bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probing the multiscale structure, composition and nanomechanical properties of lipids and biopolymers in natural systems: a few examples
Authors: Gaillard Cédric 
Published: December 2016

The natural systems as plants or animal tissues possess a highly complex organisation of numerous components: micronutriments, proteins, polyssacharides, lipids, water, …. Their natural arrangement gives very fine structures that range from the nanometer up to few meters scale range (typically from the protein to the whole plant). Native architectures have a direct influence on the functional, chemical, organoleptic and nutritional macroscopic properties relevant for designing sustainable performant products for environmentally compatible food and non–food uses.
The development and application of experimental methodologies to probe the assemblies of lipids, biopolymers, mineral nutrients as well as structural water from the sub‐cellular to the molecular levels is then a permanent challenge. The parallel use of a set of complementary microscopy tools that provides relevant information may be needed to overcome the complexity of hydrated natural systems and to get both their structural, composition and nanomechanical properties. Most of the time, the experimental sample preparation is also a critical prerequisite to adapt the biological samples to the features of the analytical tool while keeping as most as possible the structures in their native shape. Thanks to this step, the microscopy tools can be operated through a direct or indirect correlation approach.
Using few applications we developed on biopolymer‐based nanoparticles as well as animal cells or plant tissues (see Figure 1), we will show how to probe the structure/composition/nanomechanical properties focusing on the strong complementarity of AFM imaging and force mapping, Raman mapping, SEM/EDX, and scanning transmission X‐ray spectrometry (STXM). We will also discuss about the samples preparation strategies, and about data processing in relation to the information expected.
Cryo‐electron microscopy from vitreous thin films in complement to
AFM
for understanding the multiscale supramolecular assemblies: a few examples
Authors: Gaillard Cédric 
Published: December 2016

The considerable growth of nano‐technologies and nano‐sciences requires the implementation of very well adapted characterization tools and methods to combine both a nanometer resolution and a good preservation of the nano‐objects. This point is absolutely critical when the nanostructures are made of hydrated and organic compounds. Cryo‐electron microscopy (cryo‐TEM) made from vitrified thin films has proved to be a method of choice for characterizing the hierarchy of supramolecular assemblies of proteins and hydroxy fatty acids with maximum resolution and minimal damage.
We aim here to present a selection of applications of cryo‐TEM showing the characterization of dispersions of organic or hybrid organic/inorganic nanoparticles with a large range of sizes, shapes and composition (synthetic polymers, polysaccharides, proteins, lipids).
In particular, we will detail how cryo‐TEM helped to elucidate the supramolecular self‐assembling of fatty acids through a multiscale approach. The unique benefits as well as the limitations of cryo‐TEM will be discussed and compared with conventional SEM and TEM techniques as well as with liquid AFM.
Raman imaging of biology and soft matter samples: a few examples
Authors: Gaillard Cédric 
Published: December 2016

Electron microscopy (SEM, TEM) is widely used to characterize the internal structures with micrometer spatial resolution. AFM is also commonly employed for analyzing the surface topography with a superior spatial resolution. However, confocal Raman microspectrometry is a unique way to complete such structural investigation by knowledge on chemical information. Raman imaging combines the spatial resolution of optical microscopy with the molecular analysis capabilities of Raman scattering. Then, it is very well adapted to provide direct information about conformation, structure and behavior of lipids and biopolymers (proteins, polysaccharides) from micronsized zones of interest.Also, the mainly structure‐sensitive bands in protein and lipid spectra makes them suitable for multivariate analysis techniques such as principal component analysis (PCA) to deduce structural relationships.Raman microspectrometry is then a method of choice for the compositional investigation with a high spectral resolution of hydrated biological systems of food interest along with the structural investigation performed conjointly with laser scanning confocal microscopy, AFM or electron microscopy with a superior spatial resolution.We aim here to review few examples of Raman imaging performed on different biological systems (algae, plant and animal tissues) and on soft‐matter based systems (highly diluted gels, dispersions) relevant in food industry, see Figures 1 and 2. We will focus on the complementarity with the other types of microscopy, and on the practical details concerning the sample preparation (choice of objectives, choice and influence of supports, smoothing or not of the surfaces,…).
Analytical electron microscopy and atom probe tomography investigation of interfacial segregation
Authors: Danoix F. , Sauvage X. , Gouné M. , Gault B. , Cuvilly F. 
Published: December 2016

