food authenticity testing. NGS allows for the simultaneous detection of thousands of potential food contaminants in a single test, overcoming limitations of current polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA) methods. NGS involves amplifying DNA from all species in a mixed sample, sequencing the amplified products, and comparing the sequences to a reference database to identify contaminants. While a major improvement, NGS also has limitations, such as an inability to currently quantify contamination levels.
ACR2016 Wermuth Exosome poster
The exosomes isolated from serum of patients with systemic sclerosis contained higher levels of profibrotic miRNAs and lower levels of antifibrotic miRNAs compared to exosomes from healthy individuals. When applied to normal dermal fibroblasts in culture, the scleroderma patient exosomes stimulated the expression of profibrotic genes, mimicking the phenotype of scleroderma fibroblasts. This effect was partially reduced when the exosomes were pre-treated to degrade either the RNA or protein content, indicating both components contribute to the exosomes' ability to induce a profibrotic phenotype in target cells and suggesting a potential mechanism for the transmission and progression of fibrosis in scleroderma.
Biotecnika Times Newspaper 6th December 2018
This summary provides the key details from the multi-page document in 3 sentences:
The document reports on recent scientific studies, including the development of a new type of biological data recorder using genetically modified E. coli bacteria. It also describes new "kill switch" mechanisms engineered into bacteria to ensure they self-destruct under certain conditions. Additionally, the document summarizes a study that found the process of clearing dying cancer cells (efferocytosis) can unexpectedly promote tumor growth in bone metastases of prostate cancer by stimulating the release of a pro-inflammatory protein.
Human Cell Line Authentication. Why is it so important?
The differences between a cow and a monkey are clear. It is easy to tell a moth from a mosquito. So why are there still scientific studies that mix them up? The answer is simple: hundreds of cell lines stored and used by modern laboratories have been wrongly identified. Some pig cells are labelled as coming from a chicken; cell lines advertised as human have been shown to contain material from hamsters, rats, mice and monkeys. Problems have already been found with more than 400 cell lines. (Cited from Nature 520 (2015)).
An increasing number of scientific publications (i.e. Nature journals) are now sistematically asking for cell line authentication at the moment of paper submission. To help researchers to meet this requirement, UAT is starting to offer a new service for human cell line authentication.
NAISTビッグデータシンポジウム - バイオ久保先生
This document summarizes a presentation given by Minoru Kubo on single cell analyses for plant reprogramming studies. The presentation covered how next generation sequencing and single cell analyses have changed biological research. It discussed single cell transcriptomics for analyzing plant reprogramming at the single cell level. The goal is to identify reprogramming genes, understand cell-cell interactions during reprogramming, and validate theories of reprogramming using the moss Physcomitrella patens as a model organism. Positioning information from single cell analyses could provide new insights into cell lineages, interactions, and multicellular development.
Recommended
Extracellular RNA Communication: Mechanisms, Biomarkers, and Therapies
The document summarizes work from the Extracellular RNA Communication Consortium (ERCC) on extracellular RNA (exRNA). It describes how exRNA profiles differ between biofluids like plasma, urine, saliva and cerebrospinal fluid (CSF). For example, over 60% of RNA in plasma is YRNA. It also highlights studies from the ERCC on the biogenesis of exRNAs, their potential as biomarkers for diseases like glioblastoma, and therapies using exosomes from stem cells which rescued mice from lethal liver failure.
Third Natural Eukaryotic Epigenetic Mark Found.pdf
A group at the Marine Biology Laboratory (MBL) now found a third epigenetic mark in this freshwater invertebrate, Adineta vaga, which has previously been found only in bacteria. For the first time, a horizontally transferred gene has been shown to remodel gene regulatory systems in eukaryotes.
Undergraduate Research Grant
This grant proposal aims to analyze protein-protein interactions within the type-III secretion system (T3SS) of the pathogenic bacterium Chromobacterium violaceum. The researchers will use molecular techniques like PCR and the yeast two-hybrid system to study interactions between 11 proteins that are thought to be involved in Cpi-2, one of two T3SSs found in C. violaceum. Understanding these interactions could help identify new drug targets and vaccine components to treat infections caused by this antibiotic-resistant bacterium. The proposal outlines experiments to clone the genes of interest, test protein interactions using yeast two-hybrid screens, and build an interaction map of the Cpi-2 T3SS apparatus.
Testing for Food Authenticity
This document discusses food authenticity testing and the issues with current testing methods. It introduces next generation sequencing (NGS) as a new method for food authenticity testing. NGS allows for the simultaneous detection of thousands of potential food contaminants in a single test, overcoming limitations of current polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA) methods. NGS involves amplifying DNA from all species in a mixed sample, sequencing the amplified products, and comparing the sequences to a reference database to identify contaminants. While a major improvement, NGS also has limitations, such as an inability to currently quantify contamination levels.
ACR2016 Wermuth Exosome poster
The exosomes isolated from serum of patients with systemic sclerosis contained higher levels of profibrotic miRNAs and lower levels of antifibrotic miRNAs compared to exosomes from healthy individuals. When applied to normal dermal fibroblasts in culture, the scleroderma patient exosomes stimulated the expression of profibrotic genes, mimicking the phenotype of scleroderma fibroblasts. This effect was partially reduced when the exosomes were pre-treated to degrade either the RNA or protein content, indicating both components contribute to the exosomes' ability to induce a profibrotic phenotype in target cells and suggesting a potential mechanism for the transmission and progression of fibrosis in scleroderma.
Biotecnika Times Newspaper 6th December 2018
This summary provides the key details from the multi-page document in 3 sentences:
The document reports on recent scientific studies, including the development of a new type of biological data recorder using genetically modified E. coli bacteria. It also describes new "kill switch" mechanisms engineered into bacteria to ensure they self-destruct under certain conditions. Additionally, the document summarizes a study that found the process of clearing dying cancer cells (efferocytosis) can unexpectedly promote tumor growth in bone metastases of prostate cancer by stimulating the release of a pro-inflammatory protein.
Human Cell Line Authentication. Why is it so important?
The differences between a cow and a monkey are clear. It is easy to tell a moth from a mosquito. So why are there still scientific studies that mix them up? The answer is simple: hundreds of cell lines stored and used by modern laboratories have been wrongly identified. Some pig cells are labelled as coming from a chicken; cell lines advertised as human have been shown to contain material from hamsters, rats, mice and monkeys. Problems have already been found with more than 400 cell lines. (Cited from Nature 520 (2015)).
An increasing number of scientific publications (i.e. Nature journals) are now sistematically asking for cell line authentication at the moment of paper submission. To help researchers to meet this requirement, UAT is starting to offer a new service for human cell line authentication.
NAISTビッグデータシンポジウム - バイオ久保先生
This document summarizes a presentation given by Minoru Kubo on single cell analyses for plant reprogramming studies. The presentation covered how next generation sequencing and single cell analyses have changed biological research. It discussed single cell transcriptomics for analyzing plant reprogramming at the single cell level. The goal is to identify reprogramming genes, understand cell-cell interactions during reprogramming, and validate theories of reprogramming using the moss Physcomitrella patens as a model organism. Positioning information from single cell analyses could provide new insights into cell lineages, interactions, and multicellular development.
