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The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium’s collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com, we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form.
This article seeks to build a bridge between the empirical scholarship rooted in the traditional theory of political representation and constructivist theory on representation by focusing on the authorization of claims. It seeks to answer how claims can be authorized beyond elections - selecting three democratic innovations and tracing claims through the claim-making process. Different participatory democratic innovations are selected - providing various claims and taking place in different institutional contexts, i.e., (elected) members of the Council of Foreigners Frankfurt; individual citizens in participatory budgeting procedures in Münster; and citizen’s associations elected politicians in the referendum campaign in Hamburg. We first analyze the claims raised by the different claim-makers to identify their claimed constituency eligible to authorize claims. In the second step, we focus on the authorization by the claimed constituency and the relevant decision-making authority. The article finds that claim-making in democratic innovations is fractured and incomplete. Nevertheless, this is not the reason to dismiss democratic innovations as possible loci of representation; on the contrary, seen through the prism of claim-making, all representation – electoral and nonelectoral – is partial. Focusing on the authorization of claims in democratic innovations provides novel inferences about the potential and limits of democratic innovations for broadening democratic representation.
Radiotherapy is a frequently used treatment for prostate cancer. It does not only causes the intended damage to cancer cells, but also affects healthy surrounding tissue. As a result radiation-induced urethral strictures occur in 2.2% of prostate cancer patients. Management of urethral strictures is challenging due to the presence of poor vascularized tissue for reconstruction and the proximity of the sphincter, which can impair the functional outcome. This review provides a literature overview of risk factors, diagnostics and management of radiation-induced urethral strictures.
Many early taxonomic works on North American bees were published by Europeans using specimens collected in the New World, some with type locations so imprecise that uncertainty on the nomenclatural status remains to this day. Two examples come from Fabricius (1745–1808) who described Andrena virescens Fabricius, 1775 and Apis viridula Fabricius, 1793 from “America” and “Boreal America”, respectively. The former species of Agapostemon Guérin-Méneville, 1844 occurs across most of the United States and southern Canada, the latter presumed an endemic to Cuba. The type materials of these two taxa have never been compared to each other, though a morphology-based phylogenetic analysis placed both in distinct species groups. Here we synonymize Apis viridula under Ag. virescens, thereby making Ag. femoralis (Guérin-Méneville, 1844) available as the name for the Cuban species. A lectotype for Ag. femoralis (the type species for the genus Agapostemon) is hereby designated to stabilize this taxonomy. We also synonymize Ag. obscuratus Cresson, 1869 under Ag. femoralis, suggesting that it represents a dark colour polymorphism. As Ag. cubensis Roberts, 1972 is a junior secondary homonym of Ag. cubensis (Spinola, 1851), we offer Ag. robertsi as a replacement name for the former.
The Smicridea (Smicridea) fasciatella species group occurs from the southwestern USA, throughout Central America, the Greater Antilles islands, and most of South America, except for the Chilean subregion. It is characterized by the phallic apparatus being a simple tube with eversible internal sclerites at the apex. The fasciatella group is composed of 61 species, of which only 11 occur in Brazil, mainly in the Atlantic Forest biome in the southeastern region. In order to reduce the Linnean and Wallacean shortfalls for the Smicridea Brazilian fauna, we diagnose, describe, and illustrate males of six new species in the fasciatella group: Smicridea (Smicridea) blahniki Desiderio, Pes & Hamada sp. nov., S. (Smicridea) brevitruncata Desiderio, Pes & Hamada sp. nov., S. (Smicridea) caaguara Desiderio, Pes & Hamada sp. nov., S. (Smicridea) ipiranga Desiderio, Pes & Hamada sp. nov., S. (Smicridea) jeaneae Desiderio, Pes & Hamada sp. nov., and S. (Smicridea) polyacantha Desiderio, Pes &; Hamada sp. nov. Additionally, we provide distributional data for S. (Smicridea) albosignata Ulmer, 1907, S. (Smicridea) bivittata (Hagen, 1861), S. (Smicridea) erecta Flint, 1974, S. (Smicridea) obliqua Flint, 1974, S. (Smicridea) paranensis Flint, 1983, and S. (Smicridea) sattleri Denning & Sykora, 1968. The number of S. (Smicridea) species in Brazil increases from 21 to 27 and Smicridea is recorded from the states of Acre, Amapá, and Sergipe for the first time.
