A Proteogenomic Pipeline for the Analysis of Protein Biosynthesis Errors in the Human Pathogen Candida albicans.

Candida albicans is a diploid pathogen known for its ability to live as a commensal fungus in healthy individuals but causing both superficial infections and disseminated candidiasis in immunocompromised patients where it is associated with high morbidity and mortality. Its success in colonizing the human host is attributed to a wide range of virulence traits that modulate interactions between the host and the pathogen, such as optimal growth rate at 37 °C, the ability to switch between yeast and hyphal forms, and a remarkable genomic and phenotypic plasticity. A fascinating aspect of its biology is a prominent heterogeneous proteome that arises from frequent genomic rearrangements, high allelic variation, and high levels of amino acid misincorporations in proteins. This leads to increased morphological and physiological phenotypic diversity of high adaptive potential, but the scope of such protein mistranslation is poorly understood due to technical difficulties in detecting and quantifying amino acid misincorporation events in complex protein samples. We have developed and optimized mass spectrometry and bioinformatics pipelines capable of identifying rare amino acid misincorporation events at the proteome level. We have also analyzed the proteomic profile of an engineered C. albicans strain that exhibits high level of leucine misincorporation at protein CUG sites and employed an in vivo quantitative gain-of-function fluorescence reporter system to validate our LC-MS/MS data. C. albicans misincorporates amino acids above the background level at protein sites of diverse codons, particularly at CUG, confirming our previous data on the quantification of leucine incorporation at single CUG sites of recombinant reporter proteins, but increasing misincorporation of Leucine at these sites does not alter the translational fidelity of the other codons. These findings indicate that the C. albicans statistical proteome exceeds prior estimates, suggesting that its highly plastic phenome may also be modulated by environmental factors due to translational ambiguity.

Unveiling the molecular landscape of cognitive aging: insights from polygenic risk scores, DNA methylation, and gene expression.

BACKGROUND: Aging represents a significant risk factor for the occurrence of cerebral small vessel disease, associated with white matter (WM) lesions, and to age-related cognitive alterations, though the precise mechanisms remain largely unknown. This study aimed to investigate the impact of polygenic risk scores (PRS) for WM integrity, together with age-related DNA methylation, and gene expression alterations, on cognitive aging in a cross-sectional healthy aging cohort. The PRSs were calculated using genome-wide association study (GWAS) summary statistics for magnetic resonance imaging (MRI) markers of WM integrity, including WM hyperintensities, fractional anisotropy (FA), and mean diffusivity (MD). These scores were utilized to predict age-related cognitive changes and evaluate their correlation with structural brain changes, which distinguish individuals with higher and lower cognitive scores. To reduce the dimensionality of the data and identify age-related DNA methylation and transcriptomic alterations, Sparse Partial Least Squares-Discriminant Analysis (sPLS-DA) was used. Subsequently, a canonical correlation algorithm was used to integrate the three types of omics data (PRS, DNA methylation, and gene expression data) and identify an individual "omics" signature that distinguishes subjects with varying cognitive profiles. RESULTS: We found a positive association between MD-PRS and long-term memory, as well as a correlation between MD-PRS and structural brain changes, effectively discriminating between individuals with lower and higher memory scores. Furthermore, we observed an enrichment of polygenic signals in genes related to both vascular and non-vascular factors. Age-related alterations in DNA methylation and gene expression indicated dysregulation of critical molecular features and signaling pathways involved in aging and lifespan regulation. The integration of multi-omics data underscored the involvement of synaptic dysfunction, axonal degeneration, microtubule organization, and glycosylation in the process of cognitive aging. CONCLUSIONS: These findings provide valuable insights into the biological mechanisms underlying the association between WM coherence and cognitive aging. Additionally, they highlight how age-associated DNA methylation and gene expression changes contribute to cognitive aging.

Emerging Roles of tRNAs in RNA Virus Infections.

