Data-independent mass spectrometry activates all ion species isolated within a given mass-to-charge window (
m/z
) regardless of their abundance. This acquisition strategy overcomes the traditional ...data-dependent ion selection boosting data reproducibility and sensitivity. However, several tandem mass (MS/MS) spectra of the same precursor ion are acquired during chromatographic elution resulting in large data redundancy. Also, the significant number of chimeric spectra and the absence of accurate precursor ion masses hamper peptide identification. Here, we describe an algorithm to preprocess data-independent MS/MS spectra by filtering out noise peaks and clustering the spectra according to both the chromatographic elution profiles and the spectral similarity. In addition, we developed an approach to estimate the
m/z
value of precursor ions from clustered MS/MS spectra in order to improve database search performance. Data acquired using a small 3
m/z
units precursor mass window and multiple injections to cover a
m/z
range of 400–1400 was processed with our algorithm. It showed an improvement in the number of both peptide and protein identifications by 8 % while reducing the number of submitted spectra by 18 % and the number of peaks by 55 %. We conclude that our clustering method is a valid approach for data analysis of these data-independent fragmentation spectra. The software including the source code is available for the scientific community.
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MicroRNAs (miRNAs) are a class of small non-coding RNA molecules involved in the regulation of key biological processes. Different miRNAs with pro-oncogenic and anti-oncogenic properties have been ...identified in glioblastomas. We decided to analyze expression profiles of 10 mature miRNAs (miR-7-1, miR-10а, miR-17, miR-20а, miR-21, miR-23а, miR-26а, miR-137, and miR-222) in post-surgery glioma specimens of different grades in order to find whether the expression level correlates with tumor grades. We also measured expression of six key genes such as PTEN, p21/CDKN1A, MDR1, ABCG2, BAX, and BCL-2 involved in the regulation of critical glioma signaling pathways to establish the effect of miRNAs on these signaling mechanisms.
Using RT-PCR, we performed expression analysis of 25 tumor fresh samples (grades II-IV).
We found gradual increase in miR-21 and miR-23a levels in all tumor grades whereas miR-7 and miR-137 were significantly down-regulated depending on the glioma grade. MDR, ABCG2, and p21/CDKN1A levels were significantly up-regulated while expression of PTEN was down-regulated in tumor samples compared to the normal brain tissue.
These observations provide new insights into molecular pathogenic mechanisms of glioma progression and suggest about a potential value of miRNAs as a putative diagnostic marker of brain tumors.
High throughput protein identification and quantification analysis based on mass spectrometry are fundamental steps in most proteomics projects. Here, we present EasyProt (available at ...http://easyprot.unige.ch), a new platform for mass spectrometry data processing, protein identification, quantification and unexpected post-translational modification characterization. EasyProt provides a fully integrated graphical experience to perform a large part of the proteomic data analysis workflow. Our goal was to develop a software platform that would fulfill the needs of scientists in the field, while emphasizing ease-of-use for non-bioinformatician users. Protein identification is based on OLAV scoring schemes and protein quantification is implemented for both, isobaric labeling and label-free methods. Additional features are available, such as peak list processing, isotopic correction, spectra filtering, charge-state deconvolution and spectra merging. To illustrate the EasyProt platform, we present two identification and quantification workflows based on isobaric tagging and label-free methods.
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► Fully graphical, easy-to-use and multi-user platform for proteomics data analysis from MS/MS data ► Protein identification featuring on-the-fly false positives removal ► Protein quantification through both isobaric tagging and label-free methods ► Characterization of unexpected post-translational modifications ► Peak lists conversion and processing
We consider initial boundary value problem for a reaction-diffusion system with nonlinear and nonlocal boundary conditions and nonnegative initial data. We prove local existence, uniqueness, and ...nonuniqueness of solutions.
