Light microscopy has been a favorite tool of biological studies for almost a century, recently producing detailed images with exquisite molecular specificity achieving spatial resolution at nanoscale. However, light microscopy is insufficient to provide chemical information as a standalone technique. An increasing amount of evidence demonstrates that optical photothermal infrared microspectroscopy (O-PTIR) is a valuable imaging tool that can extract chemical information to locate molecular structures at submicron resolution. To further investigate the applicability of sub-micron infrared microspectroscopy for biomedical applications, we analyzed the contribution of substrate chemistry to the infrared spectra acquired from individual neurons grown on various imaging substrates. To provide an example of correlative immunofluorescence/O-PTIR imaging, we used immunofluorescence to locate specific organelles for O-PTIR measurement, thus capturing molecular structures at the sub-cellular level directly in cells, which is not possible using traditional infrared microspectroscopy or immunofluorescence microscopy alone.

The transition from terrestrial to marine environments by secondarily aquatic tetrapods necessitates a suite of adaptive changes associated with life in the sea, e.g., the scaleless skin in adult individuals of the extant leatherback turtle. A partial, yet exceptionally preserved hard-shelled (Pan-Cheloniidae) sea turtle with extensive soft-tissue remains, including epidermal scutes and a virtually complete flipper outline, was recently recovered from the Eocene Fur Formation of Denmark. Examination of the fossilized limb tissue revealed an originally soft, wrinkly skin devoid of scales, together with organic residues that contain remnant eumelanin pigment and inferred epidermal transformation products. Notably, this stem cheloniid—unlike its scaly living descendants—combined scaleless limbs with a bony carapace covered in scutes. Our findings show that the adaptive transition to neritic waters by the ancestral pan-chelonioids was more complex than hitherto appreciated, and included at least one evolutionary lineage with a mosaic of integumental features not seen in any living turtle.

Alzheimer’s disease affects millions of lives worldwide. This terminal disease is characterized by the formation of amyloid aggregates, so-called amyloid oligomers. These oligomers are composed of β-sheet structures, which are believed to be neurotoxic. However, the actual secondary structure that contributes most to neurotoxicity remains unknown. This lack of knowledge is due to the challenging nature of characterizing the secondary structure of amyloids in cells. To overcome this and investigate the molecular changes in proteins directly in cells, we used synchrotron-based infrared microspectroscopy, a label-free and non-destructive technique available for in situ molecular imaging, to detect structural changes in proteins and lipids. Specifically, we evaluated the formation of β-sheet structures in different monogenic and bigenic cellular models of Alzheimer’s disease that we generated for this study. We report on the possibility to discern different amyloid signatures directly in cells using infrared microspectroscopy and demonstrate that bigenic (amyloid-β, α-synuclein) and (amyloid-β, Tau) neuron-like cells display changes in β-sheet load. Altogether, our findings support the notion that different molecular mechanisms of amyloid aggregation, as opposed to a common mechanism, are triggered by the specific cellular environment and, therefore, that various mechanisms lead to the development of Alzheimer’s disease.

Alzheimer’s disease (AD) accounts for about 70% of neurodegenerative diseases and is a cause of cognitive decline and death for one-third of seniors. AD is currently underdiagnosed, and it cannot be effectively prevented. Aggregation of amyloid-β (Aβ) proteins has been linked to the development of AD, and it has been established that, under pathological conditions, Aβ proteins undergo structural changes to form β-sheet structures that are considered neurotoxic. Numerous intensive in vitro studies have provided detailed information about amyloid polymorphs; however, little is known on how amyloid β-sheet-enriched aggregates can cause neurotoxicity in relevant settings. We used scattering-type scanning near-field optical microscopy (s-SNOM) to study amyloid structures at the nanoscale, in individual neurons. Specifically, we show that in well-validated systems, s-SNOM can detect amyloid β-sheet structures with nanometer spatial resolution in individual neurons. This is a proof-of-concept study to demonstrate that s-SNOM can be used to detect Aβ-sheet structures on cell surfaces at the nanoscale. Furthermore, this study is intended to raise neurobiologists’ awareness of the potential of s-SNOM as a tool for analyzing amyloid β-sheet structures at the nanoscale in neurons without the need for immunolabeling.

