Ecology of mycophagous collimonas bacteria in soil

Bacteria belonging to the genus Collimonas consist of soil bacteria that can grow at expense of living fungal hyphae i.e. they are mycophagous. This PhD studies deals with the ecology of mycophagous bacteria in soil using collimonads as model organisms. Collimonads were found to be widely distributed in different types of soils albeit at low densities. Highest numbers were present in fungal-rich grassland soils and lowest numbers in fungal-poor arable soils. Yet, no significant positive correlation between numbers of collimonads and fungal biomass densities was obtained when all soils were included in the analysis. Actual growth of indigenous collimonads in soils upon invasion by fungal hyphae was demonstrated using a newly, developed Collimonas-specific qPCR assay. The fungal-induced increase in numbers of collimonads was moderate and did not result in an increased turn-over of fungal biomass. In contrast to the effects on fungal-biomass turn-over, effects of presence of collimonads on soil fungal community composition were strong. This implies that collimonads can change the competitive relationships between soil fungal species. Hence, our conclusion is that a small component of the soil microbial community can have a huge impact on this community.NWO-ALW:813.04.009UBL - phd migration 201

Microwave-Assisted Synthesis of Core–Shell Nanoparticles—Insights into the Growth of Different Geometries

Microwave irradiation is utilized for the rapid synthesis of gold–silver core–shell bimetallic nanoparticles (NPs) in a two-step process. A strategy of establishing a bilayer organic barrier around the core using citrate and ascorbic acid as capping agents, providing a means to achieve a well-defined boundary layer between the core and the shell material, is reported. These boundary layers are essential for synthesizing different core–shell morphologies and the approach results in tunable bimetallic NPs with defined core–shell structures, both for spherical as well as for triangular seed cores. In addition, theoretical calculations of the plasmonic characteristics based on the boundary element method of different classes of NPs are conducted. These investigations enable conclusions to be drawn on the influence of the core morphology on the tunability of their localized surface plasmon resonances. © 2020 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinhei

Resolution and enhancement in nanoantenna-based fluorescence microscopy

Single gold nanoparticles can act as nanoantennas for enhancing the fluorescence of emitters in their near-fields. Here we present experimental and theoretical studies of scanning antenna-based fluorescence microscopy as a function of the diameter of the gold nanoparticle. We examine the interplay between fluorescence enhancement and spatial resolution and discuss the requirements for deciphering single molecules in a dense sample. Resolutions better than 20 nm and fluorescence enhancement up to 30 times are demonstrated experimentally. By accounting for the tip shaft and the sample interface in finite-difference time-domain calculations, we explain why the measured fluorescence enhancements are higher in the presence of an interface than the values predicted for a homogeneous environment.Comment: 10 pages, 3 figures. accepted for publication in Nano Letter

B Cells as Prognostic Biomarker After Surgery for Colorectal Liver Metastases

Background: The aim of this study was to identify more accurate variables to improve prognostication of individual patients with colorectal liver metastases (CRLM). Clinicopathological characteristics only partly explain the large range in survival rates. Methods: MessengerRNA expression profiles of resected CRLM of two patient groups were analysed by mRNA sequencing: poor survivors (death from recurrent disease 60 months after surgery). Tumour and adjacent liver parenchyma samples were analysed. Results: MessengerRNA expression profiling of the tumour samples identified 77 genes that were differentially expressed between the two survival groups at a False Discovery Rate (FDR) <0.1. In the adjacent liver parenchyma samples only one gene, MTRNR2L1, showed significantly higher expression in the good survivors. Pathway analysis showed higher expression of immune-related and stroma-related genes in tumour samples from good survivors. Expression data was then validated by immunohistochemistry in two cohorts comprising a total of 125 patients. Immunohistochemical markers that showed to be associated with good survival in the total cohort were: high K/L+ infiltration in tumour stroma [p = 0.029; OR 2.500 (95% CI 1.100–5.682)] and high CD79A+ infiltration in tumour stroma [p = 0.036; OR 2.428 (95%CI 1.062–5.552)]. Conclusions: A high stromal infiltration of CD79A+ B cells and K/L+ plasma cells might be favourable prognostic biomarkers after surgery for CRLM