The chemistry of internal interfaces plays a key role in modern physical metallurgy, in particular for the development of the new generations of steels. Despite the tremendous instrumental developments over the last decade, the atomic scale characterization of these interfaces in steels is still a very challenging problem.
Analytical electron microscopy (EDX and EELS in STEM mode) and atom probe tomography are the two techniques presenting spatial and analytical resolutions suitable for such characterizations. Their respective advantages and complementarity will be illustrated on the basis of quantitative determination of segregated amounts of interstitial and substitutional elements at interfaces, with particular emphasis on the intensive specimen preparation efforts required to reach their ultimate capabilities.
Studying biological samples in their native liquid environment using electron microscopy
Authors: Hermannsdörfer Justus , Weatherup Robert , Hofmann Stephan , De Jonge Niels 
Published: December 2016

It is now possible to study biological systems (e.g. eukaryotic cells) at nanometer spatial resolution in their native liquid environment using electron microscopy [1–3]. In contrast to conventional procedures, these new methods do not involve complex preparation steps like embedding, cutting, or freeze‐sectioning. It is further possible to minimize negative drying artifacts by adjusting experimental conditions that represent the native state as close as possible, i.e. the presence of water. Several different approaches meeting these requirements have been developed to study whole cells of different sizes:
Method 1: Two silicon microchips with electron transparent windows can be used to realize a microfluidic chamber that is sealed from the vacuum in the electron microscope (Figure 1). The chamber between the two microchips is thick enough to contain whole cells, yet thin enough to ensure a sufficient transmission of electrons. It is further possible to create bubbles in the liquid cell compartment by inducing a high density of electron dose on the sample. This increases the obtained contrast due to the minimized amount of scattering solvent. The liquid cell compartment can be used in a standard Transmission electron microscope (TEM). Method 2: Environmental scanning electron microscopy (ESEM) can be used to study cells covered in a thin layer of liquid surrounded by a saturated water atmosphere. The thickness of the liquid layer is controlled by adjusting the temperature and the environmental pressure within the vacuum chamber. Method 3: The wet sample is attached to an electron transparent support (e.g. graphene, carbon, silicon nitride) and covered with a thin membrane (e.g. mono or multilayer graphene) to realize a thin layer of liquid around the sample [4]. This method allows for high resolution imaging as the amount of solvent is reduced to a minimum. It can be used in any conventional TEM and SEM with scanning transmission electron microscopy (STEM) detection. The presence of water can be confirmed by beam‐induced bubbles.
Each of these three methods can be used to study the location and stoichiometry of transmembrane proteins within the intact plasma membrane [2, 3] with relevance to cancer research [5]. Nanoparticles, specifically attached to proteins, provide enough contrast for imaging (Figure 2). Also correlative light‐ and electron microscopy is readily possible, so that large numbers of cells can be screened, while selected regions can be studied with high resolution [5].
Electrical properties of atomic carbon chains measured by in‐situ TEM
Authors: Banhart Florian , La Torre Alessandro , Ben Romdhane Ferdaous , Cretu Ovidiu , Botello‐Mendez Andrés , Charlier Jean‐Christophe 
Published: December 2016

Carbon in the

sp
1

hybridization (carbyne) is able to form atomic chains that constitute the elementary one‐dimensional phase of carbon [1]. Despite many efforts, the synthesis of carbon chains in appreciable quantities remains difficult and even the existence of bulk carbyne is subject of an ongoing controversy. However, the existence of individual carbon chains is undisputed since they have been observed in
in‐situ
TEM studies. The present work allowed, for the first time, to measure the electrical properties of carbon chains by using a dedicated specimen stage for establishing electrical contacts in the TEM.

