The aquaculture supply chain in the time of covid-19 pandemic: Vulnerability, resilience, solutions and priorities at the global scale.

The COVID-19 global pandemic has had severe, unpredictable and synchronous impacts on all levels of perishable food supply chains (PFSC), across multiple sectors and spatial scales. Aquaculture plays a vital and rapidly expanding role in food security, in some cases overtaking wild caught fisheries in the production of high-quality animal protein in this PFSC. We performed a rapid global assessment to evaluate the effects of the COVID-19 pandemic and related emerging control measures on the aquaculture supply chain. Socio-economic effects of the pandemic were analysed by surveying the perceptions of stakeholders, who were asked to describe potential supply-side disruption, vulnerabilities and resilience patterns along the production pipeline with four main supply chain components: a) hatchery, b) production/processing, c) distribution/logistics and d) market. We also assessed different farming strategies, comparing land- vs. sea-based systems; extensive vs. intensive methods; and with and without integrated multi-trophic aquaculture, IMTA. In addition to evaluating levels and sources of economic distress, interviewees were asked to identify mitigation solutions adopted at local / internal (i.e., farm-site) scales, and to express their preference on national / external scale mitigation measures among a set of a priori options. Survey responses identified the potential causes of disruption, ripple effects, sources of food insecurity, and socio-economic conflicts. They also pointed to various levels of mitigation strategies. The collated evidence represents a first baseline useful to address future disaster-driven responses, to reinforce the resilience of the sector and to facilitate the design reconstruction plans and mitigation measures, such as financial aid strategies.

New insights about the monomer and homodimer structures of the human AOX1.

Human aldehyde oxidase (hAOX1) is a molybdenum dependent enzyme that plays an important role in the metabolism of various compounds either endogenous or xenobiotics. Due to its promiscuity, hAOX1 plays a major role in the pharmacokinetics of many drugs and therefore has gathered a lot of attention from the scientific community and, particularly, from the pharmaceutical industry. In this work, homology modelling, molecular docking and molecular dynamics simulations were used to study the structure of the monomer and dimer of human AOX. The results with the monomer of hAOX1 allowed to shed some light on the role played by thioridazine and two malonate ions that are co-crystalized in the recent X-ray structure of hAOX1. The results show that these molecules endorse several conformational rearrangements in the binding pocket of the enzyme and these changes have an impact in the active site topology as well as in the stability of the substrate (phthalazine). The results show that the presence of both molecules open two gates located at the entrance of the binding pocket, from which results the flooding of the active site. They also endorse several modifications in the shape of the binding pocket (namely the position of Lys893) that, together with the presence of the solvent molecules, favour the release of the substrate to the solvent. Further insights were also obtained with the assembled homodimer of hAOX1. The allosteric inhibitor (THI) binds closely to the region where the dimerization of both monomers occur. These findings suggest that THI can interfere with protein dimerization.

Protocol for Computational Enzymatic Reactivity Based on Geometry Optimisation.

Enzymes play a biologically essential role in performing and controlling an important share of the chemical processes occurring in life. However, despite their critical role in nature, attaining a clear understanding of the way an enzyme acts is still cumbersome. Computational enzymology is playing an increasingly important role in this field of research. It allows the elucidation of a complete and detailed mechanism of an enzymatic reaction, including the characterization of reaction intermediates and transition states from both structural and energetic points of view, which is something that no other single experiment can produce alone. In this review, we present a general computational strategy to study enzymatic mechanisms based on adiabatic mapping and free geometry optimization. These methods allow chemical reactions to be studied with high theoretical levels, and allow a more exhaustive exploration of the chemical reactional space than other available methods, albeit being limited to the extent that they explore the enzyme conformational space. Special attention is given to the choice of the theoretical levels, as well as describing the model systems that are currently used to study enzymatic reactions. With this, we aim to provide a good introduction for non-specialised users in this field of research. We also provide a selection of hand-picked examples from our own work that illustrate the power of computational enzymology to study catalytic mechanisms. Some of these studies constitute pioneering work in the field that were later validated by experimental means.

The mechanism of the Ser-(cis)Ser-Lys catalytic triad of peptide amidases.