Defense Against Infectious Disease (Core)
Here are the key steps in order:
1. Chemotaxis - Phagocytes are attracted to the site of infection.
2. Attachment - The phagocyte attaches to the pathogen via cell surface receptors binding to proteins on the pathogen.
3. Phagocytosis - The phagocyte membrane envelops and engulfs the pathogen, forming an internal vesicle called a phagosome.
4. Phagosome formation - The phagosome containing the engulfed pathogen forms inside the phagocyte.
5. Lysosome fusion - Lysosomes containing digestive enzymes fuse with the phagosome.
6. Digestion - Enzymes within the phagolysosome break down the pathogen.
7
Grindberg - PNAS
This document describes a method for performing RNA sequencing on single nuclei. Key points:
1) The authors demonstrate that double-stranded cDNA can be synthesized from single mouse neural progenitor cell nuclei and hippocampal tissue nuclei, allowing for whole transcriptome sequencing.
2) On average, sequencing of single nuclei detected over 16,000 of the approximately 24,000 mouse protein-coding genes.
3) Analysis of single nuclei avoids issues with dissociating intact cells from complex tissues, is applicable across eukaryotic species, and provides insight into nuclear gene regulation.
4) RNA sequencing of single nuclei is a powerful new method for investigating gene expression at the single cell level without disrupting cells.
6.남영도110923
This document describes a comparative analysis of the human gut microbiota of Koreans using barcoded pyrosequencing. It finds that the Korean gut microbiome has high diversity at the species and strain levels, with over 800 species-level phylotypes identified on average per individual. The analysis identifies 14 core genera that are consistently present across Korean guts, including Bacteroides, Prevotella, Clostridium, and Ruminococcus. The phylum-level diversity of the Korean gut microbiome is similar to other human populations.
Fogarty Report
Dr. Manjeet K. Sharma conducted research from May 2004 to October 2005 at the University of Virginia under an NIH Fogarty International Fellowship. The goal was to develop a gene targeting construct to knockout the mouse Cabyr gene, which codes for a calcium binding sperm protein, in order to study its role in sperm motility and develop it as a target for male contraception. By the end of the fellowship period, Dr. Sharma had successfully cloned the 5' and 3' arms of the Cabyr gene into a targeting vector. Electroporation of the targeting vector into mouse embryonic stem cells was attempted but was unsuccessful. Further work would be needed to generate Cabyr knockout mice.
Benchmarking 16S rRNA gene sequencing and bioinformatics tools for identifica...
High-throughput DNA sequencing continue to offer comprehensive insights into microbial ecosystems1. Several bioinformatics tools have been inconclusively benchmarked2, yet variations in algorithms are known to impact the microbiome results3. Thus, there is need for detailed benchmarking of bioinformatics tools. Here we validated 16S rRNA amplicon sequencing and four bioinformatics tools for microbiome analyses.
Functional profile of the pre- to post-mortem transition in blood
This document summarizes research analyzing gene expression data from pre-mortem and post-mortem blood samples to characterize the functional changes that occur after death. Five main functional responses were identified, including immune response deactivation, cell division arrest, and metabolism deactivation. Specific signaling pathways involved in processes like response to hypoxia, hemostasis, and apoptosis were found to change activity levels. Computational models were used to quantify changes in signaling activity over cell functions, providing a more informative analysis than examining single genes. This approach could help understand post-mortem tissue preservation for transplantation.
Gene expression profile analysis of human hepatocellular carcinoma using sage...
Researchers performed SAGE and LongSAGE analysis on normal liver tissue, hepatocellular carcinoma (HCC) tissue, and HepG2 liver cancer cells. Approximately 50,000 tags were identified in each library. LongSAGE tags had higher specificity than SAGE tags. 224 genes related to cancer processes were differentially expressed between normal and HCC tissue. Overexpression of some genes was validated via RT-PCR. Two neighboring genes on chromosome 7, SGCE and PEG10, both showed enhanced expression in HCC, indicating a shared deregulation mechanism. The study provides insights into the molecular mechanisms of HCC.
[論文紹介] Asgardアーキアのゲノムはアクチンを制御するプロフィリンをコードしている (Genomes of Asgard archaea enco...
論文紹介 (2018)
Genomes of Asgard archaea encode profilins that regulate actin
Asgardアーキアのゲノムはアクチンを制御するプロフィリンをコードしている
※なぜか文字が表示されない場合は全画面表示や保存をすると表示されるようです。
A look at the human mutational load from the systems biology perspective
Molecular Evolution and Medicine Symposium
Temple University, Philadelphia, USA
16-17 September, 2017
CRISPER Cas & Food supply chain Application
The prokaryote-derived CRISPR–Cas genome editing systems have transformed our ability to manipulate, detect, image and annotate specific DNA and RNA sequences in living cells of diverse species. The ease of use and robustness of this technology have revolutionized genome editing for research ranging from fundamental science to translational medicine. Initial successes have inspired efforts to discover new systems for targeting and manipulating nucleic acids, including those from Cas9, Cas12, Cascade and Cas13 orthologues.
Lena Bengtsson CIRM Poster 2016
This document describes a study investigating the mechanisms underlying X chromosome counting in female embryonic stem cells (ESCs). The researchers conducted an RNA interference screen targeting proteins involved in chromosome structure to identify those necessary for the unique organization of X-linked genes observed in XX ESCs, which is a signature of counting. Knockdown of the loading factor Nipbl for the cohesin complex decreased doublet signals and increased singlet signals without changing cell morphology. Knockdown of Smc2, a subunit of the condensin complex, had no effect. In total, 15 targets were identified that may affect counting.
Knock out technology (final)
Gene knock out technology uses embryonic stem cells to introduce targeted mutations into the mouse genome, allowing the study of gene function. A targeting vector containing the mutated gene sequence flanked by homologous DNA is introduced into embryonic stem cells. Cells with the mutation incorporated via homologous recombination are identified and injected into blastocysts, generating chimeric mice. Breeding of these mice can produce strains lacking the gene of interest, enabling investigation into the effects of its absence. This technology was developed in the 1980s-1990s and its creators were awarded the 2007 Nobel Prize in Physiology or Medicine.
103BL-F14_PosterSmallQuality_PhageHunters
1) Researchers isolated and characterized a novel bacteriophage (Horchata) that infects Mycobacterium smegmatis from a soil sample.
2) Transmission electron microscopy revealed that Horchata has an icosahedral head and long non-contractile tail, characteristic of the Siphoviridae morphology.
3) Genome sequencing and annotation showed that Horchata has a 67,863 bp genome with 30 genes of putative function and 71 genes of unknown function.
Cloning_vector_vanshika_varshney
A cloning vector is a genome that can accept the target DNA and increase the number of copies through its own autonomous replication.