Viruses rely on the host cell translation machinery for efficient synthesis of their own proteins. Emerging evidence highlights different roles for host transfer RNAs (tRNAs) in the process of virus replication. For instance, different RNA viruses manipulate host tRNA pools to favor viral protein translation. Interestingly, specific host tRNAs are used as reverse transcription primers and are packaged into retroviral virions. Recent data also demonstrate the formation of tRNA-derived fragments (tRFs) upon infection to facilitate viral replication. Here, we comprehensively discuss how RNA viruses exploit distinct aspects of the host tRNA biology for their benefit. In light of the recent advances in the field, we propose that host tRNA-related pathways and mechanisms represent promising cellular targets for the development of novel antiviral strategies.

Segmentation of X-ray coronary angiography with an artificial intelligence deep learning model: Impact in operator visual assessment of coronary stenosis severity.

BACKGROUND: Visual assessment of the percentage diameter stenosis (%DSVE ) of lesions is essential in coronary angiography (CAG) interpretation. We have previously developed an artificial intelligence (AI) model capable of accurate CAG segmentation. We aim to compare operators' %DSVE in angiography versus AI-segmented images. METHODS: Quantitative coronary analysis (QCA) %DS (%DSQCA ) was previously performed in our published validation dataset. Operators were asked to estimate %DSVE of lesions in angiography versus AI-segmented images in separate sessions and differences were assessed using angiography %DSQCA as reference. RESULTS: A total of 123 lesions were included. %DSVE was significantly higher in both the angiography (77% ± 20% vs. 56% ± 13%, p < 0.001) and segmentation groups (59% ± 20% vs. 56% ± 13%, p < 0.001), with a much smaller absolute %DS difference in the latter. For lesions with %DSQCA of 50%-70% (60% ± 5%), an even higher discrepancy was found (angiography: 83% ± 13% vs. 60% ± 5%, p < 0.001; segmentation: 63% ± 15% vs. 60% ± 5%, p < 0.001). Similar, less pronounced, findings were observed for %DSQCA < 50% lesions, but not %DSQCA > 70% lesions. Agreement between %DSQCA /%DSVE across %DSQCA strata (<50%, 50%-70%, >70%) was approximately twice in the segmentation group (60.4% vs. 30.1%; p < 0.001). %DSVE inter-operator differences were smaller with segmentation. CONCLUSION: %DSVE was much less discrepant with segmentation versus angiography. Overestimation of %DSQCA < 70% lesions with angiography was especially common. Segmentation may reduce %DSVE overestimation and thus unwarranted revascularization.

Building the Bridge to a Participatory Citizenship: Curricular Integration of Communal Environmental Issues in School Projects Supported by the Internet of Things.

Generally, there is much to praise about the rise in acknowledging the need for young citizens to exercise their rights and duties, but the belief remains that this is not yet entrenched in young citizens' overall democratic involvement. A lack of citizenship and engagement in community issues was revealed by a recent study conducted by the authors in a secondary school from the outskirts of Aveiro, Portugal, during the 2019/2020 school year. Under the umbrella of a Design-Based Research methodological framework, citizen science strategies were implemented in the context of teaching, learning, and assessment, and at the service of the educational project of the target school, in a STEAM approach, and under Domains of Curricular Autonomy activities. The study's findings suggest that to build the bridge for participatory citizenship, teachers should engage students in collecting and analyzing data regarding communal environmental issues in a Citizen Science approach supported by the Internet of Things. The new pedagogies addressing the lack of citizenship and engagement in community issues promoted students' involvement at school and in the community, contributed to inform municipal education policies, and promoted dialogue and communication between local actors.

Influence of Different Rootstocks on Fruit Quality and Primary and Secondary Metabolites Content of Blood Oranges Cultivars.

