Machine learning-aided engineering of hydrolases for PET depolymerization.

Plastic waste poses an ecological challenge1-3 and enzymatic degradation offers one, potentially green and scalable, route for polyesters waste recycling4. Poly(ethylene terephthalate) (PET) accounts for 12% of global solid waste5, and a circular carbon economy for PET is theoretically attainable through rapid enzymatic depolymerization followed by repolymerization or conversion/valorization into other products6-10. Application of PET hydrolases, however, has been hampered by their lack of robustness to pH and temperature ranges, slow reaction rates and inability to directly use untreated postconsumer plastics11. Here, we use a structure-based, machine learning algorithm to engineer a robust and active PET hydrolase. Our mutant and scaffold combination (FAST-PETase: functional, active, stable and tolerant PETase) contains five mutations compared to wild-type PETase (N233K/R224Q/S121E from prediction and D186H/R280A from scaffold) and shows superior PET-hydrolytic activity relative to both wild-type and engineered alternatives12 between 30 and 50 °C and a range of pH levels. We demonstrate that untreated, postconsumer-PET from 51 different thermoformed products can all be almost completely degraded by FAST-PETase in 1 week. FAST-PETase can also depolymerize untreated, amorphous portions of a commercial water bottle and an entire thermally pretreated water bottle at 50 ºC. Finally, we demonstrate a closed-loop PET recycling process by using FAST-PETase and resynthesizing PET from the recovered monomers. Collectively, our results demonstrate a viable route for enzymatic plastic recycling at the industrial scale.

The hepatocyte epidermal growth factor receptor (EGFR) pathway regulates the cellular interactome within the liver fibrotic niche.

Liver fibrosis is the consequence of chronic liver injury in the presence of an inflammatory component. Although the main executors of this activation are known, the mechanisms that lead to the inflammatory process that mediates the production of pro-fibrotic factors are not well characterized. Epidermal growth factor receptor (EGFR) signaling in hepatocytes is essential for the regenerative processes of the liver; however, its potential role in regulating the fibrotic niche is not yet clear. Our group generated a mouse model that expresses an inactive truncated form of the EGFR specifically in hepatocytes (ΔEGFR mice). Here, we have analyzed the response of WT and ΔEGFR mice to chronic treatment with carbon tetrachloride (CCl4), which induces a pro-inflammatory and fibrotic process in the liver. The results indicated that the hallmarks of liver fibrosis were attenuated in CCl4-treated ΔEGFR mice when compared with CCl4-treated WT mice, coinciding with a faster resolution of the fibrotic process and ameliorated damage. The absence of EGFR activity in hepatocytes induced changes in the pattern of immune cells in the liver, with a notable increase in the population of M2 macrophages, more related to fibrosis resolution, as well as in the population of lymphocytes related to eradication of the damage. Transcriptome analysis of hepatocytes, and secretome studies of extracellular media from in vitro experiments, allowed us to elucidate the specific molecular mechanisms regulated by EGFR that mediate hepatocyte production of both pro-fibrotic and pro-inflammatory mediators; these have consequences for the deposition of extracellular matrix proteins, as well as for the immune microenvironment. Overall, our study uncovered novel mechanistic insights regarding EGFR kinase-dependent actions in hepatocytes that reveal its key role in chronic liver damage. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Asymmetric Synthesis of α-Chloroamides via Photoenzymatic Hydroalkylation of Olefins.

Photoenzymatic intermolecular hydroalkylations of olefins are highly enantioselective for chiral centers formed during radical termination but poorly selective for centers set in the C-C bond-forming event. Here, we report the evolution of a flavin-dependent "ene"-reductase to catalyze the coupling of α,α-dichloroamides with alkenes to afford α-chloroamides in good yield with excellent chemo- and stereoselectivity. These products can serve as linchpins in the synthesis of pharmaceutically valuable motifs. Mechanistic studies indicate that radical formation occurs by exciting a charge-transfer complex templated by the protein. Precise control over the orientation of molecules within the charge-transfer complex potentially accounts for the observed stereoselectivity. The work expands the types of motifs that can be prepared using photoenzymatic catalysis.

