bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mg
‐calcite formation in a freshwater environment (Lake Balaton): nucleation, growth, structure and composition
Authors: Pósfai Mihály , Nyirő‐Kósa Ilona , Rostási Ágnes , Bereczk‐Tompa Éva , Cora Ildikó , Koblar Maja , Kovács András 
Published: December 2016

Lake Balaton can be regarded as a large scientific laboratory in which many interesting aspects of carbonate mineral formation can be studied, with relevance to the general understanding of nanoscale processes that govern crystal nucleation and growth in a natural aqueous system. The lake is extremely shallow for its size (on average 3.5 m deep and 70 km long), its calcareous water Mg‐rich (with a Mg/Ca molar ratio ranging from (~1 to 4), typically displaying a chemical gradient along the W–E long axis of the lake, as a result of the main inlet and outlet being located at opposite ends. The bottom sediment is a soft grey mud, with 30 to 80% of it consisting of Mg‐calcite, a mineral that precipitates from the water (Fig. 1a). We used SEM, TEM and STEM techniques to characterize this Mg‐calcite, in order to obtain a better understanding of its formation and role in the ecosystem.
Freshwater calcite is known to nucleate on biological material, primarily on picoplankton (cyanobacterial) cells. In contrast, the Mg‐calcite in Lake Balaton is closely associated with few‐unit‐cell‐thick stacks of clay (smectite) layers (Figs. 1b and c), suggesting that it either nucleated on smectite or adsorbed to the clay flakes. Our laboratory experiments confirm that adding smectite to filtered lakewater dramatically induces Mg‐calcite precipitation; thus, the nm‐scale clay fragments likely serve as nucleation sites. Since the lake sediments are stirred up by even gentle winds, most of the time smectite particles are readily available for Mg‐calcite nucleation. A special case occurs when the lake is frozen and even the clay particles can settle: only bacterial cells are available as nucleation sites (Fig. 2a), and encrustation of cells results in tube‐shaped, porous Mg‐calcite particles (Fig. 2b).
Mg‐calcite that formed under „normal” conditions (i.e., nucleated on smectite) typically occurs in the shape of elongated, several μm‐large, aggregate‐looking particles (Fig. 2c). Even though they appear to be composed of many smaller crystals, SAED patterns suggest that the particles are perfect single crystals (Fig. 2d). The single crystalline nature of the particles probably results from a dissolution/reprecipitation process that preserves the original shapes of particles.
The Mg content of the calcite varies from 2 to 20 mol%, depending on the water budget (dilution) and geographical location in the lake. Mg‐calcite that nucleated on bacterial cells is highly enriched in Mg; according to SAED patterns, Mg and Ca ions do not order in the structure. Our results provide new information on freshwater calcite nucleation and on the biologically assisted precipitation of high‐magnesian calcite.
Light and electron microscopic evaluation of lattice corneal dystrophy (
LCD
)
Authors: Seckin Ismail , Cicik Mustafa Erdogan , Arslan Osman Sevki , Isildar Basak , Doğan Cezmi , Burgazdere Ozan , Hagverdiyeva Samira 
Published: December 2016

Introduction

There are three types of corneal dystrophies: anterior, posterior and stromal. Lattice corneal dystrophies (LCD) are a part of stromal dystrophies and characterized by an accumulation of amyloid deposition with in the stroma. LCD is diognosed with biomicroscopic examination and the diognosis confirmed by histological examination after keratoplasty. Genetic analysis may be required for specific cases.
In our study, the corneal buttons of four patients, three of them belonging to the same family, who applied to the Ophthalmology Clinic of Cerrahpasa Medical Faculty with lattice corneal dystrophy, histologically examined with light and electron microscopies.

Material‐Method

For light microscopic examination, a portion of corneal buttons were embedded into the parafine blocks after fixation and dehidration steps. Parafine blocks were cut as 5 µ sections and stained with hematoxylen & eosin and periodic acid & Schiff (PAS). For electron microscopic examination, the other pieces of corneal buttons were fixed glutaraldehyde and osmium tetroxide (OsO
4
). After the dehidration, corneal buttons embedded into araldite and the blocks were sectioned 500‐700Å. The sections taken on copper grids were analyzed and photographed.