Blood oranges have high concentrations of bioactive compounds that are beneficial to health. In Europe, the cultivation of blood oranges is increasing due to their excellent nutritional properties. In Citrus crops, rootstocks play an important role in juice and can increase the content of bioactive compounds. The morphological, qualitative and nutritional parameters were analyzed in cultivars 'Tarocco Ippolito', 'Tarocco Lempso', 'Tarocco Tapi' and 'Tarocco Fondaconuovo' grafted onto Citrus macrophylla and Citrus reshni. 'Tarocco Lempso' grafted onto Citrus macrophylla obtained the highest values of weight (275.78 g), caliber (81.37 mm and 76.79 mm) and juice content (162.11 g). 'Tarocco Tapi' grafted onto Citrus reshni obtained the most interesting qualitative parameters (15.40 °Brix; 12.0 MI). 'Tarocco Lempso' grafted onto Citrus reshni obtained the most intense red juice (a* = 9.61). Overall, the highest concentrations of primary metabolites were in proline, aspartate, citric acid, and sucrose. The results showed that 'Tarocco Ippolito' juice grafted onto Citrus reshni had the highest levels of total hydroxycinnamic acids (263.33 mg L-1), total flavones (449.74 mg L-1) and total anthocyanins (650.42 mg L-1). To conclude, 'Tarocco Lempso' grafted onto Citrus macrophylla obtained the best values of agronomic parameters, and the cultivars grafted onto Citrus reshni obtained significantly higher concentrations in primary and secondary metabolites.

Sports entrepreneurship during COVID-19: Technology as an ally to maintain the competitiveness of small businesses.

The sports sector, specifically the field of personal trainer entrepreneurship, has been severely affected by the COVID-19 crisis. However, there are still few empirical studies that analyze how the actions taken before and during this crisis can affect sports entrepreneurs' performance. This research aims to analyze which combinations of sports entrepreneurs' personal characteristics and actions performed have been most and least effective in minimizing the negative impact of COVID-19 on their businesses. A validated online questionnaire was administered to personal trainer entrepreneurs from May to June 2020 before they reopened their facilities. Fuzzy-set qualitative comparative analysis (fsQCA) was performed to assess the impacts. The results show that both post-COVID measures (adaptation of the business model) and previous strategic orientation seemed essential. Specifically, high levels of sports entrepreneurs' resilience and innovation/R&D when competing against their closest competitors before the COVID-19 pandemic and the increased use of technologies (sports services digitization) during the pandemic have been essential to maintaining the performance of the sports business. Thus, improvements in the digital competencies of personal trainers' sports entrepreneurs, the development of strategic plans and activities related to innovation/R&D and process improvements are important measures to maintain the competitiveness of small sports businesses during crises.

Activation of Laminin γ2 by Helicobacter pylori Promotes Invasion and Survival of Gastric Cancer Cells With E-Cadherin Defects.

BACKGROUND: Helicobacter pylori infection induces cellular phenotypes relevant for cancer progression, namely cell motility and invasion. We hypothesized that the extracellular matrix (ECM) could be involved in these deleterious effects. METHODS: Microarrays were used to uncover ECM interactors in cells infected with H. pylori. LAMC2, encoding laminin γ2, was selected as a candidate gene and its expression was assessed in vitro and in vivo. The role of LAMC2 was investigated by small interference RNA (siRNA) combined with a set of functional assays. Laminin γ2 and E-cadherin expression patterns were evaluated in gastric cancer cases. RESULTS: Laminin γ2 was found significantly overexpressed in gastric cancer cells infected with H. pylori. This finding was validated in vitro by infection with clinical isolates and in vivo by using gastric biopsies of infected and noninfected individuals. We showed that laminin γ2 overexpression is dependent on the bacterial type IV secretion system and on the CagA. Functionally, laminin γ2 promotes cell invasion and resistance to apoptosis, through modulation of Src, JNK, and AKT activity. These effects were abrogated in cells with functional E-cadherin. CONCLUSIONS: These data highlight laminin γ2 and its downstream effectors as potential therapeutic targets, and the value of H. pylori eradication to delay gastric cancer onset and progression.

Cardiac microcalcification burden: Global assessment in high cardiovascular risk subjects with Na[18F]F PET-CT.

