An Efficient Algorithm for Clustering of Large-Scale Mass Spectrometry Data

High-throughput spectrometers are capable of producing data sets containing thousands of spectra for a single biological sample. These data sets contain a substantial amount of redundancy from peptides that may get selected multiple times in a LC-MS/MS experiment. In this paper, we present an efficient algorithm, CAMS (Clustering Algorithm for Mass Spectra) for clustering mass spectrometry data which increases both the sensitivity and confidence of spectral assignment. CAMS utilizes a novel metric, called F-set, that allows accurate identification of the spectra that are similar. A graph theoretic framework is defined that allows the use of F-set metric efficiently for accurate cluster identifications. The accuracy of the algorithm is tested on real HCD and CID data sets with varying amounts of peptides. Our experiments show that the proposed algorithm is able to cluster spectra with very high accuracy in a reasonable amount of time for large spectral data sets. Thus, the algorithm is able to decrease the computational time by compressing the data sets while increasing the throughput of the data by interpreting low S/N spectra.Comment: 4 pages, 4 figures, Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference o

cGAS deficiency enhances inflammasome activation in macrophages and inflammatory pathology in pristane-induced lupus

IntroductionType I interferon (IFN) plays a vital role in the pathogenesis of systemic lupus erythematosus. Cyclic GMP AMP synthase (cGAS) is a cytosolic DNA sensor that recognizes dsDNA and creates cGAMP to activate STING-mediated type I IFN production. The activation of STING induces lupus disease in Fcgr2b deficient mice through the differentiation of dendritic cells. In contrast, Cgas-deficient mice could be generated more autoantibody production and proteinuria in pristane-induced lupus (PIL). These data suggested that the other dsDNA sensors could be involved in lupus development mechanisms.MethodsThis study aimed to identify the cGAS-mediated mechanisms contributing to lupus pathogenesis in PIL. The Cgas-deficient and WT mice were induced lupus disease with pristane and subsequently analyzed autoantibody, histopathology, and immunophenotypes. The lung tissues were analyzed with the expression profiles by RT-PCR and western blot. The bone marrow-derived macrophages were stimulated with inflammasome activators and observed pyroptosis.ResultsThe Cgas-/- mice developed more severe pulmonary hemorrhage and autoantibody production than WT mice. The activated dendritic cells, IFN-g-, and IL-17a-producing T helper cells, and infiltrated macrophages in the lung were detected in Cgas-/- mice higher than in WT mice. We observed an increase in expression of Aim2, Casp11, and Ifi16 in the lung and serum IL-1a but IL-1b in pristane-injected Cgas-/- mice. The rise of Caspase-11 in the lung of pristane-injected Cgas-/- mice suggested noncanonical inflammasome activation. The activation of AIM2 and NLRP3 inflammasomes in bone marrow-derived macrophages (BMDMs) enhanced the number of dead cells in Cgas-/- mice compared with WT mice. Activation of the inflammasome significantly induced pyroptosis in Cgas-/- BMDMs. The dsDNA level, but not mitochondrial DNA, increased dramatically in pristane-injected Cgas-/- mice suggesting the dsDNA could be a ligand activating inflammasomes. The cGAS agonist-induced BMDM activation in the Cgas-/- mice indicated that the activation of DNA sensors other than cGAS enhanced activated macrophages.ConclusionThese findings suggested that cGAS hampers the unusual noncanonical inflammasome activation through other DNA sensors

A machine learning strategy for predicting localization of post-translational modification sites in protein-protein interacting regions

Definitions of true positives (TP), false positives (FP), true negatives (TN), and false negatives (FN) in this study. (DOCX 18 kb

Razlika između proteina sjemene plazme i proteina sperme za dobru i lošu sposobnost smrzavanja ejakulata nerasta

