Fold Structures Research Articles

Structural Styles of Thrust Zones of the Urals and Pay-Khoi Foredeep

The article presents an interpretation of geophysical data characterizing the structure of the frontal fold and thrust zones of the Urals and Pay-Khoi, which show the diversity of structural styles of deformations in the study region. The following structural styles of deformations are considered: classical-style thrust zones, which are in-sequence thin-skinned imbrication systems (i); areas of distribution of wedge-shaped allochthons, composed of duplex tectonic plates that are not reflected in the sub-surface layers (ii); inversion zones where faults associated with Ural rifting are transformed into thrust faults (iii); areas whose structure is determined by the deformation of salt diapirs and extrusion of salt (iv); zone, tectonic thickening of the Precambrian complexes overlain by the Paleozoic cover (v). Interpretation of historical and new data on the structure of fold belts makes it possible to significantly update understanding of the structure and development of areas such as zones of wedge-shaped thrusts, areas of development of squeezed salt diapirs, and areas where reactivation and tectonic thickening of Precambrian complexes occurred due to the reactivation of pre-existing faults. New seismic data provided constraints on the magnitude of horizontal displacements in the thrust zones as well as timing of shortening. For the first time they have revealed the development of arrays of small-scale protothrusts.

Molecular functions of the double-sided and inverted ubiquitin-interacting motif found in Xenopus tropicalis cryptochrome 6.

Cryptochromes (CRYs) are multifunctional molecules that act as a circadian clock oscillating factor, a blue-light sensor, and a light-driven magnetoreceptor. Cry genes are classified into several groups based on the evolutionary relationships. Cryptochrome 6 gene (Cry6) is present in invertebrates and lower vertebrates such as amphibians and fishes. Here we identified a Cry6 ortholog in Xenopus tropicalis (XtCry6). XtCRY6 retains a conserved long N-terminal extension (termed CRY N-terminal extension; CNE) that is not found in any CRY in the other groups. A structural prediction suggested that CNE contained unique structures; a tetrahelical fold structure topologically related to KaiA/RbsU domain, overlapping nuclear- and nucleolar-localizing signals (NLS/NoLS), and a novel motif (termed DI-UIM) overlapping a double-sided ubiquitin-interacting motif (DUIM) and an inverted ubiquitin-interacting motif (IUIM). Potential activities of the NLS/NoLS and DI-UIM were examined to infer the molecular function of XtCRY6. GFP-NLS/NoLS fusion protein exogenously expressed in HEK293 cells was mostly observed in the nucleolus, while GFP-XtCRY6 was observed in the cytoplasm. A glutathione S-transferase (GST) pull-down assay suggested that the DI-UIM physically interacts with polyubiquitin. Consistently, protein docking simulations implied that XtCRY6 DI-UIM binds two ubiquitin molecules in a relationship of a twofold rotational symmetry with the symmetry axis parallel or perpendicular to the DI-UIM helix. These results strongly suggested that XtCRY6 does not function as a circadian transcriptional repressor and that it might have another function such as photoreceptive molecule regulating light-dependent protein degradation or gene expression through a CNE-mediated interaction with ubiquitinated proteins in the cytoplasm and/or nucleolus.

Mechanistic Insights into Bioengineered Antibiofilm Enamel Pellicles

Dental caries remains the most widespread chronic disease worldwide. Basically, caries originates within biofilms accumulated on dental enamel. Despite the nonrenewable nature of the enamel tissue, targeted preventive strategies are still very limited. We previously introduced customized multifunctional proteinaceous pellicles (coatings) for controlling bacterial attachment and subsequent biofilm succession. Stemmed from our whole proteome/peptidome analysis of the in vivo acquired enamel pellicle, we designed these pellicles using hybrid mixtures of the most abundant and complementary-acting antimicrobial and antifouling proteins/peptides for synergetic suppression of early biofilms. In conjugating these domains synthetically, their bioinhibitory efficacy was remarkably boosted. Herein, we sought to explore the key structure-function relationship of these potent de novo hybridized conjugates in comparison with their individual domains, solely or in physical mixtures. Specifically, we interrelated the following facets: physicochemical and 3-dimensional folding characteristics via molecular dynamics simulations, adopted secondary structure by circular dichroism, immobilization capacity on enamel through high–spatial resolution multiphoton microscopy, and biofilm suppression potency. Our data showed consistent associations among the increased preference for protein folding structures, α-helix content, and enamel-immobilization capacity; all were inversely correlated with the attached bioburden. The expressed phenotypes could be explained by the adopted strongly amphipathic helical conformation upon conjugation, mediated by the highly anionic and acidic N-terminal pentapeptide shared region/motif for enhanced immobilization on enamel. In conclusion, conjugating bioactive proteins/peptides is a novel translational approach to engineer robust antibiofilm pellicles for caries prevention. The adopted α-helical conformation is key to enhance the antibiofilm efficacy and immobilization capacity on enamel that are promoted by certain physicochemical properties of the constituent domains. These data are valuable for bioengineering versatile therapeutics to prevent/arrest dental caries, a condition that otherwise requires invasive treatments with substantial health care expenditures.

