Research on the gut microbiome has gained high popularity and almost every disease has meanwhile been linked to alterations in microbiome composition. Typically assessed via stool samples, the microbiome displays a huge diversity with a multitude of environmental parameters already identified as contributing to its character. Despite impressive scientific progress, normal microbiome diversity remains largely unexplained and it is tempting to speculate some of the yet unexplained variance is hidden in normal gut physiology. Although a few genome/phenome-wide associations studies have recently highlighted physiological parameters such as stool frequency,known as contributing to microbiome diversity, there is a large knowledge base from decades of basic research on gut functions that can be explored for possible links to stool features and microbiome characteristics. And, when extrapolating findings from faecal samples to the biology in the intestinal lumen or the mucosal microenvironment, gut anatomy and physiology features need to be considered. Similarly, differences in anatomy and physiology between rodents and humans need attention when discussing findings in animals in relation to human physiology and nutrition.

The world of environmental microscopy provides the possibility to study and analyze transformations and reactions during realistic conditions to understand the processes better. We report on the design and development of a metal-organic chemical vapor deposition (MOCVD) system integrated with an environmental transmission electron microscope intended for real-time investigations of crystal growth. We demonstrate methods for achieving a wide range of precisely controlled concentrations of precursor gas at the sample, as well as for calibrating the sample partial pressure using the pressure measured elsewhere in the microscope column. The influences of elevated temperature and reactive gas within the pole-piece gap are evaluated with respect to imaging and spectroscopy. We show that X-ray energy-dispersive spectroscopy can be strongly affected by temperatures beyond 500$^{\circ }$C, while the spatial resolution is largely unaffected by heat and microscope pressure for the relevant conditions. Finally, the influence of the electron beam on the investigated processes is discussed. With this work, we aim to provide crucial input in the development of advanced in situ electron microscopy systems for studies of complex reactions in real time under realistic conditions, for instance as used during formation of semiconductor crystals.

A focused ion beam (FIB) technique describing the preparation of specimens for in situ thermal and electrical transmission electron microscopy is presented in detail. The method can be applied to a wide range of materials and allows the sample to be thinned down to electron transparency while it is attached to the in situ chip. This offers the advantage that the specimen can have a quality in terms of contamination and damage due to the ion beam that is comparable to samples prepared by means of conventional FIB preparation. Additionally, our technique can be performed by most commercially available FIB devices and only requires three simple, custom stubs for the procedure. This should enable a large userbase for this type of sample fabrication. One further benefit of our technique is that the in situ chip can be reused to create another sample on the same chip. The quality of the samples is demonstrated by high-resolution transmission electron microscopy as well as electron energy loss spectroscopy.

For materials characterization, obtaining insight through 3D imaging has been extremely helpful in improving our understanding of complex systems. X-ray computed tomography (CT) has proven to be an extremely useful technique in this field, allowing for non-destructive interrogation of samples of all types across many length scales. In this article we look at how micro-CT is moving from static 3D imaging into the realm of 4D data collection through dynamic CT, where CT data are collected on samples undergoing change in an uninterrupted matter.

Intermetallic γ-TiAl-based alloys are commonly used as structural materials for components in high-temperature applications, although they generally suffer from a lack of ductility and crack resistance at ambient temperatures. Within this study, the process-adapted 4th generation TNM+ alloy, exhibiting a fully lamellar microstructure, was examined using notched micro-cantilevers with defined orientations of lamellar interfaces. These configurations were tested in situ using superimposed continuous stiffness measurement methods during loading with simultaneous scanning electron microscopy observations. Subsequently, the video signal was used for visual crack length determination by computer vision and compared to values calculated from in situ changes in stiffness data. Applying this combinatorial approach enabled to determine the J-integral as a measure of the fracture toughness for microstructurally different local crack propagation paths. Thus, distinct differences in conditional fracture toughness could be determined from 3.7 MPa m1/2 for γ/γ-interface to 4.4 MPa m1/2 for α2/γ-interface.