BACKGROUND: Fluorine-18 sodium fluoride (Na[18F]F) atherosclerotic plaque uptake in positron emission tomography with computed tomography (PET-CT) identifies active microcalcification. We aim to evaluate global cardiac microcalcification activity with Na[18F]F, as a measure of unstable microcalcification burden, in high cardiovascular (CV) risk patients. METHODS AND RESULTS: Thirty-four high CV risk individuals without previous CV events were scanned with Na[18F]F PET-CT. Cardiac Na[18F]F uptake was assessed through the global molecular calcium score (GMCS), which was calculated by summing the product of the mean standardized uptake value times the area of the cardiac regions of interest times the slice thickness for all cardiac transaxial slices, divided by the total number of slices. Mean age is 63.5 ± 7.8 years and 62% male. Median GMCS is 320.9 (240.8-402.8). Individuals with more than five CV risk factors (50%) have increased GMCS [356.7 (321.0-409.6) vs. 261.1 (225.6-342.1), P = 0.01], which is positively correlated with predicted fatal CV risk by SCORE (rs = 0.32, P = 0.04). There is a positive correlation between GMCS and weight (rs = 0.61), body mass index (rs = 0.66), abdominal perimeter (rs = 0.74), thoracic fat volume (rs = 0.47), and epicardial adipose tissue (rs = 0.41), all with P ≤ 0.01. There is no correlation between GMCS and coronary calcium score nor coronary artery wall Na[18F]F uptake. CONCLUSIONS: In a high CV risk group, the global cardiac microcalcification burden is related to CV risk factors, metabolic syndrome variables and cardiac fat. Cardiac GMCS is a promising risk stratification tool, combining a straightforward and objective methodology with a comprehensive analysis of both coronary and valvular microcalcification.

The role of micropeptides in biology.

Micropeptides are small polypeptides coded by small open-reading frames. Progress in computational biology and the analyses of large-scale transcriptomes and proteomes have revealed that mammalian genomes produce a large number of transcripts encoding micropeptides. Many of these have been previously annotated as long noncoding RNAs. The role of micropeptides in cellular homeostasis maintenance has been demonstrated. This review discusses different types of micropeptides as well as methods to identify them, such as computational approaches, ribosome profiling, and mass spectrometry.

MicroRNA-186-5p controls GluA2 surface expression and synaptic scaling in hippocampal neurons.

Homeostatic synaptic scaling is a negative feedback response to fluctuations in synaptic strength induced by developmental or learning-related processes, which maintains neuronal activity stable. Although several components of the synaptic scaling apparatus have been characterized, the intrinsic regulatory mechanisms promoting scaling remain largely unknown. MicroRNAs may contribute to posttranscriptional control of mRNAs implicated in different stages of synaptic scaling, but their role in these mechanisms is still undervalued. Here, we report that chronic blockade of glutamate receptors of the AMPA and NMDA types in hippocampal neurons in culture induces changes in the neuronal mRNA and miRNA transcriptomes, leading to synaptic upscaling. Specifically, we show that synaptic activity blockade persistently down-regulates miR-186-5p. Moreover, we describe a conserved miR-186-5p-binding site within the 3'UTR of the mRNA encoding the AMPA receptor GluA2 subunit, and demonstrate that GluA2 is a direct target of miR-186-5p. Overexpression of miR-186 decreased GluA2 surface levels, increased synaptic expression of GluA2-lacking AMPA receptors, and blocked synaptic scaling, whereas inhibition of miR-186-5p increased GluA2 surface levels and the amplitude and frequency of AMPA receptor-mediated currents, and mimicked excitatory synaptic scaling induced by synaptic inactivity. Our findings elucidate an activity-dependent miRNA-mediated mechanism for regulation of AMPA receptor expression.

The Role of MicroRNAs in Proteostasis Decline and Protein Aggregation during Brain and Skeletal Muscle Aging.

Aging can be defined as the progressive deterioration of cellular, tissue, and organismal function over time. Alterations in protein homeostasis, also known as proteostasis, are a hallmark of aging that lead to proteome imbalances and protein aggregation, phenomena that also occur in age-related diseases. Among the various proteostasis regulators, microRNAs (miRNAs) have been reported to play important roles in the post-transcriptional control of genes involved in maintaining proteostasis during the lifespan in several organismal tissues. In this review, we consolidate recently published reports that demonstrate how miRNAs regulate fundamental proteostasis-related processes relevant to tissue aging, with emphasis on the two most studied tissues, brain tissue and skeletal muscle. We also explore an emerging perspective on the role of miRNA regulatory networks in age-related protein aggregation, a known hallmark of aging and age-related diseases, to elucidate potential miRNA candidates for anti-aging diagnostic and therapeutic targets.