The NADPH oxidase NOX4 regulates redox and metabolic homeostasis preventing HCC progression.

BACKGROUND AND AIMS: The NADPH oxidase NOX4 plays a tumor-suppressor function in HCC. Silencing NOX4 confers higher proliferative and migratory capacity to HCC cells and increases their in vivo tumorigenic potential in xenografts in mice. NOX4 gene deletions are frequent in HCC, correlating with higher tumor grade and worse recurrence-free and overall survival rates. However, despite the accumulating evidence of a protective regulatory role in HCC, the cellular processes governed by NOX4 are not yet understood. Accordingly, the aim of this work was to better understand the molecular mechanisms regulated by NOX4 in HCC in order to explain its tumor-suppressor action. APPROACH AND RESULTS: Experimental models: cell-based loss or gain of NOX4 function experiments, in vivo hepatocarcinogenesis induced by diethylnitrosamine in Nox4 -deficient mice, and analyses in human HCC samples. Methods include cellular and molecular biology analyses, proteomics, transcriptomics, and metabolomics, as well as histological and immunohistochemical analyses in tissues. Results identified MYC as being negatively regulated by NOX4. MYC mediated mitochondrial dynamics and a transcriptional program leading to increased oxidative metabolism, enhanced use of both glucose and fatty acids, and an overall higher energetic capacity and ATP level. NOX4 deletion induced a redox imbalance that augmented nuclear factor erythroid 2-related factor 2 (Nrf2) activity and was responsible for MYC up-regulation. CONCLUSIONS: Loss of NOX4 in HCC tumor cells induces metabolic reprogramming in a Nrf2/MYC-dependent manner to promote HCC progression.

Immunization of cattle with a Rhipicephalus microplus chitinase peptide containing predicted B-cell epitopes reduces tick biological fitness.

Rhipicephalus microplus, the cattle fever tick, is the most important ectoparasite impacting the livestock industry worldwide. Overreliance on chemical treatments for tick control has led to the emergence of acaricide-resistant ticks and environmental contamination. An immunological strategy based on vaccines offers an alternative approach to tick control. To develop novel tick vaccines, it is crucial to identify and evaluate antigens capable of generating protection in cattle. Chitinases are enzymes that degrade older chitin at the time of moulting, therefore allowing interstadial metamorphosis. In this study, 1 R. microplus chitinase was identified and its capacity to reduce fitness in ticks fed on immunized cattle was evaluated. First, the predicted amino acid sequence was determined in 4 isolates and their similarity was analysed by bioinformatics. Four peptides containing predicted B-cell epitopes were designed. The immunogenicity of each peptide was assessed by inoculating 2 cattle, 4 times at 21 days intervals, and the antibody response was verified by indirect ELISA. A challenge experiment was conducted with those peptides that were immunogenic. The chitinase gene was successfully amplified and sequenced, enabling comparison with reference strains. Notably, a 99.32% identity and 99.84% similarity were ascertained among the sequences. Furthermore, native protein recognition was demonstrated through western blot assays. Chitinase peptide 3 reduced the weight and oviposition of engorged ticks, as well as larvae viability, exhibiting a 71% efficacy. Therefore, chitinase 3 emerges as a viable vaccine candidate, holding promise for its integration into a multiantigenic vaccine against R. microplus.

Childhood obesity and its impact on the characteristics of gait stance phases: a cross-sectional study.

