Thin-section Electron Microscopy Research Articles

Diagnostic electron microscopy in human infectious diseases - Methods and applications.

Diagnostic electron microscopy (EM) is indispensable in all cases of infectious diseases which deserve or profit from the detection of the entire pathogen (i.e. the infectious unit). The focus of its application has shifted during the last decades from routine diagnostics to diagnostics of special cases, emergencies and the investigation of disease pathogenesis. While the focus of application has changed, the methods remain more or less the same. However, since the number of cases for diagnostic EM has declined as the number of laboratories that are able to perform such investigations, the preservation of the present knowledge is important. The aim of this article is to provide a review of the methods and strategies which are useful for diagnostic EM related to infectious diseases in our days. It also addresses weaknesses as well as useful variants or extensions of established methods. The main techniques, negative staining and thin section EM, are described in detail with links to suitable protocols and more recent improvements, such as thin section EM of small volume suspensions. Sample collection, transport and conservation/inactivation are discussed. Strategies of sample examination and requirements for a proper recognition of structures are outlined. Finally, some examples for the actual application of diagnostic EM related to infectious diseases are presented. The outlook section will discuss recent trends in microscopy, such as automated object recognition by machine learning, regarding their potential in supporting diagnostic EM.

Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate

Abstract Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. Here, we present a workflow for SBF SEM of adherent cells, such as Giardia parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded in situ on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. A standard sample preparation and embedding protocol for thin section electron microscopy provided already sufficient resolution and image quality to visualize larger structures. To improve resolution and image quality of SBF imaging, we stepwise tested modifications of the protocol, such as the moderate increase of the heavy metal content of the sample. Modifications of the embedding by either the reduction of the resin layer (minimal embedding) or the addition of silver colloid to the resin were evaluated at high and low vacuum imaging conditions. The optimized sample preparation protocol is very similar to the standard preparation protocol for thin section electron microscopy, so that the samples can also be used for this application. The protocol applies a higher concentration of osmium tetroxide, a higher temperature for heavy metal incubation and an additional lead en bloc staining. In summary, the presented workflow provides a generic and adaptable solution for studying adherent cells by SBF SEM.

Pore Structures and Evolution Model of Reservoirs in Different Secondary Structural Zones in the Eocene Shahejie Formation, Chezhen Sag, Bohai Bay Basin.

Although abundant unconventional oil resources have been discovered in conglomerate and sandstone reservoirs in rift basins, the mechanism of differential pore evolution in conglomerates and sandstone reservoirs within different secondary structural zones of rift basins is not yet clear. The pore structures of conglomerate and sandstone reservoirs in the distinct secondary structural zones in the Chezhen Sag were quantified in three dimensions using high-resolution microcomputed tomography (micro-CT). Thin section and scanning electron microscopy observations were used to investigate the differential evolution mechanisms of conglomerate and sandstone reservoirs. Micro-CT analysis of the pore structures of conglomerate and sandstone reservoirs revealed that sandstone reservoirs are superior to conglomerate reservoirs with regard to the pore number and pore connectivity and that sandstone reservoirs are more heterogeneous than conglomerate reservoirs. Triangles dominate the pore and pore throat geometries of sandstone and conglomerate reservoirs, while the sandstone reservoir pores are more regular than conglomerate reservoir pores. The depositional environment, mineral composition, and diagenetic intensity jointly control the quality of the reservoirs. Because of the lengthy transportation distance of their parent rocks, the compositional maturity and sorting behavior of sandstone reservoirs in depression and gentle slope zones are better than those of conglomerate reservoirs in steep slope zones, and thus sandstone reservoirs have a higher initial porosity than conglomerate reservoirs. The rapid compaction experienced by the conglomerate reservoirs in steep slope zones in their early stages creates a closed diagenetic environment, making it difficult to effectively improve reservoir porosity through dissolution. However, the widely developed microfractures in the reservoirs provide channels for fluid migration, promote the development of dissolution pores, and form a tight reservoir dominated by secondary pores. With weak compaction and an open diagenetic environment, the primary pores in sandstone reservoirs in the gentle slope zone are preserved in large quantities. Meanwhile, dissolution expands the secondary pores of the reservoir, resulting in a high-quality reservoir having both primary and secondary pores. In addition, an approach based on primary, secondary, and total porosity was proposed in the study to efficiently evaluate reservoir quality and identify reservoir evolution mechanisms.

