Determining Macromolecular Structures Using Cryo-Electron Microscopy.

Structural insights into macromolecular and protein complexes provide key clues about the molecular basis of the function. Cryogenic electron microscopy (cryo-EM) has emerged as a powerful structural biology method for studying protein and macromolecular structures at high resolution in both native and near-native states. Despite the ability to get detailed structural insights into the processes underlying protein function using cryo-EM, there has been hesitancy amongst plant biologists to apply the method for biomolecular interaction studies. This is largely evident from the relatively fewer structural depositions of proteins and protein complexes from plant origin in electron microscopy databank. Even though the progress has been slow, cryo-EM has significantly contributed to our understanding of the molecular biology processes underlying photosynthesis, energy transfer in plants, besides viruses infecting plants. This chapter introduces sample preparation for both negative-staining electron microscopy (NSEM) and cryo-EM for plant proteins and macromolecular complexes and data analysis using single particle analysis for beginners.

Repurposing Visible-Light-Excited Ene-Reductases for Diastereo- and Enantioselective Lactones Synthesis.

Repurposing enzymes to catalyze non-natural asymmetric transformations that are difficult to achieve using traditional chemical methods is of significant importance. Although radical C-O bond formation has emerged as a powerful approach for constructing oxygen-containing compounds, controlling the stereochemistry poses a great challenge. Here we present the development of a dual bio-/photo-catalytic system comprising an ene-reductase and an organic dye for achieving stereoselective lactonizations. By integrating directed evolution and photoinduced single electron oxidation, we repurposed engineered ene-reductases to steer non-natural radical C-O formations (one C-O bond for hydrolactonizations and lactonization-alkylations while two C-O bonds for lactonization-oxygenations). This dual catalysis gave a new approach to a diverse array of enantioenhanced 5- and 6-membered lactones with vicinal stereocenters, part of which bears a quaternary stereocenter (up to 99% enantiomeric excess, up to 12.9:1 diastereomeric ratio). Detailed mechanistic studies, including computational simulations, uncovered the synergistic effect of the enzyme and the externally added organophotoredox catalyst Rh6G.

"Invisible" radioactive cesium atoms revealed: Pollucite inclusion in cesium-rich microparticles (CsMPs) from the Fukushima Daiichi Nuclear Power Plant.

Understanding radioactive Cs contamination has been a central issue at Fukushima Daiichi and other nuclear legacy sites; however, atomic-scale characterization of radioactive Cs in environmental samples has never been achieved. Here we report, for the first time, the direct imaging of radioactive Cs atoms using high-resolution high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM). In Cs-rich microparticles collected from Japan, we document inclusions that contain 27 - 36 wt% of Cs (reported as Cs2O) in a zeolite: pollucite. The compositions of three pollucite inclusions are (Cs1.86K0.11Rb0.19Ba0.22)2.4(Fe0.85Zn0.84X0.31)2.0Si4.1O12, (Cs1.19K0.05Rb0.19Ba0.22)1.7(Fe0.66Zn0.32X0.41)1.4Si4.6O12, and (Cs1.27K0.21Rb0.29Ba0.15)1.9(Fe0.60Zn0.32X0.69)1.6Si4.4O12 (X includes other cations). HAADF-STEM imaging of pollucite, viewed along the [111] zone axis, revealed an array of Cs atoms, which is consistent with a simulated image using the multi-slice method. The occurrence of pollucite indicates that locally enriched Cs reacted with siliceous substances during the Fukushima meltdowns, presumably through volatilization and condensation. Beta radiation doses from the incorporated Cs are estimated to reach 106 - 107 Gy, which is more than three orders of magnitude less than typical amorphization dose of zeolite. The atomic-resolution imaging of radioactive Cs is an important advance for better understanding the fate of radioactive Cs inside and outside of nuclear reactors damaged by meltdown events.

A Monte Carlo simulation-based decision support system for radiation oncologists in the treatment of glioblastoma multiforme.