Most valvatiform genera of the gastropod family Hydrobiidae are narrow-range taxa. One exception is the genus Arganiella, which is comprised of three congeners: the type species A. pescei from the Apennine Peninsula, A. wolfi from the Iberian Peninsula and A. tabanensis from the Balkans. The genus assignment of the latter two species was based on morphological similarities with A. pescei in the shell, operculum, radula and genitalia. Given that the morphology of hydrobiids is sometimes susceptible to convergence, this study re-evaluates the taxonomic status of species of Arganiella by analysing mitochondrial (mtCOI) and nuclear (18S rRNA) sequences of topotypes or near topotypes to infer their phylogenetic position. Our phylogenetic analyses depicted Arganiella as a non-monophyletic group within Hydrobiidae, and sequence divergence among the three species ranged from 14.5 to 16.7% for mtCOI and 2.0 to 3.8% for 18S. We also re-examined the extent of morphological variation among species of Arganiella and found a few differences among them and other valvatiform genera. Consequently, we propose two new genera for A. wolfi and A. tabanensis. Our results conflict with the classification of valvatiform hydrobiid species solely based on traditional phenotypical methods and suggest further taxonomic evaluation within a molecular framework.
Selizitapia gen. nov. (Hemiptera: Fulgoromorpha: Flatidae) from tapia woodlands of Madagascar
(2021)
A new monotypic genus of flatid planthoppers (Hemiptera: Fulgoromorpha: Flatidae), Selizitapia gen. nov., is described for Selizitapia pennyi gen. et sp. nov. (type species) from the island of Madagascar. Habitus, male and female external and internal genital structures of the new species are illustrated and compared with similar taxa. Selizitapia pennyi gen. et sp. nov. is endemic to Madagascar where it is known to date only from one locality in the Central Plateau and is associated with tapia woodland formation.
This is the first part of a revision of the type specimens of the South American Sericini. Herein, we examine type specimens of Astaena described by Lawrence Webster Saylor (1913–1999). We provide diagnostic redescriptions, images of habitus, aedeagus, and labels of the type specimens of all 18 species described by him in the genus Astaena. We raise Sayloria Frey, 1973, a former subgenus of Symmela Erichson, 1835 that includes three species, to genus level. Our study results in the following new combinations and synonymy: Sayloria bicoloripes (Saylor, 1946) comb. nov. (= A. postnodata Frey, 1973 syn. nov.), S. abcora (Saylor, 1946) comb. nov. (= A. apolinarmaria Saylor, 1946 syn. nov.) and S. pottsi (Saylor, 1946) comb. nov.
Cell-free therapy using extracellular vesicles (EVs) from adipose-derived mesenchymal stromal/stem cells (ASCs) seems to be a safe and effective therapeutic option to support tissue and organ regeneration. The application of EVs requires particles with a maximum regenerative capability and hypoxic culture conditions as an in vitro preconditioning regimen has been shown to alter the molecular composition of released EVs. Nevertheless, the EV cargo after hypoxic preconditioning has not yet been comprehensively examined. The aim of the present study was the characterization of EVs from hypoxic preconditioned ASCs. We investigated the EV proteome and their effects on renal tubular epithelial cells in vitro. While no effect of hypoxia was observed on the number of released EVs and their protein content, the cargo of the proteins was altered. Proteomic analysis showed 41 increased or decreased proteins, 11 in a statistically significant manner. Furthermore, the uptake of EVs in epithelial cells and a positive effect on oxidative stress in vitro were observed. In conclusion, culture of ASCs under hypoxic conditions was demonstrated to be a promising in vitro preconditioning regimen, which alters the protein cargo and increases the anti-oxidative potential of EVs. These properties may provide new potential therapeutic options for regenerative medicine.