In this paper, we report a theoretical investigation of the catalytic mechanism of peptide amidases that involve a Ser-(cis)Ser-Lys catalytic triad. Previous suggestions propose that these enzymes should follow a distinct catalytic mechanism from the one that is present in the classic Ser-His-Asp catalytic triad. The theoretical and computational results obtained in this work indicate the opposite idea, showing that both mechanisms are very similar and only few differences are observed between both reactions. The results reveal that the different alignment of the Ser-(cis)Ser-Lys catalytic triad in relation to the classical Ser-His-Asp triad may provide a better stabilisation of the reaction intermediates, and therefore make these enzymes catalytically more efficient. The catalytic mechanism has been determined at the M06-2X/6-311++G**//B3LYP/6-31G* level of theory and requires five sequential steps instead of the two that are generally proposed: (i) nucleophilic attack of serine on the carbonyl group of the substrate, forming the first tetrahedral intermediate, (ii) formation of an acyl-enzyme complex, (ii) release of an ammonia product, (iv) nucleophilic attack of a water molecule forming the second tetrahedral intermediate, and (iv) the release of the product of the reaction, the carboxylic acid. The computational results suggest that the rate-limiting step is the first one that requires an activation free energy of 15.93 kcal mol-1. This result agrees very well with the available experimental data that predict a reaction rate of 2200 s-1, which corresponds to a free energy barrier of 14 kcal mol-1.

Replication of PTPRC as genetic biomarker of response to TNF inhibitors in patients with rheumatoid arthritis.

Genetic biomarkers could be useful for orienting treatment of patients with rheumatoid arthritis (RA), but none has been convincingly validated yet. Putative biomarkers include 14 single nucleotide polymorphisms that have shown association with response to TNF inhibitors (TNFi) in candidate gene studies and that we assayed here in 755 RA patients. Three of them, in the PTPRC, IL10 and CHUK genes, were significantly associated with response to TNFi. The most significant result was obtained with rs10919563 in PTPRC, which is a confirmed RA susceptibility locus. Its RA risk allele was associated with improved response (B=0.33, P=0.006). This is the second independent replication of this biomarker (P=9.08 × 10(-8) in the combined 3003 RA patients). In this way, PTPRC has become the most replicated genetic biomarker of response to TNFi. In addition, the positive but weaker replication of IL10 and CHUK should stimulate further validation studies.

The catalytic mechanism of carboxylesterases: a computational study.

The catalytic mechanism of carboxylesterases (CEs, EC 3.1.1.1) is explored by computational means. CEs hydrolyze ester, amide, and carbamate bonds found in xenobiotics and endobiotics. They can also perform transesterification, a reaction important, for instance, in cholesterol homeostasis. The catalytic mechanisms with three different substrates (ester, thioester, and amide) have been established at the M06-2X/6-311++G**//B3LYP/6-31G* level of theory. It was found that the reactions proceed through a mechanism involving four steps instead of two as is generally proposed: (i) nucleophilic attack of serine to the substrate, forming the first tetrahedral intermediate, (ii) formation of the acyl-enzyme complex concomitant with the release of the alcohol product, (iii) nucleophilic attack of a water or alcohol molecule forming the second tetrahedral intermediate, and (iv) the release of the second product of the reaction. The results agree very well with the available experimental data and show that the hydrolytic and the transesterification reactions are competitive processes when the substrate is an ester. In all the other studied substrates (thioester or amide), the hydrolytic and transesterification process are less favorable and some of them might not even take place under in vivo conditions.

Understanding the importance of the aromatic amino-acid residues as hot-spots.

Protein-protein interactions (PPI) are crucial for the establishment of life. However, its basic principles are still elusive and the recognition process is yet to be understood. It is important to look at the biomolecular structural space as a whole, in order to understand the principles behind conformation-function relationships. Since the application of an alanine scanning mutagenesis (ASM) study to the growth hormone it was demonstrated that only a small subset of residues at a protein-protein interface is essential for binding - the hot-spots (HS). Aromatic residues are some of the most typical HS at a protein-protein interface. To investigate the structural role of the interfacial aromatic residues in protein-protein interactions, we performed Molecular Dynamic (MD) simulations of protein-protein complexes in a water environment and calculated a variety of physical-chemical characteristics. ASM studies of single residues and of dimers or high-order clusters were performed to check for cooperativity within aromatic residues. Major differences were found between the behavior of non-HS aromatic residues and HS aromatic residues that can be used to design drugs to block the critical interactions or to predict major interactions at protein-protein complexes.

Qualitative and quantitative analysis of poly(amidoamine) dendrimers in an aqueous matrix by liquid chromatography-electrospray ionization-hybrid quadrupole/time-of-flight mass spectrometry (LC-ESI-QTOF-MS).

