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  1. Article ; Online: Life stage-specific glycosylation of extracellular vesicles from Schistosoma mansoni schistosomula and adult worms drives differential interaction with C-type lectin receptors DC-SIGN and MGL

    Marije E. Kuipers / D. Linh Nguyen / Angela van Diepen / Lynn Mes / Erik Bos / Roman I. Koning / Esther N. M. Nolte-’t Hoen / Hermelijn H. Smits / Cornelis H. Hokke

    Frontiers in Molecular Biosciences, Vol

    2023  Volume 10

    Abstract: Schistosomes can survive in mammalian hosts for many years, and this is facilitated by released parasite products that modulate the host’s immune system. Many of these products are glycosylated and interact with host cells via C-type lectin receptors ( ... ...

    Abstract Schistosomes can survive in mammalian hosts for many years, and this is facilitated by released parasite products that modulate the host’s immune system. Many of these products are glycosylated and interact with host cells via C-type lectin receptors (CLRs). We previously reported on specific fucose-containing glycans present on extracellular vesicles (EVs) released by schistosomula, the early juvenile life stage of the schistosome, and the interaction of these EVs with the C-type lectin receptor Dendritic Cell-Specific Intercellular adhesion molecule-3-Grabbing Non-integrin (DC-SIGN or CD209). EVs are membrane vesicles with a size range between 30–1,000 nm that play a role in intercellular and interspecies communication. Here, we studied the glycosylation of EVs released by the adult schistosome worms. Mass spectrometric analysis showed that GalNAcβ1–4GlcNAc (LacDiNAc or LDN) containing N-glycans were the dominant glycan type present on adult worm EVs. Using glycan-specific antibodies, we confirmed that EVs from adult worms were predominantly associated with LDN, while schistosomula EVs displayed a highly fucosylated glycan profile. In contrast to schistosomula EV that bind to DC-SIGN, adult worm EVs are recognized by macrophage galactose-type lectin (MGL or CD301), and not by DC-SIGN, on CLR expressing cell lines. The different glycosylation profiles of adult worm- and schistosomula-derived EVs match with the characteristic glycan profiles of the corresponding life stages and support their distinct roles in schistosome life-stage specific interactions with the host.
    Keywords extracellular vesicles ; glycans ; glycosylation ; parasites ; schistosoma ; C-type lectin receptors ; Biology (General) ; QH301-705.5
    Subject code 572
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Human cortical spheroids with a high diversity of innately developing brain cell types

    Kim M. A. De Kleijn / Wieteke A. Zuure / Kirsten R. Straasheijm / Marijn B. Martens / M. Cristina Avramut / Roman I. Koning / Gerard J. M. Martens

    Stem Cell Research & Therapy, Vol 14, Iss 1, Pp 1-

    2023  Volume 25

    Abstract: Abstract Background Three-dimensional (3D) human brain spheroids are instrumental to study central nervous system (CNS) development and (dys)function. Yet, in current brain spheroid models the limited variety of cell types hampers an integrated ... ...

    Abstract Abstract Background Three-dimensional (3D) human brain spheroids are instrumental to study central nervous system (CNS) development and (dys)function. Yet, in current brain spheroid models the limited variety of cell types hampers an integrated exploration of CNS (disease) mechanisms. Methods Here we report a 5-month culture protocol that reproducibly generates H9 embryonic stem cell-derived human cortical spheroids (hCSs) with a large cell-type variety. Results We established the presence of not only neuroectoderm-derived neural progenitor populations, mature excitatory and inhibitory neurons, astrocytes and oligodendrocyte (precursor) cells, but also mesoderm-derived microglia and endothelial cell populations in the hCSs via RNA-sequencing, qPCR, immunocytochemistry and transmission electron microscopy. Transcriptomic analysis revealed resemblance between the 5-months-old hCSs and dorsal frontal rather than inferior regions of human fetal brains of 19–26 weeks of gestational age. Pro-inflammatory stimulation of the generated hCSs induced a neuroinflammatory response, offering a proof-of-principle of the applicability of the spheroids. Conclusions Our protocol provides a 3D human brain cell model containing a wide variety of innately developing neuroectoderm- as well as mesoderm-derived cell types, furnishing a versatile platform for comprehensive examination of intercellular CNS communication and neurological disease mechanisms.
    Keywords Brain organoid ; Brain spheroid ; Neuroectoderm ; Mesoderm ; Glial cells ; Endothelial cells ; Medicine (General) ; R5-920 ; Biochemistry ; QD415-436
    Subject code 571
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Physical and Functional Characterization of PLGA Nanoparticles Containing the Antimicrobial Peptide SAAP-148

