Grape pomace and pecan shell fortified bread: The effect of dietary fiber-phenolic compounds interaction on the in vitro accessibility of phenolic compounds and in vitro glycemic index.

Grape pomace (GP) and pecan shell (PS) are two by-products rich in phenolic compounds (PC), and dietary fiber (DF) that may be considered for the development of functional baked foods. In this study, four formulations with different GP:PS ratios (F1(8%:5%), F2(5%:5%), F3(5%:2%), F4(0%:5%), and control bread (CB)) were elaborated and characterized (physiochemical and phytochemical content). Also, their inner structure (SEM), changes in their FTIR functional group's vibrations, and the bioaccessibility of PC and sugars, including an in vitro glycemic index, were analyzed. Results showed that all GP:PS formulations had higher mineral, protein, DF (total, soluble, and insoluble), and PC content than CB. Additionally, PC and non-starch polysaccharides affected gluten and starch absorbance and pores distribution. In vitro digestion model showed a reduction in the glycemic index for all formulations, compared to CB. These findings highlight the possible health benefits of by-products and their interactions in baked goods.

Cryo-Electron Microscopy in the Study of Antiviral Innate Immunity.

Cryo-electron microscopy is a powerful methodology in structural biology and has been broadly used in high-resolution structure determination for challenging samples, which are not readily available for traditional techniques. In particular, the strength of super macro-complexes and the lack of a need for crystals for cryo-EM make this technique feasible for the structural study of complexes involved in antiviral innate immunity. This chapter presents detailed information and experimental procedures of Cryo-EM for determining the structures of the complexes using STING as an example. The procedures included a sample quality check, high-resolution data acquisition, and image processing for Cryo-EM 3D structure determination.

Colloidal platinum nanoparticles enhance resin-dentin bonding durability.

OBJECTIVES: This study aims to investigate the effect of colloidal platinum nanoparticles (CPN) on the durability of resin-dentin bonding performance with contemporary adhesives. METHODS: Sixty non-carious human maxillary premolars were subjected to microtensile bond strength (µTBS) testing and divided into two main groups: CPN-treated and untreated. Within each group, specimens were randomly allocated to Clearfil Megabond 2 (MB2), Scotchbond Universal Plus Adhesive with self-etch mode (SE-SUP), and etch-and-rinse mode (ER-SUP) subgroups (n = 10/group). CPN was applied to dentin in the MB2 and SE-SUP groups for 20 s, followed by rinsing before adhesive application. In the ER-SUP group, CPN was applied after etch-and-rinse. The µTBS was tested after 24 h, 6 months, and 1 year, and the fracture modes were observed using SEM. The µTBS data were analyzed using a two-way ANOVA and post-hoc Tukey HSD test (α = 0.05). An additional twelve premolars underwent TEM/STEM/EDX for ultra-morphological observations. RESULTS: The application of CPN significantly prevented a decline in the µTBS of both the MB2 and SE-SUP groups. No significant decrease was observed in the ER-SUP group, either with aging or CPN application. Ultra-morphological images revealed platinum nanoparticles attaching to the collagen fibrils of the hybrid layer regardless of aging. It was highlighted that the nanoparticles attached to the banded collagen in the aging groups were observed. SIGNIFICANCE: CPN exhibits the potential in enhancing the longevity of resin-dentin bonding in SE mode.

Analysis and comparison of post-translational modifications of α-synuclein filaments in multiple system atrophy and dementia with Lewy bodies.

Our previous cryogenic electron microscopy (cryoEM) analysis showed that the core structures of α-synuclein filaments accumulated in brains of patients diagnosed with dementia with Lewy bodies (DLB) and multiple system atrophy (MSA) patients are different. We analyzed the post-translational modifications (PTMs) in these filaments , and examined their relationship with the core filament structures and pathological features. Besides the common PTMs in MSA and DLB filaments, acetylation, methylation, oxidation and phosphorylation were frequently detected in MSA filaments, but not in DLB filaments. Furthermore, in DLB filament cases, the processing occurred at the C-terminal side of Asp at 119 residue and Asn at 122 residue, while in MSA cases, the processing occurred at multiple sites between residues 109-123. We have previously reported that PTMs in tau filaments depend on the filament core structure. This was considered to apply to α-synuclein filaments as well. As an example, PTMs including processing sites detected in α-synuclein filaments in early-onset DLB (an atypical form, now named juvenile-onset α-synucleinopathy) brain also supported this idea. These suggests that PTMs appeared to be closely related to the specific filament core structures.

