Immunoprecipitation methods impact the peptide repertoire in immunopeptidomics

IntroductionMass spectrometry-based immunopeptidomics is the only unbiased method to identify naturally presented HLA ligands, which is an indispensable prerequisite for characterizing novel tumor antigens for immunotherapeutic approaches. In recent years, improvements based on devices and methodology have been made to optimize sensitivity and throughput in immunopeptidomics. However, developments in ligand isolation, mass spectrometric analysis, and subsequent data processing can have a marked impact on the quality and quantity of immunopeptidomics data.MethodsIn this work, we compared the immunopeptidome composition in terms of peptide yields, spectra quality, hydrophobicity, retention time, and immunogenicity of two established immunoprecipitation methods (column-based and 96-well-based) using cell lines as well as primary solid and hematological tumor samples.ResultsAlthough, we identified comparable overall peptide yields, large proportions of method-exclusive peptides were detected with significantly higher hydrophobicity for the column-based method with potential implications for the identification of immunogenic tumor antigens. We showed that column preparation does not lose hydrophilic peptides in the hydrophilic washing step. In contrast, an additional 50% acetonitrile elution could partially regain lost hydrophobic peptides during 96-well preparation, suggesting a reduction of the bias towards the column-based method but not completely equalizing it.DiscussionTogether, this work showed how different immunoprecipitation methods and their adaptions can impact the peptide repertoire of immunopeptidomic analysis and therefore the identification of potential tumor-associated antigens

Forward pi^0 Production and Associated Transverse Energy Flow in Deep-Inelastic Scattering at HERA

Deep-inelastic positron-proton interactions at low values of Bjorken-x down to x \approx 4.10^-5 which give rise to high transverse momentum pi^0 mesons are studied with the H1 experiment at HERA. The inclusive cross section for pi^0 mesons produced at small angles with respect to the proton remnant (the forward region) is presented as a function of the transverse momentum and energy of the pi^0 and of the four-momentum transfer Q^2 and Bjorken-x. Measurements are also presented of the transverse energy flow in events containing a forward pi^0 meson. Hadronic final state calculations based on QCD models implementing different parton evolution schemes are confronted with the data.Comment: 27 pages, 8 figures and 3 table

NOD2-C2 - a novel NOD2 isoform activating NF-κB in a muramyl dipeptide-independent manner

<p>Abstract</p> <p>Background</p> <p>The innate immune system employs several receptor families that form the basis of sensing pathogen-associated molecular patterns. NOD (nucleotide-binding and oligomerization domain) like receptors (NLRs) comprise a group of cytosolic proteins that trigger protective responses upon recognition of intracellular danger signals. NOD2 displays a tandem caspase recruitment domain (CARD) architecture, which is unique within the NLR family.</p> <p>Findings</p> <p>Here, we report a novel alternative transcript of the <it>NOD2 </it>gene, which codes for a truncated tandem CARD only protein, called NOD2-C2. The transcript isoform is highest expressed in leucocytes, a natural barrier against pathogen invasion, and is strictly linked to promoter usage as well as predominantly to one allele of the single nucleotide polymorphism rs2067085. Contrary to a previously identified truncated single CARD NOD2 isoform, NOD2-S, NOD2-C2 is able to activate NF-κB in a dose dependent manner independently of muramyl dipeptide (MDP). On the other hand NOD2-C2 competes with MDPs ability to activate the NOD2-driven NF-κB signaling cascade.</p> <p>Conclusion</p> <p>NOD2 transcripts having included an alternative exon downstream of exon 3 (exon 3a) are the endogenous equivalents of a previously described <it>in vitro </it>construct with the putative protein composed of only the two N-terminal CARDs. This protein form (NOD2-C2) activates NF-κB independent of an MDP stimulus and is a potential regulator of NOD2 signaling.</p

Homo sapiens reached the higher latitudes of Europe by 45,000 years ago

The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Late Neanderthals persisted in western Europe several millennia after the occurrence of H. sapiens in eastern Europe1. Local hybridization between the two groups occurred2, but not on all occasions3. Archaeological evidence also indicates the presence of several technocomplexes during this transition, complicating our understanding and the association of behavioural adaptations with specific hominin groups4. One such technocomplex for which the makers are unknown is the Lincombian–Ranisian–Jerzmanowician (LRJ), which has been described in northwestern and central Europe5,6,7,8. Here we present the morphological and proteomic taxonomic identification, mitochondrial DNA analysis and direct radiocarbon dating of human remains directly associated with an LRJ assemblage at the site Ilsenhöhle in Ranis (Germany). These human remains are among the earliest directly dated Upper Palaeolithic H. sapiens remains in Eurasia. We show that early H. sapiens associated with the LRJ were present in central and northwestern Europe long before the extinction of late Neanderthals in southwestern Europe. Our results strengthen the notion of a patchwork of distinct human populations and technocomplexes present in Europe during this transitional period

Comprehensive Fragment Screening of the SARS-CoV-2 Proteome Explores Novel Chemical Space for Drug Development