Findings

In the light microscopic examination of hematoxylin & eosin stained corneal buttons; the local deposits seen in a circular arrangment, was observed and it was suggested that these were amyloid deposits. In only one of the four patients' corneal buttons, these deposits were seen in the stroma, but in the other three patients', belonging to the same family, deposits increased epithelial level and led to significant damage to the epithelium. When the samples were stained with periodic acid‐ Schiff reagent, positive reaction was observed in these deposits. Electron microscopic examination revealed that typical amyloid fibrils also occurred in deposits.
Despite local areas were damaged due to these amyloid deposits, no inflammation was observed.

Conclusion

As in other corneal dystrophies, a systematic approach and histopathological evaluation, including special staining and ultrastructural studies, are critical to a correct diagnosis, also in LCD. Therefore, it is important to make a histopathologic examination for all grafts clinically diagnosed or undiagnosed.
Serial section
(S)TEM
tomography of prokaryotic cells
Authors: Rachel Reinhard , Heinz Veronika , Flechsler Jennifer , Witzgall Ralph , Heimerl Thomas 
Published: December 2016

Cell complexity in prokaryotic cells, whether Bacteria or Archaea, is generally considered low, with a single compartment. A few examples, however, have been recently reported showing evidence for compartmentalization [e.g. 1,2,3]. These studies gained in particular from improved sample preparation methods (plunge freezing or high‐pressure freezing), adequate follow‐up methods, and 3D imaging of the samples, either by FIB‐SEM or by electron tomography. Here we report on our analyses of the ultrastructure of exceptional Archaea of the genera Ignicoccus and Pyrococcus, which show remarkable physiological characteristics (e.g. optimal growth at T~85 up to 100°C, under anoxic conditions), and unusual ultrastructural features. Although prokaryotes, these cells have a diameter of > 1 µm, which does not allow for reasonable cryoTEM observation without sectioning. Thus, samples were harvested by gentle concentration on ultrafiltration membranes, cryo‐immobilized by high‐pressure freezing, freeze‐substituted, and finally resin‐embedded; this enabled us to perform 3D ultrastructural analysis by (S)TEM tomography and immuno‐localization studies on sections of the same resin block.
So far, we are about to routinely investigate single or serial sections (ranging from 200 up to 800 nm in thickness), on a transmission electron microscope operated as TEM or STEM at 200 keV. For STEM, the illumination is adjusted to have an almost parallel beam, i.e. small convergence angle, resulting in an extended depth of focus [4]. Under these conditions, if the sample is imaged at high tilt angle (e.g. up to 70 deg), all visible image details are seen ‘in focus’, which greatly facilitates image alignment during 3D image reconstruction using IMOD (Boulder, Co, USA). In addition, the system in use allows parallel acquisition of BF and DF signal. Reconstruction and visualization is done using either WBP or SIRT in IMOD, and final manual segmentation using AMIRA®.

Our 3D data show novel and remarkable ultrastructural features: (A) Ignicoccus cells possess two membranes; in the intermembrane compartment, there is a complex endogenous membrane system. Attached to the outer cellular membrane, we have localized enzyme complexes for proton gradient generation, ATP and acetyl‐CoA synthesis, and CO
2
fixation [5]. (B) Pyrococccus cells possess flagella of the archaeal type [6], i.e. extracellular filaments involved in motility and cell‐cell interaction, and a cytoplasmic membrane and an S‐layer, and a so far unknown layer inside the cytoplasm presumbably involved in anchoring or organizing the flagellar bundle.
In‐situ observations of nanoparticles of carbon supported copper electrocatalyst during electrochemical cycling
Authors: Pacaud Jerome , Demortiere Arnaud , Dachraoui Walid , Sahin Niat Ege , Habrioux Aurelien , Comminges Clément , Napporn Tekko , Kokoh Boniface , Aguy Stephane 
Published: December 2016