Nucleoredoxin (NXN) is a redox regulator of Disheveled and thereby of WNT signaling. Deficiency in mice leads to cranial dysmorphisms and defects of heart, brain, and bone, suggesting defects of cell fate determination. We used shRNA-mediated knockdown of NXN in SH-SY5Y neuroblastoma cells to study its impact on neuronal cells. We expected that shNXN cells would easily succumb to redox stress, but there were no differences in viability on stimulation with hydrogen peroxide. Instead, the proliferation of naïve shNXN cells was increased with a higher rate of mitotic cells in cell cycle analyses. In addition, basal respiratory rates were higher, whereas the relative change in oxygen consumption upon mitochondrial stressors was similar to control cells. shNXN cells had an increased expression of redox-sensitive heat shock proteins, Hsc70/HSPA8 and HSP90, and autophagy markers suggested an increase in autophagosome formation upon stimulation with bafilomycin and higher flux under low dose rapamycin. A high rate of self-renewal, autophagy, and upregulation of redox-sensitive chaperones appears to be an attractive anti-aging combination if it were to occur in neurons in vivo for which SH-SY5Y cells are a model.
Recent proposals suggest that timing in acquisition, i.e., the age at which a phenomenon is mastered by monolingual children, influences acquisition of the L2, interacting with age of onset of bilingualism and amount of L2 input. Here, we examine whether timing affects acquisition of the bilingual child’s heritage language, possibly modulating the effects of environmental and child-internal factors. The performance of 6- to 12-year-old Greek heritage children residing in Germany (age of onset of German: 0–4 years) was assessed across a range of nine syntactic structures via the Greek LITMUS (Language Impairment Testing in Multilingual Settings) Sentence Repetition Task. Based on previous studies on monolingual Greek, the structures were classified as “early” (main clauses (SVO), coordination, clitics, complement clauses, sentential negation, non-referential wh-questions) or as “late” (referential wh-questions, relatives, adverbial clauses). Current family use of Greek and formal instruction in Greek (environmental), chronological age, and age of onset of German (child-internal) were assessed via the Questionnaire for Parents of Bilingual Children (PABIQ); short-term memory (child-internal) was measured via forward digit recall. Children’s scores were generally higher for early than for late acquired structures. Performance on the three early structures with the highest scores was predicted by the amount of current family use of Greek. Performance on the three late structures was additionally predicted by forward digit recall, indicating that higher short-term memory capacity is beneficial for correctly reconstructing structurally complex sentences. We suggest that the understanding of heritage language development and the role of child-internal and environmental factors will benefit from a consideration of timing in the acquisition of the different structures.
This paper intends to provide some speculative remarks on how consistency and continuity in language use practices within and across contexts inform heritage language acquisition outcomes. We intend “consistency” as maintenance of similar patterns of home language use over the years. “Continuity” refers to the possibility for heritage language speakers to be exposed to formal education in the heritage language. By means of a questionnaire study, we analyze to what extent Italian heritage families in Germany are consistent in their use of the heritage language with their children. Furthermore, by analyzing the educational offer related to Italian as a heritage language across different areas in Germany, we reflect on children’s opportunities to experience continuity between home and school language practices. Finally, we interpret the results of previous studies on Italian heritage language acquisition through the lens of consistency and continuity of language experience. In particular, we show that under the appropriate language experience conditions (involving consistency and continuity), heritage speakers may be successful even in the acquisition of linguistic phenomena that have been shown to be acquired late in first language acquisition.
Based on recent perturbative and non-perturbative lattice calculations with almost quark flavors and the thermal contributions from photons, neutrinos, leptons, electroweak particles, and scalar Higgs bosons, various thermodynamic quantities, at vanishing net-baryon densities, such as pressure, energy density, bulk viscosity, relaxation time, and temperature have been calculated up to the TeV-scale, i.e., covering hadron, QGP, and electroweak (EW) phases in the early Universe. This remarkable progress motivated the present study to determine the possible influence of the bulk viscosity in the early Universe and to understand how this would vary from epoch to epoch. We have taken into consideration first- (Eckart) and second-order (Israel–Stewart) theories for the relativistic cosmic fluid and integrated viscous equations of state in Friedmann equations. Nonlinear nonhomogeneous differential equations are obtained as analytical solutions. For Israel–Stewart, the differential equations are very sophisticated to be solved. They are outlined here as road-maps for future studies. For Eckart theory, the only possible solution is the functionality, H(a(t)), where H(t) is the Hubble parameter and a(t) is the scale factor, but none of them so far could to be directly expressed in terms of either proper or cosmic time t. For Eckart-type viscous background, especially at finite cosmological constant, non-singular H(t) and a(t) are obtained, where H(t) diverges for QCD/EW and asymptotic EoS. For non-viscous background, the dependence of H(a(t)) is monotonic. The same conclusion can be drawn for an ideal EoS. We also conclude that the rate of decreasing H(a(t)) with increasing a(t) varies from epoch to epoch, at vanishing and finite cosmological constant. These results obviously help in improving our understanding of the nucleosynthesis and the cosmological large-scale structure.
