Bacterial riboproteogenomics : the era of N-terminal proteoform existence revealed

With the rapid increase in the number of sequenced prokaryotic genomes, relying on automated gene annotation became a necessity. Multiple lines of evidence, however, suggest that current bacterial genome annotations may contain inconsistencies and are incomplete, even for so-called well-annotated genomes. We here discuss underexplored sources of protein diversity and new methodologies for high-throughput genome re-annotation. The expression of multiple molecular forms of proteins (proteoforms) from a single gene, particularly driven by alternative translation initiation, is gaining interest as a prominent contributor to bacterial protein diversity. In consequence, riboproteogenomic pipelines were proposed to comprehensively capture proteoform expression in prokaryotes by the complementary use of (positional) proteomics and the direct readout of translated genomic regions using ribosome profiling. To complement these discoveries, tailored strategies are required for the functional characterization of newly discovered bacterial proteoforms

Lost and found : re-searching and re-scoring proteomics data aids genome annotation and improves proteome coverage

Prokaryotic genome annotation is heavily dependent on automated gene annotation pipelines that are prone to propagate errors and underestimate genome complexity. We describe an optimized proteogenomic workflow that uses ribosome profiling (ribo-seq) and proteomic data for Salmonella enterica serovar Typhimurium to identify unannotated proteins or alternative protein forms. This data analysis encompasses the searching of cofragmenting peptides and postprocessing with extended peptide-to-spectrum quality features, including comparison to predicted fragment ion intensities. When this strategy is applied, an enhanced proteome depth is achieved, as well as greater confidence for unannotated peptide hits. We demonstrate the general applicability of our pipeline by reanalyzing public Deinococcus radiodurans data sets. Taken together, our results show that systematic reanalysis using available prokaryotic (proteome) data sets holds great promise to assist in experimentally based genome annotation

N-terminal proteomics assisted profiling of the unexplored translation initiation landscape in Arabidopsis thaliana

Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in genome annotations. We constructed a proteogenomic pipeline specific for the analysis of N-terminal proteomics data, with the aim of discovering novel translational start sites outside annotated protein coding regions. In summary, unidentified MS/MS spectra were matched to a specific N-terminal peptide library encompassing protein N termini encoded in the Arabidopsis thaliana genome. After a stringent false discovery rate filtering, 117 protein N termini compliant with N-terminal methionine excision specificity and indicative of translation initiation were found. These include N-terminal protein extensions and translation from transposable elements and pseudogenes. Gene prediction provided supporting protein-coding models for approximately half of the protein N termini. Besides the prediction of functional domains (partially) contained within the newly predicted ORFs, further supporting evidence of translation was found in the recently released Araport11 genome re-annotation of Arabidopsis and computational translations of sequences stored in public repositories. Most interestingly, complementary evidence by ribosome profiling was found for 23 protein N termini. Finally, by analyzing protein N-terminal peptides, an in silico analysis demonstrates the applicability of our N-terminal proteogenomics strategy in revealing protein-coding potential in species with well-and poorly-annotated genomes

Prevention and modulation of aminoglycoside ototoxicity (Review)

More than 60 years after their isolation and characterization, aminoglycoside (AG) antibiotics remain powerful agents in the treatment of severe gram-negative, enterococcal or mycobacterial infections. However, the clinical use of AGs is hampered by nephrotoxicity and ototoxicity, which often develop as a consequence of prolonged courses of therapy, or of administration of increased doses of these drugs. The discovery of non-ototoxic antibacterial agents, showing a wider spectrum of activity, has gradually decreased the use of AGs as first line antibiotics for many systemic infections. However, AGs are now undergoing an unexpected revival, being increasingly indicated for the treatment of severe emerging infections caused by organisms showing resistance to most first-line agents (e.g., multidrug-resistant tuberculosis, complicated nosocomially-acquired acute urinary tract infections). Increasing adoption of aminoglycosides poses again to scientists and physicians the problem of toxicity directed to the kidneys and to the inner ear. In particular, aminoglycoside-induced deafness can be profound and irreversible, especially in genetically predisposed patients. For this reason, an impressive amount of molecular strategies have been developed in the last decade to counteract the ototoxic effect of aminoglycosides. The present article overviews: i) the molecular mechanisms by which aminoglycosides exert their bactericidal activity, ii) the mechanisms whereby AGs exert their ototoxic activity in genetically-predisposed patients, iii) the drugs and compounds that have so far proven to prevent or modulate AG ototoxicity at the preclinical and/or clinical level, and iv) the dosage regimens that have so far been suggested to decrease the incidence of episodes of AG-induced ototoxicity