Carbohydrate esterases involved in deacetylation of food components by the human gut microbiota.

Non-carbohydrate modifications such as acetylations are widespread in food stuffs as well as they play important roles in diverse biological processes. These modifications meet the gut environment and are removed from their carbohydrate substrates by the resident microbiota. Among the most abundant modifications are O-acetylations, contributing to polysaccharides physico-chemical properties such as viscosity and gelling ability, as well as reducing accessibility for glycosyl hydrolases, and thus hindering polysaccharide degradation. Of particular note, O-acetylations increase the overall complexity of a polymer, thus requiring a more advanced degrading machinery for microbes to utilize it. This minireview describes acetylesterases from the gut microbiota that deacetylate various food polysaccharides, either as natural components of food, ingredients, stabilizers of microbial origin, or as part of microbes for food and beverage preparations. These enzymes include members belonging to at least 8 families in the CAZy database, as well as a large number of biochemically characterized esterases that have not been classified yet. Despite different structural folds, most of these acetylesterases have a common acid-base mechanism and belong to the SGNH hydrolase superfamily. We highlight examples of acetylesterases that are highly specific to one substrate and to the position of the acetyl group on the glycosyl residue of the carbohydrate, while other members that have more broad substrate specificity. Current research aimed at unveiling the functions and regioselectivity of acetylesterases will help providing fundamental mechanistic understanding on how dietary components are utilized in the human gut and will aid developing applications of these enzymes to manufacture novel industrial products.

Controlling the Supramolecular Polymerization of Squaraine Dyes by a Molecular Chaperone Analogue

Molecular chaperones are proteins that assist in the (un)folding and (dis)assembly of other macromolecular structures toward their biologically functional state in a non-covalent manner. Transferring this concept from nature to artificial self-assembly processes, here, we show a new strategy to control supramolecular polymerization via a chaperone-like two-component system. A new kinetic trapping method was developed that enables efficient retardation of the spontaneous self-assembly of a squaraine dye monomer. The suppression of supramolecular polymerization could be regulated with a cofactor, which precisely initiates self-assembly. The presented system was investigated and characterized by ultraviolet-visible, Fourier transform infrared, and nuclear magnetic resonance spectroscopy, atomic force microscopy, isothermal titration calorimetry, and single-crystal X-ray diffraction. With these results, living supramolecular polymerization and block copolymer fabrication could be realized, demonstrating a new possibility for effective control over supramolecular polymerization processes.

Effect of physiological pH on the molecular characteristics, rheological behavior, and molecular dynamics of κ-carrageenan/casein.

During gastrointestinal digestion, κ-carrageenan (κ-CGN) undergoes physicochemical changes, which associated with the risk of colitis. To understand the effect of physiological pH on the conformational transition and binding stability of κ-CGN and κ-carrageenan/casein (κ-CC), we conducted experiments at pH 3.0 (gastric environment) and pH 7.0 (intestinal environment). We evaluated zeta potential, free sulfate group content, Fourier transform infrared spectroscopy, thermodynamic properties, microstructure, and molecular mechanism. Our results revealed that the helical conformation of κ-CGN and κ-CC were more ordered and stable, and sulfate group exposure both lower in the intestinal environment (pH 7.0). However, in gastric environment (pH 3.0), the charge density of κ-CGN decreased, accompanied by random curling conformation and free sulfate group content increased. In contrast, the intermolecular interactions between κ-CGN and casein increased in gastric acid environments due to casein flocculation and secondary structure folding, and significantly reduced the exposure of free sulfate groups of κ-CGN. Our research results provide an important theoretical basis for elucidating the molecular mechanism and structure-activity relationship of κ-CGN under casein matrix to protect the mucosal barrier and inhibit colitis, and are of great significance for guiding and expanding the safe application of κ-CGN, thus assisting food nutrition to be absorbed.