The incidence of invasive mold disease (IMD) has significantly increased over the last decades, and IMD of the central nervous system (CNS) is a particularly severe form of this infection. Solid data on the incidence of CNS IMD in the pediatric setting are lacking, in which Aspergillus spp. is the most prevalent pathogen, followed by mucorales. CNS IMD is difficult to diagnose, and although imaging tools such as magnetic resonance imaging have considerably improved, these techniques are still unspecific. As microscopy and culture have a low sensitivity, non-culture-based assays such as the detection of fungal antigens (e.g., galactomannan or beta-D-glucan) or the detection of fungal nucleic acids by molecular assays need to be validated in children with suspected CNS IMD. New and potent antifungal compounds helped to improve outcome of CNS IMD, but not all agents are approved for children and a pediatric dosage has not been established. Therefore, studies have to rapidly evaluate dosage, safety and efficacy of antifungal compounds in the pediatric setting. This review will summarize the current knowledge on diagnostic tools and on the management of CNS IMD with a focus on pediatric patients.
Osteoarthritis (OA) is a slow-progressing joint disease, leading to the degradation and remodeling of the cartilage extracellular matrix (ECM). The usually quiescent chondrocytes become reactivated and accumulate in cell clusters, become hypertrophic, and intensively produce not only degrading enzymes, but also ECM proteins, like the cartilage oligomeric matrix protein (COMP) and thrombospondin-4 (TSP-4). To date, the functional roles of these newly synthesized proteins in articular cartilage are still elusive. Therefore, we analyzed the involvement of both proteins in OA specific processes in in vitro studies, using porcine chondrocytes, isolated from femoral condyles. The effect of COMP and TSP-4 on chondrocyte migration was investigated in transwell assays and their potential to modulate the chondrocyte phenotype, protein synthesis and matrix formation by immunofluorescence staining and immunoblot. Our results demonstrate that COMP could attract chondrocytes and may contribute to a repopulation of damaged cartilage areas, while TSP-4 did not affect this process. In contrast, both proteins similarly promoted the synthesis and matrix formation of collagen II, IX, XII and proteoglycans, but inhibited that of collagen I and X, resulting in a stabilized chondrocyte phenotype. These data suggest that COMP and TSP-4 activate mechanisms to protect and repair the ECM in articular cartilage.
Nematophilic bacteria as a source of novel macrocyclised antimicrobial non-ribosomal peptides
(2020)
A solution to ineffective clinical antimicrobials is the discovery of new ones from under-explored sources such as macrocyclic non-ribosomal peptides (NRP) from nematophilic bacteria. In this dissertation an antimicrobial discovery process –from soil sample to inhibitory peptide– is demonstrated through investigations on six nematophilic bacteria: Xenorhabdus griffiniae XN45, X. griffiniae VH1, Xenorhabdus sp. nov. BG5, Xenorhabdus sp. nov. BMMCB, X. ishibashii and Photorhabdus temperata. To demonstrate the first step of bacterium isolation and species delineation, endosymbionts were isolated from Steinernema sp. strains BG5 and VH1 that were isolated directly from soil samples in Western Kenya. After genome sequencing and assembly of novel Xenorhabdus isolates VH1 and BG5, species delineation was done via three overall genome relatedness indices. VH1 was identified as X. griffiniae VH1, BG5 as Xenorhabdus sp. nov. BG5 and X. griffiniae BMMCB was emended to Xenorhabdus sp. nov. BMMCB. The nematode host of X. griffiniae XN45, Steinernema sp. scarpo was highlighted as a putative novel species. To demonstrate the second step of genome mining and macrocyclic non-ribosomal peptide structure elucidation, chemosynthesis and biosynthesis, the non-ribosomal peptide whose production is encoded by the ishA-B genes in X. ishibashii was investigated. Through a combination of refactoring the ishA-B operon by a promoter exchange mechanism, isotope labelling experiments, high resolution tandem mass spectrometry analysis, bioinformatic protein domain analysis and chemoinformatic comparisons of actual to hypothetical mass spectrometry spectra, the structures of Ishipeptides were elucidated and confirmed by chemical synthesis. Ishipeptide A was a branch cyclic depsidodecapeptide macrocyclised via an ester bond between serine and the terminal glutamate. It chemosynthesis route was via a late stage macrolactamation and linearised Ishipeptide B was synthesised via solid phase iterative synthesis. Ishipeptides were not N-terminally acylated despite being biosynthesised from the IshA protein that had a C-starter domain. It was highlighted that more than restoration of the histidine active site of this domain is required to restore N-terminal acylation activity.