Lead-free perovskite layers may provide a good alternative to the commonly used lead-halide-based perovskite absorber layers in photovoltaics. Energy level alignment of the active semiconductor with contact layers is a key factor in device performance. Kelvin probe force microscopy was used during vapor deposition of C60 onto formamidinium tin iodide to investigate contact formation with detailed local resolution of these materials that are significant for photovoltaic cells. Significant differences dependent on the growth rate of C60 were detected. Sufficiently high deposition rates were essential to reach compact C60 films needed for good contact. A space charge layer larger than 90 nm within the C60 layer was established without indication of interfacial dipoles. The present analysis gives a clear indication of a well-functioning contact of fullerenes to formamidinium tin iodide that is suitable for the use in photovoltaic devices provided that thin compact fullerene films are formed.

An ultraviolet (UV) irradiation-based in situ silver nanoparticle (AgNP) synthesis approach has drawn significant attention for functionalizing a great variety of biomaterials. Here, we designed an AgNP-functionalized 3D-printed polylactic acid (PLA) composite scaffold with a green physical approach by employing the UV irradiation (1, 2, and 3 h) method without using any reducing agent or heat treatments. In situ AgNP synthesis was performed under different UV exposure times. The zeta sizer analysis results demonstrated that AgNPs were highly monodisperse with the particle size of 20 ± 2.2, 30 ± 3.6, and 50 ± 4.8 nm under various UV light exposure times. In situ synthesis of AgNPs on 3D-printed PLA scaffolds significantly changed the surface hydrophilicity of the 3D-printed scaffolds. These results showed that UV irradiation-based in situ AgNP synthesis on 3D-printed PLA scaffolds can be useful in various biomedical applications, such as cell culture scaffolds, biosensors, and wound healing applications.

Advanced Ni8W/Ni12W/Ni8W alloy composite substrates used in YBCO-coated conductors with a strong cube texture and high yield strength have been fabricated, and a CeO2 buffer layer film was successfully deposited on the composite substrates. Through in situ tensile testing coupled with electron backscattered diffraction (EBSD) analysis, the stability of the cube texture of Ni8W/Ni12W/Ni8W alloy composite substrates has been investigated. The stress–strain curve shows that the yield strength (at 0.2% strain) of the composite substrates exceeds 250 Mpa. The orientation of grains and boundaries on the surface of the substrates was almost unchanged, while the strain exceeds 0.2%, which indicated that the composite substrates are adequate for depositing buffer layers and YBCO layers by the reel-to-reel process.

One of the biggest challenges for in situ heating transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) is the ability to measure the local temperature of the specimen accurately. Despite technological improvements in the construction of TEM/STEM heating holders, the problem of being able to measure the real sample temperature is still the subject of considerable discussion. In this study, we review the present literature on methodologies for temperature calibration. We analyze calibration methods that require the use of a thermometric material in addition to the specimen under study, as well as methods that can be performed directly on the specimen of interest without the need for a previous calibration. Finally, an overview of the most important characteristics of all the treated techniques, including temperature ranges and uncertainties, is provided in order to provide an accessory database to consult before an in situ TEM/STEM temperature calibration experiment.

The desire to image specimens in liquids has led to the development of open-cell and closed-cell techniques in transmission electron microscopy (TEM). The closed-cell approach is currently more common in TEM and has yielded new insights into a number of biological and materials processes in liquid environments. The open-cell approach, which requires an environmental TEM (ETEM), is technically challenging but may be advantageous in certain circumstances due to fewer restrictions on specimen and detector geometry. Here, we demonstrate a novel approach to open-cell liquid TEM, in which we use salt particles to facilitate the in situ formation of droplets of aqueous solution that envelope specimen particles coloaded with the salt. This is achieved by controlling sample temperature between 1 and 10°C and introducing water vapor to the ETEM chamber above the critical pressure for the formation of liquid water on the salt particles. Our use of in situ hydration enables specimens to be loaded into a microscope in a dry state using standard 3 mm TEM grids, allowing specimens to be prepared using trivial sample preparation techniques. Our future aim will be to combine this technique with an in situ light source to study photocorrosion in aqueous environments.