    Muhanad Ali / Miriam E. van Gent / Amy M. de Waal / Bjorn R. van Doodewaerd / Erik Bos / Roman I. Koning / Robert A. Cordfunke / Jan Wouter Drijfhout / Peter H. Nibbering

    International Journal of Molecular Sciences, Vol 24, Iss 2867, p

    2023  Volume 2867

    Abstract: Synthetic antimicrobial and antibiofilm peptide (SAAP-148) commits significant antimicrobial activities against antimicrobial resistant (AMR) planktonic bacteria and biofilms. However, SAAP-148 is limited by its low selectivity index, i.e., ratio between ...

    Abstract Synthetic antimicrobial and antibiofilm peptide (SAAP-148) commits significant antimicrobial activities against antimicrobial resistant (AMR) planktonic bacteria and biofilms. However, SAAP-148 is limited by its low selectivity index, i.e., ratio between cytotoxicity and antimicrobial activity, as well as its bioavailability at infection sites. We hypothesized that formulation of SAAP-148 in PLGA nanoparticles (SAAP-148 NPs) improves the selectivity index due to the sustained local release of the peptide. The aim of this study was to investigate the physical and functional characteristics of SAAP-148 NPs and to compare the selectivity index of the formulated peptide with that of the peptide in solution. SAAP-148 NPs displayed favorable physiochemical properties [size = 94.1 ± 23 nm, polydispersity index (PDI) = 0.08 ± 0.1, surface charge = 1.65 ± 0.1 mV, and encapsulation efficiency (EE) = 86.7 ± 0.3%] and sustained release of peptide for up to 21 days in PBS at 37 °C. The antibacterial and cytotoxicity studies showed that the selectivity index for SAAP-148 NPs was drastically increased, by 10-fold, regarding AMR Staphylococcus aureus and 20-fold regarding AMR Acinetobacter baumannii after 4 h. Interestingly, the antibiofilm activity of SAAP-148 NPs against AMR S. aureus and A. baumannii gradually increased overtime, suggesting a dose–effect relationship based on the peptide’s in vitro release profile. Using 3D human skin equivalents (HSEs), dual drug SAAP-148 NPs and the novel antibiotic halicin NPs provided a stronger antibacterial response against planktonic and cell-associated bacteria than SAAP-148 NPs but not halicin NPs after 24 h. Confocal laser scanning microscopy revealed the presence of SAAP-148 NPs on the top layers of the skin models in close proximity to AMR S. aureus at 24 h. Overall, SAAP-148 NPs present a promising yet challenging approach for further development as treatment against bacterial infections.
    Keywords antimicrobial peptide ; skin infection ; PLGA ; nanoparticle ; drug delivery system ; bacterial ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 571
    Language English
    Publishing date 2023-02-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Automated vitrification of cryo-EM samples with controllable sample thickness using suction and real-time optical inspection

    Roman I. Koning / Hildo Vader / Martijn van Nugteren / Peter A. Grocutt / Wen Yang / Ludovic L. R. Renault / Abraham J. Koster / Arnold C. F. Kamp / Michael Schwertner

    Nature Communications, Vol 13, Iss 1, Pp 1-

    2022  Volume 10

    Abstract: Faster cryo specimen preparation can advance cryo electron microscopy (cryoEM). Here, the authors present a vitrification device with automated sample handling for cryoEM of proteins, suspensions and cells, enabling blot-free sample thinning, dew-point ... ...

    Abstract Faster cryo specimen preparation can advance cryo electron microscopy (cryoEM). Here, the authors present a vitrification device with automated sample handling for cryoEM of proteins, suspensions and cells, enabling blot-free sample thinning, dew-point control and characterization of cryo grids prior to data acquisition.
    Keywords Science ; Q
    Language English
    Publishing date 2022-05-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: Correlative microscopy for structural microbiology

    Howes, Stuart C / Abraham J Koster / Roman I Koning

    Current opinion in microbiology. 2018 June, v. 43

    2018  

    Abstract: Understanding how microbes utilize their environment is aided by visualizing them in their natural context at high resolution. Correlative imaging enables efficient targeting and identification of labelled viral and bacterial components by light ... ...