To demonstrate the final step of determination of antimicrobial activity, minimum inhibitory concentrations of Ishipeptides and Photoditritide from Photorhabdus temperata against fungi and bacteria were determined. None were antifungal while only the macrocyclic compounds were inhibitory, with Ishipeptide A inhibitory to Gram-positive bacteria at 37 µM. The cationic Photoditritide, a cyclic hexapeptide macrocyclised via a lactam bond between homoarginine and tryptophan, was 12 times more inhibitory (3.0 µM), even more effective than a current clinical compound, Ampicillin (4.2 µM). For both, macrocyclisation was hypothesised to contribute to antimicrobial activity. Ultimately, this dissertation demonstrated not only nematophilic bacteria as a source of novel macrocyclic antimicrobial non-ribosomal peptides but also a process of antimicrobial discovery–from soil sample to inhibitory peptide– from these useful bacteria genera. This is significant for the fight against antimicrobial resistance.
Bacterial and fungal toll-like receptor activation elicits type I IFN responses in mast cells
(2021)
Next to their role in IgE-mediated allergic diseases and in promoting inflammation, mast cells also have antiinflammatory functions. They release pro- as well as antiinflammatory mediators, depending on the biological setting. Here we aimed to better understand the role of mast cells during the resolution phase of a local inflammation induced with the Toll-like receptor (TLR)-2 agonist zymosan. Multiple sequential immunohistology combined with a statistical neighborhood analysis showed that mast cells are located in a predominantly antiinflammatory microenvironment during resolution of inflammation and that mast cell-deficiency causes decreased efferocytosis in the resolution phase. Accordingly, FACS analysis showed decreased phagocytosis of zymosan and neutrophils by macrophages in mast cell-deficient mice. mRNA sequencing using zymosan-induced bone marrow-derived mast cells (BMMC) revealed a strong type I interferon (IFN) response, which is known to enhance phagocytosis by macrophages. Both, zymosan and lipopolysaccharides (LPS) induced IFN-β synthesis in BMMCs in similar amounts as in bone marrow derived macrophages. IFN-β was expressed by mast cells in paws from naïve mice and during zymosan-induced inflammation. As described for macrophages the release of type I IFNs from mast cells depended on TLR internalization and endosome acidification. In conclusion, mast cells are able to produce several mediators including IFN-β, which are alone or in combination with each other able to regulate the phagocytotic activity of macrophages during resolution of inflammation.
The paper examines the importance of international labour standards for ESG reporting. International labour standards exist today for almost all working conditions. There are many reasons why ESG criteria should be based on these standards. This is already happening to some extent. However, the references to international labor standards should be expanded and the existing references deepened.
According to the standard account, IPRs allocate objects to owners, just like ownership allocates real property. In this paper, I explain that this simplistic paradigm operates on the basis of three fictions: The first – truly Polanyian – fiction concerns IP subject matter that was originally not produced for sale but created for other purposes, e.g. private pleasure. The second fiction is that IP is treated as a marketable good whereas much IP, in particular works and signs, are embedded in communication. Finally, IP is a fictitious concept in that we speak of works, inventions, and other IP objects as of tangible commodities, where in fact IP objects only exist insofar and because we speak and regulate as if they exist as abstract “goods” of value.
Three types of post-translation modifications (PTMs) containing N-glycosylation, phosphorylation, ubiquitylation were characterized in diffuse large B-cell lymphoma (DLBCL) on a global scale using quantitative mass spectrometry based proteomics technology in this study.
DLBCL is the most common type of malignant lymphomas and has a heterogeneous gene expression profiling, phenotype and clinical response to chemotherapy. DLBCL is a good model for the correct classification of cancers into molecularly different subtypes, which benefits for the selection of rational therapeutic strategies. It resulted in two histologically indistinguishable subtypes-activated B-cell-like (ABC) subgroup and germinal center B-cell-like (GCB) subgroup according to gene expression profiling. Signals originating from the B-cell receptor (BCR), the key protein on the surface of B cells, promote growth and survival of DLBCL. Antigen-dependent/independent BCR signaling is found in DLBCL subtypes.