Front Cover: Protein Backbone Alteration in Non‐Hairpin β‐Turns: Impacts on Tertiary Folded Structure and Folded Stability (ChemBioChem 11/2023)

Backbone modification in β-turns is vital in the development of protein mimetics. Prior work has focused on the subset of turns that join strands of a β-sheet. The cover image, rendered in a style inspired by Pittsburgh native Andy Warhol, depicts four modification schemes among a series examined in a helix-loop-helix domain. Optimal artificial residue placement yields variants of the prototype sequence with native-like tertiary structure and improved thermal stability. More information can be found in the Research Article by T. W. Harmon and W. S. Horne.

Ore Mineralogy and Typomorphism of Native Gold of the Spokoininsky Cluster of the Aldan–Stanovoy Gold Province

The ore mineralogy of a new promising target of the Aldan–Stanovoy gold province—the Spokoininsky cluster—is considered. Gold mineralization is represented by a volumetric, nonlinear type, unconventional for the region; it is related to elements of fold structures and reverse fault in the enclosing metamorphic basement rocks. Vein-disseminated sulfide–(pyrite)–quartz ores build up deposit-like bodies in beresites from gneisses and granite gneisses and are associated with Mesozoic igneous rocks of subalkaline formations. Mineralization is characterized by polysulfide (Fe-Cu-Pb); gold–bismuth (Au-Bi) and gold–silver–telluride (Au-Ag-Te) mineral types. Different mineral types have their own typomorphic minerals and typochemistry (fineness and impurities) of native gold. The widespread distribution of telluride mineralization and its great importance in the formation of gold mineralization on the Aldan shield is confirmed. The distribution area of bismuth (including tellurium–bismuth) mineralization in the southern part of the Aldan shield, in the zone of influence of the Stanovoy deep fault, has been identified.

Thraustochytrid hosts for expression of proteins relevant to SARS-CoV-2 intervention.

The emergence of COVID-19 as a global pandemic had sharply illustrated the limitations of research and development pipelines and scaled manufacturing. Although existing vaccines were created in record time, global deployment remains limited by regional production scales. Similarly, the most effective treatments for infected COVID-19 patients are also constrained by production scales as well as by the cost of production and thus expense per treatment. The need to produce these interventions more cost-effectively, at larger scales, in less time while retaining high quality is paramount. The ConamaxTM platform is based on a Thraustochytrid-an order of microorganisms well established in industry for world-scale production of omega-3 fatty acids by fermentation. Thraustochytrids, and the species Aurantiochytrium acetophilum in particular, possess a number of innate qualities which make it ideal for production of monoclonal antibodies and other biotherapeutic proteins. In this study, the Conamax system was used to produce several targets which may be relevant as interventions in the fight against COVID-19; an anti-SARS-CoV-2 antibody (CR3022), tocilizumab, and the ACE2 receptor. Our system was capable of producing all of these targets and each was assayed in vitro for an activity which confirmed proper structural folding. Purified CR3022 antibody produced from Conamax was capable of reducing the cytopathic effect of SARS-CoV-2. Conamax-derived tocilizumab was shown to bind to its target IL6R. Both the full-length and soluble versions of ACE2 protein produced in the Conamax platform exhibited ACE2-specific proteolytic activity. These data indicate that the Conamax platform has great potential in the production of therapeutic agents.