This study aimed to investigate the variations in foot type, laxity, dynamic characteristics of gait, and the characteristics of the stance phase of gait, in relation to body mass index (BMI) and groups of children of different ages. Additionally, it aimed to explore the correlations between BMI and these variables across children groups of different ages. A cross-sectional study was conducted involving 196 infants aged between 5 and 10 years old. The variables assessed included BMI, foot type, laxity, dynamic variables, and characteristics of the stance phase of gait. Significant variations were observed in foot type, laxity, certain dynamic variables, and characteristics of the stance phase of gait between normoweight (NW) and overweight/obese (OW/OB) groups among children aged between 5 and 10 years old (p ranged between 0.019 and 0.050). Moreover, BMI was also positively associated with the initial forefoot contact, heel off, total duration of the step, and forefoot contact phase of children 7 to 10 years of age (p ranged between < 0.010 and 0.040).   Conclusion: Children who are OW/OB had alterations at different stages of gait. Being OW/OB is related to alterations of the phases of gait mainly from 7 to 10 years of age, and spending more time in each of the phases of walking. This could indicate that children who are OW/OB, in addition to walking slower, overload the musculoskeletal system, subjecting their joints and muscles to greater stress. What is Known: • Children who are overweight (OW) and obese (OB) can experience changes in their musculoskeletal systems, posture, and gait due to increased body mass index. • OW and OB children experience additional stress on their musculoskeletal systems, impacting posture, biomechanics, mobility, physical activity, and daily tasks. Excessive plantar loading is linked to foot pain in adults. What is New: • Body mass index was positively associated with initial forefoot contact, heel off, total duration of the step, and forefoot contact phase in children aged 7 to 10 years old. OW/OB children aged 5-6 exhibited less ankle dorsiflexion and smaller relaxed calcaneal stance position (RCSP) as compared to normal-weight children. • Obese children aged 5-6 showed less pronation excursion, suggesting altered frontal plane movement due to RCSP differences. Children aged 7-8 who are OW/OB spent more time in certain gait phases, particularly in the forefoot contact phase. Being OW/OB is linked to altered gait parameters such as initial forefoot, heel off, total step duration, and forefoot contact phase. Being OW/OB was associated with a longer forefoot contact phase, particularly in the right foot.

Improved Bst DNA Polymerase Variants Derived via a Machine Learning Approach.

The DNA polymerase I from Geobacillus stearothermophilus (also known as Bst DNAP) is widely used in isothermal amplification reactions, where its strand displacement ability is prized. More robust versions of this enzyme should be enabled for diagnostic applications, especially for carrying out higher temperature reactions that might proceed more quickly. To this end, we appended a short fusion domain from the actin-binding protein villin that improved both stability and purification of the enzyme. In parallel, we have developed a machine learning algorithm that assesses the relative fit of individual amino acids to their chemical microenvironments at any position in a protein and applied this algorithm to predict sequence substitutions in Bst DNAP. The top predicted variants had greatly improved thermotolerance (heating prior to assay), and upon combination, the mutations showed additive thermostability, with denaturation temperatures up to 2.5 °C higher than the parental enzyme. The increased thermostability of the enzyme allowed faster loop-mediated isothermal amplification assays to be carried out at 73 °C, where both Bst DNAP and its improved commercial counterpart Bst 2.0 are inactivated. Overall, this is one of the first examples of the application of machine learning approaches to the thermostabilization of an enzyme.

Mapping the Initial Stages of a Protective Pathway that Enhances Catalytic Turnover by a Lytic Polysaccharide Monooxygenase.