Recent researches reveal that glycosylation plays role in human cells via site-specific regulation. Aberrant N-glycosylation in BCR-related effectors, such as, CD79a, immunoglobulin M or G (IgM or IgG), has been found to be associated with lymphoid malignancies. However, accurate quantification of intact glycopeptides and their individual glycan moieties in a cell-wide manner is still challenging. Here we established a site-specific quantitative N-glycoproteomics platform termed SugarQuant. It included a fast sample preparation workflow using Protein Aggregation Capture (PAC), an optimized multi-notch MS3 acquisition workflow (Glyco-SPS-MS3), a self-developed R-based tool (GlycoBinder). The robustness and accuracy of quantitation in SugarQuant were proved in a study using the different amounts of TMT-labelled IgM N-glycopeptides spiked into a background of TMT-labelled yeast peptides. Next, we used SugarQuant to identify and quantify more than 5000 unique glycoforms in Burkitt’s lymphoma cells treated with a series of doses of 2-deoxy-2-fluoro-L-fucose (2FF) and determine the more accurate site-specific glycosylation changes that occurred upon inhibition of fucosylation compared to using MS2 analysis. It revealed that 2FF-sensitive N-glycosylation on key players in BCR-mediated signaling in DG75. Furthermore, 2FF treatment also affects phosphorylation of the key players involving in B cell receptor signaling.
Then we investigated the site-specific quantitative N-glycoproteome in the cell lines of DLBCL subtypes using SugarQuant. More than 7000 unique intact glycopeptides (glycoforms) were quantified in five ABC DLBCL and four GCB DLBCL cell lines. The glycoproteome mapping (intact glycopeptide expressions) in each cell line allows to segregate DLBCL subtypes. The majority of these glycoforms were from the key cell-surface BCR effectors, such as IgM, CD79 and PTPRC. Lastly, we investigated the change of fucosylated glycopeptides in TMD8 cell line upon knockout of the fucosyltransferase FUT8, which is responsible for core-fucose synthesis, and by the treatment with 2FF. The results revealed that FUT8 might also regulate the synthesis of sub/terminal fucose on glycan chain and the inhibition of fucosylation increased the sialyated glycopeptide expression.
Phosphorylation is involved in regulating multiple processes as an important mediator in BCR signaling. Likewise, ubiquitylation plays vital roles in the activation of the nuclear factor-kappaB (NF-κB) pathway in BCR signaling. There are two vital upstream BCR-proximal tyrosine kinases, Bruton’s tyrosine kinase (BTK) and spleen tyrosine kinase (SYK), which regulate the auto-phosphorylation and phosphorylation of other proteins in BCR signaling pathway. Here we investigated the dynamics of downstream phosphorylation and ubiquitylation signaling in ABC DLBCL and GCB DLBCL cell lines upon the inhibitions of BTK and SYK using quantitative proteomics strategy. In the phosphoproteome analysis, a large dataset of quantified phosphorylation sites was obtained in the three ABC and four GCB DLBCL cell lines. BCR signaling in the subtypes of DLBCL cell lines was found to be highly individual in distinct cell lines. These significantly regulated phosphorylation events in each cell line with individual treatment were involved in multiple Reactome pathways, such as, M phase, signaling by Rho GTPases and diseases of signal transduction. Moreover, the gene regulation-related biological processes including chromosome organization and medication, DNA metabolic process, nuclear export, were involved in the DLBCL cell lines. In the ubiquitinome analysis, we identified more than 15,000 ubiquitylation sites in two ABC and one GCB cell lines upon the inhibition of BTK and SYK. The different ubiquitylation events observed in ABC and GCB subtypes revealed distinct BCR signaling pathways in two subtypes. The similar signaling perturbations across each cell line upon BTK and SYK inhibition, which were obtained from the significantly regulated ubiquitylated peptides expression, revealed the cell-type-specific concordance in ubiquitylation regulation upon BTK and SYK inhibition. These ubiquitylation modified proteins who bore the significantly regulated ubi-peptides in the samples were also found to be highly involved in gene regulatory processes.
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