In the present research, we have developed a model-based crisp logic function statistical classifier decision support system supplemented with treatment planning systems for radiation oncologists in the treatment of glioblastoma multiforme (GBM). This system is based on Monte Carlo radiation transport simulation and it recreates visualization of treatment environments on mathematical anthropomorphic brain (MAB) phantoms. Energy deposition within tumour tissue and normal tissues are graded by quality audit factors which ensure planned dose delivery to tumour site thereby minimising damages to healthy tissues. The proposed novel methodology predicts tumour growth response to radiation therapy from a patient-specific medicine quality audit perspective. Validation of the study was achieved by recreating thirty-eight patient-specific mathematical anthropomorphic brain phantoms of treatment environments by taking into consideration density variation and composition of brain tissues. Dose computations accomplished through water phantom, tissue-equivalent head phantoms are neither cost-effective, nor patient-specific customized and is often less accurate. The above-highlighted drawbacks can be overcome by using open-source Electron Gamma Shower (EGSnrc) software and clinical case reports for MAB phantom synthesis which would result in accurate dosimetry with due consideration to the time factors. Considerable dose deviations occur at the tumour site for environments with intraventricular glioblastoma, haematoma, abscess, trapped air and cranial flaps leading to quality factors with a lower logic value of 0. Logic value of 1 depicts higher dose deposition within healthy tissues and also leptomeninges for majority of the environments which results in radiation-induced laceration.

Breakthrough electroneutron multi-response miniature dosimetry/spectrometry in medical accelerator.

Breakthrough multi-response miniature dosimetry/spectrometry of electroneutrons (EN) was made on surface and in-depths of whole-body polyethylene phantom under 10 cm × 10 cm electron beam of 20 MV Varian Clinac 2100C electron medical accelerator commonly applied for prostate treatment. While dosimetry/spectrometry of photoneutrons (PN) has been well characterized for decades, those of ENs lagged behind due to very low EN reaction cross section and lack of sensitive neutron dosimeters/spectrometers meeting neutron dosimetry requirements. Recently, Sohrabi "miniature neutron dosimeter/spectrometer" and "Stripe polycarbonate dosimeter" have broken this barrier and determined seven EN ambient dose equivalent (ENDE) (µSv.Gy-1) responses from electron beam and from albedo ENs including beam thermal (21 ± 2.63), albedo thermal (43 ± 3.70), total thermal (64 ± 6.33), total epithermal (32 ± 3.90), total fast (112.00), total thermal + epithermal (l96 ± 10), and total thermal + epithermal + fast (208 ± 10.23) ENs. Having seven ENDE responses of this study and seven PNDE responses of previous study with the same accelerator obtained at identical conditions by the same principle author provided the opportunity to compare the two sets of responses. The PNDE (µSv.Gy-1) responses have comparatively higher values and 22.60 times at isocenter which provide for the first time breakthrough ENDE responses not yet reported in any studies before worldwide.

Mechanism of Interfacial Molecular Interactions Reveals the Intrinsic Factors for the Highly Enhanced Sensing Performance of Ag-Loaded Co3O4.

The noble metal-loaded strategy can effectively improve the gas-sensing performances of metal oxide sensors. However, the gas-solid interfacial interactions between noble metal-loaded sensing materials and gaseous species remain unclear, posing a significant challenge in correlating the physical and chemical processes during gas sensing. In this study, in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) and in situ Raman spectroscopy were conducted to collaboratively investigate the interfacial interactions involved in the ethanol gas-sensing processes over Co3O4 and Ag-loaded Co3O4 sensors. In situ DRIFTS revealed differences in the compositions and quantities of sensing reaction products, as well as in the adsorption-desorption interactions of surface species, among Co3O4 and Ag-loaded Co3O4 materials. In parallel, in situ Raman spectroscopy demonstrated that the ethanol atmosphere can modulate the electron scattering of Ag-loaded Co3O4 materials but not of raw Co3O4. In situ experimental results revealed the intrinsic reason for the highly enhanced sensing performances of the Ag-loaded Co3O4 sensors toward ethanol gas, including a decreased optimal working temperature (from 250 to 150 °C), an improved gas response level (from 24 to 257), and accelerated gas recovery dynamics. This work provides an effective platform to investigate the interfacial interactions of sensing processes at the molecular level and further advances the development of high-performance gas sensors.

Development of eco-friendly biofilms by utilizing microcrystalline cellulose extract from banana pseudo-stem.