Microwave assisted synthesis of metallic nanoparticles is an attractive way for the elaboration of electrocatalysts using energy efficient processes. This method consists in the use of a weak reducing agent that acts as solvent with high boiling point at the same time. Among the possible solvents, diethylene glycol is one of the most suitable molecules for microwave absorption and heating. Since microwave energy leads to a more uniform heat‐treatment than a conventional heating process, the overall activation energy for metal ion reduction decreases under microwave exposure. The carbon supported copper catalyst described herein is a good candidate for electrocatalytic processes due to the fact that copper is an abundant and effective transition metal for a number of reactions.
Observations were conducted in a Tecnai G2 fitted with a FEG, an EDX spectrometer and GIF Quantum. STEM‐HAADF was the primary technique of image recording. Scan speed was kept high in order to follow the kinetic of the evolution of the system. In this experiment, we use a sealed TEM cell recently developed by Protochips , i.e. liquid/bias TEM specimen holder (Poseidon 510). This system permits to study materials under electrochemical environment in TEM instrument. The sample (Copper nanoparticles on carbon) that is inside the sealed TEM cell (liquid gap is from 500 nm to 3000 nm) is immersed in the liquid electrolyte introduced by micro‐fluidic system (here aqueous electrolyte KCl/H2O at 0.01ML) and then electrochemically cycled using designed working electrode (glassy carbon) on transparent SixN1‐x windows. For electrochemical measurement, the applied currents were between 100 nA and 500 nA. Voltammogram was taken to ensure the correct oxidation and reduction of the copper atoms during a cycle. A strong corrosion of the supporting carbon is then observed. Experiments at constant current (chronopotentiometry) show the coalescence of large Cu grains and their disappearance depending on the applied current (See figure 1 and 2). Gas bubble formation is also observed (Figure 3). In these specific liquid experiments, optimized conditions remain to be found for TEM observation and in‐situ cycling, especially for electrocatalysis which is particularly demanding in terms of control of the experimental condition.
Application of
FIB‐SEM
tomography for analyses of ceramic coatings deposited on titanium alloy and material‐cell interface
Authors: Karbowniczek Joanna , Gruszczyński Adam , Kruk Adam , Czyrska‐Filemonowicz Aleksandra 
Published: December 2016

Biomedical engineering is a fast developing field of medicine, employing biomaterials to replace or augment damaged and diseased tissues. Growing population with osteoarthritis problems and extending life span contributes to increased demand for effective solutions in arthroplasty. Titanium alloys are the materials of the choice in case of elements of artificial joints. They are implanted directly into the bones. Long lasting performance of those implants depends on their integration with surrounding tissues. Surface modification of titanium alloys is performed to improve osseointegration. It can be achieved by deposition of porous, ceramic coatings. Such a structure facilitates bone cells ingrowth and stable anchorage of the implant in the bone. Understanding of the reactions at the interface between materials and cells will help to optimize the design of new implants with improved performance.
In current work, a titanium alloy (Ti6Al7Nb) was used as a substrate in micro‐arc oxidation (MAO) process. As the effect of this electrochemical reaction the protective and bioactive coating composed of titanium dioxides, calcium titanate and calcium phosphates was formed on the metallic sample. The obtained complex ceramic, porous layer was investigated by SEM and SEM‐EDS (Merlin Gemini II, Zeiss) and FIB‐SEM tomography (NEON CrossBeam 40EsB, Zeiss) to analyze microstructure, chemical composition and internal structure, including pores network.

In vitro
cell culture is a standard method to evaluate biocompatibility of new or modified materials. Thus, osteoblast‐like cells line MG‐63 were cultured for three days at the surface of coated titanium alloy samples. Subsequently cells attached to the ceramic coating were fixed, dehydrated and gold sputtered for electron microscopy investigations. Cells shape and distribution at rough and porous structure of the coating containing hydroxyapatite (HA) in the outer layer was investigated based on plain view SEM images (Fig. 1a). Area prepared for tomography by FIB milling of surrounding material is presented at Fig. 1b (marked by red square). FIB‐SEM tomography enables to see both material surface and cells at nanometer scale (Fig. 1c). The 3D reconstruction allows for visualization and investigations of the interface between coated material and cell in the analyzed sample volume.
A simple shortcut for observing unroofed cells by either
TEM
or
SEM
Authors: Franck Agathe , Lainé Jeanne , Bitoun Marc , Frébourg Ghislaine , Trichet Michaël , Vassilopoulos Stéphane 
Published: December 2016