Chronic edematous-polypous laryngitis (Reinke – Gayek disease) as a cause of hoarseness. Personalized approach to the surgical treatment

Introduction. Chronic edematous-polypous laryngitis, Reinke – Gayek’s edema accounts for 5.5% of all benign diseases of the vocal folds. Surgical treatment of Reinke – Gayek disease consists in removing excess mucosa, or “stripping” – tearing off a strip of mucosa with forceps from the vocal fold. The principle of laryngeal surgery is to preserve the structures of the vocal fold, to obtain flexible vibration of the muscular-membranous part and the mucous membrane of the vocal fold.Purpose. Improving the effectiveness of the treatment of patients with Reinke – Hayek edema by developing sparing methods of surgical treatment using a carbon dioxide laser. To develop criteria for choosing a method of sparing surgical treatment of Reinke – Hayek edema using a carbon dioxide laser, depending on the type of edema according to the Yonekawa classification.Materials and methods. 80 patients with Reinke – Gayek’s disease, 59 women and 21 men, from 29 to 77 years old, divided into two subgroups, and a control group were treated. Preoperative examination included endoscopic examination, laryngostroboscopy. The type was determined according to the H. Yonekawa classification. In type II, subgroup 1 – aspiration technique, n = 30. In type III, subgroup 2 – M-shaped technique, n = 30. Control group, it includes patients with type II and III edema, resection technique, n = 20.Results. Patients in the preoperative period were surveyed with the SF-36 Health Status Survey questionnaire, the dysphonia severity index (DSI), as well as the time of maximum phonation. In the postoperative period, they were examined, 1 month after the operation and 6 months after the operation. There is an increase in indicators, an increase in the time of maximum phonation, an increase in SF-36 scores.Conclusion. The use of this technique made it possible to significantly accelerate the recovery of the voice, reduce the time spent in the hospital, minimally damaging the structure of the mucous membrane of the vocal folds.

Exaptation of Inactivated Host Enzymes for Structural Roles in Orthopoxviruses and Novel Folds of Virus Proteins Revealed by Protein Structure Modeling.

Viruses with large, double-stranded DNA genomes captured the majority of their genes from their hosts at different stages of evolution. The origins of many virus genes are readily detected through significant sequence similarity with cellular homologs. In particular, this is the case for virus enzymes, such as DNA and RNA polymerases or nucleotide kinases, that retain their catalytic activity after capture by an ancestral virus. However, a large fraction of virus genes have no readily detectable cellular homologs, meaning that their origins remain enigmatic. We explored the potential origins of such proteins that are encoded in the genomes of orthopoxviruses, a thoroughly studied virus genus that includes major human pathogens. To this end, we used AlphaFold2 to predict the structures of all 214 proteins that are encoded by orthopoxviruses. Among the proteins of unknown provenance, structure prediction yielded clear indications of origin for 14 of them and validated several inferences that were previously made via sequence analysis. A notable emerging trend is the exaptation of enzymes from cellular organisms for nonenzymatic, structural roles in virus reproduction that is accompanied by the disruption of catalytic sites and by an overall drastic divergence that precludes homology detection at the sequence level. Among the 16 orthopoxvirus proteins that were found to be inactivated enzyme derivatives are the poxvirus replication processivity factor A20, which is an inactivated NAD-dependent DNA ligase; the major core protein A3, which is an inactivated deubiquitinase; F11, which is an inactivated prolyl hydroxylase; and more similar cases. For nearly one-third of the orthopoxvirus virion proteins, no significantly similar structures were identified, suggesting exaptation with subsequent major structural rearrangement that yielded unique protein folds. IMPORTANCE Protein structures are more strongly conserved in evolution than are amino acid sequences. Comparative structural analysis is particularly important for inferring the origins of viral proteins that typically evolve at high rates. We used a powerful protein structure modeling method, namely, AlphaFold2, to model the structures of all orthopoxvirus proteins and compared them to all available protein structures. Multiple cases of recruitment of host enzymes for structural roles in viruses, accompanied by the disruption of catalytic sites, were discovered. However, many viral proteins appear to have evolved unique structural folds.