12 pags., 4 figs., 3 tabs.SARS-CoV-2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti-virals. Within the international Covid19-NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80 % of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR-detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure-based drug design against the SCoV2 proteome.Work at BMRZ is supported by the state of Hesse. Work in Covid19-NMR was supported by the Goethe Corona Funds, by the IWBEFRE-program 20007375 of state of Hesse, the DFG through CRC902: “Molecular Principles of RNA-based regulation.” and through infrastructure funds (project numbers: 277478796, 277479031, 392682309, 452632086, 70653611) and by European Union’s Horizon 2020 research and innovation program iNEXT-discovery under grant agreement No 871037. BY-COVID receives funding from the European Union’s Horizon Europe Research and Innovation Programme under grant agreement number 101046203. “INSPIRED” (MIS 5002550) project, implemented under the Action “Reinforcement of the Research and Innovation Infrastructure,” funded by the Operational Program “Competitiveness, Entrepreneurship and Innovation” (NSRF 2014–2020) and co-financed by Greece and the EU (European Regional Development Fund) and the FP7 REGPOT CT-2011-285950—“SEE-DRUG” project (purchase of UPAT’s 700 MHz NMR equipment). The support of the CERM/CIRMMP center of Instruct-ERIC is gratefully acknowledged. This work has been funded in part by a grant of the Italian Ministry of University and Research (FISR2020IP_02112, ID-COVID) and by Fondazione CR Firenze. A.S. is supported by the Deutsche Forschungsgemeinschaft [SFB902/B16, SCHL2062/2-1] and the Johanna Quandt Young Academy at Goethe [2019/AS01]. M.H. and C.F. thank SFB902 and the Stiftung Polytechnische Gesellschaft for the Scholarship. L.L. work was supported by the French National Research Agency (ANR, NMR-SCoV2-ORF8), the Fondation de la Recherche Médicale (FRM, NMR-SCoV2-ORF8), FINOVI and the IR-RMN-THC Fr3050 CNRS. Work at UConn Health was supported by grants from the US National Institutes of Health (R01 GM135592 to B.H., P41 GM111135 and R01 GM123249 to J.C.H.) and the US National Science Foundation (DBI 2030601 to J.C.H.). Latvian Council of Science Grant No. VPP-COVID-2020/1-0014. National Science Foundation EAGER MCB-2031269. This work was supported by the grant Krebsliga KFS-4903-08-2019 and SNF-311030_192646 to J.O. P.G. (ITMP) The EOSC Future project is co-funded by the European Union Horizon Programme call INFRAEOSC-03-2020—Grant Agreement Number 101017536. Open Access funding enabled and organized by Projekt DEALPeer reviewe

Uncertain progress in Swiss perioperative mortality 1998-2014 for 22 operation groups.

BACKGROUND The perioperative mortality rate (POMR) is used as a quality indicator to monitor health care system performance at regional and national levels. The Swiss Federal Office of Public Health publishes national in-hospital mortality rates for several indicator conditions and indicator operation types (IORs). We investigated long-term time trends of POMRs from 1998&ndash;2014. In view of continual advances in perioperative care, we expected to find decreasing trends. METHODS Non-cardiosurgical IORs containing aggregated age- and sex-specific data (number of operations and deaths) for all years of the study period were included to calculate age-standardised POMRs using the 2013 European Standard Population. We assessed calendar time trends of POMRs using multivariable Poisson regression. We categorised IORs according to the type of time trend (decreasing, unchanged, or increasing incident rate ratio) and mean risk levels (age-adjusted POMR). RESULTS A total of 22 IORs were included, comprising 1,561,012 operations and 22,140 deaths (overall crude POMR 1.42%). POMR trends decreased for 6 IORs representing 26.8% of operations, remained unchanged for 13 IORs (56.9% of operations), and increased for 3 IORs (16.4% of operations). IOR categorisation according to POMR trends and to risk levels yielded four groups. (1) Decreasing POMR trends, low- to intermediate-risk IORs (age-adjusted POMR 0.2&ndash;2.2%): cholecystectomy; arterial pelvic/leg aneurysm or dissection operation; femoral neck fracture; trochanteric fractures; gastric, duodenal or jejunal ulcer resection; major pulmonary or bronchial resection. (2) Unchanged POMR trends, low-risk IORs (0.1&ndash;0.9%): transurethral resection of the prostate (TUR prostate); hernia repair without intestinal operation; hysterectomy; extracranial vascular operation; nephrectomy; amputation foot, non-traumatic. (3) Unchanged POMR trends, intermediate-risk IORs (1.7&ndash;3.8%): hernia repair with intestinal operation; gastric carcinoma resection; non-ruptured abdominal aortic aneurysm (open operation); arterial pelvic/leg thromboembolic operation; colorectal resection, pancreatic resection; complex oesophageal procedure. (4) Increasing POMR trends, low- to high-risk IORs (0.1&ndash;5.2%): hip endoprosthesis; cystectomy; amputation lower limb. Impact of sex on POMR: hysterectomy and TUR prostate comprised 19.7% of all operations; among the remaining operations, 68.5% showed significantly lower and 27.1% significantly higher POMRs in females. 4.4% showed no sex difference. CONCLUSIONS In Switzerland, in-hospital POMR trends from 1998&ndash;2014 were unchanged or even increasing for the majority of IORs (73% of included operations). Our analysis used age-standardisation but cannot account for changes in coding practices and organisation of healthcare delivery. POMR trends should be systematically monitored at the national level and used to guide priorities in national quality improvement strategies

Techniques culturales simplifiées: Définition

National audienceLes techniques culturales simplifiées (TCS) forment une partie des techniques culturales sans labour (TCSL), l’autre étant le semis direct. Les TCS regroupent l’ensemble des itinéraires techniques de travail du sol sans retournement de ce dernier. Elles incluent aussi bien une opération de pseudo-labour ou un travail superficiel, qu’une implantation en strip-till. Les TCS font partie des techniques de l’agriculture de conservation des sols. Elles ont été développées suite au phénomène du « dust-bowl » aux Etats-Unis et en Amérique Latine dans les années 1930, pour prévenir l’érosion éolienne en laissant des débris végétaux en surface pour protéger les sols..