    Abstract Understanding how microbes utilize their environment is aided by visualizing them in their natural context at high resolution. Correlative imaging enables efficient targeting and identification of labelled viral and bacterial components by light microscopy combined with high resolution imaging by electron microscopy. Advances in genetic and bioorthogonal labelling, improved workflows for targeting and image correlation, and large-scale data collection are increasing the applicability of correlative imaging methods. Furthermore, developments in mass spectroscopy and soft X-ray imaging are expanding the correlative imaging modalities available. Investigating the structure and organization of microbes within their host by combined imaging methods provides important insights into mechanisms of infection and disease which cannot be obtained by other techniques.
    Keywords data collection ; electron microscopy ; image analysis ; labeling techniques ; light microscopy ; mass spectrometry ; microorganisms ; X-radiation
    Language English
    Dates of publication 2018-06
    Size p. 132-138.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 1418474-6
    ISSN 1879-0364 ; 1369-5274
    ISSN (online) 1879-0364
    ISSN 1369-5274
    DOI 10.1016/j.mib.2018.01.009
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: Cross-membranes orchestrate compartmentalization and morphogenesis in Streptomyces

    Katherine Celler / Roman I. Koning / Joost Willemse / Abraham J. Koster / Gilles P. van Wezel

    Nature Communications, Vol 7, Iss 1, Pp 1-

    2016  Volume 8

    Abstract: Streptomycetes are multicellular bacteria that grow as multinucleoid filaments with infrequent cross-walls. Here, the authors describe a membrane system that forms protein-impermeable barriers and compartmentalizes the multinucleoid filaments ... ...

    Abstract Streptomycetes are multicellular bacteria that grow as multinucleoid filaments with infrequent cross-walls. Here, the authors describe a membrane system that forms protein-impermeable barriers and compartmentalizes the multinucleoid filaments independently from the FtsZ-guided cell division machinery.
    Keywords Science ; Q
    Language English
    Publishing date 2016-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article: Characterisation of the size and swelling kinetics of copolymer nano-spheres extracted from an emulsion

    Lenchenkov, Nikita S / Cor van Kruijsdijk / Erik Bos / Flavia Cassiola / Gerard Glasbergen / Milos Vulovic / Roman I. Koning

    Colloids and surfaces. 2017 Dec. 20, v. 535

    2017  

    Abstract: The size distribution and swelling kinetics of copolymer nano-spheres extracted from an W/O emulsion was studied with dynamic light scattering (DLS) and transmission electron microscopy (TEM).TEM results were compared against DLS results. It was ... ...

    Abstract The size distribution and swelling kinetics of copolymer nano-spheres extracted from an W/O emulsion was studied with dynamic light scattering (DLS) and transmission electron microscopy (TEM).TEM results were compared against DLS results. It was demonstrated that the size distribution for agglomerates (clusters) of particles match well with the size distribution obtained from DLS. Hence, less time consuming DLS tests can be used for the estimation of the size of nano-spheres in the future.Next, a novel procedure for the study of agglomeration and swelling rates separately with TEM was designed. The results of the study revealed that the spheres agglomerate and swell over time. The kinetics of the agllomeration is used for a population balance model to predict the size of spheres over time. This approach helps to understand how well the spheres can propagate in an oil reservoir over time.
    Keywords composite polymers ; emulsions ; light scattering ; models ; nanospheres ; oil fields ; transmission electron microscopy
    Language English
    Dates of publication 2017-1220
    Size p. 265-273.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 1500517-3
    ISSN 0927-7757
    ISSN 0927-7757
    DOI 10.1016/j.colsurfa.2017.09.024
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  8. Article ; Online: USP32 regulates late endosomal transport and recycling through deubiquitylation of Rab7

    Aysegul Sapmaz / Ilana Berlin / Erik Bos / Ruud H. Wijdeven / Hans Janssen / Rebecca Konietzny / Jimmy J. Akkermans / Ayse E. Erson-Bensan / Roman I. Koning / Benedikt M. Kessler / Jacques Neefjes / Huib Ovaa

    Nature Communications, Vol 10, Iss 1, Pp 1-

    2019  Volume 18

    Abstract: Though ubiquitin is known to broadly influence endosomal trafficking, few ubiquitin-utilizing enzymes targeting endosomal regulators are known. Here, the authors find that the deubiquitylating enzyme (DUB) USP32 influences endosomal membrane dynamics by ... ...