Banana pseudo-stem, often considered as an underutilized plant part was explored as a potential reinforced material to develop an eco-friendly biofilm for food packaging applications. In this study, Microcrystalline cellulose (MCC) was extracted from banana pseudo-stem by alkali and acid hydrolysis treatment. The extracted MCC was used as a reinforced material in different concentrated polyvinyl alcohol (PVA) matrix alone as well as both PVA and Carboxymethyl Cellulose (CMC) matrix to develop biofilm by solvent casting method. The synthesized MCC powder was characterized by scanning electron microscope to ensure its microcrystalline structure and to observe surface morphology. The biofilms composed of MCC, PVA, and CMC were assessed through Fourier-transform infrared spectroscopy (FTIR), mechanical properties, water content, solubility, swelling degree, moisture barrier property (Water Vapor Permeability - WVP), and light barrier property (Light Transmission and Transparency). The FTIR analysis showed the rich bonding between the materials of the biofilms. The film incorporating a combination of PVA, CMC, and MCC (S6) exhibited the highest tensile strength at 26.67 ± 0.152 MPa, making it particularly noteworthy for applications in food packaging. MCC incorporation increased the tensile strength. The WVP content of the films was observed low among the MCC-induced films which is parallel to other findings. The lowest WVP content was showed by 1% concentrated PVA with MCC (S4) (0.223 ± 0.020 10-9 g/Pahm). The WVP content of S6 film was also considerably low. MCC-incorporated films also acted as a good UV barrier. Transmittance of the MCC induced films at UV range were observed on average 38% (S2), 36% (S4) and 6% (S6) which were almost 6% lower than the control films. The S6 film demonstrated the lowest swelling capacity (1.42%) and water content, indicating a significantly low solubility of the film. The film formulated with mixing of PVA, CMC and MCC (S6) was ahead in terms of food packaging characteristics than other films. Also, the outcomes of this study point out that MCC can be a great natural resource for packaging applications and in that regard, banana pseudo-stem proves to be an excellent source for waste utilization.

Crucial roles of soil inherent Fe-bearing minerals in enhanced Cr(VI) reduction by biochar: The electronegativity neutralization and electron transfer mediation.

Biochar has been used for soil Cr(VI) remediation in the last decade due to its enriched redox functional groups and good electrochemical properties. However, the role of soil inherent Fe-bearing minerals during the reduction of Cr(VI) has been largely overlooked. In this study, biochar with different electron-donating capacities (EDCs) was produced at 400 °C (BC400) and 700 °C (BC700), and their performance for Cr(VI) reduction in soils with varied properties (e.g., Fe content) was investigated. The addition of BC400 caused around 14.2-36.0 mg g-1 Cr(VI) reduction after two weeks of incubation in red soil, paddy soil, loess soil, and fluvo-aquic soil, while a less Cr(VI) was reduced by BC700 (2.57-16.7 mg g-1) with smaller EDCs. The Cr(VI) reduction by both biochars in different soils was closely related to Fe content (R2 = 0.93-0.98), so red soil with the richest Fe (14.8% > 1.79-3.49%) showed the best reduction capability, and the removal of soil free Fe oxides (e.g., hematite) resulted in 71.9% decrease of Cr(VI) reduction by BC400. On one hand, Fe-bearing minerals could increase the soil acidity, neutralize the surface negative charge of biochar, enhance the contact between Cr(VI) and biochar, and thus facilitate the direct Cr(VI) reduction by biochar in soils. On the other hand, Fe-bearing minerals could also facilitate the indirect Cr(VI) reduction by mediating the electron from biochar to Cr(VI) with the cyclic transformation of Fe(II)/Fe(III). This study demonstrates the key role of soil Fe-bearing minerals in Cr(VI) reduction by biochar, which advances our understanding on the biochar-based remediation mechanism of Cr(VI)-contaminated soils.

The Effect of Food Polymers (Pectin, Alginate, and Gum Arabic) on Carbonated Drink-Induced Enamel Demineralization: An In Vitro Study.