Clathrin assemblies at a glance.

Clathrin assembles into honeycomb-like lattices at the plasma membrane but also on internal membranes, such as at the Golgi and tubular endosomes. Clathrin assemblies primarily regulate the intracellular trafficking of different cargoes, but clathrin also has non-endocytic functions in cell adhesion through interactions with specific integrins, contributes to intraluminal vesicle formation by forming flat bilayered coats on endosomes and even assembles on kinetochore k-fibers during mitosis. In this Cell Science at a Glance article and the accompanying poster, we review our current knowledge on the different types of canonical and non-canonical membrane-associated clathrin assemblies in mammalian cells, as observed by thin-section or platinum replica electron microscopy in various cell types, and discuss how the structural plasticity of clathrin contributes to its functional diversity.

First results of electron microscopic study of sandstones of the Salikhovo Formation Vendian (The East-European platform)

For the first time, for the platform Vendian deposits, along with lithological and petrographic methods of studying rocks in sections and quantitative mineralogical analysis of the heavy fraction of concentrate, a study was carried out by scanning electron microscopy in thin sections. The use of scanning electron microscopy made it possible to significantly refine the mineral composition of rock-forming, secondary and accessory minerals. For the first time, it was indicated that the sandstones have their own minerals of rare earth elements (monazite and xenotime) and thorium (torite), and some geochemical features of REE concentrator minerals (apatite and zircon) have been identified. Additional information on the mineral and geochemical composition of the rocks of the Salikhov Formation can be used in the future to reconstruct the composition of the feeding provinces and the conditions for the formation of sedimentary paleobasins.

Detection of Cell Wall-Anchoring Machinery by Immunogold-Labeling Thin-Section Electron Microscopy.

Cell wall anchoring of surface proteins and pili in Gram-positive bacteria is mediated by sortase - a highly conserved transpeptidase enzyme. Early studies have demonstrated the membrane-associated nature of this enzyme in close proximity with its cognate substrates, using immunogold-labeling thin-section electron microscopy. Here, we provide a detail protocol of this methodology, including specimen preparation, ultrathin sectioning, and immunogold-labeling electron microscopic procedures, with an experimental model of sortase enzymes from Actinomyces oris. In principle, this protocol can be employed for any bacterial ultrathin-section samples to detect subcellular localization of proteins and organelles by immuno-electron microscopy.

Inactivating Host Bacteria for Characterization and Use of Phages

Phage characterization for research and therapy can involve newly isolated phages propagated in pathogenic bacteria. If so, characterization requires safety-managing the bacteria. In the current study, we adapt a common and inexpensive reagent, PrimeStore (Longhorn Vaccines and Diagnostics, San Antonio, TX, USA), to safety-manage bacteria in 20 min by selectively inactivating the bacteria. No bacterial survivors are observed among >109 bacteria per ml for a representative of both Gram-negative bacteria (Escherichia coli) and Gram-positive bacteria (Bacillus thuringiensis). This procedure causes no detected inactivation of podophage T3, myophage T4 and siphophage 0105phi7-2. Margins of safety for PrimeStore concentration exist for bacterial inactivation and phage non-inactivation. Thus, general applicability is expected. Subsequent dialysis is used to block long-term effects on phages. Nonetheless, comparable tests should be performed for each pathogenic bacterial strain/phage. Electron microscopy of thin sections reveals inactivation-altered bacterial cytoplasm and a non-disintegrated bacterial envelope (ghosts). Ghosting of E. coli includes re-arrangement of the cytoplasm and the release of endotoxin. The activity of the released endotoxin is >99% reduced after subsequent dialysis, which also removes PrimeStore components. Ghosting of B. thuringiensis includes apparent phase separation within the cytoplasm. The primary application envisaged is biophysical and other screening of phages for therapy of infectious disease.