An adapter or adaptor, or a linker in genetic engineering is a short, chemically synthesized, single-stranded or double-stranded oligonucleotide that can be ligated to the ends of other DNA or RNA molecules. It may be used to add sticky ends to cDNA allowing it to be ligated into the plasmid much more efficiently.
Poster MQCB
This document describes a method for constructing conditional depletion mutants of essential genes in Caulobacter crescentus in order to study loss-of-function phenotypes. The method involves tagging endogenous essential genes with a degradation tag (ssrA) and introducing a second copy under control of a xylose promoter. This allows depletion of the essential gene when xylose is removed. As a proof of concept, genes mreB (essential) and creS (non-essential) were depleted, showing expected phenotypes with and without xylose. The method enables high-throughput generation and screening of depletion strains to study the roles of essential genes in cell shape and structure.
Comparative analysis of gene regulation in mouse rat and human
Which is the most suitable model mouse or rat even in the use of the latest gene editing tool-CRISPR/Cas 9 ?
Final Project presentaion on BSc Human Biology
CRISPR: what it is, and why it is having a profound impact on human health
This document summarizes a webinar on CRISPR that included presentations from experts in gene editing and bioinformatics. The webinar provided an overview of CRISPR and how it works using the Cas9 enzyme and guide RNA to make precise cuts in DNA. It discussed how CRISPR is being used for gene knockout studies, clinical trials to treat diseases like cystic fibrosis and cancer, and the challenges of predicting off-target effects. The webinar highlighted both the promise and challenges of CRISPR for accelerating scientific discovery and developing new gene therapies.
Pluripotent Stem Cells and their applications in disease modelling, drug disc...
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive functioning. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
The Beta Amyloid Cleaving Enzymes: From Drug Discovery to Evolution and Back
Slides presented at the University of Edinburgh in Jan 2014, based on our paper "A tale of two drug targets: the evolutionary history of BACE1 and BACE2" http://www.ncbi.nlm.nih.gov/pubmed/24381583
The beta amyloid (APP) cleaving enzyme (BACE1) has been a drug target for Alzheimer's Disease (AD) since 1999 with lead inhibitors now entering clinical trials. In 2011, the paralog, BACE2, became a new target for type II diabetes (T2DM) having been identified as a TMEM27 secretase regulating pancreatic β cell function. However, the normal roles of both enzymes are unclear. This study outlines their evolutionary history and new opportunities for functional genomics. We identified 30 homologs (UrBACEs) in basal phyla including Placozoans, Cnidarians, Choanoflagellates, Porifera, Echinoderms, Annelids, Mollusks and Ascidians (but not Ecdysozoans). UrBACEs are predominantly single copy, show 35–45% protein sequence identity with mammalian BACE1, are ~100 residues longer than cathepsin paralogs with an aspartyl protease domain flanked by a signal peptide and a C-terminal transmembrane domain. While multiple paralogs in Trichoplax and Monosiga pre-date the nervous system, duplication of the UrBACE in fish gave rise to BACE1 and BACE2 in the vertebrate lineage. The latter evolved more rapidly as the former maintained the emergent neuronal role. In mammals, Ka/Ks for BACE2 is higher than BACE1 but low ratios for both suggest purifying selection. The 5' exons show higher Ka/Ks than the catalytic section. Model organism genomes show the absence of certain BACE human substrates when the UrBACE is present. Experiments could thus reveal undiscovered substrates and roles. The human protease double-target status means that evolutionary trajectories and functional shifts associated with different substrates will have implications for the development of clinical candidates for both AD and T2DM. A rational basis for inhibition specificity ratios and assessing target-related side effects will be facilitated by a more complete picture of BACE1 and BACE2 functions informed by their evolutionary context.
Tetrad analysis, positive and negative interference, mapping through somatic ...
- This document discusses various genetic mapping techniques including tetrad analysis, somatic cell hybridization, and using human-mouse cell hybrids.
- Tetrad analysis allows observation of all four products of meiosis which can be used to determine if loci are linked based on parental and non-parental ditype frequencies.
- Somatic cell hybridization involves fusing human and mouse cells to create hybrids containing some human chromosomes. This allows assignment of human genes to chromosomes.
- Specific selection techniques using HAT medium allow isolation of hybrid cells. Analysis of hybrid cell lines then maps human genes by determining synteny or assignment.
Assignment Of Protein Function And Discovery Of Novel Nucleolar Proteins Base...
This document describes a system for automatically assigning protein functions and predicting novel nucleolar proteins based on analysis of the entire MEDLINE database. The system uses vocabulary terms to map information from literature to proteins identified in a nucleolar proteomics study. It facilitates direct association of sequence data to biological text describing function. Comparison to manual annotation showed the automated method to be highly effective. The system accurately identified functional subfamilies within a conserved protein family. It also visualized the nucleolar proteome by function and predicted previously unidentified nucleolar proteins that were later experimentally confirmed.
JoB spike in manuscript 2014
This document discusses how normalization methods for gene expression measurements that assume equal cellular RNA content across experimental conditions can mask differences in total RNA yield per cell. The authors demonstrate that total RNA yield from Chinese Hamster Ovary (CHO) cells varies between experimental treatments and cell lines expressing recombinant proteins. They apply a normalization method using synthetic spike-in RNA standards added proportionally to cell number, which reveals differences in cellular RNA content and allows detection of global transcriptional amplification or repression. They use this method to assess gene expression in CHO cell lines of different sizes treated with cell cycle or mTOR inhibitors, or subjected to high osmolarity conditions. They find that a cell cycle inhibitor increases cell size and transcriptional amplification, an mTOR inhibitor causes
More Related Content
What's hot
Defense Against Infectious Disease (Core)
Here are the key steps in order:
1. Chemotaxis - Phagocytes are attracted to the site of infection.
2. Attachment - The phagocyte attaches to the pathogen via cell surface receptors binding to proteins on the pathogen.
3. Phagocytosis - The phagocyte membrane envelops and engulfs the pathogen, forming an internal vesicle called a phagosome.
4. Phagosome formation - The phagosome containing the engulfed pathogen forms inside the phagocyte.
5. Lysosome fusion - Lysosomes containing digestive enzymes fuse with the phagosome.
6. Digestion - Enzymes within the phagolysosome break down the pathogen.
7
Grindberg - PNAS
This document describes a method for performing RNA sequencing on single nuclei. Key points:
1) The authors demonstrate that double-stranded cDNA can be synthesized from single mouse neural progenitor cell nuclei and hippocampal tissue nuclei, allowing for whole transcriptome sequencing.
2) On average, sequencing of single nuclei detected over 16,000 of the approximately 24,000 mouse protein-coding genes.
3) Analysis of single nuclei avoids issues with dissociating intact cells from complex tissues, is applicable across eukaryotic species, and provides insight into nuclear gene regulation.
4) RNA sequencing of single nuclei is a powerful new method for investigating gene expression at the single cell level without disrupting cells.