The “unroofing” technique has been successfully used to observe the cytoplasmic side of the plasma membrane (PM) using either light or electron microscopy. Combined to transmission electron microscopy (TEM), it is an invaluable method to reveal the composition of the PM and to directly observe macromolecular complexes including the cytoskeleton and endocytic membrane invaginations. This method has been optimized over decades to preserve membranes close to their native states by the combination of quick freezing of exposed membranes, followed by deep etching and rotary replication (the so‐called “QF‐DE‐RR” technique). However, a serious setback in implementing unroofing combined with QF‐DE‐RR stems from the necessity to use complicated apparatus, such as quick freezing and freeze‐fracturing devices, along with strong expertise to handle them. Moreover, the technical complexity renders these techniques time consuming and reduces the number of samples that can be processed simultaneously.
Here, we present a simple and straightforward protocol for observation of the cytoplasmic side of plasma membrane which only requires chemical treatment of samples prior to replication This method has been optimized towards sample preparation at room temperature, chemical fixation, dehydration, solvent drying and sequential metal coating. Moreover, this technique is easily amenable to higher throughput. We compared either TEM or high resolution SEM analysis of unroofed membranes from adherent cells and show the advantages and disadvantages of each technique towards visualization of the cytoskeleton and different endocytic structures such as clathrin coated pits and caveolae.
The Effect of Vitamin
E
on Ovarian Damage Caused by Nicotine Administration
Authors: Sezer Zehra , Yılmaz Tuğba Ekiz , Güngör Zeynep , Guzel Elif 
Published: December 2016

Nicotine causes the formation of free radicals and oxidative damage. Vitamin E which is required in reproduction is a potent antioxidant found in nature. In our study, due to increasing tobacco consumption in women in especially recent years it was aimed to examine the nicotine induced damage in ovary, its mechanisms and the curative effects of vitamin E on these damages.
In our study, rats (12 week old‐ Wistar female rats) were treated with nicotine (1 mg/kg/day, intraperitoneally (ip)) and vitamin E (α‐tocopherol) (200 mg/kg/day, ip) alone or in combination in experimental groups. Levels of 17ß‐estradiol, LPO (Lipid peroxidation) and MDA (Malondialdehyde) were measured in serum of the animals. Hematoxylin and eosin (H+E) staining and labeling of Ki‐67 (a cellular marker for proliferation), 4‐HNE (4‐Hydroxynonenal; produced by lipid peroxidation in cells) and TUNEL (Terminal deoxynucleotidyl transferase (TdT)‐mediated dUTP nick end labeling;Apoptosis Detection) in paraffin sections of the ovaries was performed, immunohistochemical changes were assessed by scoring system. Ultrastructural changes in araldite sections were evaluated with the electron microscopy. The data were compared statistically.
Decreased estrogen level and increased levels of LPO and MDA in serum; decreased the number of ovarian follicles and Ki‐67‐labeling in granulosa cells of follicles; increased 4‐HNE immunoreactivity and TUNEL‐labeling were observed in nicotine‐treated rats. In these animals, nicotine co‐treatment with vitamin E significantly reduced the increased levels of LPO and MDA in serum and 4‐HNE immunoreactivity and TUNEL‐labeling in ovary sections; significantly increased serum estrogen level, the number of ovarian follicles and Ki‐67‐labeling in granulosa cells of follicles. Vitamin E demonstrated positive and curative effect on biochemical and histological parameters compared to the control group. Ultrastructurally, frequent apoptotic profiles were observed in granulosa cells in follicles in nicotine group and vitamin E co‐administration led to ultrastructural alleviation of apoptotic process.
In conclusion, our biochemical, immunohistochemical and ultrastructural level findings demonstrated that oxidative stress‐induced adverse effects caused by nicotine in folliculogenesis and streoidogenesis occur via lipid peroxidation in granulosa cells. Our data suggest that vitamin E may represent an alternative of pharmacologic treatment for preserving fertility owing to its beneficial effects on the nicotine induced damages occurred in the granulosa cells.
Understanding the Self‐Assembly of a Janus‐type
POM
‐
POSS
Co‐Cluster from low‐dose
STEM
Authors: Kuebel Christian , Yan L.T. , Wang Wei 
Published: December 2016