A New Method for Comprehensive and Quantitative Characterization of Shale Microfractures: A Case Study of the Lacustrine Shale in the Yuanba Area, Northern Sichuan Basin

Microfractures can connect isolated pores within shale, significantly increasing the shale’s storage capacity and permeability, and benefiting shale gas exploitation. Therefore, the quantitative characteristics of microfractures are important parameters for shale reservoir evaluation. In this paper, taking the Jurassic Da’anzhai Member (J1z4) lacustrine shale in the Yuanba area of the northern Sichuan Basin as an example, we propose a method for comprehensive and quantitative characterization of shale microfractures that combines rock thin section (RTS) and scanning electron microscopy (SEM) observations. The different magnifications of RTSs and SEM images lead to the identification and characterization of microfractures of different scales using these two methods. RTSs are mainly used to characterize microfractures with widths larger than 10 μm, while SEM is mainly used to characterize microfractures with widths smaller than 10 μm. These techniques can be combined to comprehensively and quantitatively characterize microfractures of different scales in shale. The microfracture characterization results show that the average total porosity of the J1z4 shale is 4.46%, and the average microfracture surface porosity is 1.20% in the Yuanba area. The calculated average percentage of microfracture porosity to total porosity is 21.09%, indicating that the J1z4 shale reservoir space is dominated by pores and has the conditions for stable shale gas production and potential for shale gas exploration. However, the percentage of microfracture porosity to total porosity of shale near faults and fold zones approaches or exceeds 50%, which may lead to the loss of shale gas. The new method proposed in this study is also useful for quantitative characterization of shale microfractures in the Sichuan Basin and other basins.

EFFECTS OF SHEAR HISTORY ON THE MECHANICAL, ELECTRICAL, AND MICROSTRUCTURAL PROPERTIES OF PARTICLE-REINFORCED RUBBER

ABSTRACT The extent and nature of networks of carbon black particles in rubber compounds play a key role in determining the mechanical hysteresis and conductivity of rubber goods. It is well known that in uncrosslinked compounds, such networks display transient and time-dependent behavior when subjected to steps or ramps in shear and temperature (often called flocculation). This study probes the observed structural recoveries of carbon black networks following various levels of imposed shear strain histories. It is demonstrated that the level of shear experienced by the compound immediately before vulcanization can have a dramatic effect on the final dynamic mechanical properties of the subsequently vulcanized materials. Significant reductions in Payne effect occur when the timescales of shear-induced structural recovery, determined from rheological experiments, exceed the kinetics of vulcanization. Electrical conductivity/resistivity is also affected, especially for compounds formulated in the electrical percolation transition region. Furthermore, the microstructure of carbon black networks is tracked at different extents of recovery by using transmission electron microscopy thin section analysis and atomic force microscopy methodologies for particle network microstructure quantification. Evidence is found that relates flocculation to the progressive relaxation of shear-induced anisotropy of the carbon black micro dispersion.

Impacts of mineralogy and pore structure on spontaneous imbibition in tight glutenite reservoirs