This work introduces a liquid chromatography-electrospray ionization-hybrid quadrupole/time-of-flight mass spectrometry (LC-ESI-QTOF-MS)-based method for qualitative and quantitative analysis of poly(amidoamine) (PAMAM) dendrimers of generations 0 to 3 in an aqueous matrix. The multiple charging of PAMAM dendrimers generated by means of ESI has provided key advantages in dendrimer identification by assignation of charge state through high resolution of isotopic clusters. Isotopic distribution in function of abundance of isotopes (12)C and (13)C yielded valuable and complementarity data for confident characterization. A mass accuracy below 3.8 ppm for the most abundant isotopes (diagnostic ions) provided unambiguous identification of PAMAM dendrimers. Validation of the LC-ESI-QTOF-MS method and matrix effect evaluation enabled reliable and reproducible quantification. The validation parameters, limits of quantification in the range of 0.012 to 1.73 µM, depending on the generation, good linear range (R > 0.996), repeatability (RSD < 13.4%), and reproducibility (RSD < 10.9%) demonstrated the suitability of the method for the quantification of dendrimers in aqueous matrices (water and wastewater). The added selectivity, achieved by multicharge phenomena, represents a clear advantage in screening aqueous mixtures due to the fact that the matrix had no significant effect on ionization, with what is evidenced by an absence of sensitivity loss in most generations of PAMAM dendrimers. Fig Liquid chromatography-electrospray ionization-hybrid quadrupole/time of flight mass spectrometry (LC-ESI-QTOF-MS) based method for qualitative and quantitative analysis of PAMAM dendrimers in aqueous matrix.

[Challenges and initiatives in the prevention of healthcare associated infections: Expert consensus study]. / Retos e iniciativas en la prevención de las infecciones relacionadas con la asistencia sanitaria: estudio de consenso de expertos.

INTRODUCTION: The objective of the project was to identify new strategies, agreed upon by experts, that help reduce the prevalence of Health Care Related Infections (HAIs) given the increase in their prevalence as a result of the pandemic and improve patient safety. MATERIAL AND METHODS: The project was developed in three phases. The first two are framed in a sequential explanatory mixed model. Phase 1 consisted of a quantitative study (anonymous survey) to find out the perception of healthcare professionals about HAIs, risk factors, preventive measures, protocols, disinfection products and approaches. Phase 2 consisted of a qualitative exploratory study in which a panel of 15 experts analyzed the results, using focus group techniques, integrating both phases through the elaboration of metainferences. Phase 3 consisted of a qualitative descriptive study where, through nominal group techniques, agreed proposals for strategies to prevent HAIs were prepared. RESULTS: The panel of experts defined a total of 51 proposals for new strategies: 15 in hand hygiene, 13 in surface cleaning, 13 in the use of devices, and 10 in HAI prevention training. Of all of them, 13 were agreed upon as preferable (medium-high viability and high impact) and 7 as recommendable (low viability and high impact). CONCLUSIONS: In the prevention of HAIs, experts recommend applying different strategies simultaneously, which include innovative, technological and humanization aspects, both in data collection, intervention and training, prioritizing those with the greatest impact. and feasibility.

Rifampicin-miconazole-impregnated catheters save cost in jugular venous sites with tracheostomy.

Antimicrobial-impregnated catheters are more expensive than standard catheters (S-C). A higher incidence of catheter-related bloodstream infection (CRBSI) has been found in jugular venous access with tracheostomy than without tracheostomy. The objective of this study was to determine central venous catheter (CVC)-related costs (considering only the cost of the CVC, diagnosis of CRBSI, and antimicrobial agents used to treat CRBSI) using rifampicin-miconazole-impregnated catheters (RM-C) or S-C in jugular venous access with tracheostomy. We performed a retrospective cohort study of patients admitted to the intensive care unit (ICU) with tracheostomy who received one or more jugular venous catheters. RM-C showed a lower incidence of CRBSI compared with S-C (0 vs. 20.16 CRBSI episodes/1,000 catheter-days; odds ratio=0.05; 95% confidence interval=0.001-0.32; p<0.001) and lower CVC-related costs (including the cost of the CVC, diagnosis, and treatment of CRBSI) (11.46 ± 6.25 vs. 38.11 ± 77.25; p<0.001) in jugular venous access with tracheostomy. The use of RM-C could reduce CVC-related costs in jugular venous access with tracheostomy. The results of our study may contribute to clinical decision-making and selection of those patients who could benefit from the use of antimicrobial-impregnated catheters.

Ventilator-associated pneumonia with or without toothbrushing: a randomized controlled trial.

Certain guidelines for the prevention of ventilator-associated pneumonia (VAP) recommend oral care with chlorhexidine, but none refer to the use of a toothbrush for oral hygiene. The role of toothbrush use has received scant attention. Thus, the objective of this study was to compare the incidence of VAP in critical care patients receiving oral care with and without manual brushing of the teeth. This was a randomized clinical trial developed in a 24-bed medical-surgical intensive care unit (ICU). Patients undergoing invasive mechanical ventilation for than 24 h were included. Patients were randomly assigned to receive oral care with or without toothbrushing. All patients received oral care with 0.12 % chlorhexidine digluconate. Tracheal aspirate samples were obtained during endotracheal intubation, then twice a week, and, finally, on extubation. There were no significant differences between the two groups of patients in the baseline characteristics. We found no statistically significant differences between the groups regarding the incidence of VAP (21 of 217 [9.7 %] with toothbrushing vs. 24 of 219 [11.0 %] without toothbrushing; odds ratio [OR] = 0.87, 95 % confidence interval [CI] = 0.469-1.615; p = 0.75). Adding manual toothbrushing to chlorhexidine oral care does not help to prevent VAP in critical care patients on mechanical ventilation.