Oxygenase and peroxygenase enzymes generate intermediates at their active sites which bring about the controlled functionalization of inert C-H bonds in substrates, such as in the enzymatic conversion of methane to methanol. To be viable catalysts, however, these enzymes must also prevent oxidative damage to essential active site residues, which can occur during both coupled and uncoupled turnover. Herein, we use a combination of stopped-flow spectroscopy, targeted mutagenesis, TD-DFT calculations, high-energy resolution fluorescence detection X-ray absorption spectroscopy, and electron paramagnetic resonance spectroscopy to study two transient intermediates that together form a protective pathway built into the active sites of copper-dependent lytic polysaccharide monooxygenases (LPMOs). First, a transient high-valent species is generated at the copper histidine brace active site following treatment of the LPMO with either hydrogen peroxide or peroxyacids in the absence of substrate. This intermediate, which we propose to be a CuII-(histidyl radical), then reacts with a nearby tyrosine residue in an intersystem-crossing reaction to give a ferromagnetically coupled (S = 1) CuII-tyrosyl radical pair, thereby restoring the histidine brace active site to its resting state and allowing it to re-enter the catalytic cycle through reduction. This process gives the enzyme the capacity to minimize damage to the active site histidine residues "on the fly" to increase the total turnover number prior to enzyme deactivation, highlighting how oxidative enzymes are evolved to protect themselves from deleterious side reactions during uncoupled turnover.

Mitochondrial bioenergetics boost macrophage activation, promoting liver regeneration in metabolically compromised animals.

BACKGROUND AND AIMS: Hepatic ischemia-reperfusion injury (IRI) is the leading cause of early posttransplantation organ failure as mitochondrial respiration and ATP production are affected. A shortage of donors has extended liver donor criteria, including aged or steatotic livers, which are more susceptible to IRI. Given the lack of an effective treatment and the extensive transplantation waitlist, we aimed at characterizing the effects of an accelerated mitochondrial activity by silencing methylation-controlled J protein (MCJ) in three preclinical models of IRI and liver regeneration, focusing on metabolically compromised animal models. APPROACH AND RESULTS: Wild-type (WT), MCJ knockout (KO), and Mcj silenced WT mice were subjected to 70% partial hepatectomy (Phx), prolonged IRI, and 70% Phx with IRI. Old and young mice with metabolic syndrome were also subjected to these procedures. Expression of MCJ, an endogenous negative regulator of mitochondrial respiration, increases in preclinical models of Phx with or without vascular occlusion and in donor livers. Mice lacking MCJ initiate liver regeneration 12 h faster than WT and show reduced ischemic injury and increased survival. MCJ knockdown enables a mitochondrial adaptation that restores the bioenergetic supply for enhanced regeneration and prevents cell death after IRI. Mechanistically, increased ATP secretion facilitates the early activation of Kupffer cells and production of TNF, IL-6, and heparin-binding EGF, accelerating the priming phase and the progression through G1 /S transition during liver regeneration. Therapeutic silencing of MCJ in 15-month-old mice and in mice fed a high-fat/high-fructose diet for 12 weeks improves mitochondrial respiration, reduces steatosis, and overcomes regenerative limitations. CONCLUSIONS: Boosting mitochondrial activity by silencing MCJ could pave the way for a protective approach after major liver resection or IRI, especially in metabolically compromised, IRI-susceptible organs.

Use of Artificial Intelligence in the Identification and Diagnosis of Frailty Syndrome in Older Adults: Scoping Review.