6.남영도110923
This document describes a comparative analysis of the human gut microbiota of Koreans using barcoded pyrosequencing. It finds that the Korean gut microbiome has high diversity at the species and strain levels, with over 800 species-level phylotypes identified on average per individual. The analysis identifies 14 core genera that are consistently present across Korean guts, including Bacteroides, Prevotella, Clostridium, and Ruminococcus. The phylum-level diversity of the Korean gut microbiome is similar to other human populations.
Fogarty Report
Dr. Manjeet K. Sharma conducted research from May 2004 to October 2005 at the University of Virginia under an NIH Fogarty International Fellowship. The goal was to develop a gene targeting construct to knockout the mouse Cabyr gene, which codes for a calcium binding sperm protein, in order to study its role in sperm motility and develop it as a target for male contraception. By the end of the fellowship period, Dr. Sharma had successfully cloned the 5' and 3' arms of the Cabyr gene into a targeting vector. Electroporation of the targeting vector into mouse embryonic stem cells was attempted but was unsuccessful. Further work would be needed to generate Cabyr knockout mice.
Benchmarking 16S rRNA gene sequencing and bioinformatics tools for identifica...
High-throughput DNA sequencing continue to offer comprehensive insights into microbial ecosystems1. Several bioinformatics tools have been inconclusively benchmarked2, yet variations in algorithms are known to impact the microbiome results3. Thus, there is need for detailed benchmarking of bioinformatics tools. Here we validated 16S rRNA amplicon sequencing and four bioinformatics tools for microbiome analyses.
Functional profile of the pre- to post-mortem transition in blood
This document summarizes research analyzing gene expression data from pre-mortem and post-mortem blood samples to characterize the functional changes that occur after death. Five main functional responses were identified, including immune response deactivation, cell division arrest, and metabolism deactivation. Specific signaling pathways involved in processes like response to hypoxia, hemostasis, and apoptosis were found to change activity levels. Computational models were used to quantify changes in signaling activity over cell functions, providing a more informative analysis than examining single genes. This approach could help understand post-mortem tissue preservation for transplantation.
Gene expression profile analysis of human hepatocellular carcinoma using sage...
Researchers performed SAGE and LongSAGE analysis on normal liver tissue, hepatocellular carcinoma (HCC) tissue, and HepG2 liver cancer cells. Approximately 50,000 tags were identified in each library. LongSAGE tags had higher specificity than SAGE tags. 224 genes related to cancer processes were differentially expressed between normal and HCC tissue. Overexpression of some genes was validated via RT-PCR. Two neighboring genes on chromosome 7, SGCE and PEG10, both showed enhanced expression in HCC, indicating a shared deregulation mechanism. The study provides insights into the molecular mechanisms of HCC.
[論文紹介] Asgardアーキアのゲノムはアクチンを制御するプロフィリンをコードしている (Genomes of Asgard archaea enco...
論文紹介 (2018)
Genomes of Asgard archaea encode profilins that regulate actin
Asgardアーキアのゲノムはアクチンを制御するプロフィリンをコードしている
※なぜか文字が表示されない場合は全画面表示や保存をすると表示されるようです。
A look at the human mutational load from the systems biology perspective
Molecular Evolution and Medicine Symposium
Temple University, Philadelphia, USA
16-17 September, 2017
CRISPER Cas & Food supply chain Application
The prokaryote-derived CRISPR–Cas genome editing systems have transformed our ability to manipulate, detect, image and annotate specific DNA and RNA sequences in living cells of diverse species. The ease of use and robustness of this technology have revolutionized genome editing for research ranging from fundamental science to translational medicine. Initial successes have inspired efforts to discover new systems for targeting and manipulating nucleic acids, including those from Cas9, Cas12, Cascade and Cas13 orthologues.
Lena Bengtsson CIRM Poster 2016
This document describes a study investigating the mechanisms underlying X chromosome counting in female embryonic stem cells (ESCs). The researchers conducted an RNA interference screen targeting proteins involved in chromosome structure to identify those necessary for the unique organization of X-linked genes observed in XX ESCs, which is a signature of counting. Knockdown of the loading factor Nipbl for the cohesin complex decreased doublet signals and increased singlet signals without changing cell morphology. Knockdown of Smc2, a subunit of the condensin complex, had no effect. In total, 15 targets were identified that may affect counting.
Knock out technology (final)
Gene knock out technology uses embryonic stem cells to introduce targeted mutations into the mouse genome, allowing the study of gene function. A targeting vector containing the mutated gene sequence flanked by homologous DNA is introduced into embryonic stem cells. Cells with the mutation incorporated via homologous recombination are identified and injected into blastocysts, generating chimeric mice. Breeding of these mice can produce strains lacking the gene of interest, enabling investigation into the effects of its absence. This technology was developed in the 1980s-1990s and its creators were awarded the 2007 Nobel Prize in Physiology or Medicine.
103BL-F14_PosterSmallQuality_PhageHunters
1) Researchers isolated and characterized a novel bacteriophage (Horchata) that infects Mycobacterium smegmatis from a soil sample.
2) Transmission electron microscopy revealed that Horchata has an icosahedral head and long non-contractile tail, characteristic of the Siphoviridae morphology.
3) Genome sequencing and annotation showed that Horchata has a 67,863 bp genome with 30 genes of putative function and 71 genes of unknown function.
Cloning_vector_vanshika_varshney
A cloning vector is a genome that can accept the target DNA and increase the number of copies through its own autonomous replication.
An adapter or adaptor, or a linker in genetic engineering is a short, chemically synthesized, single-stranded or double-stranded oligonucleotide that can be ligated to the ends of other DNA or RNA molecules. It may be used to add sticky ends to cDNA allowing it to be ligated into the plasmid much more efficiently.
Poster MQCB
This document describes a method for constructing conditional depletion mutants of essential genes in Caulobacter crescentus in order to study loss-of-function phenotypes. The method involves tagging endogenous essential genes with a degradation tag (ssrA) and introducing a second copy under control of a xylose promoter. This allows depletion of the essential gene when xylose is removed. As a proof of concept, genes mreB (essential) and creS (non-essential) were depleted, showing expected phenotypes with and without xylose. The method enables high-throughput generation and screening of depletion strains to study the roles of essential genes in cell shape and structure.
Comparative analysis of gene regulation in mouse rat and human
Which is the most suitable model mouse or rat even in the use of the latest gene editing tool-CRISPR/Cas 9 ?
Final Project presentaion on BSc Human Biology
CRISPR: what it is, and why it is having a profound impact on human health
This document summarizes a webinar on CRISPR that included presentations from experts in gene editing and bioinformatics. The webinar provided an overview of CRISPR and how it works using the Cas9 enzyme and guide RNA to make precise cuts in DNA. It discussed how CRISPR is being used for gene knockout studies, clinical trials to treat diseases like cystic fibrosis and cancer, and the challenges of predicting off-target effects. The webinar highlighted both the promise and challenges of CRISPR for accelerating scientific discovery and developing new gene therapies.
Pluripotent Stem Cells and their applications in disease modelling, drug disc...