Spontaneous imbibition plays a critical role in the two-phase flow in hydraulic fractures of tight reservoirs. Although massive contributions have been devoted to addressing this issue, very few studies focus on tight glutenite reservoirs, which is an important member of tight reservoirs. As a result, the imbibition mechanism and its influencing factors are still unclear, several key factors fail to be captured, and in-depth analyses are lacking in spontaneous imbibition for tight glutenite reservoirs. In light of the current knowledge gaps, this study conducted a series of water imbibition experiments, combined with X-ray diffraction tests, thin section and scanning electron microscopy observations, high-pressure mercury intrusion experiments, and corrected contact angle experiments to reveal the impacts of rock mineralogy and pore structure on spontaneous imbibition, and significance levels of main influential factors were determined by grey relation analysis. Results show that: 1) the hydrophilic mineral that exceeds 94% provides a strong driving force for water imbibition. Intergranular pore and gravel boost imbibition recovery through enhancing imbibition and drainage ability, respectively. However, intergranular dissolved pore is unfavorable for water imbibition due to extremely rough surface and small radius. Medium-size sand also has a negative impact because of incremental flow tortuosity and pore coordination number reduction; 2) A large percentage of micropore and macropore can significantly enhance imbibition rate and recovery. Three fractal characteristics in micropore, identified for the first time, complicates water imbibition process in tight glutenites. A critical total fractal dimension of micropore is observed, above which the negative influence magnitude of complex pore structure on spontaneous imbibition gradually decreases; 3) Water imbibition sequence and diversities of imbibition phenomena are significantly affected by the combination of multi-fractal dimensions and heterogeneous distributions of pore volume in different fractal regions. The superposition of smallest fractal dimension and the largest pore volume leads to the best imbibition recovery in the transition stage of imbibition, which is an extremely time-consuming process; 4) Upon grey relation analysis, oil drainage ability is the most critical factor for water imbibition in tight glutenites. These observations deepen our understanding of the distinctive imbibition mechanisms in tight glutenite reservoirs.

Multiple geological events controlling rock types development: A case study of Wufeng-Longmaxi formation in southern Sichuan Basin, China

During Late Ordovician to Early Silurian, global geological events such as volcanic activity, glaciation, and mass extinction affected sedimentary environments and organic matter (OM) accumulation, and controlled the development of organic-rich shales. Taking the Wufeng-Longmaxi Formation (WF-L Fm) shales in southern Sichuan Basin as the research object, based on the core, thin section and scanning electron microscopy (SEM) observations, combined with X-ray fluorescence (XRF) two-dimensional element distribution maps, X-ray diffraction (XRD), trace elements, carbon isotope composition and total organic carbon (TOC) data, the relationship between geological events and sedimentary environments, OM accumulation as well as rock types development are analyzed, and the sedimentary environments response to geological events is elaborated. Eight rock types have been identified, and the minerals occurrence model has been characterized. By using Cu content, Mo content, δ13C and TOC to measure paleoproductivity, Sr content and Sr/Cu to judge paleoclimate, Sr/Ba to measure paleosalinity, and U/Th, V/Cr, V/Ni, and Ni/Co to analyze redox conditions, the sedimentary environments of the WF-L Fm shales can be furtherly divided into 7 intervals. In general, the deep water hypoxic-anoxic environments from Interval Ⅰ to Interval Ⅴ is conducive to the formation of organic-rich shales. The organic-rich shales formed in the anoxic environments from Interval Ⅰ to Interval Ⅴ are related to the fact that volcanic activities not only release a large amount of nutrients, promote biological prosperity and improve productivity, but also make the water in a sulfide anoxic environment, which is conducive to the preservation of OM. The rapid rise and fall of sea level caused by the Hirnantian glaciation harmed the living environments of organisms, led to the mass extinctions and provided material sources for OM accumulation, resulting in high TOC in the rock types of Interval IV. Irregular gravity flow can enhance terrigenous input in deep water for a short time and dilute OM, which is one of the reasons for the low TOC in the rock types of Interval Ⅵ to Interval VII. Upwelling current enhances nutrient flux in surface water and improves primary productivity of water, thus affecting the development of WF-L Fm organic-rich shales. Based on the aforementioned interpretations, the sedimentary model of the southern Sichuan Basin was established.