Blood parasites in Passeriformes in central Germany: prevalence and lineage diversity of Haemosporida (Haemoproteus, Plasmodium and Leucocytozoon) in six common songbirds

Background Avian Haemosporida are vector-borne parasites that commonly infect Passeriformes. Molecular analyses revealed a high number of different lineages and lineage specific traits like prevalence and host-specificity, but knowledge of parasite prevalence and lineage diversity in wild birds in Central Germany is still lacking. Results Blood samples from a total of 238 adult and 122 nestling songbirds belonging to six species were investigated for infections with avian haemosporidian genera and lineages (Haemoproteus spp., Plasmodium spp., Leucocytozoon spp.) and Trypanosoma avium using PCR, targeting the parasite mitochondrial cytochrome b gene and 18S ribosomal RNA. In total, the prevalence in adult birds was 31.3% infected with Haemoproteus, 12.5% with Plasmodium and 71.0% with Leucocytozoon (nestlings excluded). None of the tested birds was infected with Trypanosoma avium. Only in two nestling birds, aged 12–17 days, a Leucocytozoon spp. infection was proven. Among 225 successfully sequenced samples, we found four Haemoproteus, three Plasmodium and 19 Leucocytozoon lineages, including two new Leucocytozoon lineages. Furthermore, we report two new host-lineage associations. Conclusions As first study investigating avian haemosporidian parasites in Central Germany, we provide new information on genetic diversity of Haemosporida infecting Passeriformes. We show that even with a small sample size new lineages as well as previously unknown linkages between certain lineages and host species can be detected. This may help to elucidate the diversity of lineages as well as lineage-host-connections of avian Haemosporida

Evidence, detailed characterization and clinical context of complement activation in acute multisystem inflammatory syndrome in children

Multisystem inflammatory syndrome in children (MIS-C) is a rare, life-threatening complication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. MIS-C develops with high fever, marked inflammation and shock-like picture several weeks after exposure to, or mild infection with SARS-CoV-2. Deep immune profiling identified activated macrophages, neutrophils, B-plasmablasts and CD8 + T cells as key determinants of pathogenesis together with multiple inflammatory markers. The disease rapidly responds to intravenous immunoglobulin (IVIG) treatment with clear changes of immune features. Here we present the results of a comprehensive analysis of the complement system in the context of MIS-C activity and describe characteristic changes during IVIG treatment. We show that activation markers of the classical, alternative and terminal pathways are highly elevated, that the activation is largely independent of anti-SARS-CoV-2 humoral immune response, but is strongly associated with markers of macrophage activation. Decrease of complement activation is closely associated with rapid improvement of MIS-C after IVIG treatment

Ontwikkeling van een meetlat voor immuuncompetentie in varkens, vleeskuikens en vleeskalveren

Het doel van dit project is om een “meetlat” te ontwikkelen die de effecten van (voedings)interventies gericht op de verbetering van de immuuncompetentie van varkens, pluimvee en vleeskalveren kan vaststellen. Immuuncompetentie is binnen dit project gedefinieerd als het vermogen van dieren om effectieve responsen van het immuunsysteem te tonen op het moment dat de gezondheid van het dier onder druk wordt gezet. Een meetlat voor immuuncompetentie kan in de toekomst door de diervoedingssector gebruikt worden bij de ontwikkeling en evaluatie van nieuwe voerconcepten, ingrediënten en additieven gericht op de verbetering en ondersteuning van diergezondheid. Het is bekend dat de samenstelling van de voeding van jonge dieren invloed heeft op de functionele ontwikkeling van het maagdarmkanaal en op de samenstelling van de daarin aanwezige microbiota. De interacties tussen de microbiota en de weefsels van het darmkanaal (cross talk) hebben een belangrijke invloed op de ontwikkeling van immuuncompetentie. Daarom wordt in dit project gefocust op de effecten van (voedings)interventies op de microbiota, genexpressie veranderingen in darmweefsel, en morfologische en immunologische veranderen in de darm. De hier gepresenteerde meetlat voor immuuncompetentie is gebaseerd op de resultaten van onderzoek binnen het VDI programma van Feed4Foodure (projecten VDI-11; vleeskuikens, VDI-12; biggen, VDI- 13; gespeende biggen en kalveren) waarin m.b.v. model interventies de effecten van variatie in voersamenstelling op de microbiota samenstelling in het darmkanaal, de biologische responsen van darmweefsel en de zoötechnische dierprestaties zijn onderzocht. In de hier gepresenteerde meetlat worden gemeten effecten in deze studies aan elkaar gerelateerd en functioneel inzichtelijk gemaakt. Dit rapport beschrijft de ontwikkeling en totstandkoming van een eerste versie van de meetlat. Hierbij worden gemaakte keuzes, beperkingen en mogelijkheden van de meetlat bediscussieerd. Tenslotte wordt inzicht gegeven in de mogelijkheden tot verdere verfijningen en de toepasbaarheid van de meetlat

