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Gene activity and transcript patterns visualized for the first time in thousands of single cells

Gene activity and transcript patterns visualized for the first time in thousands of single cells | Systems biology and bioinformatics | Scoop.it
Biologists of the University of Zurich have developed a method to visualize the activity of genes in single cells. The method is so efficient that, for the first time, a thousand genes can be studied in parallel in ten thousand single human cells.

 

Applications lie in fields of basic research and medical diagnostics. The new method shows that the activity of genes, and the spatial organization of the resulting transcript molecules, strongly vary between single cells. Whenever cells activate a gene, they produce gene specific transcript molecules, which make the function of the gene available to the cell. The measurement of gene activity is a routine activity in medical diagnostics, especially in cancer medicine. Today's technologies determine the activity of genes by measuring the amount of transcript molecules. However, these technologies can neither measure the amount of transcript molecules of one thousand genes in ten thousand single cells, nor the spatial organization of transcript molecules within a single cell. The fully automated procedure, developed by biologists of the University of Zurich under the supervision of Prof. Lucas Pelkmans, allows, for the first time, a parallel measurement of the amount and spatial organization of single transcript molecules in ten thousands single cells. The results, which were recently published in the scientific journal Nature Methods, provide completely novel insights into the variability of gene activity of single cells.

 

The method developed by Pelkmans' PhD students Nico Battich and Thomas Stoeger is based upon the combination of robots, an automated fluorescence microscope and a supercomputer. "When genes become active, specific transcript molecules are produced. We can stain them with the help of a robot", explains Stoeger. Subsequently, fluorescence microscope images of brightly glowing transcript molecules are generated. Those images were analyzed with the supercomputer Brutus, of the ETH Zurich. With this method, one thousand human genes can be studied in ten thousand single cells. According to Pelkmans, the advantages of this method are the high number of single cells and the possibility to study, for the first time, the spatial organization of the transcript molecules of many genes.

The analysis of the new data shows that individual cells distinguish themselves in the activity of their genes. While the scientists had been suspecting a high variability in the amount of transcript molecules, they were surprised to discover a strong variability in the spatial organization of transcript molecules within single cells and between multiple single cells. The transcript molecules adapted distinctive patterns.

 

The importance of these new insights was summarized by Pelkmans: "Our method will be of importance to basic research and the understanding of cancer tumors because it allows us to map the activity of genes within single tumor cells.


Via Dr. Stefan Gruenwald
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Dmitry Alexeev's curator insight, October 7, 2013 11:45 PM

i would expect to find more tricky distributions of the gene expression pattern among cells - but... however it looks that the high throughputness is being reaching via automatization and robotization either then novell principles

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The proteomics quantification dilemma

The proteomics quantification dilemma | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

completely adore this author for his principial position on the subject - no to bottom up proteomics

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Mel Melendrez-Vallard's curator insight, April 14, 5:47 AM

For those that have access to the journal.

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Within-Host Bacterial Diversity Hinders Accurate Reconstruction of Transmission Networks from Genomic Distance Data

Within-Host Bacterial Diversity Hinders Accurate Reconstruction of Transmission Networks from Genomic Distance Data | Systems biology and bioinformatics | Scoop.it
PLOS Computational Biology is an open-access
Dmitry Alexeev's insight:

stream of knowledge lately has been working to keep us thinking tight

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Alexander Tyakht's curator insight, April 8, 11:42 PM

genomic diversity with focus on pathogen populations

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GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

it is becoming used more

The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters.

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Annual Progress Report - DOE Joint Genome Institute

Annual Progress Report - DOE Joint Genome Institute | Systems biology and bioinformatics | Scoop.it
The institute's annual report of its activities.
Dmitry Alexeev's insight:

cumulative of 1000 papaers Joint Genoe Institute report 2013

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No paradox, no progress: inverse cancer comorbidity in people with other complex diseases

Dmitry Alexeev's insight:

something good to know)

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Pathogens | Free Full-Text | Heat Shock Proteins: Intestinal Gatekeepers that Are Influenced by Dietary Components and the Gut Microbiota

Pathogens | Free Full-Text | Heat Shock Proteins: Intestinal Gatekeepers that Are Influenced by Dietary Components and the Gut Microbiota | Systems biology and bioinformatics | Scoop.it
Trillions of microorganisms that inhabit the intestinal tract form a diverse and intricate ecosystem with a deeply embedded symbiotic relationship with their hosts. As more detailed information on gut microbiota complexity and functional diversity accumulates, we are learning more about how diet-microbiota interactions can influence the immune system within and outside the gut and host health in general. Heat shock proteins are a set of highly conserved proteins that are present in all types of cells, from microbes to mammals. These proteins carry out crucial intracellular housekeeping functions and unexpected extracellular immuno-regulatory features in order to maintain the mucosal barrier integrity and gut homeostasis. It is becoming evident that the enteric microbiota is one of the major determinants of heat shock protein production in intestinal epithelial cells. This review will focus on the interactions between diet, gut microbiota and their role for regulating heat shock protein production and, furthermore, how these interactions influence the immune system and the integrity of the mucosal barrier.
Dmitry Alexeev's insight:

microbiota and heatshock - some of the topics we unite in our research

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Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition

Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

hey did we miss that one?

