Reduction of Cross-Reactive Carbohydrate Determinants in Plant Foodstuff: Elucidation of Clinical Relevance and Implications for Allergy Diagnosis

Background: A longstanding debate in allergy is whether or not specific immunoglobulin-E antibodies (sIgE), recognizing cross-reactive carbohydrate determinants (CCD), are able to elicit clinical symptoms. In pollen and food allergy, $20% of patients display in-vitro CCD reactivity based on presence of a1,3-fucose and/or b1,2-xylose residues on N-glycans of plant (xylose/fucose) and insect (fucose) glycoproteins. Because the allergenicity of tomato glycoallergen Lyc e 2 was ascribed to N-glycan chains alone, this study aimed at evaluating clinical relevance of CCD-reduced foodstuff in patients with carbohydrate-specific IgE (CCD-sIgE). Methodology/Principal Findings: Tomato and/or potato plants with stable reduction of Lyc e 2 (tomato) or CCD formation in general were obtained via RNA interference, and gene-silencing was confirmed by immunoblot analyses. Two different CCD-positive patient groups were compared: one with tomato and/or potato food allergy and another with hymenopteravenom allergy (the latter to distinguish between CCD- and peptide-specific reactions in the food-allergic group). Nonallergic and CCD-negative food-allergic patients served as controls for immunoblot, basophil activation, and ImmunoCAP analyses. Basophil activation tests (BAT) revealed that Lyc e 2 is no key player among other tomato (glyco)allergens. CCDpositive patients showed decreased (re)activity with CCD-reduced foodstuff, most obvious in the hymenoptera venomallergic but less in the food-allergic group, suggesting that in-vivo reactivity is primarily based on peptide- and not CCDsIgE. Peptide epitopes remained unaffected in CCD-reduced plants, because CCD-negative patient sera showed reactivity similar to wild-type. In-house-made ImmunoCAPs, applied to investigate feasibility in routine diagnosis, confirmed BAT results at the sIgE level. Conclusions/Significance: CCD-positive hymenoptera venom-allergic patients (control group) showed basophil activation despite no allergic symptoms towards tomato and potato. Therefore, this proof-of-principle study demonstrates feasibility of CCD-reduced foodstuff to minimize ‘false-positive results’ in routine serum tests. Despite confirming low clinical relevance of CCD antibodies, we identified one patient with ambiguous in-vitro results, indicating need for further component-resolved diagnosis

Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018.

Over the past decade, the Nomenclature Committee on Cell Death (NCCD) has formulated guidelines for the definition and interpretation of cell death from morphological, biochemical, and functional perspectives. Since the field continues to expand and novel mechanisms that orchestrate multiple cell death pathways are unveiled, we propose an updated classification of cell death subroutines focusing on mechanistic and essential (as opposed to correlative and dispensable) aspects of the process. As we provide molecularly oriented definitions of terms including intrinsic apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell death, autophagy-dependent cell death, immunogenic cell death, cellular senescence, and mitotic catastrophe, we discuss the utility of neologisms that refer to highly specialized instances of these processes. The mission of the NCCD is to provide a widely accepted nomenclature on cell death in support of the continued development of the field

Minimal information for studies of extracellular vesicles 2018 (MISEV2018):a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles (“MISEV”) guidelines for the field in 2014. We now update these “MISEV2014” guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points