Carbon chains are unusual conductors that may occur either as metallic cumulene with double bonds or as semiconducting polyyne with alternating single and triple bonds. Now, as it became possible to characterize them electrically, these two electronic configurations can be distinguished. A piezo‐driven tip (Nanofactory), integrated into the specimen holder of a TEM, allowed to establish contacts to graphenic material and, by controlled retraction of the electrodes, to unravel chains of carbon atoms (fig. 1a). At the same time, the electrical properties could be measured [2, 3]. By recording current‐voltage curves of individual carbon chains, both cumulene and polyyne were identified (fig. 1b). It was found experimentally and by quantum conductance calculations (fig. 1c) that transport through narrow resonant states makes the conductivity much lower than predicted in previous theoretical work. At high applied bias, however, a sudden rise in current occurs, showing the absence of conduction channels at lower energy and their presence at higher energy.
When the 1D system is under strain, the chains exhibit a semiconducting behavior, corresponding to polyyne. Conversely, when the chain is unstrained, an ohmic behavior, corresponding to cumulene, is observed (fig. 1b) [4]. This confirms a recent theoretical prediction, namely that the Peierls distortion, which would stabilize polyyne, is suppressed by zero‐point vibrations in an unstrained chain so that cumulene is the stable configuration. In the presence of strain, however, polyyne is favoured by the Peierls instability. Thus, a metal‐insulator transition can be induced by adjusting the strain. Furthermore, it is shown that these atomic chains can act as rectifying diodes when they are in a non‐symmetric contact configuration, i.e., between a carbon and a metal contact or between two carbon contacts of different type.
The effect of tau hyperphosphorylation on Pin1 expression in primary cortical neurons: in okadaic acid induced
AD
model
Authors: Metin Derya , Ak Duygu Gezen , Dursun Erdinç , Atasoy İrem , Yılmazer Selma , Korkmaz Arzu Karabay , Ozturk Melek 
Published: December 2016

Hyperphosphorylation of tau leading to neurofibrillary tangles (NFT) is a key pathological hallmarks in neurodegenerative disorders such as Alzheimer's disease (AD) (1). Peptidyl‐prolyl cis‐trans isomerase (Pin1) regulates the phosphorylation of Ser/Thr sites of tau protein, and promote microtubule assembly (2). In this study, we aimed to determine the interaction between Pin1 expression and tau hyperphosphorylation in primary cortical neurons using okadaic acid (OKA) model (3) utilized to study AD.
Cortical neurons were obtained from embryonic day 16(E16) Sprague Dawley rat embryos. The neurons were treated with 25 nM OKA on day 7 of culture. Then at 4, 8 and 24 hours after treatment OKA, tau phosphorylation was analyzed by western blot using anti‐tau antibodies including Thr231 and Tau‐1. Immunocytochemistry was used for Pin1 protein expression and localization. Pin1 mRNA expression was determined by qRT‐PCR at 4, 8 and 24 hours. For cytotoxicity LDH analysis was performed by ELISA. At 8 hours with OKA, tau phosphorylation at Thr231 was increased and non‐phosphorylated Tau‐1 was decreased compared with the untreated control. Pin1 mRNA expression levels at both 4 and 8 hours post‐OKA treatment were lower than the control group. No significant differences at Pin1 mRNA and protein expression levels were observed between the OKA‐treated group and the untreated control group at 24 hours of treatment. Pin1 was mainly localized in the nucleus of control groups, whereas was found in cytoplasm of OKA‐treated group. Apoptotic nuclear morphology in OKA‐treated group was detected more than the control neurons. In OKA‐treated group the LDH release was not significantly different than the other groups at 4 and 8 hours, whereas it significantly increased at 24 hours.
Our study indicates that OKA induces the tau‐hyperphosphorylation, affects Pin‐1 expression, and causes to translocation of Pin‐1 proteins into cytoplasm from nucleus. This study will provide a new approach for AD molecular pathophysiology of in OKA‐ induced AD model.
Electron Tomography at the Frontiers of Materials Chemistry
Authors: Leary Rowan 
Published: December 2016

