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This report is the outcome of an EFSA procurement (OC/EFSA/GMO/2021/02 – LOT1) aiming at developing an in silico strategy to predict the toxicity of (novel) proteins. Up‐to‐date, commercially available tools predicting protein toxicity based on primary structures were evaluated for their accuracy and usability, using a curated dataset of annotated toxins and non‐toxins from UniProt. ToxinPred2 and Toxify emerged as the top performers, showing both high accuracy and suitability for integration into an automated pipeline. Additional bioinformatics methods were explored, which provide sequence similarity‐based information rather than direct predictions (BLAST, InterPro HMM profiles). By converting their outputs into features for machine learning models, a high prediction accuracy was achieved, though there is potential for improvement to reduce overfitting risks. An Artificial Intelligence (AI)‐based consensus pipeline, integrating results from ToxinPred2, Toxify, and our machine learning models was developed. This consensus model reached a 95% accuracy rate in distinguishing toxins from non‐toxins. Noteworthy, our BLAST‐based machine learning model ‐ although performance‐wise comparable to BLAST ‐ offers higher sensitivity and specificity across diverse queries than BLAST; it relies on database‐based evolutionary relationships, which may significantly limit its applicability to novel or mutated toxins. Structure‐based prediction methods are deemed impractical due to their resource intensity and reliance on accurate structural data; AI‐driven structure prediction methods ‐ like Rosetta and AlphaFold ‐ are promising, however they are still under development and may not be suitable for the regulatory context yet. Recommendations are provided, including enhancement of the proposed consensus pipeline to create an independent open‐source, user‐friendly tool for evaluating the safety of (novel) proteins in food and feed; regular updates of the proposed databases and models; incorporation of 3D structures and in general validation of AI and machine learning models for regulatory uses. [ABSTRACT FROM AUTHOR]

Cytochrome P450 (CYP450) enzymes comprise a highly diverse superfamily of heme-thiolate proteins that responsible for catalyzing over 90 % of enzymatic reactions associated with xenobiotic metabolism in humans. Accurately predicting whether chemicals are substrates or inhibitors of different CYP450 isoforms can aid in pre-selecting hit compounds for the drug discovery process, chemical toxicology studies, and patients treatment planning. In this work, we investigated in silico studies on CYP450s specificity over past twenty years, categorizing these studies into structure-based and ligand-based approaches. Subsequently, we utilized 100 of the most frequently prescribed drugs to test eleven machine learning-based prediction models which were published between 2015 and 2024. We analyzed various aspects of the evaluated models, such as their datasets, algorithms, and performance. This will give readers with a comprehensive overview of these prediction models and help them choose the most suitable one to do prediction. We also provide our insights for future research trend in both structure-based and ligand-based approaches in this field., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.)