Alzheimer’s disease (AD) is the most common cause of dementia, costing about 1% of the global economy. Failures of clinical trials targeting amyloid-β protein (Aβ), a key trigger of AD, have been explained by drug inefficiency regardless of the mechanisms of amyloid neurotoxicity, which are very difficult to address by available technologies. Here, we combine two imaging modalities that stand at opposite ends of the electromagnetic spectrum, and therefore, can be used as complementary tools to assess structural and chemical information directly in a single neuron. Combining label-free super-resolution microspectroscopy for sub-cellular imaging based on novel optical photothermal infrared (O-PTIR) and synchrotron-based X-ray fluorescence (S-XRF) nano-imaging techniques, we capture elemental distribution and fibrillary forms of amyloid-β proteins in the same neurons at an unprecedented resolution. Our results reveal that in primary AD-like neurons, iron clusters co-localize with elevated amyloid β-sheet structures and oxidized lipids. Overall, our O-PTIR/S-XRF results motivate using high-resolution multimodal microspectroscopic approaches to understand the role of molecular structures and trace elements within a single neuronal cell.

The functionalisation of silicon nanoparticles with a terminal thiocyanate group, producing isothiocyanate-capped silicon nanoparticles (ITC-capped SiNPs) has been successfully attained. The procedure for the synthesis is a two-step process that occurs via thermally induced hydrosilylation of hydrogen terminated silicon nanoparticles (H-SiNPs) and further reaction with potassium thiocyanate (KSCN). The synthesis was confirmed by Fourier transform infrared (FTIR) spectroscopy and X-Ray photoelectron spectroscopy (XPS). At the same time, the internalisation and the cytotoxicity of the ITC-capped SiNPs in vitro were assessed in two cell lines: Caco-2, human colorectal cancer cells and CCD-841, human colon "normal" cells. The results showed that above concentrations of 15 µg ml-1, the cell viability of both cell lines was depleted significantly when treated with ITC SiNPs, particularly over a 48 hour period, to approximately 20% cell viability at the highest treatment concentration (70 µg ml-1). Flow cytometry was employed to determine cellular uptake in Caco-2 cells treated with ITC SiNPs. It was observed that at lower SiNP concentrations, uptake efficiency was significantly improved for time periods under 12 hours; overall it was noted that cellular uptake was positively dependent on the period of incubation and the temperature of incubation. As such, it was concluded that the mechanism of uptake of ITC SiNPs was through endocytosis. Synchrotron FTIR spectroscopy, by means of line spectral analysis and IR imaging, provided further evidence to suggest the internalisation of ITC SiNPs displays a strong localisation, with an affinity for the nucleus of treated Caco-2 cells.

In this study, we investigate the molecular structural characteristics of organic remains in various cellular organelles from a 180 Ma Jurassic royal fern belonging to the Osmundaceae family of ferns, and compare their carbon isotopic compositions to a now-living species of royal fern (Osmunda regalis). We discovered molecular structural variations indicated by Raman and infrared spectral parameters obtained from various fossilized cellular organelles. The organic remains preserved in the chromosomes and cell nuclei show marked structural heterogeneities compared to the cell walls during different stages of the cell cycle. The fossil and extant fern have similar delta C-13 values obtained from bulk samples, supporting evolutionary stasis in this plant lineage and an unchanged metabolic pathway of carbon assimilation since the Jurassic. The organic remains in the cellular organelles of the fossil seem to be less heterogeneous than those in the extant fern, likely due to the preferential preservation of certain cellular compounds during fossilization. Taphonomic processes appear to have diminished the subcellular isotopic heterogeneities. Our research sheds light on the functioning of ancient plant cellular organelles during mitosis, provides insights to the taphonomic processes operating at molecular and isotopic levels, and shows the practicability of in situ techniques in studying the evolution and behaviors of ancient cells.

Ichthyosaurs are extinct marine reptiles that display a notable external similarity to modern toothed whales. Here we show that this resemblance is more than skin deep. We apply a multidisciplinary experimental approach to characterize the cellular and molecular composition of integumental tissues in an exceptionally preserved specimen of the Early Jurassic ichthyosaur Stenopterygius . Our analyses recovered still-flexible remnants of the original scaleless skin, which comprises morphologically distinct epidermal and dermal layers. These are underlain by insulating blubber that would have augmented streamlining, buoyancy and homeothermy. Additionally, we identify endogenous proteinaceous and lipid constituents, together with keratinocytes and branched melanophores that contain eumelanin pigment. Distributional variation of melanophores across the body suggests countershading, possibly enhanced by physiological adjustments of colour to enable photoprotection, concealment and/or thermoregulation. Convergence of ichthyosaurs with extant marine amniotes thus extends to the ultrastructural and molecular levels, reflecting the omnipresent constraints of their shared adaptation to pelagic life.