BACKGROUND: Frailty syndrome (FS) is one of the most common noncommunicable diseases, which is associated with lower physical and mental capacities in older adults. FS diagnosis is mostly focused on biological variables; however, it is likely that this diagnosis could fail owing to the high biological variability in this syndrome. Therefore, artificial intelligence (AI) could be a potential strategy to identify and diagnose this complex and multifactorial geriatric syndrome. OBJECTIVE: The objective of this scoping review was to analyze the existing scientific evidence on the use of AI for the identification and diagnosis of FS in older adults, as well as to identify which model provides enhanced accuracy, sensitivity, specificity, and area under the curve (AUC). METHODS: A search was conducted using PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) guidelines on various databases: PubMed, Web of Science, Scopus, and Google Scholar. The search strategy followed Population/Problem, Intervention, Comparison, and Outcome (PICO) criteria with the population being older adults; intervention being AI; comparison being compared or not to other diagnostic methods; and outcome being FS with reported sensitivity, specificity, accuracy, or AUC values. The results were synthesized through information extraction and are presented in tables. RESULTS: We identified 26 studies that met the inclusion criteria, 6 of which had a data set over 2000 and 3 with data sets below 100. Machine learning was the most widely used type of AI, employed in 18 studies. Moreover, of the 26 included studies, 9 used clinical data, with clinical histories being the most frequently used data type in this category. The remaining 17 studies used nonclinical data, most frequently involving activity monitoring using an inertial sensor in clinical and nonclinical contexts. Regarding the performance of each AI model, 10 studies achieved a value of precision, sensitivity, specificity, or AUC ≥90. CONCLUSIONS: The findings of this scoping review clarify the overall status of recent studies using AI to identify and diagnose FS. Moreover, the findings show that the combined use of AI using clinical data along with nonclinical information such as the kinematics of inertial sensors that monitor activities in a nonclinical context could be an appropriate tool for the identification and diagnosis of FS. Nevertheless, some possible limitations of the evidence included in the review could be small sample sizes, heterogeneity of study designs, and lack of standardization in the AI models and diagnostic criteria used across studies. Future research is needed to validate AI systems with diverse data sources for diagnosing FS. AI should be used as a decision support tool for identifying FS, with data quality and privacy addressed, and the tool should be regularly monitored for performance after being integrated in clinical practice.

Effect of toothpaste tablets on gloss and surface roughness of resin-based composite materials.

PURPOSE: To evaluate the effects of toothpaste tablets on the gloss and surface roughness of resin-based composite materials and determine the relationship between gloss and roughness. METHODS: Rectangular jigs were designed and printed. Wells (2 mm deep x 7 mm diameter) were filled with Filtek Supreme Ultra A2B, light-cured and polished. A small-area glossmeter was used for gloss (GU) measurements and a profilometer for roughness measurements (Ra) at baseline and after challenge with each toothpaste. An automated tooth-brushing machine was set at 120 strokes/minute for a total of 10,000 strokes to evaluate four test groups with 16 specimens in each group. NC: Brushing with distilled water; TABS: Colgate Anywhere Travel Tooth Tabs; CP: Colgate Cavity Protection Toothpaste and AW: Colgate Whitening Advanced Toothpaste. Kruskal-Wallis test was used to test the difference in gloss and surface roughness among the groups and Pearson correlation was used to compare the relationship between gloss and roughness. RESULTS: There was no statistically significant difference in gloss and roughness among the four groups at baseline. At post-brushing, there was a statistically significant difference among the groups (P< 0.001) with increased roughness and decreased gloss for CP and AW when compared to TABS. There was a statistically significant correlation between post-brushing roughness and post-brushing gloss (P< 0.001, rho: -0.815). Thus, the higher the surface roughness the lower the gloss. CLINICAL SIGNIFICANCE: Toothpaste tablets retain better gloss and roughness of resin-based composite materials when compared to conventional toothpastes.

Thermal resting pattern and acute skin temperature response to exercise in older adults: Role of cardiorespiratory fitness.

BACKGROUND: Infrared thermography is a growing area of interest in sports science due to the potential of skin temperature (Tsk) measurements to provide valuable information from rest to exercise. However, limited research exists on Tsk in older adults and the impact of factors such as sex and cardiorespiratory fitness (CRF) on Tsk. This study aims to investigate Tsk at rest and after acute exercise in older adults and assess whether sex or CRF influences Tsk. METHODS: Ninety-two participants (41 women, 68.48 ± 3.01 years) were examined with a thermographic camera in a conditioned room (23.02 ± 3.01 °C) at rest and after a graded protocol. The Tsk of 25 regions of interest (ROIs) were extracted and analysed. RESULTS: Men had higher overall Tsk at rest in 76% of ROIs, showing significant differences (p < 0.010) in six specific ROIs, independent of CRF. Both sexes had similar Tsk responses after graded exercise, with increases in distal parts (1.06 ± 0.50 °C), decreases in proximal parts (-0.62 ± 0.42 °C), and stable central Tsk (0.23 ± 0.59 °C). Increases in lower limb Tsk were significantly associated with CRF in men and women (ß = 0.438, p = 0.001, and ß = 0.535, p < 0.001, respectively), explaining 17% and 27% of the variance, respectively. CONCLUSIONS: This study demonstrates a sex-specific effect on resting Tsk in older adults, suggesting that sex-specific Tsk patterns should be considered when analysing Tsk in this population. Additionally, the association between increases in lower limb Tsk and CRF suggests that Tsk could be a promising predictor of CRF in older adults.