This presentation will follow two themes. The first considers recent contributions of electron tomography in materials chemistry, with particular focus on rationally designed multi‐scale and multi‐component systems. Second, developments and future prospects in electron tomographic methodology will be discussed.
Summarised in Figures 1 and 2, for example, is a recent study of Au nanorpisms decorated with Pt nanoparticles of size relevant for catalysis [1]. The tomographic analyses disclosed otherwise ambiguous details of the multi‐component architecture, revealing that both pseudospherical protrusions and dendritic Pt nanoparticles grow on all faces of the nanoprisms, the faceted or occasionally twisted morphologies of which were also revealed, and shedding light on alignment of the Pt nanoparticles. Complementary electron energy‐loss spectrum imaging showed that the Au nanoprisms support multiple localized surface plasmon resonances despite the presence of pendant Pt nanoparticles. These insights suggest potential applications in plasmon‐enhanced catalysis and in situ monitoring of chemical processes via surface‐enhanced spectroscopy, and pave the way toward comprehensive engineering of such multi‐functional nanostructures.
With the widespread adoption of scanning transmission electron microscopy and high‐angle annular‐dark field imaging, structural electron tomographic studies have reached a consistently high standard. The fidelity of such studies has also been raised significantly by the development of advanced reconstruction algorithms, such as those based on compressed sensing [2]. These are undergoing continual evolution to address the range of contexts and challenges faced in contemporary nanoscale investigations, including quantitative, low‐dose and analytical electron tomography.

Significant advances in hardware, such as fast and efficient X‐ray and electron energy‐loss spectrometers, and new camera technologies, have opened the flood gates to analytical electron tomography [3]. New ‘big data’ challenges are faced in the processing and analysis of multi‐dimensional tomography data sets. In this regard,
post facto
‘computational microscopy’ is becoming increasingly important; and versatile computational approaches can yield rich rewards. Indeed, computational analysis combined with advanced reconstruction can enable capture of the salient information content in a powerful and efficient manner. Computational modelling also offers the opportunity to utilise signals that have traditionally been thought unsuitable for tomography. Combined, hardware and computational advances are enabling a new era of analytical electron tomography, providing sophisticated 3D mapping at the nanoscale, spanning composition, crystallography, chemical, optical and electronic properties.
3D
imaging via
FIB‐SEM
tomography at nanoscale for tissue engineering applications
Authors: Urszula Stachewicz , Szewczyk Piotr , Kruk Adam , Barber Asa , Czyrska‐Filemonowicz Aleksandra 
Published: December 2016

The use of electrospun nanofibers for guided bone regeneration or bone scaffolds are becoming increasingly important in tissue engineering for next‐generation healthcare. However, understanding the interaction between the nanofiber scaffolds that organize into complex 3D organizations and cells for optimized growth is a recurrent problem yet to be overcome.
In this study we exploit high resolution 3D imaging using scanning electron microscopy (SEM) and focussed ion beam (FIB) microscopy to evaluate cryo‐prepared electrospun nanofiber scaffolds. Specifically, a biodegradable electrospun nanofiber membrane fabricated from poly(D,L‐lactide‐co‐glycolide) (PLGA) is used for guided bone regeneration for orthopaedic applications. The electrospun scaffolds are produced with randomly oriented and aligned nanofibers, creating a range of void sizes, which are crucial for controlling cells penetration into electrospun scaffolds. The secondary electron imaging in Figure 1 and 2 demonstrates osteoblasts spreading over the random and aligned nanofiber mat surface respectively and within the fibrous membrane after 4 days in culture. Osteoblasts tend to growth both along the principal fiber axis and migrate in all directions towards neighboring fibrous filopodia, localized at the edges of osteoblasts, help the sheets of cells to align in the nanofiber direction and participate in cell‐cell adhesion. It is presumed that these filopodia–like–protrusions are responsible for osteoblast elongation and migration into the 3D network of the electrospun nanofiber mat.