Precise Size Determination of Supported Catalyst Nanoparticles via Generative AI and Scanning Transmission Electron Microscopy.

Transmission electron microscopy (TEM) plays a crucial role in heterogeneous catalysis for assessing the size distribution of supported metal nanoparticles. Typically, nanoparticle size is quantified by measuring the diameter under the assumption of spherical geometry, a simplification that limits the precision needed for advancing synthesis-structure-performance relationships. Currently, there is a lack of techniques that can reliably extract more meaningful information from atomically resolved TEM images, like nuclearity or geometry. Here, cycle-consistent generative adversarial networks (CycleGANs) are explored to bridge experimental and simulated images, directly linking experimental observations with information from their underlying atomic structure. Using the versatile Pt/CeO2 (Pt particles centered ≈2 nm) catalyst synthesized by impregnation, large datasets of experimental scanning transmission electron micrographs and physical image simulations are created to train a CycleGAN. A subsequent size-estimation network is developed to determine the nuclearity of imaged nanoparticles, providing plausible estimates for ≈70% of experimentally observed particles. This automatic approach enables precise size determination of supported nanoparticle-based catalysts overcoming crystal orientation limitations of conventional techniques, promising high accuracy with sufficient training data. Tools like this are envisioned to be of great use in designing and characterizing catalytic materials with improved atomic precision.

Morphological structure of salivary glands, alimentary canal, and Malpighian tubules in adult Eurydema spectabilis Horváth, 1882 (Heteroptera, Pentatomidae).

Eurydema spectabilis (Heteroptera: Pentatomidae) has a piercing-sucking mouth type and feeds on plant sap. In this study, the morphological structure of the salivary glands, alimentary canal, and Malpighian tubules of E. spectabilis was examined using light and scanning electron microscopy. Salivary glands consist of the principal and accessory salivary glands. In E. spectabilis, digestion begins in the mouth and ends in the anus. Alimentary canal is divided into three parts: foregut, midgut, and hindgut. The foregut consists of pharynx, esophagus, and proventriculus. The esophagus connects to the proventriculus and resembles a narrow tube. The wall of the proventriculus has a recessed structure and is surrounded by a single cylindrical layer of epithelium and muscle. The midgut is divided into three regions: the first, second, and third ventricles (V1-V3). V1 and V2 consist of single-layered cylindrical epithelium. V3 contains a single layer of cuboidal epithelium. Gastric caeca were found in the midgut. The hindgut consisted of a pylorus followed by a well-developed rectum. The wall of the rectum consists of a single-layer cuboidal epithelium and muscle. Its lumen contains numerous bacteria and uric acid crystals. The pylorus consists of a single-layered cylindrical epithelium. It is also the origin of Malpighian tubules. Malpighian tubules consist of two regions: proximal and distal. The morphological structure of the salivary glands, alimentary canal, and Malpighian tubules of E. spectabilis, which has not been studied before, was examined and discussed in comparison with other orders. It is also aimed to contribute to future studies. RESEARCH HIGHLIGHTS: In E. spectabilis, the salivary glands are divided into principal and accessory salivary glands. Microvilli and numerous secretory granules were found in Malpighian tubules. Numerous uric acid crystals and bacteria were found in the rectum lumen.

Cassia alata: Helminth and Bacteria Fighter.

