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Creators/Authors contains: "Firlar, Emre"

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  1. Ferritin is a protein that regulates the iron ions in humans by storing them in the form of iron oxides. Despite extensive efforts to understand the ferritin iron oxide structures, it is still not clear how ferritin proteins with a distinct light (L) and heavy (H) chain subunit ratio impact the biomineralization process. In situ graphene liquid cell-transmission electron microscopy (GLC-TEM) provides an indispensable platform to study the atomic structure of ferritin mineral cores in their native liquid environment. In this study, we report differences in the iron oxide formation in human spleen ferritins (HSFs) and human heart ferritins (HHFs) using in situ GLC-TEM. Scanning transmission electron microscopy (STEM) along with selected area electron diffraction (SAED) of the mineral core and electron energy loss spectroscopy (EELS) analyses enabled the visualization of morphologies, crystal structures and the chemistry of iron oxide cores in HSFs and HHFs. Our study revealed the presence of metastable ferrihydrite (5Fe 2 O 3 ·9H 2 O) as a dominant phase in hydrated HSFs and HHFs, while a stable hematite (α-Fe 2 O 3 ) phase predominated in non-hydrated HSFs and HHFs. In addition, a higher Fe 3+ /Fe 2+ ratio was found in HHFs in comparison with HSFs. This study provides new understanding on iron-oxide phases that exist in hydrated ferritin proteins from different human organs. Such new insights are needed to map ferritin biomineralization pathways and possible correlations with various iron-related disorders in humans. 
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  2. Understanding the biomineralization pathways in living biological species is a grand challenge owing to the difficulties in monitoring the mineralization process at sub-nanometer scales. Here, we monitored the nucleation and growth of magnetosome nanoparticles in bacteria and in real time using a transmission electron microscope (TEM). To enable biomineralization within the bacteria, we subcultured magnetotactic bacteria grown in iron-depleted medium and then mixed them with iron-rich medium within graphene liquid cells (GLCs) right before imaging the bacteria under the microscope. Using in situ electron energy loss spectroscopy (EELS), the oxidation state of iron in the biomineralized magnetosome was analysed to be magnetite with trace amount of hematite. The increase of mass density of biomineralized magnetosomes as a function of incubation time indicated that the bacteria maintained their functionality during the in situ TEM imaging. Our results underpin that GLCs enables a new platform to observe biomineralization events in living biological species at unprecedented spatial resolution. Understanding the biomineralization processes in living organisms facilitates the design of biomimetic materials, and will enable a paradigm shift in understanding the evolution of biological species. 
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  3. Abstract Calcium oxalate (CaOx) is the major phase in kidney stones and the primary calcium storage medium in plants. CaOx can form crystals with different lattice types, water contents, and crystal structures. However, the conditions and mechanisms leading to nucleation of particular CaOx crystals are unclear. Here, liquid‐cell transmission electron microscopy and atomistic molecular dynamics simulations are used to study in situ CaOx nucleation at different conditions. The observations reveal that rhombohedral CaOx monohydrate (COM) can nucleate via a classical pathway, while square COM can nucleate via a non‐classical multiphase pathway. Citrate, a kidney stone inhibitor, increases the solubility of calcium by forming calcium‐citrate complexes and blocks oxalate ions from approaching calcium. The presence of multiple hydrated ionic species draws additional water molecules into nucleating CaOx dihydrate crystals. These findings reveal that by controlling the nucleation pathways one can determine the macroscale crystal structure, hydration state, and morphology of CaOx. 
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