The interaction between osteoblasts and osteoblast‐derived mineralized nodule formation on the nanofiber membrane is visualized using 3D FIB‐SEM imaging based on a ‘slice‐and‐view’ approach. The 3D imaging highlights a coherent interface at small length scales between osteoblasts and nanofiber surfaces through connections between osteoblast, their filopodia and the nanofibers that promote cell growth. These imaging results are supported by biochemical approaches that indicate the formation of proteins responsible for focal adhesion in osteoblasts.
1
The presented 3D tomography therefore presents a new approach in high resolution visualization the cell growth on electrospun nanofibers, and potentially other biomaterials, that will develop and design new biomaterials for a range of clinically important applications including orthopaedics of this work.
A closer look at high‐resolution electron holography
Authors: Niermann Tore , Lehmann Michael 
Published: December 2016

In the recent years high‐resolution off‐axis electron holography made huge advancements. Electron microscopes with increased numbers of electron optical biprisms and electron lenses allow more flexible ray paths. Due to the combination of double biprism holography and higher magnification at the lower biprism, holograms in the high resolution regime are now recorded with negligible artifacts [1]. Furthermore, smart averaging schemes for hologram series allow to prolong the effective exposure time for a hologram to time scales, where the experimental errors are not dominated by the shot noise anymore [2].
One of the advantages of holography is the posterior correction of residual aberrations. However, the aberrations still have to be sufficiently known. By quantitative comparison of reconstructed wave functions with calculations the imaging parameters can be retrieved with sufficient precision allowing the reconstruction of aberration corrected exit‐wave functions. Thus nowadays holograms with (sub‐)angstrom resolution can be obtained on a regular basis.
In off‐axis holography only the side‐band channel of the information recorded in the hologram is reconstructed. As hologram series are recorded and the reconstructed wave function can be propagated to arbitrary defocus values anyway, also focal series of conventional images (center‐band) can be obtained in the same measurement.
In the figures the reconstructed exit waves of a GaAs wedge, obtained by inline and off‐axis holography are shown [3, 4]. While differences in the low‐frequency reconstruction are expected, also significant differences in thicker specimen parts are found. The latter can be easily recognized on the left side of the linescan profiles, where the amplitudes signals at the columns positions exhibit different behaviours. There are several possible reasons for this discrepancy. The numerical inversion of the imaging process within the inline method becomes worse conditioned since the thicker parts exhibit stronger non‐linear imaging. Thus the reconstruction algorithm might converge in a wrong minimum of the overall error figure. Also, any changes of the object during the acquisition of the series will exhibit different behaviour in the measurement. Furthermore, both channels (side‐band and center‐band) refer to different parts of the density matrix due to the different quantum‐mechanical nature of the underlying interference experiment.
Our muscle at near‐atomic resolution ‐ Cryo‐EM structure of the F‐actin‐tropomyosin complex
Authors: von der Ecken Julian , Müller Mirco , Lehman William , Manstein Dietmar J. , Penczek Pawel A. , Raunser Stefan 
Published: December 2016

Muscular movement plays an essential role not only in our lives but also describes a fundamental mechanism of force production. Filamentous actin (F‐actin) is the major protein of muscle thin filaments, and actin microfilaments are the main component of the eukaryotic cytoskeleton. The interaction of myosin with actin filaments is the central feature of muscle contraction and cargo movement along actin filaments.In striated muscle fibres, this interplay is mainly regulated by tropomyosin and troponin. Although crystal structures for monomeric actin are available, the difficulty of obtaining diffracting crystals, however, has prevented structure determination by crystallography of F‐actin. High‐resolution structures of F‐actin in complex are still missing, hampering our understanding of how disease‐causing mutations affect the function of thin muscle filaments and affecting skeletal and cardiac muscles.
We solved the three‐dimensional structure of F‐actin in complex with tropomyosin at a resolution of 3.7 Å (von der Ecken et al., 2015). We used cutting edge transmission electron cryomicroscopy and direct electron detectors and implemented new methods for processing of the data. The structure reveals insights in the inner interaction of the F‐actin subunits and the interplay of F‐actin and tropomyosin at near‐atomic resolution.