Quantum Oblivious Transfer: A Short Review.

Quantum cryptography is the field of cryptography that explores the quantum properties of matter. Generally, it aims to develop primitives beyond the reach of classical cryptography and to improve existing classical implementations. Although much of the work in this field covers quantum key distribution (QKD), there have been some crucial steps towards the understanding and development of quantum oblivious transfer (QOT). One can show the similarity between the application structure of both QKD and QOT primitives. Just as QKD protocols allow quantum-safe communication, QOT protocols allow quantum-safe computation. However, the conditions under which QOT is fully quantum-safe have been subject to intense scrutiny and study. In this review article, we survey the work developed around the concept of oblivious transfer within theoretical quantum cryptography. We focus on some proposed protocols and their security requirements. We review the impossibility results that daunt this primitive and discuss several quantum security models under which it is possible to prove QOT security.

Protein synthesis inhibition and GADD34 control IFN-ß heterogeneous expression in response to dsRNA.

In innate immune responses, induction of type-I interferons (IFNs) prevents virus spreading while viral replication is delayed by protein synthesis inhibition. We asked how cells perform these apparently contradictory activities. Using single fibroblast monitoring by flow cytometry and mathematical modeling, we demonstrate that type-I IFN production is linked to cell's ability to enter dsRNA-activated PKR-dependent translational arrest and then overcome this inhibition by decreasing eIF2α phosphorylation through phosphatase 1c cofactor GADD34 (Ppp1r15a) expression. GADD34 expression, shown here to be dependent on the IRF3 transcription factor, is responsible for a biochemical cycle permitting pulse of IFN synthesis to occur in cells undergoing protein synthesis inhibition. Translation arrest is further demonstrated to be key for anti-viral response by acting synergistically with MAVS activation to amplify TBK1 signaling and IFN-ß mRNA transcription, while GADD34-dependent protein synthesis recovery contributes to the heterogeneous expression of IFN observed in dsRNA-activated cells.

The role of non-standard translation in Candida albicans pathogenesis.

Candida albicans typically resides in the human gastrointestinal tract and mucosal membranes as a commensal organism. To adapt and cope with the host immune system, it has evolved a variety of mechanisms of adaptation such as stress-induced mutagenesis and epigenetic regulation. Niche-specific patterns of gene expression also allow the fungus to fine-tune its response to specific microenvironments in the host and switch from harmless commensal to invasive pathogen. Proteome plasticity produced by CUG ambiguity, on the other hand is emerging as a new layer of complexity in C. albicans adaptation, pathogenesis, and drug resistance. Such proteome plasticity is the result of a genetic code alteration where the leucine CUG codon is translated mainly as serine (97%), but maintains some level of leucine (3%) assignment. In this review, we dissect the link between C. albicans non-standard CUG translation, proteome plasticity, host adaptation and pathogenesis. We discuss published work showing how this pathogen uses the fidelity of protein synthesis to spawn novel virulence traits.

Sodium fluoride in cardiovascular disorders: A systematic review.

BACKGROUND: 18-Fluorine sodium fluoride is a well-known radiotracer used for bone metastasis diagnosis. Its uptake correlation with cardiovascular (CV) risk was primarily suggested in oncological patients. Moreover, as a specific marker of microcalcification, it seems to correlate with CV disease progression and plaque instability. METHODS AND RESULTS: Our purpose was to systematically review clinical studies that characterized the use of this marker in CV conditions. In atherosclerosis, most studies report a positive correlation with the burden of CV risk factors and vascular calcification. A higher uptake was found in culprit plaques/rupture sites in coronary and carotid arteries and it was also linked to high-risk features in histology and intravascular imaging analysis of the plaques. In aortic stenosis, this tracer displayed an increasing uptake with disease severity. CONCLUSIONS: Sodium fluoride positron emission tomography is a promising non-invasive technique to identify high-risk plaques, which sets ground to a potential use of this tracer in evaluating atherosclerotic disease progression and degenerative changes in aortic valve stenosis. Nevertheless, there is a need for further prospective evidence that demonstrates this technique's value in predicting clinical events, adjusting treatment strategies, and improving patient outcomes.

tRNA-modifying enzyme mutations induce codon-specific mistranslation and protein aggregation in yeast.