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive functioning. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
The Beta Amyloid Cleaving Enzymes: From Drug Discovery to Evolution and Back
Slides presented at the University of Edinburgh in Jan 2014, based on our paper "A tale of two drug targets: the evolutionary history of BACE1 and BACE2" http://www.ncbi.nlm.nih.gov/pubmed/24381583
The beta amyloid (APP) cleaving enzyme (BACE1) has been a drug target for Alzheimer's Disease (AD) since 1999 with lead inhibitors now entering clinical trials. In 2011, the paralog, BACE2, became a new target for type II diabetes (T2DM) having been identified as a TMEM27 secretase regulating pancreatic β cell function. However, the normal roles of both enzymes are unclear. This study outlines their evolutionary history and new opportunities for functional genomics. We identified 30 homologs (UrBACEs) in basal phyla including Placozoans, Cnidarians, Choanoflagellates, Porifera, Echinoderms, Annelids, Mollusks and Ascidians (but not Ecdysozoans). UrBACEs are predominantly single copy, show 35–45% protein sequence identity with mammalian BACE1, are ~100 residues longer than cathepsin paralogs with an aspartyl protease domain flanked by a signal peptide and a C-terminal transmembrane domain. While multiple paralogs in Trichoplax and Monosiga pre-date the nervous system, duplication of the UrBACE in fish gave rise to BACE1 and BACE2 in the vertebrate lineage. The latter evolved more rapidly as the former maintained the emergent neuronal role. In mammals, Ka/Ks for BACE2 is higher than BACE1 but low ratios for both suggest purifying selection. The 5' exons show higher Ka/Ks than the catalytic section. Model organism genomes show the absence of certain BACE human substrates when the UrBACE is present. Experiments could thus reveal undiscovered substrates and roles. The human protease double-target status means that evolutionary trajectories and functional shifts associated with different substrates will have implications for the development of clinical candidates for both AD and T2DM. A rational basis for inhibition specificity ratios and assessing target-related side effects will be facilitated by a more complete picture of BACE1 and BACE2 functions informed by their evolutionary context.
Tetrad analysis, positive and negative interference, mapping through somatic ...
- This document discusses various genetic mapping techniques including tetrad analysis, somatic cell hybridization, and using human-mouse cell hybrids.
- Tetrad analysis allows observation of all four products of meiosis which can be used to determine if loci are linked based on parental and non-parental ditype frequencies.
- Somatic cell hybridization involves fusing human and mouse cells to create hybrids containing some human chromosomes. This allows assignment of human genes to chromosomes.
- Specific selection techniques using HAT medium allow isolation of hybrid cells. Analysis of hybrid cell lines then maps human genes by determining synteny or assignment.
What's hot (20)
Benchmarking 16S rRNA gene sequencing and bioinformatics tools for identifica...
Benchmarking 16S rRNA gene sequencing and bioinformatics tools for identifica...
Functional profile of the pre- to post-mortem transition in blood
Functional profile of the pre- to post-mortem transition in blood
Gene expression profile analysis of human hepatocellular carcinoma using sage...
Gene expression profile analysis of human hepatocellular carcinoma using sage...
[論文紹介] Asgardアーキアのゲノムはアクチンを制御するプロフィリンをコードしている (Genomes of Asgard archaea enco...
[論文紹介] Asgardアーキアのゲノムはアクチンを制御するプロフィリンをコードしている (Genomes of Asgard archaea enco...
A look at the human mutational load from the systems biology perspective
A look at the human mutational load from the systems biology perspective
Comparative analysis of gene regulation in mouse rat and human
Comparative analysis of gene regulation in mouse rat and human
CRISPR: what it is, and why it is having a profound impact on human health
CRISPR: what it is, and why it is having a profound impact on human health
Pluripotent Stem Cells and their applications in disease modelling, drug disc...
Pluripotent Stem Cells and their applications in disease modelling, drug disc...
The Beta Amyloid Cleaving Enzymes: From Drug Discovery to Evolution and Back
The Beta Amyloid Cleaving Enzymes: From Drug Discovery to Evolution and Back
Tetrad analysis, positive and negative interference, mapping through somatic ...
Tetrad analysis, positive and negative interference, mapping through somatic ...
Similar to Refining Gene Ontology to Include Terms and Relationships Relevant to exRNA Communications
Assignment Of Protein Function And Discovery Of Novel Nucleolar Proteins Base...
This document describes a system for automatically assigning protein functions and predicting novel nucleolar proteins based on analysis of the entire MEDLINE database. The system uses vocabulary terms to map information from literature to proteins identified in a nucleolar proteomics study. It facilitates direct association of sequence data to biological text describing function. Comparison to manual annotation showed the automated method to be highly effective. The system accurately identified functional subfamilies within a conserved protein family. It also visualized the nucleolar proteome by function and predicted previously unidentified nucleolar proteins that were later experimentally confirmed.
JoB spike in manuscript 2014
This document discusses how normalization methods for gene expression measurements that assume equal cellular RNA content across experimental conditions can mask differences in total RNA yield per cell. The authors demonstrate that total RNA yield from Chinese Hamster Ovary (CHO) cells varies between experimental treatments and cell lines expressing recombinant proteins. They apply a normalization method using synthetic spike-in RNA standards added proportionally to cell number, which reveals differences in cellular RNA content and allows detection of global transcriptional amplification or repression. They use this method to assess gene expression in CHO cell lines of different sizes treated with cell cycle or mTOR inhibitors, or subjected to high osmolarity conditions. They find that a cell cycle inhibitor increases cell size and transcriptional amplification, an mTOR inhibitor causes
GtoPdb_ITMAT_2017
Poster titled "The imperative of small, high quality data for underpinning big data: the IUPHAR/BPS Guide to PHARMACOLOGY". Presented by Dr. Christopher Southan, at the British Society of Pharmacology, Institute for Translational Medicine & Therapeutics (ITMAT) Meeting, Edinburgh, March 2017, ‘Big Data & the Development of New Medicines’.
Exploiting Edinburgh's Guide to PHARMACOLOGY database as a source of protein ...
Presented by Jamie Davies at the SULSA Synthetic Biology Meeting, Edinburgh, 10 June 2014
http://www.eventbrite.co.uk/e/sulsa-synthetic-biology-meeting-registration-11251454403?aff=eorg
Abstract: Synthetic creation of new biological systems typically incorporates pathways and signaling modules from known protein building blocks. Testing the models underpinning the synthetic engineering thus needs the experimental manipulation of individual proteins, for example, ablating a specific enzyme activity via RNAi, SNP mutation, or knockout. However, the option of small-molecule inhibition as the system perturbation has the advantages of 1) rapid onset 2) dose-response 3) analog testing for structure-activity relationships, 4) exploring mixtures for combinatorial effects 5) pulsing and reversal by wash-out. 6) accurate measurements of added substances and 7) a vast precedent of published results in natural systems from medicinal chemistry, pharmacology, and chemical biology. For the synthetic biologists the GToPdb1 can thus be considered as compendium of the latter. It encompasses an interaction matrix between ~4000 small molecules and ~1000 human proteins with a focus on drugs, clinical candidates, research compounds and peptide ligands These not only have ~ 10,000 mapped binding constants but also the spectrum of documented modulation extends across enzymes, receptors, channels and transporters. It thus becomes an increasingly plausible option to choose a “Lego protein” from GToPdb as a synthetic system component that can have experimentally useable activity probes available from chemical vendors. Even if it does not currently have a suitable target-probe pair, as knowledge base (and expertise resource via the curation team who populate it) GToPdb is an ideal starting point from which to walk out to wider chemogenomic spaces. For example, while an approved drug and its target might seem a logical choice, analogs from the lead series or different chemotypes from which the drug was optimized, or even failed in development, can have superior probe-like properties for in vitro experiments (e.g. be more potent, specific and soluble). The GToPdb facilitates access to such compound data via curated papers and patents.
