抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Efficient analysis of very large amounts of raw data for peptide identification and protein quantification is a principal challenge in mass spectrometry (MS)-based proteomics. Here we describe MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data. Using correlation analysis and graph theory, MaxQuant detects peaks, isotope clusters and stable amino acid isotope-labeled (SILAC) peptide pairs as three-dimensional objects in m/z, elution time and signal intensity space. By integrating multiple mass measurements and correcting for linear and nonlinear mass offsets, we achieve mass accuracy in the p.p.b. range, a sixfold increase over standard techniques. We increase the proportion of identified fragmentation spectra to 73% for SILAC peptide pairs via unambiguous assignment of isotope and missed-cleavage state and individual mass precision. MaxQuant automatically quantifies several hundred thousand peptides per SILAC-proteome experiment and allows statistically robust identification and quantification of >4,000 proteins in mammalian cell lysates.

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Resolving the molecular details of proteome variation in the different tissues and organs of the human body will greatly increase our knowledge of human biology and disease. Here, we present a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level. Our tissue-based analysis detected more than 90% of the putative protein-coding genes. We used this approach to explore the human secretome, the membrane proteome, the druggable proteome, the cancer proteome, and the metabolic functions in 32 different tissues and organs. All the data are integrated in an interactive Web-based database that allows exploration of individual proteins, as well as navigation of global expression patterns, in all major tissues and organs in the human body.

Tissue-based map of the human proteome

Recent successes illustrate the role of mass spectrometry-based proteomics as an indispensable tool for molecular and cellular biology and for the emerging field of systems biology. These include the study of protein-protein interactions via affinity-based isolations on a small and proteome-wide scale, the mapping of numerous organelles, the concurrent description of the malaria parasite genome and proteome, and the generation of quantitative protein profiles from diverse species. The ability of mass spectrometry to identify and, increasingly, to precisely quantify thousands of proteins from complex samples can be expected to impact broadly on biology and medicine.

Mass spectrometry-based proteomics

La presente invention concerne des complexes multiproteiques tires d'eukaryotes. Les complexes peuvent etre obtenus par utilisation d'une proteine en tant qu'appât et par isolement de l'ensemble de proteines qui lui est attache a partir de cellules. Ces complexes proteiques peuvent contenir jusqu'a trente proteines distinctes.

Complexes de proteines et leurs procedes d'utilisation

/pdf/author-correction-target-deconvolution-of-hdac-pharmacopoeia-h68f5x59.pdf

Author Correction: Target deconvolution of HDAC pharmacopoeia reveals MBLAC2 as common off-target

La presente invention concerne des complexes proteiques intervenant dans des processus cellulaires, dont il a ete demontre qu'ils sont critiques pour l'evolution de diverses formes de maladies neurologiques. Elle concerne egalement des proteines constitutives de ces complexes, des fragments et des derives desdites proteines constitutives, et des anticorps specifiques de ces complexes. L'invention concerne en outre des methodes d'utilisation des complexes, et leurs proteines interagissant, entre autres, dans des criblages, diagnostics ou traitements. Elle concerne enfin des methodes de preparation de ces complexes.

Complexes proteiques impliques dans des maladies neurologiques

http://www.mcponline.org/article/S1535947623001238/pdf

Unified workflow for the rapid and in-depth characterization of bacterial proteomes.

The invention concerns a compound, wherein the compound is a substance according to the following formula (I) 
wherein R 1 is 
-SO 3 H, 1-methyl-4,5-dihydro-1H-imidazol-2-yl, 
wherein the ring A is a pyrrolidine, piperidine, morpholine, or imidazole residue or a substituted pyrrolidine, piperidine, morpholine, or imidazole residue, Q is -NH-, -NH-alkyl-, -O-, or -S- and R 7 is -H, a substituted or non-substituted pyrrolidine, piperidine, morpholine, triazine, or imidazole residue, or a substituted or non-substituted alkylpyrrolidine, alkylpiperidine, alkylmorpholine, alkyltriazine, or alkylimidazole residue, alkyl, alkylester, alkenyl, alkenylester, alkynyl, alkynylester, aminoalkyl, cyanyl, -NO 2 , methylsulfonyl residue, or a substituted or non-substituted form of any of the following residues: cycloalkyl, cycloalkylalkyl, cycloalkenyl, cycloalkenylalkyl, bicycloalkyl, bicycloalkylalkyl, bicycloalkenyl, bicycloalkenylalkyl, or another bicyclic residue, aryl, aminoaryl, heteroaryl, heteroaminoaryl, cyclyl, aminocyclyl, heterocyclyl, heteroaminocyclyl, aralkyl, aminoaralkyl, heterocycloalkyl, or heteroaminocycloalkyl, 
R 2 is 
-H, -Cl, -Br, -CF 3 , -CH=CH 2 or another alkenyl, -C=CH or another alkynyl, phenyl or substituted phenyl, triazolyl or another heteroaryl, substituted triazolyl or another substituted heteroaryl, a residue of 9-BBN (9-borabicyclo[3.3.1]nonane), OBBD (9-oxa-10-borabicyclo[3.3.2]decane), trifluoroborate, boronic acid, or an ester of boronic acid and pinacol, methyliminodiacetic acid (MIDA), catechol, pinane diol, ethylene glycol, or propane diol or another boronic acid ester, 
wherein the ring A is a pyrrolidine, piperidine, morpholine, or imidazole residue or a substituted pyrrolidine, piperidine, morpholine, or imidazole residue, Q is -NH-, -NH-alkyl-, -O-, or -S- and R 7 is -H, a substituted or non-substituted pyrrolidine, piperidine, morpholine, triazine, or imidazole residue, or a substituted or non-substituted alkylpyrrolidine, alkylpiperidine, alkylmorpholine, alkyltriazine, or alkylimidazole residue, alkyl, alkylester, alkenyl, alkenylester, alkynyl, alkynylester, aminoalkyl, cyanyl, -NO 2 , methylsulfonyl residue, or a substituted or non-substituted form of any of the following residues: cycloalkyl, cycloalkylalkyl, cycloalkenyl, cycloalkenylalkyl, bicycloalkyl, bicycloalkylalkyl, bicycloalkenyl, bicycloalkenylalkyl, or another bicyclic residue, aryl, aminoaryl, heteroaryl, heteroaminoaryl, cyclyl, aminocyclyl, heterocyclyl, heteroaminocyclyl, aralkyl, aminoaralkyl, heterocycloalkyl, or heteroaminocycloalkyl, 
R 3 is -H or -CH 3 , 
R 4 is -H, -Cl, -Br, -CH 3 , -CH(CH 3 ) 2 or -C(CH 3 ) 3 , 
R 5 is -H, -CH 3 , -CH(CH 3 ) 2 or -C(CH 3 ) 3 , and 
R 6 is -H or -CH 3 , 
or a salt of said substance.

Bernhard Kuster

Papers

Complexes de proteines et leurs procedes d'utilisation

Author Correction: Target deconvolution of HDAC pharmacopoeia reveals MBLAC2 as common off-target

Complexes proteiques impliques dans des maladies neurologiques

Unified workflow for the rapid and in-depth characterization of bacterial proteomes.

Compound, compound for use in the treatment of a pathological condition, a pharmaceutical composition and a method for preparing said compound