Selective laser sintering methods are workhorses for additively manufacturing polymer-based components. The ease of rapid prototyping also means it is easy to produce illicit components. It is necessary to have a data-calibrated in-situ physical model of the build process in order to predict expected and defective microstructure characteristics that inform component provenance. Toward this end, sintering models are calibrated and characteristics such as component defects are explored. This is accomplished by assimilating multiple data streams, imaging analysis, and computational model predictions in an adaptive Bayesian parameter estimation algorithm. From these data sources, along with a phase-field model, bulk porosity distributions are inferred. Model parameters are constrained to physically-relevant search directions by sensitivity analysis, and then matched to predictions using adaptive sampling. Using this feedback loop, data-constrained estimates of sintering model parameters along with uncertainty bounds are obtained.

Melting, solidification and solid-state transformation of the intermetallic Ni3Sn compound were investigated in situ using synchrotron high-energy X-ray diffraction. It was observed that the compound undergoes a hexagonal to cubic transition before melting. In solidification, a disordered cubic phase crystallizes from the liquid at a large undercooling but it is reordered prior to bulk solidification. In melting and solidification, forced or natural flows are active bringing about significant changes of crystal orientations. These in situ observations provided insights into phase transformations of Ni3Sn at elevated temperatures and their roles in formation of metastable microstructure consisting of coarse grains and subgrains.

Many nanoparticles in fields such as heterogeneous catalysis undergo surface structural fluctuations during chemical reactions, which may control functionality. These dynamic structural changes may be ideally investigated with time-resolved in situ electron microscopy. We have explored approaches for extracting quantitative information from large time-resolved image data sets with a low signal to noise recorded with a direct electron detector on an aberration-corrected transmission electron microscope. We focus on quantitatively characterizing beam-induced dynamic structural rearrangements taking place on the surface of CeO2 (ceria). A 2D Gaussian fitting procedure is employed to determine the position and occupancy of each atomic column in the nanoparticle with a temporal resolution of 2.5 ms and a spatial precision of 0.25 Å. Local rapid lattice expansions/contractions and atomic migration were revealed to occur on the (100) surface, whereas (111) surfaces were relatively stable throughout the experiment. The application of this methodology to other materials will provide new insights into the behavior of nanoparticle surface reconstructions that were previously inaccessible using other methods, which will have important consequences for the understanding of dynamic structure–property relationships.

In situ X-ray diffraction is one of the most useful tools for studying a variety of processes, among which crystallization of nanoparticles where phase purity and size control are desired. Growth kinetics of a single phase can be completely resolved by proper analysis of the diffraction peaks as a function of time. The peak width provides a parameter for monitoring the time evolution of the particle size distribution (PSD), while the peak area (integrated intensity) is directly related to the whole diffracting volume of crystallized material in the sample. However, to precisely describe the growth kinetics in terms of nucleation and coarsening, the correlation between PSD parameters and diffraction peak widths has to be established in each particular study. Corrections in integrated intensity values for physical phenomena such as variation in atomic thermal vibrations and dynamical diffraction effects have also to be considered in certain cases. In this work, a general correlation between PSD median value and diffraction peak width is deduced, and a systematic procedure to resolve time-dependent lognormal PSDs from in situ XRD experiments is described in details. A procedure to correct the integrated intensities for dynamical diffraction effects is proposed. As a practical demonstration, this analytical procedure has been applied to the single-phase crystallization process of bismuth ferrite nanoparticles.

Crop wild relatives (CWR) are a vital source of traits for crop improvement – therefore, conserving CWR diversity is critical to ensure food, nutrition and economic security. Efficient CWR conservation planning is a critical first step to maintain this natural resource for future use. The development of National Strategic Action Plans (NSAPs) for the conservation and sustainable use of CWR is an effective means of conservation planning and also plays an important role in sensitizing policy makers and other stakeholders to the importance of CWR. Tools to guide and facilitate countries in CWR national conservation planning and NSAP development have been prepared, namely: an ‘Interactive Toolkit for CWR Conservation Planning’, a ‘Template for the Preparation of a NSAP for the Conservation and Sustainable Use of CWR’, a ‘Template for the Preparation of a Technical Background Document for a NSAP for the Conservation and Sustainable Use of CWR’, a ‘CWR Checklist and Inventory Data Template’ and an ‘Occurrence Data Collation Template’. In this short communication, we briefly explain what these tools are, how they were developed, how they can be used and where they can be found.