Direct Oral FXa Inhibitors Binding to Human Serum Albumin: Spectroscopic, Calorimetric, and Computational Studies.

Direct FXa inhibitors are an important class of bioactive molecules (rivaroxaban, apixaban, edoxaban, and betrixaban) applied for thromboprophylaxis in diverse cardiovascular pathologies. The interaction of active compounds with human serum albumin (HSA), the most abundant protein in blood plasma, is a key research area and provides crucial information about drugs' pharmacokinetics and pharmacodynamic properties. This research focuses on the study of the interactions between HSA and four commercially available direct oral FXa inhibitors, applying methodologies including steady-state and time-resolved fluorescence, isothermal titration calorimetry (ITC), and molecular dynamics. The HSA complexation of FXa inhibitors was found to occur via static quenching, and the complex formation in the ground states affects the fluorescence of HSA, with a moderate binding constant of 104 M-1. However, the ITC studies reported significantly different binding constants (103 M-1) compared with the results obtained through spectrophotometric methods. The suspected binding mode is supported by molecular dynamics simulations, where the predominant interactions were hydrogen bonds and hydrophobic interactions (mainly π-π stacking interactions between the phenyl ring of FXa inhibitors and the indole moiety of Trp214). Finally, the possible implications of the obtained results regarding pathologies such as hypoalbuminemia are briefly discussed.

Supramolecular co-encapsulation of a photosensitizer and chemotherapeutic drug in cucurbit[8]uril for potential chemophototherapy.

Supramolecular strategies as well as combinatorial approaches have been proposed to improve cancer therapeutics. In this work, we investigated the encapsulation of the photosensitizer acridine orange (AO) and the chemotherapeutic drug oxaliplatin (OxPt) in cucurbit[8]uril (CB[8]), and tested their effect both separate and combined on tumoral cells cultivated in vitro. Binding constants and enthalpies of reaction for the AO@CB[8], (AO)2@CB[8] and OxPt@CB[8] complexes were determined by isothermal titration calorimetry. In the case of AO, a negative cooperativity for the binding of the second AO molecule was found, in agreement with previous fluorescence titration data. We show herein that the AO@CB[8] complex was effectively incorporated within the cells and showed important phototoxicity, while the OxPt@CB[8] complex was cytotoxic only at long incubation times (24 h). Pre-treatment of the cells with the OxPt@CB[8] complex for 24 h inhibited any photodynamic action by the later treatment with the AO@CB[8] complex. However, when both complexes were co-incubated for 90 min, the combined cytotoxicity/phototoxicity was superior to any of the treatments individually. A cooperative effect was identified that added up to an extra 30% cytotoxicity/phototoxicity. The results point to an interesting system where a photosensitizer and chemotherapeutic drug are co-encapsulated in a macrocycle to develop chemophototherapy applications.

Pharmacological and somatic treatment effects on suicide in adults: A systematic review and meta-analysis.