    Abstract Though ubiquitin is known to broadly influence endosomal trafficking, few ubiquitin-utilizing enzymes targeting endosomal regulators are known. Here, the authors find that the deubiquitylating enzyme (DUB) USP32 influences endosomal membrane dynamics by deubiquitinating Rab7.
    Keywords Science ; Q
    Language English
    Publishing date 2019-03-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: USP32 regulates late endosomal transport and recycling through deubiquitylation of Rab7

    Aysegul Sapmaz / Ilana Berlin / Erik Bos / Ruud H. Wijdeven / Hans Janssen / Rebecca Konietzny / Jimmy J. Akkermans / Ayse E. Erson-Bensan / Roman I. Koning / Benedikt M. Kessler / Jacques Neefjes / Huib Ovaa

    Nature Communications, Vol 10, Iss 1, Pp 1-

    2019  Volume 18

    Abstract: Though ubiquitin is known to broadly influence endosomal trafficking, few ubiquitin-utilizing enzymes targeting endosomal regulators are known. Here, the authors find that the deubiquitylating enzyme (DUB) USP32 influences endosomal membrane dynamics by ... ...

    Abstract Though ubiquitin is known to broadly influence endosomal trafficking, few ubiquitin-utilizing enzymes targeting endosomal regulators are known. Here, the authors find that the deubiquitylating enzyme (DUB) USP32 influences endosomal membrane dynamics by deubiquitinating Rab7.
    Keywords Science ; Q
    Language English
    Publishing date 2019-03-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: WNT3a and WNT5a Transported by Exosomes Activate WNT Signaling Pathways in Human Cardiac Fibroblasts

    Edyta Działo / Michał Rudnik / Roman I. Koning / Marcin Czepiel / Karolina Tkacz / Monika Baj-Krzyworzeka / Oliver Distler / Maciej Siedlar / Gabriela Kania / Przemysław Błyszczuk

    International Journal of Molecular Sciences, Vol 20, Iss 6, p

    2019  Volume 1436

    Abstract: WNT signaling plays an important role in fibrotic processes in the heart. Recently, exosomes have been proposed as novel extracellular transporters for WNT proteins. In this study, we analyzed whether WNT3a and WNT5a carried by exosomes could activate ... ...

    Abstract WNT signaling plays an important role in fibrotic processes in the heart. Recently, exosomes have been proposed as novel extracellular transporters for WNT proteins. In this study, we analyzed whether WNT3a and WNT5a carried by exosomes could activate downstream molecular pathways in human cardiac fibroblasts. Exosomes were isolated from conditioned medium of control, WNT3a- and WNT5a-producing L cells by differential ultracentrifugations. Obtained exosomes showed size ranging between 20–150 nm and expressed exosomal markers ALG-2-interacting protein X (ALIX) and CD63. Treatment with WNT3a-rich exosomes inhibited activity of glycogen synthase kinase 3β (GSK3β), induced nuclear translocation of β-catenin, and activated T-cell factor (TCF)/lymphoid enhancer factor (LEF) transcription factors as well as expression of WNT/β-catenin responsive genes in cardiac fibroblasts, but did not coactivate extracellular signal-regulated kinase (ERK), c-Jun N-terminal kinase (JNK), and activator protein 1 (AP-1) signaling pathways. In contrast, exosomes produced by WNT5a-producing L cells failed to activate β-catenin-dependent response, but successfully triggered phosphorylation of ERK1/2 and JNK and stimulated IL-6 production. In conclusion, exosomes containing WNT proteins can functionally contribute to cardiac fibrosis by activating profibrotic WNT pathways on cardiac fibroblasts and may represent a novel mechanism of spreading profibrotic signals in the heart.
    Keywords exosomes ; WNT3a ; WNT5a ; cardiac fibroblasts ; canonical WNT ; non-canonical WNT ; cardiovascular diseases ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Language English
    Publishing date 2019-03-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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