Cereal crops are one of the most widely consumed and most valuable crops for humankind. The species have been domesticated for over 10,000 years and as such have lost much of the genetic diversity that is present within their wild relatives. Future breeding efforts will require the use of genetic diversity from crop wild relatives (CWRs) to help improve our cereal crops. This study aims to identify an in situ conservation network within the Mediterranean Basin and west Asia for the four cereal crops, barley (Hordeum L.), oat (Avena L.), rye (Secale L.) and wheat (Aegilops L., Amblyopyrum L., Triticum L.). This region is a centre of diversity for these taxa and an area of potentially high genetic diversity, which if left unprotected will not be available for plant breeders to utilize in the future. Presence point data for a total of 90 taxa were collected from GBIF and resulted in 76,343 individual presence points across the 44 countries in the study region. Geographic Information System (GIS) software was used to identify potential in situ reserve networks per crop genepool and for all crops combined. Results indicate a network of 10 locations across the region which would protect over 80% of the taxa. The number one priority reserve is found within the Fertile Crescent region on the border of Israel, Syria and Jordan. This proposed reserve location contains 93 currently protected areas (i.e. National Parks) and as such, it may only be necessary to alter management plans to effectively protect CWR populations. For taxa not found within protected areas ex situ conservation may be more appropriate and should be implemented as a backup to the in situ reserve network.

Crop wild relatives (CWR) are wild plant taxa relatively closely related to crops that can contribute beneficial traits for crop improvement, such as biotic and abiotic stress resistance. Turkey has a rich flora of approximately 11,000 higher plant taxa, has two Vavilov centres of crop diversity (i.e. the Mediterranean and the Near East), is recognized as the cradle of agriculture providing the northern boundary of the Fertile Crescent, and has recently been identified as the country with the highest concentration of CWR diversity. The objective of this paper is to present the results of a gap analysis of CWR genetic diversity in Turkey using existing data sources of 458 of the 764 priority CWR taxa with available georeferenced data. In total, 27,597 presence points were obtained from the Global Biodiversity Information Facility, Aegean Agricultural Research Institute in Menemen and Field Crops Central Research Institute, Ankara. Geographic Information System (GIS) software was used to identify taxon richness, sampling bias, future ex situ population collection and location where existing protected sites could form the basis of national network of in situ genetic reserves. CWR taxon richness was located along the Aegean Coast, Syrian border and southern Mediterranean coast. Current ex situ representation of CWR taxa is inadequate and further collection across the entire country is required. The highest priority in situ reserve location is found in Izmir, Sanliurfa and Antalya province, which reflects overall CWR richness.

High resolution (< 1 µm) computed tomography is an attractive tool in materials research due to its ability to non-destructively visualize the three-dimensional internal microstructures of the material. Recently, this technique has been further empowered by adding a fourth (temporal) dimension to study the time-lapse material response under load. Such studies are referred to as four-dimensional or in situ testing. In this snapshot review, we highlight three representative examples of in situ testing using synchrotron radiation computed tomography (SRCT) for composites failure analysis, measurement of local corrosion rate in alloys, and visualization and quantification of electrochemical reactions in lithium-ion batteries, as well as forward-looking integration of machine learning with in situ CT. Lastly, the future opportunities and challenges of in situ SRCT testing are discussed.

Multifunctionality was created by coupling an electronic charge carrier transport with ionic conductivity or ferroelectricity in polarized liquid crystal phases. Liquid-crystalline perylene bisimide derivatives bearing cyclotetrasiloxane rings and triethylene oxide chains formed nanosegregated columnar structures which could conduct ions as well as electrons. The spin-coated thin films could be insolubilized by the exposure on acid vapors and display electrochromism. Phenylterthiophene derivatives bearing a chiral alkyl side chain exhibited a ferroelectric phase, in which a photovoltaic effect was caused by the interaction between photogenerated charge carriers with the internal electric field formed by the spontaneous polarization of the ferroelectric phase.