Protein synthesis rate and accuracy are tightly controlled by the cell and are essential for proteome homoeostasis (proteostasis); however, the full picture of how mRNA translational factors maintain protein synthesis accuracy and co-translational protein folding are far from being fully understood. To address this question, we evaluated the role of 70 yeast tRNA-modifying enzyme genes on protein aggregation and used mass spectrometry to identify the aggregated proteins. We show that modification of uridine at anticodon position 34 (U34) by the tRNA-modifying enzymes Elp1, Elp3, Sml3 and Trm9 is critical for proteostasis, the mitochondrial tRNA-modifying enzyme Slm3 plays a fundamental role in general proteostasis and that stress response proteins whose genes are enriched in codons decoded by tRNAs lacking mcm5U34, mcm5s2U34, ncm5U34, ncm5Um34, modifications are overrepresented in protein aggregates of the ELP1, SLM3 and TRM9 KO strains. Increased rates of amino acid misincorporation were also detected in these strains at protein sites that specifically mapped to the codons sites that are decoded by the hypomodified tRNAs, demonstrating that U34 tRNA modifications safeguard the proteome from translational errors, protein misfolding and proteotoxic stress.

De novo sequencing of proteins by mass spectrometry.

INTRODUCTION: Proteins are crucial for every cellular activity and unraveling their sequence and structure is a crucial step to fully understand their biology. Early methods of protein sequencing were mainly based on the use of enzymatic or chemical degradation of peptide chains. With the completion of the human genome project and with the expansion of the information available for each protein, various databases containing this sequence information were formed. AREAS COVERED: De novo protein sequencing, shotgun proteomics and other mass-spectrometric techniques, along with the various software are currently available for proteogenomic analysis. Emphasis is placed on the methods for de novo sequencing, together with potential and shortcomings using databases for interpretation of protein sequence data. EXPERT OPINION: As mass-spectrometry sequencing performance is improving with better software and hardware optimizations, combined with user-friendly interfaces, de-novo protein sequencing becomes imperative in shotgun proteomic studies. Issues regarding unknown or mutated peptide sequences, as well as, unexpected post-translational modifications (PTMs) and their identification through false discovery rate searches using the target/decoy strategy need to be addressed. Ideally, it should become integrated in standard proteomic workflows as an add-on to conventional database search engines, which then would be able to provide improved identification.

Phenotypic heterogeneity promotes adaptive evolution.

Genetically identical cells frequently display substantial heterogeneity in gene expression, cellular morphology and physiology. It has been suggested that by rapidly generating a subpopulation with novel phenotypic traits, phenotypic heterogeneity (or plasticity) accelerates the rate of adaptive evolution in populations facing extreme environmental challenges. This issue is important as cell-to-cell phenotypic heterogeneity may initiate key steps in microbial evolution of drug resistance and cancer progression. Here, we study how stochastic transitions between cellular states influence evolutionary adaptation to a stressful environment in yeast Saccharomyces cerevisiae. We developed inducible synthetic gene circuits that generate varying degrees of expression stochasticity of an antifungal resistance gene. We initiated laboratory evolutionary experiments with genotypes carrying different versions of the genetic circuit by exposing the corresponding populations to gradually increasing antifungal stress. Phenotypic heterogeneity altered the evolutionary dynamics by transforming the adaptive landscape that relates genotype to fitness. Specifically, it enhanced the adaptive value of beneficial mutations through synergism between cell-to-cell variability and genetic variation. Our work demonstrates that phenotypic heterogeneity is an evolving trait when populations face a chronic selection pressure. It shapes evolutionary trajectories at the genomic level and facilitates evolutionary rescue from a deteriorating environmental stress.

Correction: Phenotypic heterogeneity promotes adaptive evolution.

[This corrects the article DOI: 10.1371/journal.pbio.2000644.].