The activity of sirtuin 1 (SIRT1, a member of the NAD + -dependent deacetylases family) decreases during aging as NAD + levels naturally decline, thus increasing the risk of several age-associated diseases. Several sirtuin-activating compounds (STACs) have been developed to counteract the age-associated reduction in SIRT1 activity, and some of them are currently under development in clinical trials. STACs induce SIRT1 activation, either through allosteric activation of the enzyme in the presence of NAD + , or by increasing NAD + levels by inhibiting its degradation or by supplying a key precursor in biosynthesis. In this study, we have identified (E)-2'-des-methyl sulindac analogues as a novel class of STACs that act also in the absence of NAD + , a peculiar behavior demonstrated through enzymatic and mass spectrometry experiments, both in vitro and in cell lines. The activation of the SIRT1 pathway was confirmed in vivo through gene expression and metabolomics analysis. Our data suggest that these compounds could serve as candidate leads for a novel therapeutic strategy aimed at addressing a key metabolic deficiency that may contribute to metabolic and age-associated diseases., Competing Interests: Declaration of Competing Interest The authors declare that they have no conflict of interest., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The Organic Cation Transporter Novel 1 (OCTN1), also known as SLC22A4, is widely expressed in various human tissues, and involved in numerous physiological and pathological processes remains. It facilitates the transport of organic cations, zwitterions, with selectivity for positively charged solutes. Ergothioneine, an antioxidant compound, and acetylcholine (Ach) are among its substrates. Given the lack of experimentally solved structures of this protein, this study aimed at generating a reliable 3D model of OCTN1 to shed light on its substrate-binding preferences and the role of sodium in substrate recognition and transport. A chimeric model was built by grafting the large extracellular loop 1 (EL1) from an AlphaFold-generated model onto a homology model. Molecular dynamics simulations revealed domain-specific mobility, with EL1 exhibiting the highest impact on overall stability. Molecular docking simulations identified cytarabine and verapamil as highest affinity ligands, consistent with their known inhibitory effects on OCTN1. Furthermore, MM/GBSA analysis allowed the categorization of substrates into weak, good, and strong binders, with molecular weight strongly correlating with binding affinity to the recognition site. Key recognition residues, including Tyr211, Glu381, and Arg469, were identified through interaction analysis. Ach demonstrated a low interaction energy, supporting the hypothesis of its one-directional transport towards to outside of the membrane. Regarding the role of sodium, our model suggested the involvement of Glu381 in sodium binding. Molecular dynamics simulations of systems at increasing levels of Na+ concentrations revealed increased sodium occupancy around Glu381, supporting experimental data associating Na+ concentration to molecule transport. In conclusion, this study provides valuable insights into the 3D structure of OCTN1, its substrate-binding preferences, and the role of sodium in the recognition. These findings contribute to the understanding of OCTN1 involvement in various physiological and pathological processes and may have implications for drug development and disease management., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Mariem et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Angiopoietin-like protein 3 (ANGPTL3) is a plasmatic protein that plays a crucial role in lipoprotein metabolism by inhibiting the lipoprotein lipase (LPL) and the endothelial lipase (EL) responsible for the hydrolysis of phospholipids on high-density lipoprotein (HDL). Interest in developing new pharmacological therapies aimed at inhibiting ANGPTL3 has been growing due to the hypolipidemic and antiatherogenic profile observed in its absence. The goal of this study was the in silico characterization of the interaction between ANGPTL3 and EL. Because of the lack of any structural information on both the trimeric coiled-coil N-terminal domain of ANGPTL3 and the EL homodimer as well as data regarding their interactions, the first step was to obtain the three-dimensional model of these two proteins. The models were then refined via molecular dynamics (MD) simulations and used to investigate the interaction mechanism. The analysis of interactions in different docking poses and their refinement via MD allowed the identification of three specific glutamates of ANGPTL3 that recognize a positively charged patch on the surface of EL. These ANGPTL3 key residues, i.e., Glu154, Glu157, and Glu160, could form a putative molecular recognition site for EL. This study paves the way for future investigations aimed at confirming the recognition site and at designing novel inhibitors of ANGPTL3.

Innervation of the hypothalamic median eminence by Gonadotropin-Releasing Hormone (GnRH) neurons is vital to ensure puberty onset and successful reproduction. However, the molecular and cellular mechanisms underlying median eminence development and pubertal timing are incompletely understood. Here we show that Semaphorin-6A is strongly expressed by median eminence-resident oligodendrocytes positioned adjacent to GnRH neuron projections and fenestrated capillaries, and that Semaphorin-6A is required for GnRH neuron innervation and puberty onset. In vitro and in vivo experiments reveal an unexpected function for Semaphorin-6A, via its receptor Plexin-A2, in the control of median eminence vascular permeability to maintain neuroendocrine homeostasis. To support the significance of these findings in humans, we identify patients with delayed puberty carrying a novel pathogenic variant of SEMA6A. In all, our data reveal a role for Semaphorin-6A in regulating GnRH neuron patterning by tuning the median eminence vascular barrier and thereby controlling puberty onset., (© 2023. The Author(s).)