INTRODUCTION: The concurrent presence of helminthiasis and bacterial diseases imposes a dual burden, worsening the challenges associated with each condition independently. This cohabitation intensifies the economic impact, creating a compounding effect on public health and economic well-being. METHOD: Phytochemical analysis of Cassia alata Extract (CAE) using infrared spectroscopy has revealed the presence of various functional groups. In addition, GC mass analysis has confirmed the presence of 26 active compounds. An assessment of the anthelmintic activity of CAE against mature earthworms has demonstrated comparable efficacy to the conventional anthelmintic, albendazole. The optimal dosage of 500 mg/ml has induced a rapid onset of paralysis (2.7 ± 0.5 min) and death (20.1 ± 1.7 min), outperforming albendazole (20 mg/mL) in terms of faster paralysis and death times (21.8 ± 1.1 and 30.14 ± 3.2 min, respectively). Structural modifications induced by CAE have been observed through light microscopy and Scanning Electron Microscopy (SEM). Control worms have exhibited normal body architecture, while CAE-treated worms have displayed size reduction, uniform body wall shrinkage, and increased cuticular thickness. Similar alterations have been observed in albendazole-treated worms. RESULTS: The antibacterial activity of CAE has been evaluated through a broth dilution assay, which has revealed a dose-response effect. At 6.25 mg/ml, CAE has exhibited 100% inhibitory action against both Gram-positive and Gram-negative bacteria. Significant differences in bacterial viability have been noted at lower concentrations, with no significant variation at 0.3906 mg/ml of CAE. CONCLUSION: The findings have highlighted the multifaceted bioactivity of CAE, showcasing its potential as an anthelmintic agent and antimicrobial agent against a spectrum of bacterial strains. The observed structural alterations in treated worms have provided insights into the potential mechanisms underlying the anthelmintic effects.

Welcoming Alejandro Buschiazzo, Dorothee Liebschner and Stephen Muench as Co-editors of Acta Crystallographica F - Structural Biology Communications.

The Section Editors welcome and introduce three new Co-editors to the journal and summarize their expertise in computational structural biology, experimental structural biology and cryo-electron microscopy.

Ejectosome of Pectobacterium bacteriophage ΦM1.

Podophages that infect gram-negative bacteria, such as Pectobacterium pathogen ΦM1, encode tail assemblies too short to extend across the complex gram-negative cell wall. To overcome this, podophages encode a large protein complex (ejectosome) packaged inside the viral capsid and correspondingly ejected during infection to form a transient channel that spans the periplasmic space. Here, we describe the ejectosome of bacteriophage ΦM1 to a resolution of 3.32 Å by single-particle cryo-electron microscopy (cryo-EM). The core consists of tetrameric and octameric ejection proteins which form a ∼1.5-MDa ejectosome that must transition through the ∼30 Å aperture created by the short tail nozzle assembly that acts as the conduit for the passage of DNA during infection. The ejectosome forms several grooves into which coils of genomic DNA are fit before the DNA sharply turns and goes down the tunnel and into the portal. In addition, we reconstructed the icosahedral capsid and hybrid tail apparatus to resolutions between 3.04 and 3.23 Å, and note an uncommon fold adopted by the dimerized decoration proteins which further emphasize the structural diversity of podophages. These reconstructions have allowed the generation of a complete atomic model of the ΦM1, uncovering two distinct decoration proteins and highlighting the exquisite structural diversity of tailed bacteriophages.

Obtaining 3D Atomic Reconstructions from Electron Microscopy Images Using a Bayesian Genetic Algorithm: Possibilities, Insights, and Limitations.

The Bayesian genetic algorithm (BGA) is a powerful tool to reconstruct the 3D structure of mono-atomic single-crystalline metallic nanoparticles imaged using annular dark field scanning transmission electron microscopy. The number of atoms in a projected atomic column in the image is used as input to obtain an accurate and atomically precise reconstruction of the nanoparticle, taking prior knowledge and the finite precision of atom counting into account. However, as the number of parameters required to describe a nanoparticle with atomic detail rises quickly with the size of the studied particle, the computational costs of the BGA rise to prohibitively expensive levels. In this study, we investigate these computational costs and propose methods and control parameters for efficient application of the algorithm to nanoparticles of at least up to 10 nm in size.

The effects of environments and adhesive layer thickness on the failure modes of composite material bonded joints.