 

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Decontaminating Sequencing Samples - Bio-IT World

Decontaminating Sequencing Samples - Bio-IT World | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

Appistry piplines 

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Evolution and transmission of drug-resistant tuberculosis in a Russian population : Nature Genetics : Nature Publishing Group

Evolution and transmission of drug-resistant tuberculosis in a Russian population : Nature Genetics : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
Francis Drobniewski and colleagues report the whole-genome sequencing of 1,000 Mycobacterium tuberculosis strains obtained prospectively from patients over a 2-year period in Samara, Russia, a region with a high incidence of multidrug resistant...
Dmitry Alexeev's insight:

tubi from russia

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Human–microbe mismatch boosts risk of stomach cancer

Human–microbe mismatch boosts risk of stomach cancer | Systems biology and bioinformatics | Scoop.it
H. pylori strains more likely to cause tumours when they did not co-evolve with their hosts.
Dmitry Alexeev's insight:

This is AMAZING!!!

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Alexander Tyakht's curator insight, January 14, 10:59 PM

news about geo-tracked bacterium tracked by M. Achtman before.

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Integrated metagenomics/metaproteomics reveals huma... [PLoS One. 2012] - PubMed - NCBI

Integrated metagenomics/metaproteomics reveals huma... [PLoS One. 2012] - PubMed - NCBI | Systems biology and bioinformatics | Scoop.it
PubMed comprises more than 23 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Dmitry Alexeev's insight:

crohn's metaproteomics - we'll save it for later

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The Hologenomic Basis of Speciation: Gut Bacteria Cause Hybrid Lethality in the Genus Nasonia

Dmitry Alexeev's insight:

all your base are belong to us! - metagenome controlling species hybrid survival - hologenome proofs)

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Discovery and saturation analysis of cancer genes across 21 tumour types : Nature : Nature Publishing Group

Discovery and saturation analysis of cancer genes across 21 tumour types : Nature : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

more NGS, more cancers more genes

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Network Biology

Network Biology | Systems biology and bioinformatics | Scoop.it
Network Biology
Dmitry Alexeev's insight:

the page camoe useful for me with marveloous collection of works and refernces

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Global modeling of transcriptional responses in interaction networks

Global modeling of transcriptional responses in interaction networks | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions and the associated transcriptional responses are often unknown. Organism-wide modeling of network activation can reveal unique and shared mechanisms between tissues, and potentially as yet unknown processes. The same method can also be applied to cell-biological conditions in one or more tissues.

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Cell - A Whole-Cell Computational Model Predicts Phenotype from Genotype

Cell - A Whole-Cell Computational Model Predicts Phenotype from Genotype | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

we are up into whole cell modelling)

and what are you up to today?))

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A Second-generation Protein-Protein Interaction Network of Helicobacter pylori

Dmitry Alexeev's insight:

This is exactly what we need now - a comprehensive wide network of PPI fro helicobacter pylori

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Polyphasic Analysis of a Middle Ages Coprolite Microbiota, Belgium

Polyphasic Analysis of a Middle Ages Coprolite Microbiota, Belgium | Systems biology and bioinformatics | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
Dmitry Alexeev's insight:

Medieval coprolites! Wonder is amount of pathogens found ... makes us think)

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Addendum: Enterotypes of the human gut microbiome : Nature : Nature Publishing Group

Addendum: Enterotypes of the human gut microbiome : Nature : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

"It has been drawn to our attention that the methods described in the main text and the Supplementary Information of this Article have been considered by some researchers to be insufficient to enable them to identify enterotypes in their own data sets."

Good start for the Nature addendum - and yes we were among those researchers who were unable to identify )))



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Manipulation of the Microbiota for Treatment of IBS and IBD—Challenges and Controversies

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issues of biota manipulation

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Molecular biology: A second layer of information in RNA

Molecular biology: A second layer of information in RNA | Systems biology and bioinformatics | Scoop.it

Three studies have characterized the full complement of RNA folding in cells. They find large numbers of secondary structures in RNA, some of which may have functional consequences for the cell.

 

Molecular biology: A second layer of information in RNA
Silvia B. V. Ramos & Alain Laederach

Nature 505, 621–622 (30 January 2014) http://dx.doi.org/10.1038/505621a


Via Complexity Digest
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Rescooped by Dmitry Alexeev from Complexity - Complex Systems Theory
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Marie Curie says stop hating on quilt plots already. | Simply Statistics

Marie Curie says stop hating on quilt plots already. | Simply Statistics | Systems biology and bioinformatics | Scoop.it

"There are sadistic scientists who hurry to hunt down error instead of establishing the truth." -Marie Curie (http://en.wikiquote.org/wiki/Marie_Curie)


Via Bernard Ryefield
Dmitry Alexeev's insight:

we support no ntrolling quiltplots)

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Connecting the Dots between PubMed Abstracts

Connecting the Dots between PubMed Abstracts | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

somformulas but i like)

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Probabilistic inference of biochemical reac... [PLoS Comput Biol. 2013] - PubMed - NCBI

Probabilistic inference of biochemical reac... [PLoS Comput Biol. 2013] - PubMed - NCBI | Systems biology and bioinformatics | Scoop.it
PubMed comprises more than 23 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Dmitry Alexeev's insight:

have to read this one

 

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CoNet

CoNet | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

cytoscape tool for metagenomics networks

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