Aβ is a class of aggregation-prone proteins, which may misfold into stable, β-sheet rich fibrils. Aβ is linked to the development of synaptic pathology in Alzheimer's disease (AD). However, a main question in the AD field is how Aβ contributes to AD neuropathology? Up to now there is little evidence for protein structural changes in diseased neuron. Our aim is to study the distribution of β-sheet structures in AD transgenic neurons in order to uncover sub-cellular mechanism(s) by which amyloid β-sheet structures are involved in AD pathology.

The Ediacaran Doushantuo Formation (DST) is renowned for exceptionally preserved Precambrian fossils including metazoans. Some of these fossils, particularly microfossils such as multicellular algae and acanthomorphic acritarchs, are preserved in DST chert nodules. To better understand the geomicrobiological processes that contributed to the authigenic formation of DST chert nodules and facilitated exceptional fossil preservation, we analyzed organic matter in these chert nodules and the surrounding matrix (calcareous mudstone) using multiple in-situ techniques: confocal laser Raman spectroscopy, micro-Fourier transform infrared spectroscopy (FTIR), and secondary ion mass spectroscopy (SIMS). We found strong ultrastructural, chemical, and isotopic heterogeneities in the organic matter as indicated by the Raman spectral parameter 1-1350/1600 ranging from 0.49 to 0.88, the infrared spectral index R-3/2 from 0.12 to 0.90, and an estimated delta 13C(org-SIMS) range of 44%, (V-PDB). These micron-scale heterogeneities imply that the organic matter preserved in the DST chert nodules is derived from different carbonaceous sources in a diverse microbial ecosystem, including eukaryotic and/or prokaryotic photoautotrophs, as well as chemotrophs involved in the fermentation and probably anaerobic oxidation of organic remains. Thus, the microbial ecosystems in Ediacaran ocean waters and sediments were more complex than previously thought, and these microbial processes controlled dynamic micro-environments in DST sediments where chert nodules were formed and fossils were mineralized. The results also show that variations in the relative abundances, activities, and interactions of co-existing microorganisms in DST sediments may have modulated delta 13C(org), shifts, causing local decoupling between delta 13C(org) and delta 13C(carb) as measured in bulk samples. (C) 2017 Elsevier B.V. All rights reserved.

Reducing levels of the aggregation-prone Aβ peptide that accumulates in the brain with Alzheimer’s disease (AD) has been a major target of experimental therapies. An alternative approach may be to stabilize the physiological conformation of Aβ. To date, the physiological state of Aβ in brain remains unclear, since the available methods used to process brain tissue for determination of Aβ aggregate conformation can in themselves alter the structure and/or composition of the aggregates. Here, using synchrotron-based Fourier transform infrared micro-spectroscopy, non-denaturing gel electrophoresis and conformational specific antibodies we show that the physiological conformations of Aβ and amyloid precursor protein (APP) in brain of transgenic mouse models of AD are altered before formation of amyloid plaques. Furthermore, focal Aβ aggregates in brain that precede amyloid plaque formation localize to synaptic terminals. These changes in the states of Aβ and APP that occur prior to plaque formation may provide novel targets for AD therapy.

The Paleo- and Mesoproterozoic fossil record of multicellular eukaryotes is scarce but extremely important in studying the evolution of life in the Precambrian Era. Typically, fossils heralded as 'multicellular eukaryotes' that are older than the Ediacaran are met with controversy. To confront such debates, we investigate the chemical, isotopic, and molecular structural characteristics of organic matter from carbonaceous compressions in the 1630 Ma Tuanshanzi Formation in northern China, some of the earliest putative macroscopic multicellular eukaryote fossils (Zhu and Chen, 1995). The large-size and relative complexity of these fossils and similar remains from the 1.56 Ga Gaoyuzhuang Formation have led to their interpretation as eukaryotes. Raman spectral parameters give an estimated peak-metamorphic temperature Tmax in the range of 202-286 degrees C, confirming the good preservation of the organic remains. Two-dimensional Raman maps of the carbonaceous compressions show ultrastructural variations that suggest diverse subcellular compounds being consistent with multicellular eukaryotes. The organic matter has carbon isotopic composition delta(13)Corg-sills between -45.3 and -32.2 parts per thousand, and a branching index of carbon chain measured by the micro-FTIR spectral parameter R-3/2 between 0.17 and 0.31. Together with their large-size and morphology, the isotopic, geochemical and ultrastructural data supports an interpretation of the Tuanshanzi Formation carbonaceous compressions as derived from phototrophic, multi cellular eukaryotic algae. Our data support the early evolution of macroscopic multicellular eukaryotes in the sulfidic and low-oxygen conditions that prevailed in the Paleo- and Mesoproterozoic oceans.