BACKGROUND: Suicide is a public health crisis. We conducted a systematic review and meta-analysis of the effects of psychopharmacologic and somatic therapies on suicide risk. METHODS: A systematic search of MEDLINE for studies evaluating the effects of pharmacologic (excluding antidepressants) or somatic interventions on suicide risk was conducted. Studies were included if they used a comparison group, reported on suicide death, assessed a psychopharmacological or somatic intervention, and included adults. Study quality was assessed using the Newcastle-Ottawa scale. Fifty-seven studies were included from 2940 reviewed citations. RESULTS: In bipolar disorder, lithium was associated with a reduction in the odds of suicide compared to active controls (odds ratio [OR] = .58, p = .005; k = 12) and compared to placebo/no lithium (OR = .46, p = .009; k = 9). In mixed diagnostic samples, lithium was associated with a reduction in the odds of suicide compared to placebo/no lithium (OR = .27, p < .001; k = 12), but not compared to active controls (OR = .89, p = .468; k = 7). In psychotic disorders, clozapine was associated with a reduction in the odds of suicide (OR = .46, p = .007; k = 7). Associations between suicide death and electroconvulsive therapy (OR = .77, p = .053; k = 11), non-clozapine antipsychotics in bipolar disorder (OR = .73, p = .090; k = 6) and antipsychotics in psychotic disorders (OR = .39, p = .069; k = 6) were not significant. There was no consistent relationship between antiepileptic mood stabilizers and suicide. There were insufficient studies to meta-analyze associations of suicide risk with vagus nerve stimulation, transcranial magnetic stimulation, magnetic seizure therapy, or transcranial direct current stimulation. CONCLUSION: Lithium and clozapine have consistent data supporting protective effects against suicide in certain clinical contexts.

Discrete Models in Epidemiology: New Contagion Probability Functions Based on Real Data Behavior.

Mathematical modeling is a tool used for understanding diseases dynamics. The discrete-time model is an especial case in modeling that satisfactorily describes the epidemiological dynamics because of the discrete nature of the real data. However, discrete models reduce their descriptive and fitting potential because of assuming a homogeneous population. Thus, in this paper, we proposed contagion probability functions according to two infection paradigms that consider factors associated with transmission dynamics. For example, we introduced probabilities of establishing an infectious interaction, the number of contacts with infectious and the level of connectivity or social distance within populations. Through the probabilities design, we overcame the homogeneity assumption. Also, we evaluated the proposed probabilities through their introduction into discrete-time models for two diseases and different study zones with real data, COVID-19 for Germany and South Korea, and dengue for Colombia. Also, we described the oscillatory dynamics for the last one using the contagion probabilities alongside parameters with a biological sense. Finally, we highlight the implementation of the proposed probabilities would improve the simulation of the public policy effect of control strategies over an infectious disease outbreak.

Learning the local landscape of protein structures with convolutional neural networks.

One fundamental problem of protein biochemistry is to predict protein structure from amino acid sequence. The inverse problem, predicting either entire sequences or individual mutations that are consistent with a given protein structure, has received much less attention even though it has important applications in both protein engineering and evolutionary biology. Here, we ask whether 3D convolutional neural networks (3D CNNs) can learn the local fitness landscape of protein structure to reliably predict either the wild-type amino acid or the consensus in a multiple sequence alignment from the local structural context surrounding site of interest. We find that the network can predict wild type with good accuracy, and that network confidence is a reliable measure of whether a given prediction is likely going to be correct or not. Predictions of consensus are less accurate and are primarily driven by whether or not the consensus matches the wild type. Our work suggests that high-confidence mis-predictions of the wild type may identify sites that are primed for mutation and likely targets for protein engineering.

Clathrin switches transforming growth factor-ß role to pro-tumorigenic in liver cancer.