Ninety-day complication rate based on 532 Latarjet procedures in Dutch hospitals with different operation volumes

Background: In this study, we aimed to provide insight into the 90-day complication rates following the Latarjet procedure. Data from 2015 were collected from multiple hospitals in the Netherlands, with different volumes of Latarjet procedures. Our second aim was to examine which patient and surgical factors were associated with complications.Methods: We conducted a retrospective chart review of 13 hospitals between 2015 and 2022. Data regarding complications within 90 days of Latarjet procedures were extracted. The effect of sex, age, body mass index (BMI), smoking, previous shoulder operations, fixation material, hospital volume, screw size, and operation time on the complication rate was assessed by multivariable logistic regression analysis.Results: Of the 532 included patients, 58 (10.9%) had complications. The most common complications were material failure (n = 19, 3.6%) and nerve injury (n = 13, 2.4%). The risk of complications was lower for male patients than for female patients (odds ratio, 0.40; 95% confidence interval, 0.21-0.77; P = .006). Age, BMI, smoking, previous shoulder operations, type of fixation material, hospital volume, screw size, and operation time were not associated with complications.Conclusion: The 90-day complication rate after the Latarjet procedure was 10.9% and was higher in female patients than in male patients. Age, BMI, smoking, previous shoulder operations, type of fixation material, hospital volume, screw size, and operation time did not affect complication rates. We advise setting up a national registry to prevent under-reporting of complications.</p

Characteristics and outcomes of older patients hospitalised for COVID-19 in the first and second wave of the pandemic in The Netherlands:the COVID-OLD study

BACKGROUND: as the coronavirus disease of 2019 (COVID-19) pandemic progressed diagnostics and treatment changed. OBJECTIVE: to investigate differences in characteristics, disease presentation and outcomes of older hospitalised COVID-19 patients between the first and second pandemic wave in The Netherlands. METHODS: this was a multicentre retrospective cohort study in 16 hospitals in The Netherlands including patients aged ≥ 70 years, hospitalised for COVID-19 in Spring 2020 (first wave) and Autumn 2020 (second wave). Data included Charlson comorbidity index (CCI), disease severity and Clinical Frailty Scale (CFS). Main outcome was in-hospital mortality. RESULTS: a total of 1,376 patients in the first wave (median age 78 years, 60% male) and 946 patients in the second wave (median age 79 years, 61% male) were included. There was no relevant difference in presence of comorbidity (median CCI 2) or frailty (median CFS 4). Patients in the second wave were admitted earlier in the disease course (median 6 versus 7 symptomatic days; P < 0.001). In-hospital mortality was lower in the second wave (38.1% first wave versus 27.0% second wave; P < 0.001). Mortality risk was 40% lower in the second wave compared with the first wave (95% confidence interval: 28–51%) after adjustment for differences in patient characteristics, comorbidity, symptomatic days until admission, disease severity and frailty. CONCLUSIONS: compared with older patients hospitalised in the first COVID-19 wave, patients in the second wave had lower in-hospital mortality, independent of risk factors for mortality. The better prognosis likely reflects earlier diagnosis, the effect of improvement in treatment and is relevant for future guidelines and treatment decisions