The present study was performed to compare the expression of sperm proteins, i.e. triosephosphate isomerase (TPI) and acrosin binding protein (ACRBP) and seminal plasma proteins, i.e. glutathione peroxidase 5 (GPX5) and fibronectin 1 (FN1), in boar semen with good, moderate and poor freezability. The study was conducted by determining the protein contents in 32 sperm samples and 38 seminal plasma samples of semen. The ejaculated semen was divided into two portions: the first portion was centrifuged to separate the pellet of sperm from the seminal plasma and the second portion was cryopreserved. After thawing, the ejaculates were classified into three groups according to their post-thawed sperm motility: good (60.2 ± 1.7%), moderate (29.3 ± 2.0%) and poor (16.6 ± 2.2%) freezabilities. The expressions of GPX5 and FN1 in seminal plasma and TPI and ACRBP in sperm were determined using Western blot analysis. It was found that, for sperm proteins, the level of TPI was negatively correlated with the post-thawed total sperm motility (r = -0.38, P = 0.029). For seminal plasma proteins, the level of FN1 in the seminal plasma was positively correlated with the post-thawed total sperm motility (r = 0.37, P = 0.021) and progressive motility (r = 0.39, P = 0.016). The expression of GPX5 was not correlated with any of the frozen–thawed sperm qualities (P > 0.05). In conclusions, boar semen containing a high level of FN1 in seminal plasma has better freezability. Frozen–thawed sperm motility was positively correlated with the level of FN1 in boar seminal plasma and negatively correlated with TPI in boar spermatozoa.Ova studija provedena je u svrhu usporedbe ekspresije proteina sperme, tj. trioza-fosfat izomeraze (TPI) i akrozin-vezujućeg proteina (ACRBP) te proteina sjemene plazme, tj. glutation peroksidaze 5 (GPX5) i fibronektina 1 (FN1), u sjemenu nerasta s dobrom, umjerenom i lošom sposobnošću smrzavanja. Studija je provedena ustvrđivanjem sadržaja proteina u 32 uzorka sperme i 38 uzoraka sjemene plazme sjemena. Ejakulirano sjeme podijeljeno je u dva dijela: prvi dio je centrifugiran za odvajanje taloga sperme od sjemene plazme, a drugi je dio je krioprezerviran. Nakon odmrzavanja u skladu s pokretljivošću spermija nakon odmrzavanja ejakulati su klasificirani u tri skupine: dobra (60,2 ± 1,7%), umjerena (29,3 ± 2,0%) i loša (16,6 ± 2,2%) sposobnost smrzavanja. Ekspresije GPX5 i FN1 u sjemenoj plazmi te TPI i ACRBP u spermi ustvrđene su „Western blot“ analizom. Za proteine sperme je otkriveno da je razina TPI nakon odmrzavanja negativno povezana s ukupnom pokretljivošću sperme (r = -0,38, P = 0,029). Za proteine sjemene plazme, razina FN1 u sjemenoj plazmi nakon odmrzavanja pozitivno je povezana s ukupnom pokretljivošću sperme nakon odmrzavanja (r = 0,37, P = 0,021) i progresivnom pokretljivošću (r = 0,39, P = 0,016). Ekspresija GPX5 nije povezana ni sa kakvim kvalitetama smrznute pa odmrznute sperme (P > 0,05). Zaključno, sjeme nerasta koje sadrži visoku razinu FN1 u sjemenoj plazmi ima bolju sposobnost smrzavanja. Pokretljivost sperme koja je smrznuta pa odmrznuta pozitivno je povezana s razinom FN1 u sjemenoj plazmi nerasta, a negativno s razinom TPI u spermijima nerasta

Impact of mAb-induced A475V substitution on viral fitness and antibody neutralization of SARS-CoV-2 omicron variants in the presence of monoclonal antibodies and human convalescent sera

The emergence and rapid evolution of SARS-CoV-2 variants have posed a major challenge to the global efforts to control the COVID -19 pandemic. In this study, we investigated the potential of two SARS-CoV-2 variants, BA.2 and BA.5, to evade neutralization by a human monoclonal antibody targeting the virus’s spike RBD (mAb 1D1). By subjecting the viruses to serial propagation in the presence of the antibody, we found that BA.2 exhibited poor growth, whereas BA.5 regained robust growth with significantly higher kinetics than the parental virus. Genetic analysis identified a single mutation, A475V, in the spike protein of BA.5 that substantially reduced the neutralizing activities of monoclonal antibodies and convalescent sera. In addition, the A475V mutation alone in BA.2 moderately reduced the neutralizing activity but completely abolished the neutralizing effect of mAb 1D1 when F486V or L452R were also present. Our results shed light on the possible evolutionary development of SARS-CoV-2 variants under selection pressure by monoclonal antibodies and have implications for the development of effective antibody therapies and vaccines against the virus