BACKGROUND & AIMS: Upon ligand binding, tyrosine kinase receptors, such as epidermal growth factor receptor (EGFR), are recruited into clathrin-coated pits for internalization by endocytosis, which is relevant for signalling and/or receptor degradation. In liver cells, transforming growth factor-ß (TGF-ß) induces both pro- and anti-apoptotic signals; the latter are mediated by the EGFR pathway. Since EGFR mainly traffics via clathrin-coated vesicles, we aimed to analyse the potential role of clathrin in TGF-ß-induced signalling in liver cells and its relevance in liver cancer. METHODS: Real-Time PCR and immunohistochemistry were used to analyse clathrin heavy-chain expression in human (CLTC) and mice (Cltc) liver tumours. Transient knockdown (siRNA) or overexpression of CLTC were used to analyse its role on TGF-ß and EGFR signalling in vitro. Bioinformatic analysis was used to determine the effect of CLTC and TGFB1 expression on prognosis and overall survival in patients with hepatocellular carcinoma (HCC). RESULTS: Clathrin expression increased during liver tumorigenesis in humans and mice. CLTC knockdown cells responded to TGF-ß phosphorylating SMADs (canonical signalling) but showed impairment in the anti-apoptotic signals (EGFR transactivation). Experiments of loss or gain of function in HCC cells reveal an essential role for clathrin in inhibiting TGF-ß-induced apoptosis and upregulation of its pro-apoptotic target NOX4. Autocrine TGF-ß signalling in invasive HCC cells upregulates CLTC expression, switching its role to pro-tumorigenic. A positive correlation between TGFB1 and CLTC was found in HCC cells and patients. Patients expressing high levels of TGFB1 and CLTC had a worse prognosis and lower overall survival. CONCLUSIONS: This work describes a novel role for clathrin in liver tumorigenesis, favouring non-canonical pro-tumorigenic TGF-ß pathways. CLTC expression in human HCC samples could help select patients that would benefit from TGF-ß-targeted therapy. LAY SUMMARY: Clathrin heavy-chain expression increases during liver tumorigenesis in humans (CLTC) and mice (Cltc), altering the cellular response to TGF-ß in favour of anti-apoptotic/pro-tumorigenic signals. A positive correlation between TGFB1 and CLTC was found in HCC cells and patients. Patients expressing high levels of TGFB1 and CLTC had a worse prognosis and lower overall survival. CLTC expression in HCC human samples could help select patients that would benefit from therapies targeting TGF-ß.

Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function.

Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.

Unintentional injuries in Mexico, 1990-2017: findings from the Global Burden of Disease Study 2017.

BACKGROUND: To date, the burden of injury in Mexico has not been comprehensively assessed using recent advances in population health research, including those in the Global Burden of Disease Study 2017 (GBD 2017). METHODS: We used GBD 2017 for burden of unintentional injury estimates, including transport injuries, for Mexico and each state in Mexico from 1990 to 2017. We examined subnational variation, age patterns, sex differences and time trends for all injury burden metrics. RESULTS: Unintentional injury deaths in Mexico decreased from 45 363 deaths (44 662 to 46 038) in 1990 to 42 702 (41 439 to 43 745) in 2017, while age-standardised mortality rates decreased from 65.2 (64.4 to 66.1) in 1990 to 35.1 (34.1 to 36.0) per 100 000 in 2017. In terms of non-fatal outcomes, there were 3 120 211 (2 879 993 to 3 377 945) new injury cases in 1990, which increased to 5 234 214 (4 812 615 to 5 701 669) new cases of injury in 2017. We estimated 2 761 957 (2 676 267 to 2 859 777) disability-adjusted life years (DALYs) due to injuries in Mexico in 1990 compared with 2 376 952 (2 224 588 to 2 551 004) DALYs in 2017. We found subnational variation in health loss across Mexico's states, including concentrated burden in Tabasco, Chihuahua and Zacatecas. CONCLUSIONS: In Mexico, from 1990 to 2017, mortality due to unintentional injuries has decreased, while non-fatal incident cases have increased. However, unintentional injuries continue to cause considerable mortality and morbidity, with patterns that vary by state, age, sex and year. Future research should focus on targeted interventions to decrease injury burden in high-risk populations.