References
1. Pawson AJ, Sharman JL, Benson HE, Faccenda E, Alexander SP, Buneman OP, Davenport AP, McGrath JC, Peters JA, Southan C, Spedding M, Yu W, Harmar AJ; NC-IUPHAR. The IUPHAR/BPS Guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands. Nucleic Acids Res. 2014 Jan 1;42(1)
Applied Bioinformatics Assignment 5docx
This document discusses various bioinformatics approaches for analyzing molecular interactions, including protein-protein interaction, protein-ligand interaction, docking, pharmacophore, and virtual screening. It provides details on each topic, describing things like how protein-protein interactions occur and are classified, common methods for studying protein-ligand interactions, the basic process and types of docking, and the definition of a pharmacophore. The key topics covered are protein-protein interaction, protein-ligand interaction analysis through methods like docking, and virtual screening using pharmacophore models.
Protein protein interaction
Protein-protein interactions are important for many biological processes. There are various types of interactions depending on their composition and duration. Methods to study interactions include yeast two-hybrid, co-immunoprecipitation, affinity chromatography, and chromatin immunoprecipitation. Databases such as IntAct and MINT provide repositories for protein interaction data.
Poster on systems pharmacology of the cholesterol biosynthesis pathway
A systems pharmacology study of the cholesterol biosynthesis pathway
Poster presented at the Pharmacology 2017 conference, London, December 2017
STRING - Prediction of a functional association network for the yeast mitocho...
The document discusses predicting functional associations between proteins in the yeast mitochondrial system using the STRING database. It summarizes how STRING integrates genomic context, experimental data, and evidence from other species to infer functional links. It then describes applying these methods to predict mitochondrial proteins in yeast and build an association network for the yeast mitochondrial system, identifying functional modules within it.
Biomedicine & Pharmacotherapy
Biomedicine & Pharmacotherapy
Discovery of drug targets and therapeutic agents based on drug
repositioning to treat lung adenocarcinoma
Guide to Pharmacology Poster - ELIXIR All Hands 2020
The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb) is an expert-driven, open database of pharmacological targets and the substances that act on them. It contains information on over 1,800 drug targets and 1,100 related proteins. The database is curated by 500 experts and provides detailed pharmacological data as well as overviews of key properties and ligands. Specialized extensions of GtoPdb include guides to immunopharmacology and malaria pharmacology that connect their fields to drug discovery. The database is continuously updated with new targets, ligands, features and access methods.
Weber_FinalProposal
This document proposes using ellipsometry to investigate ligand binding to G-protein coupled receptors (GPCRs). GPCRs are integral membrane proteins responsible for many biological processes. Ligand binding to GPCRs is currently measured using cell-based assays and surface plasmon resonance, but both have limitations. Ellipsometry is an optical technique that could quantify ligand-GPCR binding by analyzing changes in the polarization of light reflected from a sample. The proposal aims to use ellipsometry to collect baseline data on substrates and cells, relate ligand binding to changes in ellipsometry measurements, and confirm binding using ELISA. A chemokine receptor and ligand, CXCR4 and CXCL12, will serve as a model system to
Identification of PFOA linked metabolic diseases by crossing databases
The increasing amount of biological data makes possible their interpretation more accurate and richer than never before. Various way of representations and interpretations of the links between those data have been applied or developed consequently to these new elements which can be taken into account in diagnostics and soon in personalized medicine. The aim of this student project was to cross data coming from various databases to be able to link Perfluorooctaoic Acid (PFOA) to one or more human phenotypes and metabolic diseases. Our approach makes possible an easy and confident interpretation on the data kept and also allow us to rank diseases linked according to their risk of correlation to a specific set of proteins.
Yeast two hybrid
The yeast two-hybrid system allows for the identification of protein-protein interactions. It involves fusing two interacting proteins to a DNA-binding domain and transcriptional activation domain, so that interaction leads to expression of reporter genes. This in vivo technique uses yeast as a host to screen libraries or characterize proteins of interest. Some applications include identifying novel interactions, protein cascades, and mutations affecting binding.
Kegg
The document describes several key databases within the KEGG resource, including:
- The PATHWAY database containing molecular network maps of metabolic and genetic pathways.
- The BRITE database providing hierarchical classifications of biological systems beyond what is shown in pathways.
- The LIGAND database consisting of chemical compounds, carbohydrates, reactions, and enzyme information.
KEGG aims to comprehensively capture biological knowledge through integrated databases covering genomes, pathways, diseases and drugs.
Proteomics a search tool for vaccines
The document discusses using proteomics to develop vaccines. It describes how proteomics can help understand protein interactions for vaccine development. The document then focuses on developing a vaccine for Lassa fever. It outlines computational methods used to analyze the Lassa virus glycoprotein, including determining its structure, domains, and interactions within cells. The goal is to use this analysis to develop a stabilized vaccine candidate against Lassa virus that can protect humans.
Stable Drug Designing by Minimizing Drug Protein Interaction Energy Using PSO
1. The document proposes using a particle swarm optimization (PSO) algorithm to design stable drug molecules that minimize interaction energy with target proteins.
2. In the algorithm, drugs are represented as variable-length trees containing functional groups, and PSO is used to optimize van der Waals and electrostatic interaction energies.
3. Results show that PSO performs better than previous fixed-length tree methods at designing drugs that stably bind to active sites of human rhinovirus, malaria, and HIV proteins.
PTPRC as a Predictive Marker Related to PD-L1 for Prognosis and Immunotherapy...
The expression of programmed cell death protein 1 (PD-L1) has been found to be closely related to the efficacy
of immunotherapy. The aim of our study is to explore biomarkers
associated with PD-L1 expression that might influence the efficacy
of immunotherapy.
PTPRC as a Predictive Marker Related to PD-L1 for Prognosis and Immunotherapy...
The expression of programmed cell death protein 1 (PD-L1) has been found to be closely related to the efficacy of immunotherapy. The aim of our study is to explore biomarkers associated with PD-L1 expression that might influence the efficacy of immunotherapy.
PTPRC as a Predictive Marker Related to PD-L1 for Prognosis and Immunotherapy...