A New Method for Measuring the Dynamic Shape Change of Platelets

Background: Platelet shape change is a dynamic process that has been classified in different types. Exact documentation of platelet structure needs an improved method of measuring platelet shape. Methods: 10 l of platelet-rich plasma (PRP) from anticoagulated whole blood (3.2% buffered sodium citrate 0.105 mol/l) was put onto a glass slide covered with a cover slip. By use a of dark field light microscope connected with a CMOSCamera a photographic snap-shot was taken after 5 and 30 min. Diameter of platelets and length of filopodia were measured with a self-developed plugin for ImageJ software. Statistic calculation was performed with Excel WinSTAT Microsoft software. Results: We showed a swelling of the granulomer from 2.06 ± 0.56 m to 2.33 ± 0.59 m (p < 0.05), a reduction of pseudopodia (2.10 ± 0.94 vs. 1.78 ± 1.04 m; p < 0.05) in conjunction with an increase of hyalomer diameter from 3.29 ± 0.83 to 3.50 ± 0.85 m (p < 0.05), and an increase of pseudopodia length from 2.68 ± 1.45 m to 3.67 ± 1.79 m (p < 0.005) in conjunction with an increase of hyalomer diameter from 6.58 ± 1.91 m to 7.94 ± 1.87 m (p < 0.05). Conclusion: We revealed and documented a dynamic change of platelet size and filopodia structure in PRP. This method allows an exact analysis of platelet size and surface structures.Hintergrund: Der thrombozytäre Formwandel (engl. shape change) ist ein dynamischer Prozess, für den eine Klassifikation nach Typen eingeführt worden ist. Für die genaue Dokumentation der dynamischen Änderungen der Plättchenstruktur ist eine verbesserte Messmethode notwendig. Methoden: 10 l plättchenreichen Plasmas (PRP) aus antikoaguliertem Vollblut (3,2% gepuffertes Natriumcitrat, 0,105 mol/l) wurden auf einen Objektträger aufgebracht und mit einem Deckglas abgedeckt. Die digitale mikrofotografische Dokumentation 5 und 30 min nach der Präparation erfolgte unter Verwendung eines mit einer CMOS-Kamera verbundenen Dunkelfeldmikroskops. Durchmesser der Plättchen und Länge der Filopodien wurden mit einem selbstentwickelten Plugin für die Software ImageJ (NIH) vermessen. Die statistische Auswertung erfolgte mit Microsoft Excel WinSTAT. Ergebnisse: Ein Anschwellen des Granulomers von 2,06 ± 0,56 m auf 2,33 ± 0,59 m (p < 0,05), eine Verkürzung der Pseudopodien (2,10 ± 0,94 vs. 1,78 ± 1,04 m; p < 0,05) in Verbindung mit einer Zunahme der Hyalomer-Diameter von 3,29 ± 0,83 auf 3,50 ± 0,85 m (p < 0,05) und eine Verlängerung der Pseudopodien von 2,68 ± 1,45 m auf 3,67 ± 1,79 m (p < 0,005) in Verbindung mit einer Zunahme der Hyalomer-Diameter von 6,58 ± 1,91 m auf 7,94 ± 1,87 m (p < 0,05) wird dargestellt. Schlussfolgerungen: Eine dynamische Änderung der Plättchengröße und Filopodien- Struktur wird gezeigt und dokumentiert. Die Methode erlaubt eine genaue Analyse und Dokumentation dynamischer Veränderungen von Plättchen im PRP

Ischemic stroke and dose adjustment of oral Factor Xa inhibitors in patients with atrial fibrillation

Background!#!Oral Factor Xa inhibitors for the prevention of stroke in atrial fibrillation require dose adjustment based on certain clinical criteria, but the off-label use of the reduced doses is common.!##!Methods!#!Data from an observational registry including patients admitted with acute cerebral ischemia while taking oral Factor Xa inhibitors for atrial fibrillation between April 2016 and December 2018 were investigated. The dose regimen of the Xa inhibitor was classified as 'appropriate', 'underdosed' and 'overdosed' in conformity with the European Medicines Agency labelling. The effect of underdosing on the functional factor Xa plasma level on admission, the clinical stroke severity and the functional outcome after 3 months were investigated.!##!Results!#!254 patients with cerebral ischemia while on Factor Xa inhibitors were included. The dose regimen of the Factor Xa inhibitor was appropriate in 166 patients (65%), underdosed in 67 patients (26%) and overdosed in 21 patients (8%). Underdosing was associated with female sex, diabetes mellitus and higher CHA!##!Conclusion!#!One in three patients with ischemic stroke during treatment with oral Xa inhibitors used inappropriate dose regimens. Underdosing was associated with lower functional plasma levels, higher clinical stroke severity and worse functional outcome

Collecting, Comparing, and Computing Sequences: The Making of Margaret O. Dayhoff’s Atlas of Protein Sequence and Structure, 1954–1965

Collecting, comparing, and computing molecular sequences are among the most prevalent practices in contemporary biological research. They represent a specific way of producing knowledge. This paper explores the historical development of these practices, focusing on the work of Margaret O. Dayhoff, Richard V. Eck, and Robert S. Ledley, who produced the first computer-based collection of protein sequences, published in book format in 1965 as the Atlas of Protein Sequence and Structure. While these practices are generally associated with the rise of molecular evolution in the 1960s, this paper shows that they grew out of research agendas from the previous decade, including the biochemical investigation of the relations between the structures and function of proteins and the theoretical attempt to decipher the genetic code. It also shows how computers became essential for the handling and analysis of sequence data. Finally, this paper reflects on the relationships between experimenting and collecting as two distinct ‘‘ways of knowing’’ that were essential for the transformation of the life sciences in the twentieth century