The effect of novel antihypertensive drug valsartan on lysozyme aggregation: A combined in situ and in silico study

Protein misfolding can result in amyloid fiber aggregation, which is associated with various types of diseases. Therefore, preventing or treating abnormally folded proteins may provide therapeutic intervention for these diseases. Valsartan (VAL) is an angiotensin II receptor blocker (ARB) that is used to treat hypertension. In this study, we examine the anti-aggregating effect of VAL against hen egg-white lysozyme (HEWL) amyloid fibrils through spectroscopy, docking, and microscopic analysis. In vitro formation of HEWL amyloid fibrils was indicated by increased turbidity, RLS (Rayleigh light scattering), and ThT fluorescence intensity. 10 μM VAL, amyloid/aggregation was inhibited up to 83% and 72% as measured by ThT and RLS respectively. In contrast, 100 μM VAL significantly increases the fibril aggregation of HEWL. CD spectroscopy results show a stabilization of HEWL α-helical structures in the presence of 10 μM VAL while the increase in β-sheet was detected at 100 μM concentration of VAL. The hydrophobicity of HEWL was increased at 100 μM VAL, suggesting the promotion of aggregation via its self-association. Steady-state quenching revealed that VAL and HEWL interact spontaneously via hydrogen bonds and van der Waals forces. Transmission electron microscopy (TEM) images illustrate that the needle-like fibers of HEWL amyloid were reduced at 10 μM VAL, while at 100 μM the fibrils of amyloid were increased. Additionally, our computational studies showed that VAL could bind to two binding sites within HEWL. In the BS-1 domain of HEWL, VAL binds to ASN59, ILE98, ILE58, TRP108, VAL109, SER50, ASP52, ASN59, ALA107, and TRP108 residues with a binding energy of −9.72 kcal mol−1. Also, it binds to GLU7, ALA10, ALA11, CYS6, ARG128, and ARG14 in the BS-2 domain with a binding energy of −5.89 kcal mol−1. VAL, therefore, appears to have dual effect against HEWL aggregation. We suggest that VAL stabilizes HEWL's aggregation-prone region (APR) at 10 μM, preventing aggregation. Also, we assume that at 100 μM, VAL occupies BS-2 beside BS-1 and destabilizes the folding structure of HEWL, resulting in aggregation. Further studies are needed to investigate the mechanism of action and determine its potential side effects.

Protein Backbone Alteration in Non-Hairpin β-Turns: Impacts on Tertiary Folded Structure and Folded Stability.

The importance of β-turns to protein folding has motivated extensive efforts to stabilize the motif with non-canonical backbone connectivity. Prior work has focused almost exclusively on turns between strands in a β-sheet (i. e., hairpins). Turns in other structural contexts are also common in nature and have distinct conformational preferences; however, design principles for their mimicry remain poorly understood. Here, we report strategies that stabilize non-hairpin β-turns through systematic evaluation of the impacts of backbone alteration on the high-resolution folded structure and folded stability of a helix-loop-helix prototype protein. Several well-established hairpin turn mimetics are shown detrimental to folded stability and/or hydrophobic core packing, while less-explored modification schemes that reinforce alternate turn types lead to improved stability and more faithful structural mimicry. Collectively, these results have implications in control over protein folding through chemical modification as well as the design of protein mimetics.

Impact of the Dimethyl Sulfoxide Reductase Superfamily on the Evolution of Biogeochemical Cycles.

The dimethyl sulfoxide reductase (or MopB) family is a diverse assemblage of enzymes found throughout Bacteria and Archaea. Many of these enzymes are believed to have been present in the last universal common ancestor (LUCA) of all cellular lineages. However, gaps in knowledge remain about how MopB enzymes evolved and how this diversification of functions impacted global biogeochemical cycles through geologic time. In this study, we perform maximum likelihood phylogenetic analyses on manually curated comparative genomic and metagenomic data sets containing over 47,000 distinct MopB homologs. We demonstrate that these enzymes constitute a catalytically and mechanistically diverse superfamily defined not by the molybdopterin- or tungstopterin-containing [molybdopterin or tungstopterin bis(pyranopterin guanine dinucleotide) (Mo/W-bisPGD)] cofactor but rather by the structural fold that binds it in the protein. Our results suggest that major metabolic innovations were the result of the loss of the metal cofactor or the gain or loss of protein domains. Phylogenetic analyses also demonstrated that formate oxidation and CO2 reduction were the ancestral functions of the superfamily, traits that have been vertically inherited from the LUCA. Nearly all of the other families, which drive all other biogeochemical cycles mediated by this superfamily, originated in the bacterial domain. Thus, organisms from Bacteria have been the key drivers of catalytic and biogeochemical innovations within the superfamily. The relative ordination of MopB families and their associated catalytic activities emphasize fundamental mechanisms of evolution in this superfamily. Furthermore, it underscores the importance of prokaryotic adaptability in response to the transition from an anoxic to an oxidized atmosphere. IMPORTANCE The MopB superfamily constitutes a repertoire of metalloenzymes that are central to enduring mysteries in microbiology, from the origin of life and how microorganisms and biogeochemical cycles have coevolved over deep time to how anaerobic life adapted to increasing concentrations of O2 during the transition from an anoxic to an oxic world. Our work emphasizes that phylogenetic analyses can reveal how domain gain or loss events, the acquisition of novel partner subunits, and the loss of metal cofactors can stimulate novel radiations of enzymes that dramatically increase the catalytic versatility of superfamilies. We also contend that the superfamily concept in protein evolution can uncover surprising kinships between enzymes that have remarkably different catalytic and physiological functions.