The holotype (MHM-K2) of the Eocene cheloniine Tasbacka danica is arguably one of the best preserved juvenile fossil sea turtles on record. Notwithstanding compactional flattening, the specimen is virtually intact, comprising a fully articulated skeleton exposed in dorsal view. MHM-K2 also preserves, with great fidelity, soft tissue traces visible as a sharply delineated carbon film around the bones and marginal scutes along the edge of the carapace. Here we show that the extraordinary preservation of the type of T . danica goes beyond gross morphology to include ultrastructural details and labile molecular components of the once-living animal. Haemoglobin-derived compounds, eumelanic pigments and proteinaceous materials retaining the immunological characteristics of sauropsid-specific β-keratin and tropomyosin were detected in tissues containing remnant melanosomes and decayed keratin plates. The preserved organics represent condensed remains of the cornified epidermis and, likely also, deeper anatomical features, and provide direct chemical evidence that adaptive melanism – a biological means used by extant sea turtle hatchlings to elevate metabolic and growth rates – had evolved 54 million years ago.

Gene sequences form the primary basis for understanding the relationships among extant plant groups, but genetic data are unavailable from fossils to evaluate the affinities of extinct taxa. Here we show that geothermally resistant fossil cuticles of seed-bearing plants, analysed with Fourier transform infrared (FTIR) spectroscopy and hierarchical cluster analysis (HCA), retain biomolecular suites that consistently distinguish major taxa even after experiencing different diagenetic histories. Our results reveal that similarities between the cuticular biochemical signatures of major plant groups (extant and fossil) are mostly consistent with recent phylogenetic hypotheses based on molecular and morphological data. Our novel chemotaxonomic data also support the hypothesis that the extinct Nilssoniales and Bennettitales are closely allied, but only distantly related to Cycadales. The chemical signature of the cuticle of Czekanowskia (Leptostrobales) is strongly similar to that of Ginkgo leaves and supports a close evolutionary relationship between these groups. Finally, our results also reveal that the extinct putative araucariacean, Allocladus, when analysed through HCA, is grouped closer to Ginkgoales than to conifers. Thus, in the absence of modern relatives yielding molecular information, FTIR spectroscopy provides valuable proxy biochemical data complementing morphological characters to distinguish fossil taxa and to help elucidate extinct plant relationships.

After having emerged as primary contenders in the race for highly efficient optoelectronics materials, organolead halide perovskites (OHLP) are now being investigated in the nanoscale regime as promising building blocks with unique properties. For example, unlike their bulk counterpart, quantum dots of OHLP are brightly luminescent, owing to large exciton binding energies that cannot be rationalized solely on the basis of quantum confinement. Here, we establish the direct correlation between the structure and the electronic band-edge properties of CH3NH3PbBr3 nanoparticles. Complementary structural and spectroscopic measurements probing long-range and local order reveal that lattice strain influences the nature of the valence band and modifies the subtle stereochemical activity of the Pb(2+) lone-pair. More generally, this work demonstrates that the stereochemical activity of the lone-pair at the metal site is a specific physicochemical parameter coupled to composition, size and strain, which can be employed to engineer novel functionalities in OHLP nanomaterials.

At the beamline D7 at the MAX III ring at the MAX IV laboratory we have a setup for infrared microspectroscopy which is usable from 30 to 10000 cm(-1). In this project specular reflection infrared microspectroscopy was used for chemical imaging of cross-sectioned urinary stones. to determine their chemical composition and morphology simultaneously. Absorption spectral bands were recovered from reflection spectra by Kramers-Kronig transform. Use of far-infrared radiation provides high-contrast images and allows more precise constituent distribution determinations than mid-infrared because band asymmetry after the transform caused by diffuse reflection is less in the far-infrared.