In this study, a structural adhesive was used to bond unidirectional prepreg and fiber fabric in a single lap joint. The mechanical properties of the structural adhesive were investigated under room temperature dry state (RTD) and elevated temperature wet state (ETW, 71 â„ƒ/85% RH), and different adhesive layer thicknesses (0.5 mm, 1.0 mm, 1.5 mm, and 2.0 mm). The fracture surfaces of the bonded joints were examined using scanning electron microscopy (SEM), and finite element simulations were conducted to observe the failure modes and failure paths. Additionally, the specimens were immersed in water and hydraulic oil, and their tensile shear strength was tested to evaluate their liquid sensitivity. The experimental results indicated that with increasing adhesive layer thickness, the strength of the specimens decreased by 21% in the RTD and by 52% in the ETW. The strength differences between different environments were minimal for adhesive layer thicknesses of 1 mm and 1.5 mm. The shear strength of the specimens decreased after immersion in water and hydraulic oil, with reductions of 43.78% and 39.21%, compared to the room temperature dry respectively. SEM observations of the bonded joint sections revealed that the primary failure modes were adherend failure and adhesive layer failure. Finite element simulations indicated that fiber tearing and crack initiation occurred in stress concentration areas during loading, leading to structural failure.

Unveiling Spatial and Temporal Dynamics of Plasmon-Enhanced Localized Fields in Metallic Nanoframes through Ultrafast Electron Microscopy.

Plasmonic nanomaterials, particularly noble metal nanoframes (NFs), are important for applications such as catalysis, biosensing, and energy harvesting due to their ability to enhance localized electric fields and atomic efficiency via localized surface plasmon resonance (LSPR). Yet the fundamental structure-function relationships and plasmonic dynamics of the NFS are difficult to study experimentally and thus far rely predominately on computational methodologies, limiting their utilization. This study leverages the capabilities of ultrafast electron microscopy (UEM), specifically photon-induced near-field electron microscopy (PINEM), to probe the light-matter interactions within plasmonic NF structures. The effects of shape, size, and plasmonic coupling of Pt@Au core-shell NFs on spatial and temporal characteristics of plasmon-enhanced localized electric fields are explored. Importantly, time-resolved PINEM analysis reveals that the plasmonic fields around hexagonal NF prisms exhibit a spatially dependent excitation and decay rate, indicating a nuanced interplay between the spatial geometry of the NF and the temporal evolution of the localized electric field. These results and observations uncover nanophotonic energy transfer dynamics in NFs and highlight their potential for applications in biosensing and photocatalysis.

Is it really descemetocele? Morphology of extremely thin membrane that remained after severe corneal melting: a case report.

The aim of this study was to report transmission electron microscopic findings of a case with whole corneal descemetocele following infective corneal ulcer for the first time in literature. A 72-year-old male patient presented with infective corneal ulcer. After resolution of the infection, corneoscleral transplantation was performed. The excised very thin corneal membrane was processed for transmission electron microscopic examination. Transmission electron microscopic examination of the specimen revealed many layered structures that consisted of two different types of cells. The first type consisted of lighter staining polygonal cells, while the second consisted of elongated cells with relatively dense staining. All cells were connected with a large number of gap or adherens junctions with intercalation of the cell membranes of adjacent cells. A haphazard distribution of cytoplasmic microfilaments were also observed in all of the cell types. There was no evidence of the presence of endothelial cells throughout the specimen. There was also no evidence of Descemet membrane presence except for a small part adjacent to iris tissue that contained some melanosomes. Although we clinically diagnosed descemetocele, Descemet membrane was not present at the electron microscopic level, and thus, the expression "descemetocele" is inappropriate.

Understanding alpha-synuclein aggregation propensity in animals and humans.