Endothelial cells release microvesicles that harbour multivesicular bodies and secrete exosomes

AbstractExtracellular vesicles (EVs) released by endothelial cells support vascular homeostasis. To better understand endothelial cell EV biogenesis, we examined cultured human umbilical vein endothelial cells (HUVECs) prepared by rapid freezing, freeze‐substitution, and serial thin section electron microscopy (EM). Thin sections of HUVECs revealed clusters of membrane protrusions on the otherwise smooth cell surface. The protrusions contained membrane‐bound organelles, including multivesicular bodies (MVBs), and appeared to be on the verge of pinching off to form microvesicles. Beyond cell peripheries, membrane‐bound vesicles with internal MVBs were observed, and serial sections confirmed that they were not connected to cells. These observations are consistent with the notion that these multi‐compartmented microvesicles (MCMVs) pinch‐off from protrusions. Remarkably, omega figures formed by fusion of vesicles with the MCMV limiting membrane were directly observed, apparently releasing exosomes from the MCMV. In summary, MCMVs are a novel form of EV that bud from membrane protrusions on the HUVEC surface, contain MVBs and release exosomes. These observations suggest that exosomes can be harboured within and released from transiting microvesicles after departure from the parent cell, constituting a new site of exosome biogenesis occurring from endothelial and potentially additional cell types.

Depositional-diagenetic process and their implications for pore development of Wufeng-Longmaxi shales in the Jiangdong block, Fuling shale gas field, SW China

Depositional environment and diagenesis are important factors affecting pore characteristics, whereas how differential depositional and diagenetic processes affect pore development and preservation in shale remains controversial. In this study, based on geochemical analysis, low-temperature gas (including N2 and CO2) physisorption, core observation, thin section and field emission-scanning electron microscopy, the influences of various paleoenvironmental conditions and diagenetic pathways on pore development of the Wufeng and Longmaxi Formations are investigated. The results indicate that paleoenvironmental conditions determine primary mineral composition and content of organic matter, resulting in the various shale lithofacies. Subsequently, minerals in different shale lithofacies experienced various diagenetic events and evolution pathways, finally affecting pore generation and evaluation. Three system tracts, including transgressive systems tract (TST), early highstand systems tract (EHST) and late highstand systems tract (LHST) are identified in the Wufeng and Longmaxi Formations. Siliceous shale, mainly deposited in the TST, contains large amounts of biogenic authigenic quartz and abundant organic matter. Authigenic quartz aggregates effectively inhibit compaction and protect abundant pores. The contents of extrabasinal components increase during the EHST, while biogenic quartz and organic matter decrease to mainly develop mixed shale. Insufficient microcrystalline authentic quartz and high content of clay minerals lead to higher degree of compaction in mixed shale than siliceous shale, resulting in fewer residual pores. In contrast, clay minerals in clay-rich shale, deposited in the LHST, undergo strong compaction and illitization of smectite during diagenesis, resulting in strong deformation and loss of primary pores. As a result, higher amount of OM pores is generated and preserved in the organic-rich siliceous shales from the bottom of Wufeng and Longmaxi Formation, and gradually decreases in the mixed shale, while clay-rich shale in the upper section of the Longmaxi has the lowest amount of pore volume.

Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy

BackgroundSARS-CoV-2 replicates efficiently in the upper airways of humans and produces high loads of virus RNA and, at least in the initial phase after infection, many infectious virus particles. Studying virus ultrastructure, such as particle integrity or presence of spike proteins, and effects on their host cells in patient samples is important to understand the pathogenicity of SARS-CoV-2.MethodsSuspensions from swab samples with a high load of virus RNA (Ct < 20) were sedimented by desktop ultracentrifugation and prepared for thin section electron microscopy using a novel method which is described in detail. Embedding was performed in Epon or in LR White resin using standard or rapid protocols. Thin sections were examined using transmission electron microscopy.ResultsVirus particles could be regularly detected in the extracellular space, embedded in a background of heterogenous material (e.g. vesicles and needle-like crystals), and within ciliated cells. Morphology (i.e. shape, size, spike density) of virus particles in the swab samples was very similar to particle morphology in cell culture. However, in some of the samples the virus particles hardly revealed spikes. Infected ciliated cells occasionally showed replication organelles, such as double-membrane vesicles. The most common cells in all samples were keratinocytes from the mucosa and bacteria.ConclusionsThe new method allows the ultrastructural visualization and analysis of coronavirus particles and of infected host cells from easy to collect naso/oropharyngeal patient swab samples.

