Here we have some of the papers we discuss in our journal club


 

12/02/2015

How gut Microbiome composition affects immunotherapy responses in mouse models of cancer

Eduardo Pareja commented about two recent papers in Science and a commentary paper also in Science that pointed to the importance of gut microbiome composition in the immunotherapy of cancer. Both of them have been done in a melanoma model in mice. The...

How gut Microbiome composition affects immunotherapy responses in mouse models of cancer

Eduardo Pareja commented about two recent papers in Science and a commentary paper also in Science that pointed to the importance of gut microbiome composition in the immunotherapy of cancer. Both of them have been done in a melanoma model in mice. The immunoptherapy (check-point blockade) was done in PD-L1 in one case and in CTLA4 in the other.

The impact of that will be at least the immediate incorporation of metagenomics analysis in experimental studies and clinical trials for cancer immunotherapy.

 

See also: http://www.ncbi.nlm.nih.gov/pubmed/26612936

04/20/15: "Population and Evolutionary Genomics: The Selective Footprint of Wolfgang Stephan" DFG Symposium in Munich

Vedran Bozicevic shared in today's journal club his impressions on the symposium that was held from March 25th to 27th by the DFG (German Research Foundation), which is the self-governing organisation for science and research in Germany. The topic for this meeting was population and evolutionary genomics, and it was done in honor of Wolfgang Stephan, whose research interests are in theoretical and empirical population genetics, and in particular the modeling and inference of natural selection in the genome of eukaryotes.

04/16/15: RNA-Seq-based transcriptome analysis of methicillin-resistant Staphylococcus aureus biofilm inhibition by ursolic acid and resveratrol.

Regina Fernandez presented this paper that shows how two natural products (ursolic acid and resveratrol) seem to be able to inhibit the formation of biofilms. Since bacterial biofilms become resistant to the majority of available antobiotics, it is of high importance to find potential antagonists that inhibit its formation. 

 

 

See also: http://www.ncbi.nlm.nih.gov/pubmed/24970710

04/07/15: Entropy-scaling search of massive biological data

Eduardo Pareja-Tobes (@eparejatobes) presented today this paper whose main idea is that one can take advantage of the triangle inequality (that any distance is required to satisfy) to reduce the search space (the database) through adequate coverings by balls of a radius that is chosen according to the desired sensitivity. The complexity of this process is then related with entropy and fractal dimension-like measures of the search space.

See also: http://arxiv.org/abs/1503.05638

04/06/15: Neoantigens in cancer immunotherapy

In today's Journal Club Eduardo Pareja (@eduardopareja) talked about this paper  that explains the current situation of cancer immunotherapy. This is thanks to recent technologies an evolving field, that allows now to identify a new class of tumor-specific antigens derived from mutated proteins that are present only in the tumor. These “neoantigens” should provide highly specific targets for antitumor immunity. It will be therefore important to engineer therapeutic interventions by which neoantigen-specific T cell reactivity is selectively enhanced. 

See also: http://www.ncbi.nlm.nih.gov/pubmed/25838375

04/06/15: The shared microbiota of humans and companion animals as evaluated from Staphylococcus carriage sites

Eduardo Pareja (@eduardopareja) presented today this paper that studied the microbiota that colonizes typical coagulase-positive Staphylococcus spp. carriage sites in humans and their companion pets and also factors that influence sharing of microbiota between pets and humans. One of the results indicated that humans in households without pets were more similar to each other than humans in pet-owning households. This suggests that companion animals may play a role in microbial transfer. 

See also: http://www.ncbi.nlm.nih.gov/pubmed/25705378

02/26/15: Current strategies for mobilome research

Marina Manrique presented this paper about the sequencing of mobile genetic elements (MGEs) today. They are very important for bacterial evolution and adaptation, but sequencing them has turned out to be a complex issue. Several approaches have been proposed to enrich plasmid DNA from community samples. In this publication they review the most recent approaches and point out possible future developments for and pitfalls of these approaches. 

See also: http://www.ncbi.nlm.nih.gov/pubmed/25657641

02/23/15: The UCSC Genome Browser database: 2014 update

In today's Journal Club Evdokim Kovach talked about the UCSC (University of California Santa Cruz) Genome Browser. It offers access to genomic sequence and annotations for a variety of organisms, with an emphasis on vertebrate, primarily human and mouse genomes. It is an Open-Source graphical viewer that allows for a rapid visualization, examination, and querying of the data at many levels.