Since the 1980s, it has been known that the administration of ganglioside GM1 to cultured cells induced or enhanced neuronal differentiation. GM1 mechanism of action relies on its direct interaction and subsequent activation of the membrane tyrosine kinase receptor, TrkA, which naturally serves as NGF receptor. This process is mediated by the sole oligosaccharide portion of GM1, the pentasaccharide β-Gal-(1-3)-β-GalNAc-(1-4)-[α-Neu5Ac-(2-3)]-β-Gal-(1-4)-β-Glc. Here we detailed the minimum structural requirements of the oligosaccharide portion of GM1 for mediating the TrkA dependent neuritogenic processing. By in vitro and in silico biochemical approaches, we demonstrated that the minimal portion of GM1 required for the TrkA activation is the inner core of the ganglioside's oligosaccharide β-Gal-(1-3)-β-GalNAc-(1-4)-[α-Neu5Ac-(2-3)]-β-Gal. The addition of a sialic acid residue at position 3 of the outer galactose of the GM1 oligosaccharide, which forms the oligosaccharide of GD1a, prevented the interaction with TrkA and the resulting neuritogenesis. On the contrary, the addition of a fucose residue at position 2 of the outer galactose, forming the Fucosyl-GM1 oligosaccharide, did not prevent the TrkA-mediated neuritogenesis., (© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Aim: The effect of liposomes bi-functionalized with phosphatidic acid and with a synthetic peptide derived from human apolipoprotein E has been evaluated on the aggregation features of different amyloidogenic proteins: human Amyloid β1-40 (Aβ 1-40 ), transthyretin (TTR) variant S52P, human β2microglobulin (β2m) variants ΔN6 and D76N, Serum Amyloid A (SAA)., Methods: The formation of fibrillar aggregates of the proteins was investigated by ThioflavinT fluorescence assay and validated by Atomic Force Microscopy., Results: The results show that liposomes are preventing the transition of non-aggregated forms to the fibrillar state, with stronger effects on Aβ 1-40 , β2m ΔN6 and SAA. Liposomes also induce disaggregation of the amyloid aggregates of all the proteins investigated, with stronger effects on Aβ 1-40 , β2 D76N and TTR.SPR assays show that liposomes bind Aβ 1-40 and SAA aggregates with high affinity (KD in the nanomolar range) whereas binding to TTR aggregates showed a lower affinity (KD in the micromolar range). Aggregates of β2m variants showed both high and low affinity binding sites. Computed Structural analysis of protein fibrillar aggregates and considerations on the multidentate features of liposomes allow to speculate a common mechanism of action, based on binding the β-stranded peptide regions responsible for the amyloid formation., Conclusion: Thus, multifunctional liposomes perform as pharmacological chaperones with anti-amyloidogenic activity, with a promising potential for the treatment of a number of protein-misfolding diseases.Key messageAmyloidosis is a group of diseases, each due to a specific protein misfolding.Anti-amyloidogenic nanoparticles have been gaining the utmost importance as a potential treatment for protein misfolding disorders.Liposomes bi-functionalized with phosphatidic acid and with a synthetic peptide derived from human apolipoprotein E showed anti-amyloidogenic activity.

Discrimination against and negative beliefs about large-bodied individuals, known as weight stigma, is pervasive and harmful. While previous research has focused on the negative consequences of weight stigma, the present study aims to highlight the lived experience of large-bodied individuals while also exploring the process of healing from harmful experiences of weight stigma. Ten adult (9/10 White, 8/10 cisgender women), large-bodied individuals recruited via snowball sampling through a nonprofit, grassroots, eating disorder advocacy organization participated in a 10-week, counselor-facilitated support group with the shared goal of healing from the impact of weight stigma. Researchers used reflexive thematic analysis to analyze video recordings and transcripts of group sessions to answer the following question: how did participants make sense of their weight stigma experiences and engage with the process of healing in community? Four primary themes were generated: (a) Community is Essential, (b) Storying, (c) Deprogramming and Changing Mindset, and (d) Expansive Healing. These results underscore the impact of weight stigma in the lives of large-bodied individuals and provide insight into how clinicians might support such individuals engaging in collective healing from these painful experiences. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

Purpose: RPH3A encodes a protein involved in the stabilization of GluN2A subunit of N-methyl-D-aspartate (NMDA)-type glutamate receptors at the cell surface, forming a complex essential for synaptic plasticity and cognition. We investigated the effect of variants in RPH3A in patients with neurodevelopmental disorders., Methods: By using trio-based exome sequencing, GeneMatcher, and screening of 100,000 Genomes Project data, we identified 6 heterozygous variants in RPH3A. In silico and in vitro models, including rat hippocampal neuronal cultures, have been used to characterize the effect of the variants., Results: Four cases had a neurodevelopmental disorder with untreatable epileptic seizures [p.(Gln73His)dn; p.(Arg209Lys); p.(Thr450Ser)dn; p.(Gln508His)], and 2 cases [p.(Arg235Ser); p.(Asn618Ser)dn] showed high-functioning autism spectrum disorder. Using neuronal cultures, we demonstrated that p.(Thr450Ser) and p.(Asn618Ser) reduce the synaptic localization of GluN2A; p.(Thr450Ser) also increased the surface levels of GluN2A. Electrophysiological recordings showed increased GluN2A-dependent NMDA ionotropic glutamate receptor currents for both variants and alteration of postsynaptic calcium levels. Finally, expression of the Rph3A Thr450Ser variant in neurons affected dendritic spine morphology., Conclusion: Overall, we provide evidence that missense gain-of-function variants in RPH3A increase GluN2A-containing NMDA ionotropic glutamate receptors at extrasynaptic sites, altering synaptic function and leading to a clinically variable neurodevelopmental presentation ranging from untreatable epilepsy to autism spectrum disorder., Competing Interests: Conflict of Interest The authors declare no conflicts of interest., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Riboflavin is an essential water-soluble vitamin that needs to be provided through the diet because of the conversion into flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN), important cofactors in hundreds of flavoenzymes. The adsorption and distribution of riboflavin is mediated by transmembrane transporters of the SLC52 family, namely RFVT1-3, whose mutations are mainly associated with two diseases, MADD and the Brown-Vialetto-Van Laere syndrome. Interest in RFVTs as pharmacological targets has increased in the last few years due to their overexpression in several cancer cells, which can be exploited both by blocking the uptake of riboflavin into the cancerous cells, and by performing cancer targeted delivery of drugs with a high affinity for RFVTs. In this work, we propose three-dimensional structural models for all three human riboflavin transporters obtained by state-of-the-art artificial intelligence-based methods, which were then further refined with molecular dynamics simulations. Furthermore, two of the most notable mutations concerning RFVT2 and RFVT3 (W31S and N21S, respectively) were investigated studying the interactions between the wild-type and mutated transporters with riboflavin., (© 2022 Wiley Periodicals LLC.)