Characterization of pore structure and reservoir properties of tight sandstone with CTS, SEM, and HPMI: A case study of the tight oil reservoir in fuyu oil layers of Sanzhao Sag, Songliao basin, NE China

Quantitative characterization of the pore throat structures and reservoir properties of the tight sandstone in Fuyu oil layers of Sanzhao Sag, Songliao Basin, NE China was carried out using cast thin section (CTS), scanning electron microscopy (SEM) and high-pressure mercury intrusion (HPMI) combined with fractal theory. cast thin section and scanning electron microscopy describe the composition, pore filling, cementation, and connectivity of tight sandstones. Six different fractal models, i.e. 2D capillary model, 3D spherical model, 3D capillary model, geometric model, thermodynamic model, and wetting phase model are used to calculate the fractal dimension of pore size distribution using capillary pressure data of high-pressure mercury intrusion, and their correlations with reservoir properties were analyzed. The images of CTS and SEM show that the main lithology of this oil reservoir is tight sandstone, and the pore types are mainly intergranular dissolved pores and intragranular dissolved pores, with uneven pore distribution and poor connectivity. The study of the HPMI data shows that the throat sorting coefficient is the main influencing factor of tight sandstone permeability. The fractal dimensions calculated from the HPMI capillary pressure data using the 3D capillary model and the wetting phase fractal model have the strongest correlations with the reservoir properties compared with the other fractal model. As the fractal dimension increases, the pore throat structures become more heterogenous and reservoir properties become poorer. For the wetting phase fractal model, the calculated fractal dimension is positively correlated with the heterogeneity of the pore throat structure of tight sandstone, which is contrary to the fractal theory and is not suitable for analyzing pore throat structures. The fractal dimensions calculated from the thermodynamic model have no obvious correlations with reservoir properties and cannot quantitatively characterize the heterogeneity of tight sandstone.

Volcanic Origin and Significance of Glauconite Grains in the Upper Cretaceous Austin Chalk Formation in the Balcones Igneous Province, South and Central Texas

Abundant glauconite grains occur in the upper Austin Chalk A and B1 units within the confines of the Balcones Igneous Province (BIP) in the area of the Maverick Basin and San Marcos Arch in Central to South Texas. Controversy exists as to whether the origin of the grains is related to sedimentary hardgrounds or to alteration of volcanic ash and lapilli. The Austin Chalk A and B1 units were deposited contemporaneously with active volcanism (i.e., BIP), and glauconite grains are closely associated with and limited to the area of the BIP. Abundant ash and lapilli are noted near volcanic mounds, where many of these grains are converted to vermiculite and glauconite. It is well established that the BIP pyroclastics underwent alteration in seawater soon after deposition. An unambiguous transition from vermiculite and glauconite-altered volcanic fragments to sand-size glauconite is clearly demonstrated by thin-section and scanning electron microscopy analysis. Grains of glauconite (highly altered ash) deposited away from volcanic mounds have the same origin as those near the mounds. The sand-size glauconite grains can retain internal outlines of gas vesicles and other volcanic microstructures. The misidentification of these volcanic grains as sedimentary-formed glauconite, and not as altered volcanic ash, can lead to misinterpretation of the geologic history and sequence stratigraphy of the upper Austin Chalk section.