INTRODUCTION: The increased use of soft drinks leads to a high prevalence of dental erosion (DE), and the use of polymers can decrease tooth demineralization by a carbonated drink. Assessment of the effect of food-approved polymers such as highly esterified pectin (HP), propylene glycol alginate (PGA), and gum arabic (GA) on their efficiency to reduce enamel demineralization on addition with a commercially available carbonated drink was the main objective of this study. MATERIALS AND METHODS: For this study, 300 premolar teeth were studied for enamel erosion and were divided into five groups consisting of 60 samples in each group. The teeth treated with distilled water had negative control, a commercially available carbonated drink with pH 2.7 had positive control, and food polymers were added individually to the carbonated drink in a specified quantity with minimal pH change and were taken as groups A, B, and C, respectively. The enamel erosion that occurred in study groups was measured using a laser fluorescence spectroscopic system with laser excitation at 404 nm at different treatment times (30, 60, and 120 seconds).  Results: Demineralization was less in samples treated with polymer added to carbonated drink solutions compared to samples exposed to plain carbonated drink. As the time of exposure increased up to 120 seconds, a significant decrease in demineralization occurred in polymer-treated groups of samples as against plain carbonated drink with HP showing more decreased demineralization with extended exposure periods compared to other polymers. The surface morphology of tooth samples exhibited the anti-erosive effect of polymers, and the scanning electron microscopic pictures revealed a smoother surface for the polymer-added group. CONCLUSION: This study shows the efficacy of HP, PGA, and GA on reducing the effect of carbonated drink-induced enamel demineralization, and these polymers' addition to drinks can be an innovative way to reduce the demineralization potential of carbonated acidic drinks.

Evaluation of cytotoxicity and adaptability of a novel bioceramic root canal sealer: An in vitro and scanning electron microscope study.

Context: Cytotoxicity and adaptability are among the highly imperative tests that should be performed on a novel endodontic material to ensure its successful implementation in endodontic treatment. Aims: Assess a recently introduced bioceramic root canal sealer CeramoSeal with TotalFill BC and AH plus sealers regarding the cytotoxicity and adaptability. Materials and Methods: Five sealer discs were prepared for each sealer and their extracts were cultured in 96-well plates containing human fibroblasts for 24 h. After their incubation, MTT solution was added to each well plate using an enzyme-linked immunosorbent assay plate reader was implemented to calculate the percentage of viable cells. Thirty mandibular single-rooted premolars were prepared using the Edge Endo rotary system, teeth were divided into three groups (n = 10) based on the sealer type: Group 1 CeramoSeal, Group 2 Totalfill, and Group 3 AH plus sealer. Teeth were sectioned longitudinally and viewed under a scanning electron microscope where the region with the gaps was identified and quantified as a percentage of the root canal's overall area. Statistical Analysis: One-way ANOVA test was used for cytotoxicity, while Kruskal-Wallis and Friedman's tests were used for adaptability. Results: Ceramoseal statistically significantly showed the lowest viability, at high concentrations AH plus showed the highest cell viability, while at lower concentration Totalfill BC sealer showed the highest cell viability percentage. The gap percentages were statistically significantly higher in Ceramoseal group, there was no statistically significant difference between AH Plus and Totalfill groups. Conclusions: Ceramoseal sealer exhibited the lowest viability and highest gap percentage compared to the other sealers.

Bacterial muropeptides promote OXPHOS and suppress mitochondrial stress in mammals.

Mitochondrial dysfunction critically contributes to many major human diseases. The impact of specific gut microbial metabolites on mitochondrial functions of animals and the underlying mechanisms remain to be uncovered. Here, we report a profound role of bacterial peptidoglycan muropeptides in promoting mitochondrial functions in multiple mammalian models. Muropeptide addition to human intestinal epithelial cells (IECs) leads to increased oxidative respiration and ATP production and decreased oxidative stress. Strikingly, muropeptide treatment recovers mitochondrial structure and functions and inhibits several pathological phenotypes of fibroblast cells derived from patients with mitochondrial disease. In mice, muropeptides accumulate in mitochondria of IECs and promote small intestinal homeostasis and nutrient absorption by modulating energy metabolism. Muropeptides directly bind to ATP synthase, stabilize the complex, and promote its enzymatic activity in vitro, supporting the hypothesis that muropeptides promote mitochondria homeostasis at least in part by acting as ATP synthase agonists. This study reveals a potential treatment for human mitochondrial diseases.

X-ray structure and enzymatic study of a bacterial NADPH oxidase highlight the activation mechanism of eukaryotic NOX.