Nanoantennas for visible and infrared radiation

Nanoantennas for visible and infrared radiation can strongly enhance the interaction of light with nanoscale matter by their ability to efficiently link propagating and spatially localized optical fields. This ability unlocks an enormous potential for applications ranging from nanoscale optical microscopy and spectroscopy over solar energy conversion, integrated optical nanocircuitry, opto-electronics and density-ofstates engineering to ultra-sensing as well as enhancement of optical nonlinearities. Here we review the current understanding of optical antennas based on the background of both well-developed radiowave antenna engineering and the emerging field of plasmonics. In particular, we address the plasmonic behavior that emerges due to the very high optical frequencies involved and the limitations in the choice of antenna materials and geometrical parameters imposed by nanofabrication. Finally, we give a brief account of the current status of the field and the major established and emerging lines of investigation in this vivid area of research.Comment: Review article with 76 pages, 21 figure

Studying Cat (Felis catus) Diabetes: Beware of the Acromegalic Imposter

Naturally occurring diabetes mellitus (DM) is common in domestic cats (Felis catus). It has been proposed as a model for human Type 2 DM given many shared features. Small case studies demonstrate feline DM also occurs as a result of insulin resistance due to a somatotrophinoma. The current study estimates the prevalence of hypersomatotropism or acromegaly in the largest cohort of diabetic cats to date, evaluates clinical presentation and ease of recognition. Diabetic cats were screened for hypersomatotropism using serum total insulin-like growth factor-1 (IGF-1; radioimmunoassay), followed by further evaluation of a subset of cases with suggestive IGF-1 (>1000 ng/ml) through pituitary imaging and/ or histopathology. Clinicians indicated pre-test suspicion for hypersomatotropism. In total 1221 diabetic cats were screened; 319 (26.1%) demonstrated a serum IGF-1>1000 ng/ml (95% confidence interval: 23.6-28.6%). Of these cats a subset of 63 (20%) underwent pituitary imaging and 56/63 (89%) had a pituitary tumour on computed tomography; an additional three on magnetic resonance imaging and one on necropsy. These data suggest a positive predictive value of serum IGF-1 for hypersomatotropism of 95% (95% confidence interval: 90-100%), thus suggesting the overall hypersomatotropism prevalence among UK diabetic cats to be 24.8% (95% confidence interval: 21.2-28.6%). Only 24% of clinicians indicated a strong pre-test suspicion; most hypersomatotropism cats did not display typical phenotypical acromegaly signs. The current data suggest hypersomatotropism screening should be considered when studying diabetic cats and opportunities exist for comparative acromegaly research, especially in light of the many detected communalities with the human disease

The role of the disulfide bond in the interaction of islet amyloid polypeptide with membranes

Human islet amyloid polypeptide (hIAPP) forms amyloid fibrils in pancreatic islets of patients with type 2 diabetes mellitus. It has been suggested that the N-terminal part, which contains a conserved intramolecular disulfide bond between residues 2 and 7, interacts with membranes, ultimately leading to membrane damage and β-cell death. Here, we used variants of the hIAPP1–19 fragment and model membranes of phosphatidylcholine and phosphatidylserine (7:3, molar ratio) to examine the role of this disulfide in membrane interactions. We found that the disulfide bond has a minor effect on membrane insertion properties and peptide conformational behavior, as studied by monolayer techniques, 2H NMR, ThT-fluorescence, membrane leakage, and CD spectroscopy. The results suggest that the disulfide bond does not play a significant role in hIAPP–membrane interactions. Hence, the fact that this bond is conserved is most likely related exclusively to the biological activity of IAPP as a hormone