The coronavirus disease outbreak in 2019 (COVID-19) has now achieved the level of a global pandemic and affected more than 100 million people on all five continents and caused over 2 million deaths. ...Russia is, needless to say, among the countries affected by SARS-CoV-2, and its health authorities have mobilized significant efforts and resources to fight the disease. The paper presents the result of a functional analysis of 155 patients in the Moscow Region who were examined at the Central Clinical Hospital of the Russian Academy of Sciences during the first wave of the pandemic (February-July, 2020). The inclusion criteria were a positive PCR test and typical, computed tomographic findings of viral pneumonia in the form of ground-glass opacities. A clinical correlation analysis was performed in four groups of patients: (1) those who were not on mechanical ventilation, (2) those who were on mechanical ventilation, and (3) those who subsequently recovered or (4) died. The correlation analysis also considered confounding comorbidities (diabetes, metabolic syndrome, hypertension, etc.). The immunological status of the patients was examined (levels of immunoglobulins of the M, A, G classes and their subclasses, as well as the total immunoglobulin level) using an original SARS-CoV-2 antibody ELISA kit. The ELISA kit was developed using linear S-protein RBD-SD1 and NTD fragments, as well as the N-protein, as antigens. These antigens were produced in the prokaryotic
system. Recombinant RBD produced in the eukaryotic CHO system (RBD CHO) was used as an antigen representing conformational RBD epitopes. The immunoglobulin A level was found to be the earliest serological criterion for the development of a SARS-CoV-2 infection and it yielded the best sensitivity and diagnostic significance of ELISA compared to that of class M immunoglobulin. We demonstrated that the seroconversion rate of "early" N-protein-specific IgM and IgA antibodies is comparable to that of antibodies specific to RBD conformational epitopes. At the same time, seroconversion of SARS-CoV-2 N-protein-specific class G immunoglobulins was significantly faster compared to that of other specific antibodies. Our findings suggest that the strong immunogenicity of the RBD fragment is for the most part associated with its conformational epitopes, while the linear RBD and NTD epitopes have the least immunogenicity. An analysis of the occurrence rate of SARS-CoV-2-specific immunoglobulins of different classes revealed that RBD- and N-specific antibodies should be evaluated in parallel to improve the sensitivity of ELISA. An analysis of the immunoglobulin subclass distribution in sera of seropositive patients revealed uniform induction of N-protein-specific IgG subclasses G1-G4 and IgA subclasses A1-A2 in groups of patients with varying severity of COVID-19. In the case of the S-protein, G1, G3, and A1 were the main subclasses of antibodies involved in the immune response.
Li atoms in Li2(VO)2(μ-OOCR)6(bpy)2 (R=CMe3 (2), CF3(3)) contribute to the weakening of spin coupling between two vanadium(IV) centers in comparison with (VO)2(μ-OH)(μ-OOCCMe3)2(bpy)2 (1). Different ...types of weak antiferromagnetic spin–spin interactions are detected in similarly constructed molecules 2 and 3: in 2 – intramolecular, but in 3 – probably intermolecular exchange.
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Crystals of binuclear complex (VO)2(µ-OH)(µ-Piv)2(bpy)2(OTf) (1) have been obtained by the reaction of VO(H2O)5(OTf)2 (OTf=CF3SO3−, Piv=(CH3)3CCO2−) with 2,2′-bipyridine (bpy) and lithium trimethylacetate (pivalate), Li(Piv), in a ratio of 1:1:2 in MeCN. Change of the reagent ratio to 1:1:3 resulted in the bimetallic compound Li2(VO)2(µ-Piv)6(bpy)2 (2), which was isolated in the form of 2·MeCN and 2·CH2Cl2 solvates. Replacement of Li(Piv) with lithium trifluoroacetate Li(Tfac) (Tfac=CF3CO2−) results in the bimetallic compound Li2(VO)2(µ-Tfac)6(bpy)2 (3). A similar reaction with lithium trichloroacetate, Li(Tcac) (Tcac=CCl3CO2−), in ethanol gives the mononuclear complex VO(Tcac)(bpy)2(OTf) (4). The structures of 1–4 were determined by single crystal X-ray diffraction. The magnetic properties (2–300K) and EPR spectra of compounds 1–3 have been studied. Using the ESEEM (electron spin echo envelope modulation) method it has been shown that the mononuclear cation VO(Tcac)(bpy)2+ of complex 4 has partial spin density transfer from the VIV atom to donor ligands (in particular, the bpy nitrogen atoms). According to EPR spectroscopy data and quantum-chemical calculations, a similar spin density distribution is observed for 2 and 3, though spin exchange in these compounds is hindered by lithium ions, which contain no spin density and block electron density delocalization in the bridging system between the “magnetic” vanadium ions. Electrochemical properties of compounds 2 and 3 confirm the vanadium(IV) oxidation state.