Alpha-synuclein (α-syn) aggregation plays a critical role in the pathogenicity of Parkinson's Disease (PD). This study aims to evaluate the aggregation propensity of α-syn fragment peptides designed using the variability found in humans and animals. Thioflavin T (ThT) and transmission electron microscopy (TEM) were used to validate the formation of fibrils to identify important amino acid residues. Human α-syn fragments 51-75, 37-61, 62-86, 76-100, and 116-140 demonstrate a significantly higher tendency to aggregate compared to fragments 1-25, 26-50, and 91-115. All species analyzed of the α-syn 37-61 and 62-86 regions were shown to form fibrils on both ThT and TEM. The α-syn 37-61 and 62-86 fragment regions exhibited a high susceptibility to aggregation, with fibril formation observed in all species. The A53T mutation in several α-syn 37-61 fragments may enhance their propensity for aggregation, suggesting a correlation between this mutation and the capacity for fibril formation. Furthermore, the presence of the non-amyloid-ß component (NAC) region, specifically in α-syn 62-86, was consistently observed in several fragments that displayed fibril formation, indicating a potential correlation between the NAC region and the process of fibril formation in α-syn. Finally, the combination of a high quantity of valine and a low quantity of acidic amino acids in these fragments may serve as indicators of α-syn fibril formation.

Early prediction of the bactericidal and bacteriostatic effect of imipenem and doxycycline using tabletop scanning electron microscopy.

Introduction: Our work aims at establishing a proof-of-concept for a method that allows the early prediction of the bactericidal and bacteriostatic effects of antibiotics on bacteria using scanning electron microscopy (SEM) as compared to traditional culture-based methods. Methods: We tested these effects using Imipenem (bactericidal) and Doxycycline (bacteriostatic) with several strains of sensitive and resistant Escherichia coli. We developed a SEM-based predictive score based on three main criteria: Bacterial Density, Morphology/Ultrastructure, and Viability. We determined the results for each of these criteria using SEM micrographs taken with the TM4000Plus II-Tabletop-SEM (Hitachi, Japan) following an optimized, rapid, and automated acquisition and analysis protocol. We compared our method with the traditional culture colony counting gold standard method and classic definitions of the two effects. Results: Our method revealed total agreement with the CFU method and classic definition by visualizing the effect of the antibiotic at 60 minutes and 120 minutes using SEM. Discussion: This early prediction allows a rapid and early identification of the bactericidal and bacteriostatic effects as compared to culture that would take a minimum of 18 hours. This has several future applications in the development of SEM-automated assays coupled to machine learning models that identify the antibiotic effect and facilitate determination of bacterial susceptibility.

Ultra-fast Digital DPC Yielding High Spatio-temporal Resolution for Low-Dose Phase Characterization.

In the scanning transmission electron microscope, both phase imaging of beam-sensitive materials and characterization of a material's functional properties using in situ experiments are becoming more widely available. As the practicable scan speed of 4D-STEM detectors improves, so too does the temporal resolution achievable for both differential phase contrast (DPC) and ptychography. However, the read-out burden of pixelated detectors, and the size of the gigabyte to terabyte sized data sets, remain a challenge for both temporal resolution and their practical adoption. In this work, we combine ultra-fast scan coils and detector signal digitization to show that a high-fidelity DPC phase reconstruction can be achieved from an annular segmented detector. Unlike conventional analog data phase reconstructions from digitized DPC-segment images yield reliable data, even at the fastest scan speeds. Finally, dose fractionation by fast scanning and multi-framing allows for postprocess binning of frame streams to balance signal-to-noise ratio and temporal resolution for low-dose phase imaging for in situ experiments.

Effects of cardanol-based phospholipid analogs on Trichomonas vaginalis.

Trichomonas vaginalis is a protist parasite of the urogenital tract, responsible for human trichomoniasis, an infection sexually transmitted that affects approximately 156 million people worldwide. This pathology is more evident in females and can cause miscarriages, premature births, and infertility. The disease can also lead to a greater predisposition to HIV infection and cervical and prostate cancer. Metronidazole (MTZ) is a drug that treats human trichomoniasis. The data from studies involving human subjects are limited regarding MTZ use during pregnancy. In addition to the toxicity of the treatment, some isolates have become resistant to MTZ. Therefore, searching for new compounds active for treating trichomoniasis becomes necessary. In the present study, we report results obtained using new phospholipid analogs. Two cardanol-based compounds designated LDT117 and LDT134 were active against T. vaginalis with an IC50 of 4.58 and 10.24 µM, respectively. These compounds were not toxic to epithelial cells in culture. Scanning electron microscopy observations revealed a rounding of the cells, a shortening of the flagella, and protrusions on the surface of drug-treated cells. Transmission electron microscopy of treated cells revealed alterations in the plasma membrane with formations of blebs, protrusions, depressions, and vacuoles with myelin figures and vacuolization in the cytoplasm after incubation. Furthermore, after treatments with the compounds LDT117 and LDT134, the parasites presented a positive reaction for TUNEL, indicating death by a mechanism like apoptosis. Given the results obtained, further in vivo studies using animal experimental models are necessary to validate that these compounds are effective for treating human trichomoniasis.