NADPH oxidases (NOX) are transmembrane proteins, widely spread in eukaryotes and prokaryotes, that produce reactive oxygen species (ROS). Eukaryotes use the ROS products for innate immune defense and signaling in critical (patho)physiological processes. Despite the recent structures of human NOX isoforms, the activation of electron transfer remains incompletely understood. SpNOX, a homolog from Streptococcus pneumoniae, can serves as a robust model for exploring electron transfers in the NOX family thanks to its constitutive activity. Crystal structures of SpNOX full-length and dehydrogenase (DH) domain constructs are revealed here. The isolated DH domain acts as a flavin reductase, and both constructs use either NADPH or NADH as substrate. Our findings suggest that hydride transfer from NAD(P)H to FAD is the rate-limiting step in electron transfer. We identify significance of F397 in nicotinamide access to flavin isoalloxazine and confirm flavin binding contributions from both DH and Transmembrane (TM) domains. Comparison with related enzymes suggests that distal access to heme may influence the final electron acceptor, while the relative position of DH and TM does not necessarily correlate with activity, contrary to previous suggestions. It rather suggests requirement of an internal rearrangement, within the DH domain, to switch from a resting to an active state. Thus, SpNOX appears to be a good model of active NOX2, which allows us to propose an explanation for NOX2's requirement for activation.

Electron FLASH radiotherapy in vivo studies. A systematic review.

FLASH-radiotherapy delivers a radiation beam a thousand times faster compared to conventional radiotherapy, reducing radiation damage in healthy tissues with an equivalent tumor response. Although not completely understood, this radiobiological phenomenon has been proved in several animal models with a spectrum of all kinds of particles currently used in contemporary radiotherapy, especially electrons. However, all the research teams have performed FLASH preclinical studies using industrial linear accelerator or LINAC commonly employed in conventional radiotherapy and modified for the delivery of ultra-high-dose-rate (UHDRs). Unfortunately, the delivering and measuring of UHDR beams have been proved not to be completely reliable with such devices. Concerns arise regarding the accuracy of beam monitoring and dosimetry systems. Additionally, this LINAC totally lacks an integrated and dedicated Treatment Planning System (TPS) able to evaluate the internal dose distribution in the case of in vivo experiments. Finally, these devices cannot modify dose-time parameters of the beam relevant to the flash effect, such as average dose rate; dose per pulse; and instantaneous dose rate. This aspect also precludes the exploration of the quantitative relationship with biological phenomena. The dependence on these parameters need to be further investigated. A promising advancement is represented by a new generation of electron LINAC that has successfully overcome some of these technological challenges. In this review, we aim to provide a comprehensive summary of the existing literature on in vivo experiments using electron FLASH radiotherapy and explore the promising clinical perspectives associated with this technology.

Structurally Flexible 2D Spacer for Suppressing the Electron-Phonon Coupling Induced Non-Radiative Decay in Perovskite Solar Cells.

This study presents experimental evidence of the dependence of non-radiative recombination processes on the electron-phonon coupling of perovskite in perovskite solar cells (PSCs). Via A-site cation engineering, a weaker electron-phonon coupling in perovskite has been achieved by introducing the structurally soft cyclohexane methylamine (CMA+) cation, which could serve as a damper to alleviate the mechanical stress caused by lattice oscillations, compared to the rigid phenethyl methylamine (PEA+) analog. It demonstrates a significantly lower non-radiative recombination rate, even though the two types of bulky cations have similar chemical passivation effects on perovskite, which might be explained by the suppressed carrier capture process and improved lattice geometry relaxation. The resulting PSCs achieve an exceptional power conversion efficiency (PCE) of 25.5% with a record-high open-circuit voltage (VOC) of 1.20 V for narrow bandgap perovskite (FAPbI3). The established correlations between electron-phonon coupling and non-radiative decay provide design and screening criteria for more effective passivators for highly efficient PSCs approaching the Shockley-Queisser limit.

Evaluation of layer-by-layer assembly systems for drug delivery and antimicrobial properties in orthopaedic application.