N-glycosylation plays a key role in modulating the bioactivity of monoclonal antibodies (mAbs), as well as the light chain (LC) isotype can influence their physicochemical properties. However, investigating the impact of such features on mAbs conformational behavior is a big challenge, due to the very high flexibility of these biomolecules. In this work we investigate, by accelerated molecular dynamics (aMD), the conformational behavior of two commercial immunoglobulins G1 (IgG1), representative of κ and λ LCs antibodies, in both their fucosylated and afucosylated forms. Our results show, through the identification of a stable conformation, how the combination of fucosylation and LC isotype modulates the hinge behavior, the Fc conformation and the position of the glycan chains, all factors potentially affecting the binding to the FcγRs. This work also represents a technological enhancement in the conformational exploration of mAbs, making aMD a suitable approach to clarify experimental results., (© 2023. The Author(s).)

Stature is a biological trait directly determined by the interaction of genetic and environmental components. As such, it is often evaluated as an indicator for the reconstruction of skeletal biological profiles, past health, and social dynamics of human populations. Based on the analysis of 549 skeletons from the CAL (Collezione Antropologica LABANOF), a study of the diachronic trend of male and female adult stature in Milan (Italy) is being proposed here, covering a time span of about 2000 years, ranging from the Roman era to present-days. The skeletons, from necropolises dedicated to the less wealthy classes of Milanese society, were assigned to one of following five historical periods: Roman Era (first-fifth centuries AD), Early Middle Ages (sixth-tenth centuries AD), Late Middle Ages (eleventh-fifteenth centuries AD), Modern Era (sixteenth-eighteenth centuries AD) and Contemporary Era (nineteenth-twentieth centuries AD), and their stature was estimated according to the regression formulae of Trotter (1970). The collected data were then subjected to statistical analyses with ANOVA using R software. Although stature values showed an ample standard deviation in all periods, statistical analyses showed that stature did not significantly vary across historical periods in Milan for both sexes. This is one of the rare studies showing no diachronic changes in the trend of stature in Europe., (© 2023. The Author(s).)

The fulfilment of the European "Farm to Fork" strategy requires a drastic reduction in the use of "at risk" synthetic pesticides; this exposes vulnerable agricultural sectors-among which is the European risiculture-to the lack of efficient means for the management of devastating diseases, thus endangering food security. Therefore, novel scaffolds need to be identified for the synthesis of new and more environmentally friendly fungicides. In the present work, we employed our previously developed 3D model of P. oryzae cytochrome bc1 (cyt bc1 ) complex to perform a high-throughput virtual screening of two commercially available compound libraries. Three chemotypes were selected, from which a small collection of differently substituted analogues was designed and synthesized. The compounds were tested as inhibitors of the cyt bc1 enzyme function and the mycelium growth of both strobilurin-sensitive (WT) and -resistant (RES) P. oryzae strains. This pipeline has permitted the identification of thirteen compounds active against the RES cyt bc1 and five compounds that inhibited the WT cyt bc1 function while inhibiting the fungal mycelia only minimally. Serendipitously, among the studied compounds we identified a new chemotype that is able to efficiently inhibit the mycelium growth of WT and RES strains by ca. 60%, without inhibiting the cyt bc1 enzymatic function, suggesting a different mechanism of action.