Lithofacies identification of shale reservoirs using a tree augmented Bayesian network: A case study of the lower Silurian Longmaxi formation in the changning block, South Sichuan basin, China

As important units for evaluating shale gas reservoirs, lithofacies exert obvious control on the abundance of shale organic matter and the enrichment degree of gas reservoirs. Therefore, it is of great significance to accurately identify the lithofacies of shale reservoirs relative to shale gas exploration and development. This paper takes the Longmaxi Formation shale in the Changning block, Sichuan Basin, China, as an example and uses a tree augmented Bayesian network for the quantitative classification and identification of lithofacies for the first time. First, based on thin section and scanning electron microscopy observations and X-ray diffraction, we can determine the shale lithofacies types of the Longmaxi Formation. Second, the logging response characteristics of different lithofacies were obtained by comparing conventional logging data. Finally, the tree augmented Bayesian network (TAN) was built according to the selected logging parameters and identified unknown lithofacies. The results are as follows: (1) Longmaxi Formation shale is rich in siliceous minerals. By comparing analysis of shale mineral composition and diagenetic characteristics, we divide the lithofacies into five types: siliceous rock, siliceous shale, argillaceous/siliceous mixed shale, calcareous/siliceous mixed shale and calcareous shale. (2) Based on the logging data, 6 logging curves (GR, AC, DEN, CNL, PE and RT) can sensitively indicate diagenesis and changes in mineral content. (3) The TAN model trained by logging information was used to identify 68 shale samples through the 5-fold cross validation method, with an accuracy rate of 95.58%. The results showed that the tree augmented Bayesian network not only can overcome the limitation of interdependence among well-logging properties but also represents an efficient and accurate new method for identifying shale lithofacies. This algorithm can be applied to lithofacies identification of shale reservoirs with only conventional well-logging data, which can help promote the development of lithofacies identification of unconventional oil and gas geology and provides a new method for shale gas reservoir evaluation.

Hydraulic fracturing as unconventional production potential for the organic-rich carbonate reservoir rocks in the Abu El Gharadig Field, north western Desert (Egypt): Evidence from combined organic geochemical, petrophysical and bulk kinetics modeling results

This paper systematically analyzes the organic geochemical, petrophysical, and petrographical properties combined with bulk kinetics modeling of the Abu Roash (F) organic-rich carbonate rocks in the Abu El Gharadig Field. The Abu Roash (F) carbonate-rich samples exhibit high organic content with total organic matter (TOC) values up to 3.04 wt%, and mainly Type II kerogen, with a slight gradient to Type II/III and III kerogens, reaching good to very good oil generation potential. This finding of hydrogen-rich kerogen and oil generation potential was also demonstrated by the abundance of fluorescent alginite, amorphous organic matter (AOM), and bituminite organic matter (OM) as established via ultra violet (UV) light microscopy. The maturity indicators demonstrate that most of the examined Abu Roash (F) carbonate-rich samples from the studied wells, with a deep burial depth of more than 3000 m, are thermally mature, thus defining an early mature to moderate-mature stage. The kinetic models suggest that the Abu Roash (F) carbonate-rich rocks in the deepest burial depth, with calculated vitrinite reflectance (%VRo) values in the range of 0.72–0.83 %, have reached kerogen transformation ratio (TR) in the range of 10–55 %, indicating a high probability of oil production. This finding is confirmed by the presence of the oil crossover in these rocks with an oil saturation index (OSI) of more than 100 mg HC/ g rock. The Abu Roash (F) organic-rich carbonates are intractable rocks as implied by low porosities (up to 2.33 %) and poor permeability in the range of 0.0017–0.0039 mD. The pores in these rocks have a wide range in size, including interparticle, fracture, and organic matter (OM) pores, as recognized in the thin section and scanning electron microscopy (SEM). The development of these pore types and their quality is mainly controlled by high mineralogical brittleness (i.e., carbonates) together with the high OM inputs. Based on the above characteristics, the Abu Roash (F) carbonate-rich rocks in the Abu El Gharadig Field are a candidate for unconventional tight oil reservoir potential, which typically require a form of hydraulic fracturing for possible oil production at deeper burial depths.