In-situ wide-angle X-ray scattering (WAXS) measurements have been conducted on atmospheric-pressure fuel-rich premixed freely propagating ethylene/oxygen flames with argon and nitrogen dilution. In this work, a novel analysis methodology able to provide quantitative information on soot/carbon particle species and concentrations was tested under heavy sooting conditions. The particle composition and concentrations were retrieved by fitting theoretical calculations of structural components from major molecular and nanometric species to the experimental WAXS data. The results show that argon dilution yields predominantly graphene-like components that are less stacked and amorphous carbon that is less structured than under nitrogen dilution. This finding was later confirmed by electron microscopy analysis on samples extracted from similar flames. In addition, the WAXS showed that most of the carbon present in the flames was bound as particles. These results constitute some of the first in-situ observations on structures and concentrations of carbon species in laboratory burner flames operating without stabilization plates.

Colour, derived primarily from melanin and/or carotenoid pigments, is integral to many aspects of behaviour in living vertebrates, including social signalling, sexual display and crypsis. Thus, identifying biochromes in extinct animals can shed light on the acquisition and evolution of these biological traits. Both eumelanin and melanin-containing cellular organelles (melanosomes) are preserved in fossils, but recognizing traces of ancient melanin-based coloration is fraught with interpretative ambiguity, especially when observations are based on morphological evidence alone. Assigning microbodies (or, more often reported, their 'mouldic impressions') as melanosome traces without adequately excluding a bacterial origin is also problematic because microbes are pervasive and intimately involved in organismal degradation. Additionally, some forms synthesize melanin. In this review, we survey both vertebrate and microbial melanization, and explore the conflicts influencing assessment of microbodies preserved in association with ancient animal soft tissues. We discuss the types of data used to interpret fossil melanosomes and evaluate whether these are sufficient for definitive diagnosis. Finally, we outline an integrated morphological and geochemical approach for detecting endogenous pigment remains and associated microstructures in multimillion-year-old fossils.

Feathers are amongst the most complex epidermal structures known and they have a well-documented evolutionary trajectory across non-avian dinosaurs and basal birds. Moreover, melanosome-like microbodies preserved in association with fossil plumage have been used to reconstruct original colour, behaviour and physiology. However, these putative ancient melanosomes might alternatively represent microorganismal residues, a conflicting interpretation compounded by a lack of unambiguous chemical data. We therefore used sensitive molecular imaging, supported by multiple independent analytical tests, to demonstrate that the filamentous epidermal appendages in a new specimen of the Jurassic paravian Anchiornis comprise remnant eumelanosomes and fibril-like microstructures, preserved as endogenous eumelanin and authigenic calcium phosphate. These results provide novel insights into the early evolution of feathers at the sub-cellular level and unequivocally determine that melanosomes can be preserved in fossil feathers.

Opaline silica deposits on Mars may be good target sites where organic biosignatures could be preserved. Potential analogues on Earth are provided by ancient cherts containing carbonaceous material (CM) permineralized by silica. In this study, we investigated the ultrastructure and chemical characteristics of CM in the Rhynie chert (c. 410 Ma, UK), Bitter Springs Formation (c. 820 Ma, Australia), and Wumishan Formation (c. 1485 Ma, China). Raman spectroscopy indicates that the CM has experienced advanced diagenesis or low-grade metamorphism at peak metamorphic temperatures of 150-350°C. Raman mapping and micro-Fourier transform infrared (micro-FTIR) spectroscopy were used to document subcellular-scale variation in the CM of fossilized plants, fungi, prokaryotes, and carbonaceous stromatolites. In the Rhynie chert, ultrastructural variation in the CM was found within individual fossils, while in coccoidal and filamentous microfossils of the Bitter Springs and formless CM of the Wumishan stromatolites ultrastructural variation was found between, not within, different microfossils. This heterogeneity cannot be explained by secondary geological processes but supports diverse carbonaceous precursors that experienced differential graphitization. Micro-FTIR analysis found that CM with lower structural order contains more straight carbon chains (has a lower R3/2 branching index) and that the structural order of eukaryotic CM is more heterogeneous than prokaryotic CM. This study demonstrates how Raman spectroscopy combined with micro-FTIR can be used to investigate the origin and preservation of silica-permineralized organics. This approach has good capability for furthering our understanding of CM preserved in Precambrian cherts, and potential biosignatures in siliceous deposits on Mars.