GPR17, a G protein-coupled receptor, is a pivotal regulator of myelination. Its endogenous ligands trigger receptor desensitization and downregulation allowing oligodendrocyte terminal maturation. In addition to its endogenous agonists, GPR17 could be promiscuously activated by pro-inflammatory oxysterols and chemokines released at demyelinating lesions. Herein, the chemokine receptors CXCR2 and CXCR4 were selected to perform both in silico modelling and in vitro experiments to establish their structural and functional interactions with GPR17. The relative propensity of GPR17 and CXCR2 or CXCR4 to form homo- and hetero-dimers was assessed by homology modelling and molecular dynamics (MD) simulations, and co-immunoprecipitation and immunoenzymatic assay. The interaction between chemokine receptors and GPR17 was investigated by determining receptor-mediated modulation of intracellular cyclic adenosine monophosphate (cAMP). Our data show the GPR17 association with CXCR2 or CXCR4 and the negative regulation of these interactions by CXCR agonists or antagonists. Moreover, GPR17 and CXCR2 heterodimers can functionally influence each other. In contrast, CXCR4 can influence GPR17 functionality, but not vice versa . According to MD simulations, all the dimers reached conformational stability and negative formation energy, confirming the experimental observations. The cross-talk between these receptors could play a role in the development of the neuroinflammatory milieu associated with demyelinating events.

Toxic aggregates of α-synuclein (αsyn) are considered key drivers of Parkinson's disease (PD) pathology. In early PD, αsyn induces synaptic dysfunction also modulating the glutamatergic neurotransmission. However, a more detailed understanding of the molecular mechanisms underlying αsyn-triggered synaptic failure is required to design novel therapeutic interventions. Here, we described the role of Rabphilin-3A (Rph3A) as novel target to counteract αsyn-induced synaptic loss in PD. Rph3A is a synaptic protein interacting with αsyn and involved in stabilizing dendritic spines and in promoting the synaptic retention of NMDA-type glutamate receptors. We found that in vivo intrastriatal injection of αsyn-preformed fibrils in mice induces the early loss of striatal synapses associated with decreased synaptic levels of Rph3A and impaired Rph3A/NMDA receptors interaction. Modulating Rph3A striatal expression or interfering with the Rph3A/αsyn complex with a small molecule prevented dendritic spine loss and rescued associated early motor defects in αsyn-injected mice. Notably, the same experimental approaches prevented αsyn-induced synaptic loss in vitro in primary hippocampal neurons. Overall, these findings indicate that approaches aimed at restoring Rph3A synaptic functions can slow down the early synaptic detrimental effects of αsyn aggregates in PD., Competing Interests: Conflicts of interest The authors declare no conflict of interest., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Objectives: The purpose of the study was to describe the influence of contralateral forced eyelid closure on intraocular pressure (IOP)., Methods: Twenty-one healthy volunteers with no ophthalmic history had their IOP measured in the supine position to simulate the intraoperative environment. Intraocular pressure was measured with a handheld tonometer over three scenarios: (1) both eyes in a relaxed state, (2) eyelid speculum in the right eye with both eyes open and relaxed, (3) eyelid speculum in the right eye with the fellow eye squeezing tightly., Results: Intraocular pressure significantly increased with forced contralateral eyelid squeezing compared with the relaxed state by a mean of 7.71±5.08 mm Hg (95% Confidence Interval of 5.40-7.37), P<0.001., Conclusions: Contralateral eyelid squeezing can significantly increase intraoperative IOP measurements., Competing Interests: The authors have no funding or conflicts of interest to disclose., (Copyright © 2022 Contact Lens Association of Ophthalmologists.)

On October 21-22, 2020 the HESI (Health and Environmental Sciences Institute) Protein Allergens, Toxins, and Bioinformatics Committee, and the Society of Toxicology Food Safety Specialty Section co-hosted a virtual workshop titled "From Protein Toxins to Applied Toxicological Testing". The workshop focused on the safety assessment of novel proteins contained in foods and feeds, was globally represented by over 200 stakeholder attendees, and featured contributions from experts in academia, government and non-government organizations, and agricultural biotechnology developers from the private sector. A range of topics relevant to novel protein safety were discussed, including: the state of protein toxin biology, modes and mechanisms of action, structures and activity, use of bioinformatic analyses to assess the safety of a protein, and ways to leverage computational biology with in silico approaches for protein toxin identification/characterization. Key outcomes of the workshop included the appreciation of the complexity of developing a definition for a protein toxin when viewed from the perspective of food and feed safety, confirming the need for a case-by-case hypothesis-driven interpretation of bioinformatic results that leverages additional metadata rather than an alignment threshold-driven interpretation, and agreement that a "toxin protein database" is not necessary, as the bioinformatic needs for toxin detection may be accomplished by existing databases such as Pfam and UniProtKB/Swiss-Prot. In this paper, a path forward is proposed., (Copyright © 2022. Published by Elsevier Inc.)