Understanding the self‐assembly process of novel cluster‐assembled materials (CAMs) is a prerequisite to optimize their structure and function. Janus‐type molecules are of particular interest as the provide the possibility to combine dissimilar properties. In this study, two kinds of unlike organo‐functionalized inorganic clusters (polyoxometalate: POM, polyhedral oligomeric silsesquioxane: POSS) have been covalently linked by a short organic tether to form a dumbbell‐shaped Janus co‐cluster. Their supramolecular assembly in nanocrystals has been analyzed in 2D and 3D using low‐dose HAADF‐STEM techniques to understand the assembly process based on the structure and the structural variations. The results have been compared to coarse grained molecular simulations.
STEM tomography reveals a honeycomb superstructure constructed by hexagonal close‐packed cylinders of the smaller POSS cluster and an orderly arranged framework of the larger POM cluster either in single or bicrystals (Fig. 1). A more detailed analysis (Fig. 2) reveals a bilayer arrangement of the POM‐POSS clusters within the hexagonal framework as the favorable structural motive. However, locally significant structural variations are observed, both in terms of the POM neighbor coordination (Fig. 2E) as well as for the tessellation of the supercell arrangement (Fig. 2F). This self‐organization demonstrates two synergistic effects controlling the structure formation: phase separation of the two immiscible blocks favoring a hexagonal framework, while crystallization or at least ordered packing of the POM clusters favors an extended bilayer leading to a geometrically frustrated structure. Close to the growth surface, this frustration leads to large structural variations with an increasing number of clusters in the basic motive, while it becomes more defined close to the core of the nanoparticles (Fig. 2D).
A series of coarse grained molecular simulations reveals that the size asymmetry of the two clusters has a significant effect on the self‐assembled structure. Ratios between 1.5 and 1.8 lead to hexagonal structures in good agreement with the experimental results. This understanding opens up new opportunities for generating novel CAMs for advanced applications.
Investigating Surface Plasmon‐Enhanced Local Electric Fields by
EELS
with tunable <60
meV
Energy Resolution
Authors: Abellan Patricia , El‐Khoury Patrick Z. , Hage Fredrik S. , Cottom Josh , Joly Alan G. , Hess Wayne P. , Brydson Rik , Ramasse Quentin M. 
Published: December 2016

Recent improvements in energy resolution, enabled by the use of electron energy monochromators, have the potential to turn EELS into a tool able to provide quantitative information of localized surface plasmons (LSPs), such as damping effects in single particles and electron kinetics of single plasmon modes.[1] Crucial to the prospect of quantitative analysis of LSPs is the requirement that the experimental energy resolution must be better than the natural line width of the plasmon resonances, all the while retaining high enough signal‐to‐noise ratio to enable an accurate determination of the properties of interest.[1] The energy resolution of EELS is customarily determined by the full‐width at half‐maximum (FWHM) of the zero‐loss (ZL) peak. The plasmon resonances, lying in the low‐loss regime, often overlap with the broad tail of the ZL peak, blurring many spectral signatures of interest. Until now, several processing techniques had to be applied to overcome these issues, relying for instance on deconvolution algorithms [2] which can introduce artifacts [3] A new generation of electron monochromators now allows for high signal‐to‐noise ratios while varying the energy resolution controllably, down to the 10meV regime [4].
Here we present recent results aimed at spatially and spectrally resolving the plasmon resonances of individual plasmonic nanostructures and of functional plasmonic devices using a Cs‐corrected and monochromated Nion UltraSTEM 100MC (‘Hermes’) microscope with a nominal energy resolution of 10meV. Figure 1 shows spatially resolved LSP modes of two individual Ag particles with different shapes and different number of crystalline domains for the energy ranges indicated in the figure. Both shape and crystallinity appear to affect the plasmonic response. We show how the energy resolution, which also affects the attainable signal‐to‐noise ratio and dictates the required integration (exposure) time, can be conveniently set and tuned, depending on the inherent properties of the system of interest. Figure 2A shows as‐recorded EEL spectra taken from the centre of a Ag nanowire (inset) and showing a narrow bulk plasmon resonance at 3.85eV. We note that the FWHM of the peak does not decrease with decreasing energy resolution from 40meV to 16meV, meaning that 40meV must be below the natural line width of the resonance. In this context, we will discuss the prospect of not only characterizing bare metallic nanostructures, but of also interrogating chemically functionalized plasmonic nanostructures using EELS. We note that the accessible energy ranges (sub‐40 meV) also allows us to probe molecules adsorbed onto metal nanostructures. In the raw spectra in Fig. 2B taken from different locations within a sample, spectroscopic signatures of aromatic thiols chemisorbed onto multiple Ag nanoparticles are shown.[5]