The expression of programmed cell death protein 1 (PD-L1) has been found to be closely related to the efficacy of immunotherapy. The aim of our study is to explore biomarkers associated with PD-L1 expression that might influence the efficacy of immunotherapy.
GLUER integrative analysis of single-cell omics and imaging data by deep neur...
GLUER integrative analysis of single-cell omics and imaging data by deep neural network
Similar to Refining Gene Ontology to Include Terms and Relationships Relevant to exRNA Communications (20)
Assignment Of Protein Function And Discovery Of Novel Nucleolar Proteins Base...
Assignment Of Protein Function And Discovery Of Novel Nucleolar Proteins Base...
Exploiting Edinburgh's Guide to PHARMACOLOGY database as a source of protein ...
Exploiting Edinburgh's Guide to PHARMACOLOGY database as a source of protein ...
Poster on systems pharmacology of the cholesterol biosynthesis pathway
Poster on systems pharmacology of the cholesterol biosynthesis pathway
STRING - Prediction of a functional association network for the yeast mitocho...
STRING - Prediction of a functional association network for the yeast mitocho...
Guide to Pharmacology Poster - ELIXIR All Hands 2020
Guide to Pharmacology Poster - ELIXIR All Hands 2020
Identification of PFOA linked metabolic diseases by crossing databases
Identification of PFOA linked metabolic diseases by crossing databases
Stable Drug Designing by Minimizing Drug Protein Interaction Energy Using PSO
Stable Drug Designing by Minimizing Drug Protein Interaction Energy Using PSO
PTPRC as a Predictive Marker Related to PD-L1 for Prognosis and Immunotherapy...
PTPRC as a Predictive Marker Related to PD-L1 for Prognosis and Immunotherapy...
PTPRC as a Predictive Marker Related to PD-L1 for Prognosis and Immunotherapy...
PTPRC as a Predictive Marker Related to PD-L1 for Prognosis and Immunotherapy...
PTPRC as a Predictive Marker Related to PD-L1 for Prognosis and Immunotherapy...
PTPRC as a Predictive Marker Related to PD-L1 for Prognosis and Immunotherapy...
GLUER integrative analysis of single-cell omics and imaging data by deep neur...
GLUER integrative analysis of single-cell omics and imaging data by deep neur...
Recently uploaded
Compexometric titration/Chelatorphy titration/chelating titration
Classification
Metal ion ion indicators
Masking and demasking reagents
Estimation of Magnisium sulphate
Calcium gluconate
Complexometric Titration/ chelatometry titration/chelating titration, introduction, Types-
1.Direct Titration
2.Back Titration
3.Replacement Titration
4.Indirect Titration
Masking agent, Demasking agents
formation of complex
comparition between masking and demasking agents,
Indicators/Metal ion indicators/ Metallochromic indicators/pM indicators,
Visual Technique,PM indicators (metallochromic), Indicators of pH, Redox Indicators
Instrumental Techniques-Photometry
Potentiometry
Miscellaneous methods.
Complex titration with EDTA.
在线办理(salfor毕业证书)索尔福德大学毕业证毕业完成信一模一样
学校原件一模一样【微信：741003700 】《(salfor毕业证书)索尔福德大学毕业证》【微信：741003700 】学位证，留信认证（真实可查，永久存档）原件一模一样纸张工艺/offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。
本公司拥有海外各大学样板无数，能完美还原。
1:1完美还原海外各大学毕业材料上的工艺：水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠。文字图案浮雕、激光镭射、紫外荧光、温感、复印防伪等防伪工艺。材料咨询办理、认证咨询办理请加学历顾问Q/微741003700
【主营项目】
一.毕业证【q微741003700】成绩单、使馆认证、教育部认证、雅思托福成绩单、学生卡等！
二.真实使馆公证(即留学回国人员证明,不成功不收费)
三.真实教育部学历学位认证（教育部存档！教育部留服网站永久可查）
四.办理各国各大学文凭(一对一专业服务,可全程监控跟踪进度)
如果您处于以下几种情况：
◇在校期间，因各种原因未能顺利毕业……拿不到官方毕业证【q/微741003700】
◇面对父母的压力，希望尽快拿到；
◇不清楚认证流程以及材料该如何准备；
◇回国时间很长，忘记办理；
◇回国马上就要找工作，办给用人单位看；
◇企事业单位必须要求办理的
◇需要报考公务员、购买免税车、落转户口
◇申请留学生创业基金
留信网认证的作用:
1:该专业认证可证明留学生真实身份
2:同时对留学生所学专业登记给予评定
3:国家专业人才认证中心颁发入库证书
4:这个认证书并且可以归档倒地方
5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息
6:个人职称评审加20分
7:个人信誉贷款加10分
8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才
Randomised Optimisation Algorithms in DAPHNE
Slides from talk:
Aleš Zamuda: Randomised Optimisation Algorithms in DAPHNE .
Austrian-Slovenian HPC Meeting 2024 – ASHPC24, Seeblickhotel Grundlsee in Austria, 10–13 June 2024
https://ashpc.eu/
Micronuclei test.M.sc.zoology.fisheries.
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
Thornton ESPP slides UK WW Network 4_6_24.pdf
ESPP presentation to EU Waste Water Network, 4th June 2024 “EU policies driving nutrient removal and recycling
and the revised UWWTD (Urban Waste Water Treatment Directive)”
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptx
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
Authoring a personal GPT for your research and practice: How we created the Q...
Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
THEMATIC APPERCEPTION TEST(TAT) cognitive abilities, creativity, and critic...
THEMATIC APPERCEPTION TEST(TAT) cognitive abilities, creativity, and critic...Abdul Wali Khan University Mardan,kP,Pakistan
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skillsApplied Science: Thermodynamics, Laws & Methodology.pdf
When I was asked to give a companion lecture in support of ‘The Philosophy of Science’ (https://shorturl.at/4pUXz) I decided not to walk through the detail of the many methodologies in order of use. Instead, I chose to employ a long standing, and ongoing, scientific development as an exemplar. And so, I chose the ever evolving story of Thermodynamics as a scientific investigation at its best.
Conducted over a period of >200 years, Thermodynamics R&D, and application, benefitted from the highest levels of professionalism, collaboration, and technical thoroughness. New layers of application, methodology, and practice were made possible by the progressive advance of technology. In turn, this has seen measurement and modelling accuracy continually improved at a micro and macro level.
Perhaps most importantly, Thermodynamics rapidly became a primary tool in the advance of applied science/engineering/technology, spanning micro-tech, to aerospace and cosmology. I can think of no better a story to illustrate the breadth of scientific methodologies and applications at their best.
Sharlene Leurig - Enabling Onsite Water Use with Net Zero Water
Sharlene Leurig - Enabling Onsite Water Use with Net Zero WaterTexas Alliance of Groundwater Districts
Presented at June 6-7 Texas Alliance of Groundwater Districts Business MeetingDescribing and Interpreting an Immersive Learning Case with the Immersion Cub...
Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
Immersive Learning That Works: Research Grounding and Paths Forward
We will metaverse into the essence of immersive learning, into its three dimensions and conceptual models. This approach encompasses elements from teaching methodologies to social involvement, through organizational concerns and technologies. Challenging the perception of learning as knowledge transfer, we introduce a 'Uses, Practices & Strategies' model operationalized by the 'Immersive Learning Brain' and ‘Immersion Cube’ frameworks. This approach offers a comprehensive guide through the intricacies of immersive educational experiences and spotlighting research frontiers, along the immersion dimensions of system, narrative, and agency. Our discourse extends to stakeholders beyond the academic sphere, addressing the interests of technologists, instructional designers, and policymakers. We span various contexts, from formal education to organizational transformation to the new horizon of an AI-pervasive society. This keynote aims to unite the iLRN community in a collaborative journey towards a future where immersive learning research and practice coalesce, paving the way for innovative educational research and practice landscapes.
The cost of acquiring information by natural selection
This is a short talk that I gave at the Banff International Research Station workshop on Modeling and Theory in Population Biology. The idea is to try to understand how the burden of natural selection relates to the amount of information that selection puts into the genome.
It's based on the first part of this research paper:
The cost of information acquisition by natural selection
Ryan Seamus McGee, Olivia Kosterlitz, Artem Kaznatcheev, Benjamin Kerr, Carl T. Bergstrom
bioRxiv 2022.07.02.498577; doi: https://doi.org/10.1101/2022.07.02.498577
8.Isolation of pure cultures and preservation of cultures.pdf
Isolation of pure culture, its various method.
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
Recently uploaded (20)
Compexometric titration/Chelatorphy titration/chelating titration
Compexometric titration/Chelatorphy titration/chelating titration
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptx
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptx
Authoring a personal GPT for your research and practice: How we created the Q...
Authoring a personal GPT for your research and practice: How we created the Q...
THEMATIC APPERCEPTION TEST(TAT) cognitive abilities, creativity, and critic...
THEMATIC APPERCEPTION TEST(TAT) cognitive abilities, creativity, and critic...
Applied Science: Thermodynamics, Laws & Methodology.pdf
Applied Science: Thermodynamics, Laws & Methodology.pdf
Sharlene Leurig - Enabling Onsite Water Use with Net Zero Water
Sharlene Leurig - Enabling Onsite Water Use with Net Zero Water
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
Immersive Learning That Works: Research Grounding and Paths Forward
Immersive Learning That Works: Research Grounding and Paths Forward
The cost of acquiring information by natural selection
The cost of acquiring information by natural selection
8.Isolation of pure cultures and preservation of cultures.pdf
8.Isolation of pure cultures and preservation of cultures.pdf
mô tả các thí nghiệm về đánh giá tác động dòng khí hóa sau đốt
mô tả các thí nghiệm về đánh giá tác động dòng khí hóa sau đốt
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
Refining Gene Ontology to Include Terms and Relationships Relevant to exRNA Communications
- 1. An ontology is used to represent domain knowledge in a standard machine-readable way to enable data annotation, discovery, and integration. The Extracellular RNA Communication Consortium has established an ontology group to work towards standardization and classification of the terms used to describe extracellular vesicles (EVs). As part of this ontology effort, we have worked with domain experts and ontology experts to propose new terms and relationships that can be added to the widely-used Gene Ontology (GO) for describing EVs and other exRNA-containing particles. Our proposal reflects broad community consensus, as it was reviewed and approved by: • International Society for Extracellular Vesicles • American Society for Exosomes and Microvesicles. In this attempt to standardize exRNA-related terminology, we strive to strike a balance between the “lumper” and “splitter” approaches in this new and incompletely understood domain. We are currently working closely with the GO Consortium to incorporate the proposed terms and relationships into the GO Cellular Component branch. Extension of GO Cellular Component branch to include terms and relationships relevant to exRNA communications Refining Gene Ontology to Include Terms and Relationships Relevant to exRNA Communications Cheung KH1, Laurent LC2, Roncaglia P3, Gould S4, Mathivanan S5, Hill AF6, Lotvall J6, Subramanian S7, Roth M7, Alexander R8, Kitchen R1, Rozowsky J1, Wauben M9, Quesenberry P10, Patel T11, Breakefield X12, Thery C13, Ezrin A14, Su A15, Galas D8, Gerstein MB1, Milosavljevic A7 1Yale University, New Haven, CT, USA; 2UC San Diego, La Jolla, CA, USA; 3European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, UK and The Gene Ontology Consortium; 4Johns Hopkins University School of Medicine, Baltimore, MD, USA; 5La Trobe University, Bundoora, Victoria, Australia; 6University of Gothenburg, Gothenburg, Sweden; 7Baylor College of Medicine, Houston, TX, USA; 8Pacific Northwest Diabetes Research Institute, Seattle, WA, USA; 9Universiteit Utrecht, Utrecht, Netherlands; 10University Medicine Comprehensive Cancer Center, Providence, RI, USA; 11Mayo Clinic, Jacksonville, FL, USA; 12Harvard Medical School, Boston, MA, USA;13Institut Curie, INSERM U932, Paris, France; 14NX PharmaGen, Louisville, KY, USA; 15The Scripps Research Institute, La Jolla, CA, USA Abstract • Add more terms and relationships that are relevant to exRNA communications • Annotate metadata (metadata working group) • Link to other ontologies • Develop use cases for ontological data integration Future Directions GO Browser GO:1990684 protein-lipid-RNA complex definition: "A macromolecular complex containing separate protein, lipid and RNA molecules. Separate in this context means not covalently bound to each other." [GOC:vesicles, PMID:21423178, PMID:22028337, PMID:23559634] comment: Examples of protein-lipid-RNA complexes are described in PMID:21423178 and PMID:23559634, both showing evidence that high-density lipoprotein (HDL) and, to a lesser extent, low-density lipoprotein (HDL) transport endogenous microRNAs (miRNAs) and deliver them to recipient cells with functional targeting capabilities. Also see fig. 1 in the review PMID:22028337. Not to be confused with GO:0034364 'high- density lipoprotein particle' or GO:0034362 'low-density lipoprotein particle', which describe complexes of proteins and lipids only, without RNAs. synonym: "miRNA-lipoprotein complex" RELATED [] is_a: GO:0032991 ! macromolecular complex relationship: has_part CHEBI:18059 ! lipid relationship: has_part CHEBI:33697 ! ribonucleic acid relationship: has_part PR:000000001 ! protein Acknowledgements • Extracellular RNA Communications Consortium • External RNA Controls Consortium • International Society for Extracellular Vesicles • American Society for Exosomes and Microvesicles • Gene Ontology Consortium • This work was supported in part by NIH Common Fund Legend: • Rectangles represent GO terms. • Ovals represent synonyms. • Arrows represent is_a relationships. • Dashed lines represent synonymous relationships. • White rectangles represent existing GO terms. • Black arrows represent existing is_a relationships. • Red markings represent either new terms/synonyms or existing terms/synonyms with new relationships.