Areoana analysis of moss leaf cell structure of two Cyrtomnium species (Mniaceae, Bryophyta)

Two species of the moss genus Cyrtomnium were studied for the parameters of their leaf cells. The computer program AREOANA, specially designed for this kind of studies, allows involving large datasets in the analysis. In this study, it processed 81 leaves with altogether 140 000 cellsyesBelgorod State National Research Universit

Areoana analysis of moss leaf cell structure of two Cyrtomnium species (Mniaceae, Bryophyta)

yesTwo species of the moss genus Cyrtomnium were studied for the parameters of their leaf cells. The computer program AREOANA, specially designed for this kind of studies, allows involving large datasets in the analysis. In this study, it processed 81 leaves with altogether 140 000 cellsBelgorod State National Research Universit

Multiomic Profiling Identified EGF Receptor Signaling as a Potential Inhibitor of Type I Interferon Response in Models of Oncolytic Therapy by Vesicular Stomatitis Virus

Cancer cell lines responded differentially to type I interferon treatment in models of oncolytic therapy using vesicular stomatitis virus (VSV). Two opposite cases were considered in this study, glioblastoma DBTRG-05MG and osteosarcoma HOS cell lines exhibiting resistance and sensitivity to VSV after the treatment, respectively. Type I interferon responses were compared for these cell lines by integrative analysis of the transcriptome, proteome, and RNA editome to identify molecular factors determining differential effects observed. Adenosine-to-inosine RNA editing was equally induced in both cell lines. However, transcriptome analysis showed that the number of differentially expressed genes was much higher in DBTRG-05MG with a specific enrichment in inflammatory proteins. Further, it was found that two genes, EGFR and HER2, were overexpressed in HOS cells compared with DBTRG-05MG, supporting recent reports that EGF receptor signaling attenuates interferon responses via HER2 co-receptor activity. Accordingly, combined treatment of cells with EGF receptor inhibitors such as gefitinib and type I interferon increases the resistance of sensitive cell lines to VSV. Moreover, sensitive cell lines had increased levels of HER2 protein compared with non-sensitive DBTRG-05MG. Presumably, the level of this protein expression in tumor cells might be a predictive biomarker of their resistance to oncolytic viral therapy

Petr Damian. Certamen spirituale.

RIASSUNTO MATĚJEK, Marek: Pier Damiani. Certamen spirituale. La licenza di teologia spirituale Ľargomento centrale della mia licenza è ľanalisi delle lettere e scritture di Pier Damiani e della vita monastica da lui praticata a Fonte Avellana. Fin dalľinizio del cristianesimo esistettero cristiani che si ritiravano in luoghi solitari per dedicarsi interamente alla contemplazione. Questa forma di vita religiosa è testimoniata per la prima volta in Egitto, nel 3. secolo. La vita eremitica si diffuse in Occidente grazie a sanťAtanasio e a san Girolamo. Dal 4. secolo troviamo eremiti in Africa e in Europa. Nelľ11. secolo furono fondati ordini religiosi di eremiti. Nella mia licenza ho cercato di identificare ľorigine della idea eremitica e lo sviluppo progressivo fino ai giorni della riforma Gregoriana. Pier Damiani è nato a Ravenna da agiata famiglia. Lui viene in custodia da un suo fratello maggiore di nome Damiano, che si preoccupò della sua educazione. I suoi studi furono fatti dapprima a Ravenna, poi a Faenza e infine a Parma, dove studiò filosofia e retorica. Nel 1034 era professore nelle arti del trivio e del quadrivio, ma nonostante cercò la solitudine per praticare la sua devozione verso Dio. Da qui si fece monaco. Nel 1042 è a San Vincenzo al Furlo, dove scrive la Vita Romualdi e nel 1043 venne eletto...Department of Theological Ethics and Theology of SpiritualityKatedra teologické etiky a spirituální teologie (do 2018)Catholic Theological FacultyKatolická teologická fakult

Proteogenomics of Malignant Melanoma Cell Lines: The Effect of Stringency of Exome Data Filtering on Variant Peptide Identification in Shotgun Proteomics

The identification of genetically encoded variants at the proteome level is an important problem in cancer proteogenomics. The generation of customized protein databases from DNA or RNA sequencing data is a crucial stage of the identification workflow. Genomic data filtering applied at this stage may significantly modify variant search results, yet its effect is generally left out of the scope of proteogenomic studies. In this work, we focused on this impact using data of exome sequencing and LC–MS/MS analyses of six replicates for eight melanoma cell lines processed by a proteogenomics workflow. The main objectives were identifying variant peptides and revealing the role of the genomic data filtering in the variant identification. A series of six confidence thresholds for single nucleotide polymorphisms and indels from the exome data were applied to generate customized sequence databases of different stringency. In the searches against unfiltered databases, between 100 and 160 variant peptides were identified for each of the cell lines using X!Tandem and MS-GF+ search engines. The recovery rate for variant peptides was ∼1%, which is approximately three times lower than that of the wild-type peptides. Using unfiltered genomic databases for variant searches resulted in higher sensitivity and selectivity of the proteogenomic workflow and positively affected the ability to distinguish the cell lines based on variant peptide signatures

Proteogenomics of Malignant Melanoma Cell Lines: The Effect of Stringency of Exome Data Filtering on Variant Peptide Identification in Shotgun Proteomics

The identification of genetically encoded variants at the proteome level is an important problem in cancer proteogenomics. The generation of customized protein databases from DNA or RNA sequencing data is a crucial stage of the identification workflow. Genomic data filtering applied at this stage may significantly modify variant search results, yet its effect is generally left out of the scope of proteogenomic studies. In this work, we focused on this impact using data of exome sequencing and LC–MS/MS analyses of six replicates for eight melanoma cell lines processed by a proteogenomics workflow. The main objectives were identifying variant peptides and revealing the role of the genomic data filtering in the variant identification. A series of six confidence thresholds for single nucleotide polymorphisms and indels from the exome data were applied to generate customized sequence databases of different stringency. In the searches against unfiltered databases, between 100 and 160 variant peptides were identified for each of the cell lines using X!Tandem and MS-GF+ search engines. The recovery rate for variant peptides was ∼1%, which is approximately three times lower than that of the wild-type peptides. Using unfiltered genomic databases for variant searches resulted in higher sensitivity and selectivity of the proteogenomic workflow and positively affected the ability to distinguish the cell lines based on variant peptide signatures