Layer-by-layer self-assembly systems were developed using monolayer and multilayer carriers to prevent infections and improve bone regeneration of porous Ti-6Al-4V scaffolds. These polymeric carriers incorporated (Gel/Alg-IGF-1 + Chi-Cef) and (4Gel/Alg-IGF-1 + Chi-Cef) on the surface of porous implants produced via electron beam melting (EBM). The results showed that the drug release from multilayer carriers was higher than that of monolayers after 14 days. However, the carrier containing Gel/Alg-IGF-1 + Chi-Cef exhibited more sustained behavior. Cell morphology was characterized, revealing that multilayer carriers had higher cell adhesion than monolayers. Additionally, cell differentiation was significantly greater for (Gel/Alg-IGF-1) + Chi-Cef, and (4Gel/Alg-IGF-1) + Chi-Cef multilayer carriers than for the monolayer groups after 7 days. Notably, the drug dosage was effective and did not interfere, and the cell viability assay showed safe results. Antibacterial evaluations demonstrated that both multilayer carriers had a greater effect on Staphylococcus aureus during treatment. The carriers containing lower alginate had notably less effect than the other studied carriers. This study aimed to test systems for controlling drug release, which will be applied to improve MG63 cell behavior and prevent bacterial accumulation during orthopaedic applications.

Structural studies of a serum amyloid A octamer that is primed to scaffold lipid nanodiscs.

Serum amyloid A (SAA) is a highly conserved acute-phase protein that plays roles in activating multiple pro-inflammatory pathways during the acute inflammatory response and is commonly used as a biomarker of inflammation. It has been linked to beneficial roles in tissue repair through improved clearance of lipids and cholesterol from sites of damage. In patients with chronic inflammatory diseases, elevated levels of SAA may contribute to increased severity of the underlying condition. The majority of circulating SAA is bound to lipoproteins, primarily high-density lipoprotein (HDL). Interaction with HDL not only stabilizes SAA but also alters its functional properties, likely through altered accessibility of protein-protein interaction sites on SAA. While high-resolution structures for lipid-free, or apo-, forms of SAA have been reported, their relationship with the HDL-bound form of the protein, and with other possible mechanisms of SAA binding to lipids, has not been established. Here, we have used multiple biophysical techniques, including SAXS, TEM, SEC-MALS, native gel electrophoresis, glutaraldehyde crosslinking, and trypsin digestion to characterize the lipid-free and lipid-bound forms of SAA. The SAXS and TEM data show the presence of soluble octamers of SAA with structural similarity to the ring-like structures reported for lipid-free ApoA-I. These SAA octamers represent a previously uncharacterized structure for lipid-free SAA and are capable of scaffolding lipid nanodiscs with similar morphology to those formed by ApoA-I. The SAA-lipid nanodiscs contain four SAA molecules and have similar exterior dimensions as the lipid-free SAA octamer, suggesting that relatively few conformational rearrangements may be required to allow SAA interactions with lipid-containing particles such as HDL. This study suggests a new model for SAA-lipid interactions and provides new insight into how SAA might stabilize protein-lipid nanodiscs or even replace ApoA-I as a scaffold for HDL particles during inflammation.

Reconstruction of an enigmatic Pennsylvanian cone reveals a relationship to Sphenophyllales.

PREMISE: We studied the 3D morphology of a small, well-preserved cone from the Pennsylvanian Mazon Creek Lagerstätte to characterize its structure and determine its systematic affinity. Previously tentatively assigned to the enigmatic Tetraphyllostrobus, we show that it differs in key respects from that genus as described. METHODS: We systematically compared the new fossil with relevant Paleozoic cone genera and employed advanced imaging techniques, including scanning electron microscopy, Airyscan confocal super-resolution microscopy, optical microscopy, and X-ray microcomputed tomography to visualize and reconstruct the fossil cone in 3D. RESULTS: The analyses demonstrate unequivocally that the sporophylls of the new Mazon Creek cone are arranged in whorls of six and have characters typical of Sphenophyllales, including epidermal cells with undulatory margins and in situ spores assignable to Columinisporites. The combination of characters, including sporophyll arrangement, anatomy, and spore type, supports the establishment of Hexaphyllostrobus kostorhysii gen. et sp. nov. within Sphenophyllales. Furthermore, we show that Tetraphyllostrobus, although originally described as possessing smooth monolete spores, actually possesses Columinisporites-type spores, indicating that it, too, was most likely a sphenophyll. CONCLUSIONS: The recognition of Hexaphyllostrobus contributes to our knowledge of Pennsylvanian sphenophyll diversity, and in particular increases the number of species with in situ Columinisporites-type spores. Attribution of Hexaphyllostrobus to Sphenophyllales calls into question current interpretations of Tetraphyllostrobus suggesting that future research on better-preserved macrofossil material may demonstrate a sphenophyllalean relationship.