Uncovering the folding mechanism of pertactin: A comparative study of isolated and vectorial folding

Autotransporters are a large family of virulence factors found in Gram-negative bacteria that play important roles in their pathogenesis. The passenger domain of autotransporters is almost always composed of a large β-helix, with only a small portion of it being relevant to its virulence function. This has led to the hypothesis that the folding of the β-helical structure aids the secretion of the passenger domain across the Gram-negative outer membrane. In this study, we used molecular dynamics simulations and enhanced sampling methods to investigate the stability and folding of the passenger domain of pertactin, an autotransporter from Bordetella pertussis. Specifically, we employed steered molecular dynamics to simulate the unfolding of the entire passenger domain as well as self-learning adaptive umbrella sampling to compare the energetics of folding rungs of the β-helix independently (“isolated folding”) versus folding rungs on top of a previously folded rung (“vectorial folding”). Our results showed that vectorial folding is highly favorable compared with isolated folding; moreover, our simulations showed that the C-terminal rung of the β-helix is the most resistant to unfolding, in agreement with previous studies that found the C-terminal half of the passenger domain to be more stable than the N-terminal one. Overall, this study provides new insights into the folding process of an autotransporter passenger domain and its potential role in secretion across the outer membrane.

Template-Based Modelling of the Structure of Fungal Effector Proteins

The discovery of new fungal effector proteins is necessary to enable the screening of cultivars for disease resistance. Sequence-based bioinformatics methods have been used for this purpose, but only a limited number of functional effector proteins have been successfully predicted and subsequently validated experimentally. A significant obstacle is that many fungal effector proteins discovered so far lack sequence similarity or conserved sequence motifs. The availability of experimentally determined three-dimensional (3D) structures of a number of effector proteins has recently highlighted structural similarities amongst groups of sequence-dissimilar fungal effectors, enabling the search for similar structural folds amongst effector sequence candidates. We have applied template-based modelling to predict the 3D structures of candidate effector sequences obtained from bioinformatics predictions and the PHI-BASE database. Structural matches were found not only with ToxA- and MAX-like effector candidates but also with non-fungal effector-like proteins—including plant defensins and animal venoms—suggesting the broad conservation of ancestral structural folds amongst cytotoxic peptides from a diverse range of distant species. Accurate modelling of fungal effectors were achieved using RaptorX. The utility of predicted structures of effector proteins lies in the prediction of their interactions with plant receptors through molecular docking, which will improve the understanding of effector–plant interactions.

Flexible SERS strip based on HKUST-1(cu)/biomimetic antibodies composite multilayer for trace determination of ethephon

A surface-enhanced Raman scattering (SERS) sensor based on the folding and assembly characteristics of the three-dimensional structure of paper fibers, the skeleton controllability of metal-organic framework materials (MOFs), and the morphology designability of plasmonic noble metal materials has been established for rapid on-site determination of ethephon in food. HKUST-1(Cu) was assembled onto a carbon-treated chromatographic paper matrix by electrodeposition, and its skeleton respiration and sponge effect were used to overcome the bottleneck problem of poor affinity of SERS substrate for target molecules. Further coupled with the targeted recognition specificity of biomimetic antibodies, a paper-based interface with high specificity of molecular sensitivity was constructed. A sandwich multi-stage progressive enhancement structure was designed to couple plasma pine branch-shaped silver material in situ at the interface to realize superposition and collaborative amplification of SERS signals. When the paper-based strip sensor was used to monitor ethephon, it demonstrated a linear range of 10−3 to 10 mg kg−1 and a detection limit of around 1.39 × 10−4 mg kg−1. The construction and application of the paper-based HKUST-1(Cu)/biomimetic antibodies/pine branch-shaped silver material sensor will provide technical means and theoretical support for the rapid and efficient identification of biological ripening agent residues in food with multi-level signal enhancement.