Shrinking-Hole Colloidal Lithography: Self-Aligned Nanofabrication of Complex Plasmonic Nanoantennas

Plasmonic nanoantennas create locally strongly enhanced electric fields in so-called hot spots. To place a relevant nanoobject with high accuracy in such a hot spot is crucial to fully capitalize on the potential of nanoantennas to control, detect, and enhance processes at the nanoscale. With state-of-the-art nanofabrication, in particular when several materials are to be used, small gaps between antenna elements are sought, and large surface areas are to be patterned, this is a grand challenge. Here we introduce self-aligned, bottom-up and self-assembly based Shrinking-Hole Colloidal Lithography, which provides (i) unique control of the size and position of subsequently deposited particles forming the nanoantenna itself, and (ii) allows delivery of nanoobjects consisting of a material of choice to the antenna hot spot, all in a single lithography step and, if desired, uniformly covering several square centimeters of surface. We illustrate the functionality of SHCL nanoantenna arrangements by (i) an optical hydrogen sensor exploiting the polarization dependent sensitivity of an Au-Pd nanoantenna ensemble; and (ii) single particle hydrogen sensing with an Au dimer nanoantenna with a small Pd nanoparticle in the hot spot

Islet expression of the DNA repair enzyme 8-oxoguanosine DNA glycosylase (Ogg1) in human type 2 diabetes

BACKGROUND: It has become increasingly clear that β-cell failure plays a critical role in the pathogenesis of type 2 diabetes. Free-radical mediated β-cell damage has been intensively studied in type 1 diabetes, but not in human type 2 diabetes. Therefore, we studied the protein expression of the DNA repair enzyme Ogg1 in pancreases from type 2 diabetics. Ogg1 was studied because it is the major enzyme involved in repairing 7,8-dihydro-8-oxoguanosine DNA adducts, a lesion previously observed in a rat model of type 2 diabetes. Moreover, in a gene expression screen, Ogg1 was over-expressed in islets from a human type 2 diabetic. METHODS: Immunofluorescent staining of Ogg1 was performed on pancreatic specimens from healthy controls and patients with diabetes for 2–23 years. The intensity and islet area stained for Ogg1 was evaluated by semi-quantitative scoring. RESULTS: Both the intensity and the area of islet Ogg1 staining were significantly increased in islets from the type 2 diabetic subjects compared to the healthy controls. A correlation between increased Ogg1 fluorescent staining intensity and duration of diabetes was also found. Most of the staining observed was cytoplasmic, suggesting that mitochondrial Ogg1 accounts primarily for the increased Ogg1 expression. CONCLUSION: We conclude that oxidative stress related DNA damage may be a novel important factor in the pathogenesis of human type 2 diabetes. An increase of Ogg1 in islet cell mitochondria is consistent with a model in which hyperglycemia and consequent increased β-cell oxidative metabolism lead to DNA damage and the induction of Ogg1 expression

Self-assembled amyloid fibrils with controllable conformational heterogeneity

Amyloid fibrils are a hallmark of neurodegenerative diseases and exhibit a conformational diversity that governs their pathological functions. Despite recent findings concerning the pathological role of their conformational diversity, the way in which the heterogeneous conformations of amyloid fibrils can be formed has remained elusive. Here, we show that microwave-assisted chemistry affects the self-assembly process of amyloid fibril formation, which results in their conformational heterogeneity. In particular, microwave-assisted chemistry allows for delicate control of the thermodynamics of the self-assembly process, which enabled us to tune the molecular structure of ??-lactoglobulin amyloid fibrils. The heterogeneous conformations of amyloid fibrils, which can be tuned with microwave-assisted chemistry, are attributed to the microwave-driven thermal energy affecting the electrostatic interaction during the self-assembly process. Our study demonstrates how microwave-assisted chemistry can be used to gain insight into the origin of conformational heterogeneity of amyloid fibrils as well as the design principles showing how the molecular structures of amyloid fibrils can be controlledopen0