Purpose: This study aimed to describe a case of keratitis secondary to Metarhizium robertsii, a soil-dwelling fungus with typical insect pathogenicity., Methods: A Case report., Results: A 58-year-old man with a ocular history of soft contact lens overwear, poor contact lens hygiene, and ocular exposure to ground well water supplying his house was referred to our university practice for a central corneal ulcer with 40% thinning. Same-day rapid microscopic detection with Giemsa stain identified the presence of many hyphae elements, and he was ultimately diagnosed with M. robertsii keratitis. The patient's course involved severe and progressive corneal thinning that stabilized over a 3-month course of antifungal therapy., Conclusions: Metarhizium robertsii seems more aggressive than other forms of fungal keratitis; therefore, this infection may be watched more closely with the risk for quick progressive corneal thinning, even while on antifungal management., Competing Interests: The authors have no conflicts of interest to disclose., (Copyright © 2021 Wolters Kluwer Health, Inc. All rights reserved.)

In this compilation we collect information about the main protein components in hemolymph and stress the continued interest in their study. The reasons for such an attention span several areas of biological, veterinarian and medical applications: from the notions for better dealing with the species - belonging to phylum Arthropoda, subphylum Crustacea, and to phylum Mollusca - of economic interest, to the development of 'marine drugs' from the peptides that, in invertebrates, act as antimicrobial, antifungal, antiprotozoal, and/or antiviral agents. Overall, the topic most often on focus is that of innate immunity operated by classes of pattern-recognition proteins. SIGNIFICANCE: The immune response in invertebrates relies on innate rather than on adaptive/acquired effectors. At a difference from the soluble and membrane-bound immunoglobulins and receptors in vertebrates, the antimicrobial, antifungal, antiprotozoal and/or antiviral agents in invertebrates interact with non-self material by targeting some common (rather than some highly specific) structural motifs. Developing this paradigm into (semi) synthetic pharmaceuticals, possibly optimized through the modeling opportunities offered by computational biochemistry, is one of the lessons today's science may learn from the study of marine invertebrates, and specifically of the proteins and peptides in their hemolymph., (Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.)

Purpose: To compare the outcomes of Pseudomonas aeruginosa keratitis (PAK) in contact lens wearers (CLWs) and non-contact lens wearers (non-CLWs) and identify risk factors for poor visual acuity (VA) outcomes in each group., Design: Retrospective cohort study METHODS: Two hundred fourteen consecutive cases of PAK were included between January 2006 and December 2019. Clinical features, microbiologic results, and treatment course were compared between CLW and non-CLW groups. Analyses of clinical features predicting poor final VA were performed., Results: This study identified 214 infected eyes in 207 patients with PAK, including 163 eyes (76.2%) in CLWs and 51 eyes (23.8%) in non-CLWs. The average age was 39.2 years in CLWs and 71.9 years in non-CLWs (P < .0001). The average logMAR visual acuity (VA) at presentation was 1.39 in CLWs and 2.17 in non-CLWs (P < .0001); average final VA was 0.76 in CLWs and 1.82 in non-CLWs (P < .0001). Stromal necrosis required a procedural or surgical intervention in 13.5% of CLWs and 49.0% of non-CLWs (P < .0001). A machine learning-based analysis yielded a list of clinical features that most strongly predict a poor VA outcome (worse than 20/40), including worse initial VA, older age, larger size of infiltrate or epithelial defect at presentation, and greater maximal depth of stromal necrosis., Conclusions: Non-CLWs have significantly worse VA outcomes and required a higher rate of surgical intervention, compared with CLWs. Our study elucidates risk factors for poor visual outcomes in non-CLWs with PAK., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Purpose of Review: Corneal collagen crosslinking (CXL) is a minimally invasive treatment that can stabilize corneal ectatic disorders including keratoconus, pellucid marginal degeneration, or postrefractive surgery ectasia. The benefits of CXL have been well documented. New research is focused on modifying current treatment protocols with the goals of maximizing corneal stability while also shortening overall procedure time., Recent Findings: Accelerated CXL protocols have the goal of delivering the same ultraviolet A intensity as conventional protocols, but over a shorter time period. Accelerated protocols have shown success to date, but there are concerns for long-term corneal stability. Pulsed protocols may increase the long-term efficacy of the accelerated designs. In addition, transepithelial crosslinking protocols have been designed with the goal of reducing postoperative pain and lower the risk of infectious complications of epithelial-off conventional protocols., Summary: Newer CXL protocols attempt to make the procedure safer and more effective. Current research is promising, but long-term studies are essential to understand how the new protocols may affect corneal stability., (Copyright © 2021 Wolters Kluwer Health, Inc. All rights reserved.)