Laser-imprinting of micro-3D printed protein hydrogels enables real-time independent modification of substrate topography and elastic modulus

Independent control over the Young's modulus and topography of a hydrogel cell culture substrate is necessary to characterize how attributes of its adherent surface affect cellular responses. Arbitrary, real-time manipulation of these parameters at the micron scale would further provide cellular biologists and bioengineers with the tools to study and control numerous highly dynamic behaviors including cellular adhesion, motility, metastasis, and differentiation. Although physical, chemical, thermal, and light-based strategies have been developed to influence Young's modulus and topography of hydrogel substrates, independent control of these physical attributes has remained elusive, spatial resolution is often limited, and features commonly must be pre-patterned. We recently reported a strategy in which biomaterials having specified three-dimensional (3D) morphologies are micro-3D printed in a two-step process: laser-scanning bioprinting of a protein-based hydrogel, followed by biocompatible hydrogel re-scanning to create microscale imprinted features at user-defined times. In this approach, a pulsed near-infrared laser beam is focused within the printed hydrogel to promote matrix contraction through multiphoton crosslinking, where scanning the laser focus projects a user-defined topographical pattern on the surface without subjecting the hydrogel-solution interface to damaging light intensities. Here, we extend this strategy, demonstrating the ability to decouple dynamic topographical changes from changes in hydrogel Young's modulus at the substrate surface by increasing the isolation distance between the surface and re-scanning planes. Using atomic force microscopy, we show that robust topographic changes can be imposed without altering the Young's modulus measured at the substrate surface by scanning at a depth of greater than ∼6 μm. Transmission electron microscopy of hydrogel thin sections reveals changes to hydrogel porosity and density distribution within scanned regions, and that such changes to the hydrogel matrix are highly localized to regions of laser exposure. These results represent valuable new capabilities for deconvolving the effects of substrate dynamic physical attributes on the behavior of adherent cells.

Understanding carbonates from Saudi Arabia: Laboratory measurements of elastic properties. Part I

Laboratory measurements of elastic properties are presented for carbonate samples from the Saudi Arabian Arab formation. Compressional and shear wave velocities (at 1 MHz) and the quasi-static strains of 37 carbonate rock samples were measured as functions of the saturating fluid and the confining pressure. Furthermore, P- and S-wave velocities of the saturated samples were measured at constant differential pressure of 15 MPa. The lithology, mineralogy, porosity, pore type and pore size distribution of each sample were obtained using a combination of thin section and scanning electron microscopy, helium porosimetry and mercury intrusion porosimetry. The samples showed a high sensitivity to the applied differential pressure especially for the high porosity samples. Due to the lack of closing microcracks and compliant pores in low porosity samples, the travel times show slight changes with the confining pressure whereas the high porosity samples showed a remarkable reduction of the travel time with an increase in confining pressure for both P- and S-waves. We found that the sample physically deformed at pressure above 25 MPa. Evidence of inelastic deformation were observed in a few samples even at a differential pressure of 25 MPa. Both P- and S-wave velocities show a visible deviation with respect to the conventional velocity-porosity inverse relationships, with large variabilities in the velocities at a given porosity. The tight samples only measured a 3% average increase in velocity over the pressure range, whereas the porous samples measured a 20% average increase in velocity over the same pressure range. Despite the nature of porosity, the measured velocities showed a general increase with pressure. Also, all measured samples showed an increase in the bulk modulus of the rock after water saturation with 60% and less than 1% increases. There was no trivial correlation between porosity and the magnitude of the bulk modulus increase. Indeed, the shear modulus of the rock should be insensitive to any changes in water saturation, however, we observed some changes. The presence of anhydrite reduced both P- and S-wave velocities and had a significant influence on the velocities of carbonate rocks at any given porosity. A second paper will build on the results and will consist of predicting and validating suitable rock physics models using the measured carbonate data. The data that support findings of this study are openly available in ERA: Education and Research Archive University of Alberta at https://doi.org/10.7939/R3091B