See also: http://www.ncbi.nlm.nih.gov/pubmed/24270787

02/09/15: The Candidate Cancer Gene Database: a database of cancer driver genes from forward genetic screens in mice

Marina Manrique talked today about The Candidate Cancer Gene Database (CCGD, http://ccgd-starrlab.oit.umn.edu/). It is a manually curated database containing all identified candidate driver genes and the genomic location of transposon common insertion sites (CISs) from all currently published transposon-based screens. It is a novel resource available to scientists interested in the identification of genetic drivers of cancer.

See also: http://www.ncbi.nlm.nih.gov/pubmed/25190456

02/05/15: FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations

Vedran Bozicevic chose to talk today about FlyBase  (http://flybase.org), a database of genetic and molecular data for D. melanogaster and other Drosophila species. These data types include mutant phenotypes,molecular characterization of mutant alleles and other deviations, cytological maps, wild-type expression patterns, anatomical images, transgenic constructs and insertions, sequence-level gene models and molecular classification of gene product functions.

See also: http://www.ncbi.nlm.nih.gov/pubmed/25398896

02/02/15: VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases

In today's journal club Rosa Martin presented VectorBase, a database for invertebrate vectors of human pathogens supported by the National Institute of Allergy and Infectious Diseases. It currently hosts the genomes of 35 organisms including a number of non-vectors for comparative analysis. Their data ranges from genome assemblies with annotated gene features, transcript and protein expression data to population genetics including variation and insecticide-resistance phenotypes.

See also: http://www.ncbi.nlm.nih.gov/pubmed/25510499

01/30/15: Tissue-based map of the human proteome

Eduardo Pareja chose for today's journal club this databe in which it is presented a map of the human tissue proteome based on quantitative transcriptomics on a tissue and organ level combined with protein profiling (using microarray-based immunochemistry) to gain information about the localization of proteins at the single-cell level. They provide a global analysis of the secreted and membrane proteins and also an analysis of the expression profiles for the proteins targeted by drugs and proteins implicated in cancer.

See also: http://www.ncbi.nlm.nih.gov/pubmed/25613900

01/27/15: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

Pablo Pareja-Tobes presented the MetaCyc database, which contains experimentally determined data about metabolic pathways and enzymes from all domains of life. It contains >2100 pathways derived from >37 000 publications, the largest curated collection of metabolic pathways currently available.

 

See also: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238876/

01/26/15: ComPPI: a cellular compartment-specific database for protein–protein interaction network analysis

We start off in our Journal Club a round of databases reviews, taken from the 2015 Nucleic Acids Research Database Issue.

Today, Alexey Alekhin presented ComPPI, a cellular compartment-specific database of proteins and their interactions. It enables the analysis of  compartmentalized protein-protein interaction networks. In this way, you can filter biologically unlikely interactions and predict novel properties. ComPPI provides confidence scores for protein subcellular localizations and protein-protein interactions.

See also: http://www.ncbi.nlm.nih.gov/pubmed/25348397

01/19/15: Differential RNA-seq: the approach behind and the biological insight gained

Transcriptomics have been lately the source of a lot of new discoveries concerning bacterial genomics. In this paper, a differential RNA-seq method is presented. Through this method it is possible to distinguish between primary and processed transcripts and it can also, among other features, provide a rich global map of transcriptional start sites. (Presented by Marina Manrique) 

See also: http://www.ncbi.nlm.nih.gov/pubmed/25024085

01/14/15: Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes

A total of 16 genomes and transcriptomes of anopheline mosquito species (vector for human malaria) have been recently sequenced. These genomes belonged to species from different locations spanning ~100 million years of evolution. The aim of this study was to get an insight on their vectorial capacity and explore new possibilities to control them. (Presented by Eduardo Pareja)

See also: http://www.ncbi.nlm.nih.gov/pubmed/25554792

01/13/15: Systematic identification of signaling pathways with potential to confer anticancer drug resistance

A group of scientists studied the effect that some mutated signaling pathways have on the resistance of cancer cells to some drugs. One interesting result is that the activation of the Notch1 pathway confers resistance to tamoxifen, a drug widely used by women suffering from breast cancer. Notch1 signaling could therefore be a potential therapeutic target in these cases in which women do not respond to the treatment with tamoxifen. (Presented by Eduardo Pareja)

See also: http://www.ncbi.nlm.nih.gov/pubmed/25538079