Purpose: To report a case of a sterile iris abscess associated with herpes zoster ophthalmicus (HZO)., Observations: A 69-year-old African American female presented to SUNY Downstate Medical Center complaining of left-sided eye pain for two weeks. The patient had a best-corrected visual acuity of 20/30 OD and 20/200 OS. On external exam, vesicles were noted on the left upper lid and tip of the nose. Anterior segment exam was notable for decreased sensation without epithelial defects. The patient had 2+ stromal edema with 3+ cell and flare. The iris was flat with 1+ nuclear sclerosis OU. The intraocular pressure (IOP) was 14 mmHg OD and 40 mmHg OS. The patient was diagnosed with HZO with secondary uveitic glaucoma.At ten weeks, anterior segment inflammation resolved and IOP stabilized. However, an iris nodule was noted superior nasal which continued to enlarge by 16 weeks follow up. Iris ultrasound revealed a 3 × 3 mm elevated lesion with internal homogeneity suggestive of an abscess.At five months, a dense, mature cataract developed. The patient underwent cataract extraction with sector iridectomy. Gram staining and cultures were negative for organisms but positive for polymorphic neutrophils. Histopathology revealed fibrosis, surface necrosis, and stromal infiltration with chronic inflammatory cells consistent with chronic iritis and a sterile abscess secondary to HZO., Conclusions and Importance: HZO is associated with a range of ocular sequelae with acquired iris nodule only mentioned once in the literature. As the second documented case, our findings will add to the general fund of knowledge regarding iris lesions and HZO., Competing Interests: The following authors have no financial disclosures: SAL, LP, NA, MB, EM, HG, ME., (© 2021 The Authors. Published by Elsevier Inc.)

The increasing emergence of fungicide-resistant pathogens requires urgent solutions for crop disease management. Here, we describe a structural investigation of new fungicides obtained by combining strobilurin and succinate dehydrogenase inhibitor pharmacophores. We identified compounds endowed with very good activity against wild-type Pyricularia oryzae , combined in some cases with promising activity against strobilurin-resistant strains. The first three-dimensional model of P. oryzae cytochrome bc1 complex containing azoxystrobin as a ligand was developed. The model was validated with a set of commercially available strobilurins, and it well explains both the resistance mechanism to strobilurins mediated by the mutation G143A and the activity of metyltetraprole against strobilurin-resistant strains. The obtained results shed light on the key recognition determinants of strobilurin-like derivatives in the cytochrome bc1 active site and will guide the further rational design of new fungicides able to overcome resistance caused by G143A mutation in the rice blast pathogen.

Lecithin:cholesterol-acyl transferase (LCAT) plays a major role in cholesterol metabolism as it is the only extracellular enzyme able to esterify cholesterol. LCAT activity is required for lipoprotein remodeling and, most specifically, for the growth and maturation of HDLs. In fact, genetic alterations affecting LCAT functionality may cause a severe reduction in plasma levels of HDL-cholesterol with important clinical consequences. Although several hypotheses were formulated, the exact molecular recognition mechanism between LCAT and HDLs is still unknown. We employed a combination of structural bioinformatics procedures to deepen the insights into the HDL-LCAT interplay that promotes LCAT activation and cholesterol esterification. We have generated a data-driven model of reconstituted HDL (rHDL) and studied the dynamics of an assembled rHDL::LCAT supramolecular complex, pinpointing the conformational changes originating from the interaction between LCAT and apolipoprotein A-I (apoA-I) that are necessary for LCAT activation. Specifically, we propose a mechanism in which the anchoring of LCAT lid to apoA-I helices allows the formation of a hydrophobic hood that expands the LCAT active site and shields it from the solvent, allowing the enzyme to process large hydrophobic substrates., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)