The genus Hemimysis (Malacostraca: Mysida: Mysidae) encompasses near-bottom, demersal and cave-dwelling mysids living in the marine, brackish and freshwater habitats around the European coast, from ...the Caspian Sea to the Scandinavian Peninsula. We conducted cladistic analysis of 52 morphological characters of all nine species and three subspecies of the genus Hemimysis. We also completed a molecular analysis based on three molecular markers of Hemimysis lamornae (Couch, 1856) found in the English Channel, the Mediterranean Sea, and the Black Sea. Bothanalyses did not support monophyly of Hemimysis lamornae. We thus consider the former subspecies H. lamornae pontica (Czerniavsky, 1882) and H. lamornae mediterranea Bacescu, 1936 as valid species. Analysis of mitochondrial cytochrome oxidase subunit I (COI) sequences of H. pontica shows no significant divergence between mysids living in the marine caves of Crimea and Bulgaria. Morphological trends in Hemimysis are discussed, H. pontica Czerniavsky, Q1 1882 is redescribed, and a new key to all 11 species of the genus is given.
INTRODUCTION. Ibrutinib is an oral small-molecule drug that irreversibly inhibits Bruton's tyrosine kinase and thus suppresses proliferation of B cells. Ibrutinib therapy in chronic lymphocytic ...leukemia (CLL) and in mantle cell lymphoma (MCL) is associated with frequent bleeding complications that were reported to be more severe in CLL. This difference was suggested to be related to differential adenosine diphosphate (ADP) disruption by CD39, expressed by tumor cells. Here we investigate platelet functional activity in CLL and MCL patients before initiation of ibrutinib.
MATERIALS. Fifty one adult patients with relapsed and refractory CLL and MCL and 20 healthy donors were included in the study. Platelet functional activity was characterized by flow cytometry before and after activation with SFLLRN plus collagen-related peptide. Levels of CD42b, CD61, CD62P, PAC1, annexin V binding, and mepacrine release were determined. Aggregation with collagen, ADP and ristocetin were measured.
RESULTS. Among 36 CLL patients 25 (69%) were men, the median age was 66 (range, 31 to 83 years) and 23 (64%) had a refractory disease. In 34 previously treated patients the median number of prior treatments was 2 (range, 1 - 6). Two CLL patients with del (17p) received ibrutinib as a first line. In a group of MCL patients (n=15) there were 12 men (80%), the median age was 63 years (range, 49-79). Seven (54%) patients had a high MIPI score. The median number of previous chemotherapy lines in MCL patients was 1 (range, 1 - 6). Lymphocyte count before initiation of ibrutinib was significantly higher in CLL group (median 17,5 х 109/L range 0,48 - 189,7) compared to MCL group (median 1,75 х 109/L, range 0,35 - 6,59, p=0,037). Initial platelets count was also different being lower in CLL than in MCL patients (127 х 109/L (15 - 248) versus 186 х 109/L (63 - 311), p=0,005). Platelets of untreated patients with CLL had statistically significant impairments in their responses compared to those with MCL. Specifically, they had decreased integrin activation in response to stimulation (46±19% versus 73±18%; for healthy donors, 100±17%), and relative mepacrine release (2.9±0.9 versus 3.5±0.8; healthy, 4.0±0.7). P-selectin release was impaired milder (77±17% versus 92±14%; healthy, 100±10%), and procogulant platelet formation impairment was not statistically significant (8±6% versus 12±7%; healthy, 12±3%). In control experiments, addition of MeS-AMP and MRS2179, selective inhibitors of ADP receptors, had comparable effects on the healthy donor platelets. Aggregation in response to ADP was dramatically impaired in CLL compared with MCL (24±18% versus 42±16%), as well as that in response to collagen (47±23% versus 72±13%). Upon ibrutinib treatment, further decrease of PAC1 binding and procoagulant platelets formation almost to the level of resting platelets were observed; activation with SFLLRN alone produced a similar result with donor platelets.
CONCLUSIONS. Patients with CLL and MCL have initially impaired response of platelets. The defects of platelet function in CLL is much greater suggesting a possible explanation of the different clinical severity.
Vorobyev:Janssen: Speakers Bureau. Ptushkin:Janssen: Speakers Bureau.
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