Genomic transfer via membrane vesicle: a strategy of giant phage phiKZ for early infection.

During infection, the giant phiKZ phage forms a specialized structure at the center of the host cell called the phage nucleus. This structure is crucial for safeguarding viral DNA against bacterial nucleases and for segregating the transcriptional activities of late genes. Here, we describe a morphological entity, the early phage infection (EPI) vesicle, which appears to be responsible for earlier gene segregation at the beginning of the infection process. Using cryo-electron microscopy, electron tomography (ET), and fluorescence microscopy with membrane-specific dyes, we demonstrated that the EPI vesicle is enclosed in a lipid bilayer originating, apparently, from the inner membrane of the bacterial cell. Our investigations further disclose that the phiKZ EPI vesicle contains both viral DNA and viral RNA polymerase (vRNAP). We have observed that the EPI vesicle migrates from the cell pole to the center of the bacterial cell together with ChmA, the primary protein of the phage nucleus. The phage DNA is transported into the phage nucleus after phage maturation, but the EPI vesicle remains outside. We hypothesized that the EPI vesicle acts as a membrane transport agent, efficiently delivering phage DNA to the phage nucleus while protecting it from the nucleases of the bacterium. IMPORTANCE: Our study shed light on the processes of phage phiKZ early infection stage, expanding our understanding of possible strategies for the development of phage infection. We show that phiKZ virion content during injection is packed inside special membrane structures called early phage infection (EPI) membrane vesicles originating from the bacterial inner cell membrane. We demonstrated the EPI vesicle fulfilled the role of the safety transport unit for the phage genome to the phage nucleus, where the phage DNA would be replicated and protected from bacterial immune systems.

Taxonomic Additions to the Neotropical Subgenus Camponotus (Myrmobrachys) Forel 1912 (Hymenoptera: Formicidae) with Emphasis on the dimorphus-Group.

We provide updated diagnoses for the senex-, burtoni- and dimorphus-groups of Camponotus (Myrmobrachys). Dichotomous keys for the C. (Myrmobrachys) groups and species of the dimorphus-group, based on type-specimens are provided. Two new species of the dimorphus-group are described, Camponotus cameloides sp. nov. and Camponotus hyalus sp. nov. We classified C. dolabratus and C. lancifer as members of the dimorphus-group and C. crassicornis, C. subcircularis, and C. championi as members of the senex-group. Scanning Electron Microscopy was used to describe the branched pilosity of C. cameloides and this is the first description of it for adult workers of Camponotini tribe.

Interpretable Structural Evaluation of Metal-Oxide Nanostructures in Scanning Transmission Electron Microscopy (STEM) Images via Persistent Homology.

Persistent homology is a powerful tool for quantifying various structures, but it is equally crucial to maintain its interpretability. In this study, we extracted interpretable geometric features from the persistent diagrams (PDs) of scanning transmission electron microscopy (STEM) images of self-assembled Pt-CeO2 nanostructures synthesized under different annealing conditions. We focused on PD quadrants and extracted five interpretable features from the zeroth and first PDs of nanostructures ranging from maze-like to striped patterns. A combination of hierarchical clustering and inverse analysis of PDs reconstructed by principal component analysis through vectorization of the PDs highlighted the importance of the number of arc-like structures of the CeO2 phase in the first PDs, particularly those that were smaller than a characteristic size. This descriptor enabled us to quantify the degree of disorder, namely the density of bends, in nanostructures formed under different conditions. By using this descriptor along with the width of the CeO2 phase, we classified 12 Pt-CeO2 nanostructures in an interpretable way.