Water Window Ptychographic Imaging with Characterized Coherent X-rays

We report on a ptychographical coherent diffractive imaging experiment in the water window with focused soft X-rays at $500~\mathrm{eV}$. An X-ray beam with high degree of coherence was selected for ptychography at the P04 beamline of the PETRA III synchrotron radiation source. We measured the beam coherence with the newly developed non-redundant array method. A pinhole $2.6~\mathrm{\mu m}$ in size selected the coherent part of the beam and was used for ptychographic measurements of a lithographically manufactured test sample and fossil diatom. The achieved resolution was $53~\mathrm{nm}$ for the test sample and only limited by the size of the detector. The diatom was imaged at a resolution better than $90~\mathrm{nm}$.Comment: 22 pages. 7 figure

Istraživanje nečiste i čiste (100) površine vanadija STM-om

Scanning tunneling microscopy is used to characterize different states of the V(100) surface during the cleaning procedure in an ultrahigh vacuum apparatus, starting with the "as received" sample and finishing with an almost perfectly clean surface. We show, for the first time, STM images of the clean V(100) surface and with atomic resolution.Primijenili smo skenirajući tunelirajući mikroskop (STM) za topografsku karakterizaciju površine V(100) prije i tijekom čišćenja u aparaturi za ultravisok vakuum, počevši s “dobivenim” uzorkom i nakon pojedinih postupaka čišćenja. Po prvi puta se pokazuju slike potpuno čiste površine V(100) s atomskim razlučivanjem, snimljene STM-om

Istraživanje nečiste i čiste (100) površine vanadija STM-om

Scanning tunneling microscopy is used to characterize different states of the V(100) surface during the cleaning procedure in an ultrahigh vacuum apparatus, starting with the "as received" sample and finishing with an almost perfectly clean surface. We show, for the first time, STM images of the clean V(100) surface and with atomic resolution.Primijenili smo skenirajući tunelirajući mikroskop (STM) za topografsku karakterizaciju površine V(100) prije i tijekom čišćenja u aparaturi za ultravisok vakuum, počevši s “dobivenim” uzorkom i nakon pojedinih postupaka čišćenja. Po prvi puta se pokazuju slike potpuno čiste površine V(100) s atomskim razlučivanjem, snimljene STM-om

Semantic Segmentation for Fully Automated Macrofouling Analysis on Coatings after Field Exposure

Biofouling is a major challenge for sustainable shipping, filter membranes, heat exchangers, and medical devices. The development of fouling-resistant coatings requires the evaluation of their effectiveness. Such an evaluation is usually based on the assessment of fouling progression after different exposure times to the target medium (e.g., salt water). The manual assessment of macrofouling requires expert knowledge about local fouling communities due to high variances in phenotypical appearance, has single-image sampling inaccuracies for certain species, and lacks spatial information. Here we present an approach for automatic image-based macrofouling analysis. We created a dataset with dense labels prepared from field panel images and propose a convolutional network (adapted U-Net) for the semantic segmentation of different macrofouling classes. The establishment of macrofouling localization allows for the generation of a successional model which enables the determination of direct surface attachment and in-depth epibiotic studies.Comment: 33 pages, 10 figure

Adherent cells avoid polarization gradients on periodically poled LiTaO\u3csub\u3e3\u3c/sub\u3e ferroelectrics

The response of fibroblast cells to periodically poled LiTaO3 ferroelectric crystals has been studied. While fibroblast cells do not show morphological differences on the two polarization directions, they show a tendency to avoid the field gradients that occur between polarization domains of the ferroelectric. The response to the field gradients is fully established after one hour, a time at which fibroblasts form their first focal contacts. If suspension cells, with a lower tendency to establish strong surface contacts are used, no influence of the field gradients is observed

Adherent cells avoid polarization gradients on periodically poled LiTaO\u3csub\u3e3\u3c/sub\u3e ferroelectrics

The response of fibroblast cells to periodically poled LiTaO3 ferroelectric crystals has been studied. While fibroblast cells do not show morphological differences on the two polarization directions, they show a tendency to avoid the field gradients that occur between polarization domains of the ferroelectric. The response to the field gradients is fully established after one hour, a time at which fibroblasts form their first focal contacts. If suspension cells, with a lower tendency to establish strong surface contacts are used, no influence of the field gradients is observed

Can BioSAXS detect ultrastructural changes of antifungal compounds in Candida albicans?–an exploratory study