KINNTREX: a neural network to unveil protein mechanisms from time-resolved X-ray crystallography.

Here, a machine-learning method based on a kinetically informed neural network (NN) is introduced. The proposed method is designed to analyze a time series of difference electron-density maps from a time-resolved X-ray crystallographic experiment. The method is named KINNTREX (kinetics-informed NN for time-resolved X-ray crystallography). To validate KINNTREX, multiple realistic scenarios were simulated with increasing levels of complexity. For the simulations, time-resolved X-ray data were generated that mimic data collected from the photocycle of the photoactive yellow protein. KINNTREX only requires the number of intermediates and approximate relaxation times (both obtained from a singular valued decomposition) and does not require an assumption of a candidate mechanism. It successfully predicts a consistent chemical kinetic mechanism, together with difference electron-density maps of the intermediates that appear during the reaction. These features make KINNTREX attractive for tackling a wide range of biomolecular questions. In addition, the versatility of KINNTREX can inspire more NN-based applications to time-resolved data from biological macromolecules obtained by other methods.

Unambiguous identification of asymmetric and symmetric synapses using volume electron microscopy.

The brain contains thousands of millions of synapses, exhibiting diverse structural, molecular, and functional characteristics. However, synapses can be classified into two primary morphological types: Gray's type I and type II, corresponding to Colonnier's asymmetric (AS) and symmetric (SS) synapses, respectively. AS and SS have a thick and thin postsynaptic density, respectively. In the cerebral cortex, since most AS are excitatory (glutamatergic), and SS are inhibitory (GABAergic), determining the distribution, size, density, and proportion of the two major cortical types of synapses is critical, not only to better understand synaptic organization in terms of connectivity, but also from a functional perspective. However, several technical challenges complicate the study of synapses. Potassium ferrocyanide has been utilized in recent volume electron microscope studies to enhance electron density in cellular membranes. However, identifying synaptic junctions, especially SS, becomes more challenging as the postsynaptic densities become thinner with increasing concentrations of potassium ferrocyanide. Here we describe a protocol employing Focused Ion Beam Milling and Scanning Electron Microscopy for studying brain tissue. The focus is on the unequivocal identification of AS and SS types. To validate SS observed using this protocol as GABAergic, experiments with immunocytochemistry for the vesicular GABA transporter were conducted on fixed mouse brain tissue sections. This material was processed with different concentrations of potassium ferrocyanide, aiming to determine its optimal concentration. We demonstrate that using a low concentration of potassium ferrocyanide (0.1%) improves membrane visualization while allowing unequivocal identification of synapses as AS or SS.

Electron beam lithography on nonplanar and irregular surfaces.

E-beam lithography is a powerful tool for generating nanostructures and fabricating nanodevices with fine features approaching a few nanometers in size. However, alternative approaches to conventional spin coating and development processes are required to optimize the lithography procedure on irregular surfaces. In this review, we summarize the state of the art in nanofabrication on irregular substrates using e-beam lithography. To overcome these challenges, unconventional methods have been developed. For instance, polymeric and nonpolymeric materials can be sprayed or evaporated to form uniform layers of electron-sensitive materials on irregular substrates. Moreover, chemical bonds can be applied to help form polymer brushes or self-assembled monolayers on these surfaces. In addition, thermal oxides can serve as resists, as the etching rate in solution changes after e-beam exposure. Furthermore, e-beam lithography tools can be combined with cryostages, evaporation systems, and metal deposition chambers for sample development and lift-off while maintaining low temperatures. Metallic nanopyramids can be fabricated on an AFM tip by utilizing ice as a positive resistor. Additionally, Ti/Au caps can be patterned around a carbon nanotube. Moreover, 3D nanostructures can be formed on irregular surfaces by exposing layers of anisole on organic ice surfaces with a focused e-beam. These advances in e-beam lithography on irregular substrates, including uniform film coating, instrumentation improvement, and new pattern transferring method development, substantially extend its capabilities in the fabrication and application of nanoscale structures.