Knowledge on mode-of-action (MOA) is required to understand toxicological effects of compounds, notably in the context of risk assessment of mixtures. Such information is generally scarce, and often complicated by the existence of multiple MOAs per compound. Here, MOAs related to developmental craniofacial malformations were derived from literature, and assembled in a MOA network. A selection of gene expression markers was based on these MOAs. Next, these markers were verified by qPCR in zebrafish embryos, after exposure to reference compounds. These were: triazoles for inhibition of retinoic acid (RA) metabolism, AM580 and CD3254 for selective activation of respectively RA-receptor (RAR) and retinoid-X-receptor (RXR), dithiocarbamates for inhibition of lysyl oxidase, TCDD for activation of the aryl-hydrocarbon-receptor (AhR), VPA for inhibition of histone deacetylase (HDAC), and PFOS for activation of peroxisome proliferator-activated receptor-alpha (PPARα). Next, marker gene profiles for these reference compounds were used to map the profiles of test compounds to known MOAs. In this way, 2,4-dinitrophenol matched with the TCDD and RAR profiles, boric acid with RAR, endosulfan with PFOS, fenpropimorph with dithiocarbamates, PCB126 with AhR, and RA with triazoles and RAR profiles. Prochloraz showed no match. Activities of these compounds in ToxCast assays, and in silico analysis of binding affinity to the respective targets showed limited concordance with the marker gene expression profiles, but still confirmed the complex MOA profiles of reference and test compounds. Ultimately, this approach could be used to support modeling of mixture effects based on upfront knowledge of (dis)similarity of MOAs., (Copyright © 2020 Elsevier Inc. All rights reserved.)

BACKGROUND Neisseria-associated conjunctivitis is a rare cause of bacterial conjunctivitis in adults, with Neisseria gonorrhoeae as the primarily identified infectious strain. Here, we present a rare case of bacterial conjunctivitis due to Neisseria sicca in a 34-year-old immunocompetent man with no prior medical or ocular history. CASE REPORT A 34-year-old man with no significant past medical or ocular history presented with a 3-day history of left periorbital edema, ocular pain, and copious purulent discharge. Bacterial conjunctivitis was suspected due to the rapidity of onset and purulence. Peripheral corneal thinning was identified. Preliminary culture results showed gram-negative diplococci, and the patient was treated for gonococcal infection. Final cultures identified Neisseria sicca, a rarely pathogenic strain of Neisseria species. CONCLUSIONS This is the second reported case of Neisseria sicca-associated conjunctivitis, and the first reported case to have corneal involvement. Neisseria sicca, while typically non-pathogenic, may manifest as conjunctivitis in immunocompetent hosts with a low-risk sexual history.

Mixtures of substances sharing the same molecular initiating event (MIE) are supposed to induce additive effects. The proposed MIE for azole fungicides is CYP26 inhibition with retinoic acid (RA) local increase, triggering key events leading to craniofacial defects. Valproic acid (VPA) is supposed to imbalance RA-regulated gene expression trough histone deacetylases (HDACs) inhibition. The aim was to evaluate effects of molecules sharing the same MIE (azoles) and of such having (hypothetically) different MIEs but which are eventually involved in the same adverse outcome pathway (AOP). An in silico approach (molecular docking) investigated the suggested MIEs. Teratogenicity was evaluated in vitro (WEC). Abnormalities were modelled by PROAST software. The common target was the branchial apparatus. In silico results confirmed azole-related CYP26 inhibition and a weak general VPA inhibition on the tested HDACs. Unexpectedly, VPA showed also a weak, but not marginal, capability to enter the CYP 26A1 and CYP 26C1 catalytic sites, suggesting a possible role of VPA in decreasing RA catabolism, acting as an additional MIE. Our findings suggest a new more complex picture. Consequently two different AOPs, leading to the same AO, can be described. VPA MIEs (HDAC and CYP26 inhibition) impinge on the two converging AOPs., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)

We report in this manuscript what is known about the protein makeup of a selection of biological fluids in the domestic dog. The samples we review - amniotic and allantoic fluid, seminal fluid, saliva, bile, synovial fluid, tears - are still very poorly characterized in this species. For some of them we can present results from our own, mainly unpublished experiments. SIGNIFICANCE: The dog is one of the most widespread companion animals, and also of medical relevance as model species for some human diseases. Still, investigation of body fluids other than serum and urine is not so commonly undertaken, although - like in humans - also these sample types may have potential for diagnostic purposes. We compile published data about proteomes of fetal fluids, seminal plasma, saliva, bile, synovial fluid and tears, enriched by some yet unpublished data of our own (proteins of amniotic and allantoic fluid, tears). Closing gaps in our knowledge on dog proteins will further our understanding of (patho)physiological processes., Competing Interests: Declaration of Competing Interest The authors declare no conflict of interest., (Copyright © 2020 The Author(s). Published by Elsevier B.V. All rights reserved.)