The opportunistic yeast Candida albicans is the most common cause of candidiasis. With only four classes of antifungal drugs on the market, resistance is becoming a problem in the treatment of fungal infections, especially in immunocompromised patients. The development of novel antifungal drugs with different modes of action is urgent. In 2016, we developed a groundbreaking new medium-throughput method to distinguish the effects of antibacterial agents. Using small-angle X-ray scattering for biological samples (BioSAXS), it is now possible to screen hundreds of new antibacterial compounds and select those with the highest probability for a novel mode of action. However, yeast (eukaryotic) cells are highly structured compared to bacteria. The fundamental question to answer was if the ultrastructural changes induced by the action of an antifungal drug can be detected even when most structures in the cell stay unchanged. In this exploratory work, BioSAXS was used to measure the ultrastructural changes of C. albicans that were directly or indirectly induced by antifungal compounds. For this, the well-characterized antifungal drug Flucytosine was used. BioSAXS measurements were performed on the synchrotron P12 BioSAXS beamline, EMBL (DESY, Hamburg) on treated and untreated yeast C. albicans. BioSAXS curves were analysed using principal component analysis (PCA). The PCA showed that Flucytosine-treated and untreated yeast were separated. Based on that success further measurements were performed on five antifungal peptides {1. Cecropin A-melittin hybrid [CA (1–7) M (2–9)], KWKLFKKIGAVLKVL; 2. Lasioglossin LL-III, VNWKKILGKIIKVVK; 3. Mastoparan M, INLKAIAALAKKLL; 4. Bmkn2, FIGAIARLLSKIFGKR; and 5. optP7, KRRVRWIIW}. The ultrastructural changes of C. albicans indicate that the peptides may have different modes of action compared to Flucytosine as well as to each other, except for the Cecropin A-melittin hybrid [CA (1–7) M (2–9)] and optP7, showing very similar effects on C. albicans. This very first study demonstrates that BioSAXS shows promise to be used for antifungal drug development. However, this first study has limitations and further experiments are necessary to establish this application

BioSAXS measurements reveal that two antimicrobial peptides induce similar molecular changes in gram-negative and gram-positive bacteria

Two highly active short broad-spectrum AMPs (14D and 69D) with unknown mode of action have been investigated in regards to their effect against the Gramnegative bacteria Escherichia coli and the Gram-positive bacteria methicillinresistant Staphylococcus aureus (MRSA). Minimal inhibitory concentration (MIC) measurements using a cell density of 108 cfu/ml resulted in values between 16 and 32 μg/ml. Time-kill experiments using 108 cfu/ml revealed complete killing, except for 69D in combination with MRSA, where bacterial load was reduced a million times. Small-angle X-ray scattering of biological samples (BioSAXS) at 108 cfu/ml was applied to investigate the ultrastructural changes in E. coli and MRSA in response to these two broad-spectrum AMPs. In addition, electron microscopy (EM) was performed to visualize the treated and non-treated bacteria. As expected, the scattering curves generated using BioSAXS show the ultrastructure of the Grampositive and Gram-negative bacteria to be very different (BioSAXS is not susceptible to the outer shape). After treatment with either peptide, the scattering curves of E.coli and MRSA cells are much more alike. Whereas in EM, it is notoriously difficult to observe changes for spherical Gram-positives; the BioSAXS results are superior and reveal strongly similar effects for both peptides induced in Gram-positive as well as Gram-negative bacteria. Given the high-throughput possibility and robust statistics, BioSAXS can support and speed up mode of action research in AMPs and other antimicrobial compounds, making a contribution toward the development of urgently needed drugs against resistant bacteria

Can BioSAXS detect ultrastructural changes of antifungal compounds in Candida albicans?–an exploratory study

The opportunistic yeast Candida albicans is the most common cause of candidiasis. With only four classes of antifungal drugs on the market, resistance is becoming a problem in the treatment of fungal infections, especially in immunocompromised patients. The development of novel antifungal drugs with different modes of action is urgent. In 2016, we developed a groundbreaking new medium-throughput method to distinguish the effects of antibacterial agents. Using small-angle X-ray scattering for biological samples (BioSAXS), it is now possible to screen hundreds of new antibacterial compounds and select those with the highest probability for a novel mode of action. However, yeast (eukaryotic) cells are highly structured compared to bacteria. The fundamental question to answer was if the ultrastructural changes induced by the action of an antifungal drug can be detected even when most structures in the cell stay unchanged. In this exploratory work, BioSAXS was used to measure the ultrastructural changes of C. albicans that were directly or indirectly induced by antifungal compounds. For this, the well-characterized antifungal drug Flucytosine was used. BioSAXS measurements were performed on the synchrotron P12 BioSAXS beamline, EMBL (DESY, Hamburg) on treated and untreated yeast C. albicans. BioSAXS curves were analysed using principal component analysis (PCA). The PCA showed that Flucytosine-treated and untreated yeast were separated. Based on that success further measurements were performed on five antifungal peptides {1. Cecropin A-melittin hybrid [CA (1–7) M (2–9)], KWKLFKKIGAVLKVL; 2. Lasioglossin LL-III, VNWKKILGKIIKVVK; 3. Mastoparan M, INLKAIAALAKKLL; 4. Bmkn2, FIGAIARLLSKIFGKR; and 5. optP7, KRRVRWIIW}. The ultrastructural changes of C. albicans indicate that the peptides may have different modes of action compared to Flucytosine as well as to each other, except for the Cecropin A-melittin hybrid [CA (1–7) M (2–9)] and optP7, showing very similar effects on C. albicans. This very first study demonstrates that BioSAXS shows promise to be used for antifungal drug development. However, this first study has limitations and further experiments are necessary to establish this application