High-Speed Videoendoscopic and Acoustic Characteristics of Inspiratory Phonation.

Given the importance of inspiratory phonation for assessment of vocal fold structure, the aim of this investigation was to evaluate and describe the vocal fold vibratory characteristics of inspiratory phonation using high-speed videoendoscopy in healthy volunteers. The study also examined the empirical relationship between cepstral peak prominence (CPP) and glottal area waveform measurements derived from simultaneous high-speed videoendoscopy and audio recordings. Vocally healthy adults (33 women, 28 men) volunteered for this investigation and completed high-speed videoendoscopic assessment of vocal fold function for two trials of an expiratory/inspiratory phonation task at normal pitch and normal loudness. Twelve glottal area waveform measures and acoustic CPP values were extracted for analyses. Inspiratory phonation resulted in shorter closing time, longer duration of the opening phase, and faster closing phase velocity compared to expiratory phonation. Sex differences were elucidated. CPP changes for inspiratory phonation were predicted by changes in the glottal area index and waveform symmetry index, whereas changes in CPP during expiratory phonation were predicted by changes in asymmetry quotient, glottal area index, and amplitude periodicity. Vocal fold vibratory differences were identified for inspiratory phonation when compared to expiratory phonation, the latter of which has been studied more extensively. This investigation provides important basic inspiratory phonation data to better understand laryngeal physiology in vivo and provides a basic model from which to further study inspiratory phonation in a larger population representing a broader age range. https://doi.org/10.23641/asha.22223812.

β-Sheet Assembly Translates Conservative Single-Site Mutation into a Perturbation in Macroscopic Structure.

Transferring structural information from amino acid sequence to macroscale assembly is a challenging approach for designing protein quaternary structure. However, the pathway by which the slight variations in sequence result in a global perturbation effect on the assembled structure is unknown. Herein, we design two synthetic peptides, QNL-His and QNL-Arg, with one amino acid substitution and use scanning tunneling microscopy (STM) to image individual peptides in the assembled state. The submolecular resolution of STM enables us to determine the folding structure and β-sheet supramolecular organization of peptides. QNL-His and QNL-Arg differ in their β-strand length distribution in pleated β-sheet association. These structural variations lead to distinguishable outcomes in their β-sheet assembled fibrils and phase transitions. The comparison of QNL-His versus QNL-Arg structures and macroscopic properties unveils the role of assembly to amplify the structural variations associated with a single-site mutation from a single-molecule scale to a macroscopic scale.

Drouetiella epilithica sp. nov. and Drouetiella lurida (Oculatellaceae, Synechococcales) isolated in the Republic of Korea based on the polyphasic approach

SUMMARYFive strains of Drouetiella (ACKU666, 667, 668, 669 and 670) were isolated from gravels in water, stone monument and coastal mudflat in Korea, and were studied using morphological and molecular traits. All five strains had thin and simple trichomes and exhibited false branching. From these strains, four strains (ACKU666, 667, 668 and 669) exhibited similar cell lengths with reddish–brown colored cells such as Drouetiella lurida. The 16S rRNA gene phylogeny showed the four strains formed a clade with Drouetiella lurida, and their DNA similarity was calculated to be 99.1–100%. The color of strain ACKU670 appeared to be in bright blue–green color like Drouetiella fasciculata, and their thylakoids showed a parietal arrangement, which is a characteristic feature of the family Oculatellaceae. Strain ACKU670 turned out to be a sister clade to the D. lurida according to the phylogenetic analysis of the 16S rRNA gene. The 16–23S rRNA internal transcribed spacer secondary folding structure (D1–D1′, Box‐B and V3 helices) confirmed the uniqueness of strain ACKU670, therefore indicating differences from the related species. Considering all the results, we described our strain ACKU670 as Drouetiella epilithica sp. nov. in accordance with the International Code of Nomenclature for Algae, Fungi and Plants.