Determination of nicotine in mushrooms by various GC/MS- and LC/MS-based methods.

Due to the basic properties of nicotine, it is not easily integrated into commonly used multiresidue methods. The present work investigates the application of two commonly employed multiresidue methods-the QuEChERS method and the ethyl acetate method-for determining nicotine in mushrooms. Both methods are employed in a modified form and an unmodified form: the former to address the special properties of nicotine and the latter, combined with the use of isotopically labelled nicotine, to compensate for poor recoveries. The QuEChERS-based methods were followed by liquid chromatography-time-of-flight mass spectrometry and those based on ethyl acetate extraction were followed by gas chromatography-triple quadrupole-mass spectrometry. All methods were validated according to European guidelines (document no. SANCO/10684/2009). Recovery studies performed on mushroom spiked at 10 and 100 µg kg(-1) yielded average recoveries in the range 80-110% with relative standard deviation (RSD) values below 9%. The linearity of the response over two orders of magnitude was demonstrated (r(2) > 0.995) for all of the determination techniques employed. The limits of detection and quantification obtained were in the 0.7 and 10 µg kg(-1) range, depending on the technique, and thus below the maximum residue level established for this toxic alkaloid by current EU legislation. Good repeatability and reproducibility were obtained in terms of the RSD of the analytical methods (0.4-13.2%). The modified QuEChERS method was tested in a proficiency test on nicotine in dried mushrooms obtaining good results. The methods were successfully applied to 20 real samples.

Dataset of working mPEG-alkyne with scCO2.

This article contains data related to the research article entitled "Carbon dioxide sorption and melting behavior of mPEG-alkyne". The presented data gives information on the thermodynamics properties of the solvent and the polymer. The time saturation of mPEG-alkyne in supercritical carbon dioxide (scCO2) was evaluated in a high-pressure variable volume cell in different period of time at different pressure at the same temperature. The effects of pressure and temperature on the density of CO2 when it is above supercritical conditions are determined with Sanchez Lacombe and Bender Equation and compared with the NIST database and values of equation of Bender. The characteristic parameters of CO2 were determined with the equations proposed by Chengyong Wang et al. [1] and the sum of squared error was calculated for each parameter. Furthermore in this work the solubility data of scCO2/polymer mixture were correlated with Sanchez Lacombe Equation of State (SL EOS) and Heuristic model proposed by Irene Pasquali et al. [2]. This work describes the methodology for solving the SL EOS between the polymer and scCO2 and the procedure of determining the solubility parameter with the group contribution method necessary to apply the heuristic model is described.

Harmonizing analytical chemistry and clinical epidemiology for human biomonitoring studies. A case-study of plastic product chemicals in urine.

There is an interdisciplinary interface between analytical chemistry and epidemiology studies with respect to the design, execution, and analysis of environmental epidemiology cohorts and studies. Extracting meaningful results linking chemical exposure to human health outcomes begins at study design and spans the entire workflow. Here we discuss analytical experimental design from an exposure science perspective, and propose a reporting checklist for the design of human biomonitoring studies. We explain key analytical chemistry concepts of blanks and limits of reporting and present a case series of plastic product chemical exposure in prenatal urine specimens from the Barwon Infant Study.

MADAMM: a multistaged docking with an automated molecular modeling protocol.

Dealing with receptor flexibility in docking methodology is still a problem. The main reason behind this difficulty is the large number of degrees of freedom that have to be considered in this kind of calculations. In this paper, we present an automated procedure, called MADAMM, that allows flexibilization of both the receptor and the ligand during a multistaged docking with an automated molecular modeling protocol. We show that the orientation of particular residues at the interface between the protein and the ligand have a crucial influence on the way they interact during the docking process, and the standard docking methodologies failed to predict their correct mode of binding. We present some examples that demonstrate the capabilities of this approach when compared with traditional docking methodologies.

ABAD: a potential therapeutic target for Abeta-induced mitochondrial dysfunction in Alzheimer's disease.

Amyloid-beta-peptide (Abetabinding to mitochondrial Abeta-binding alcohol dehydrogenase (ABAD) enzyme triggers a series of events leading to mitochondrial dysfunction characteristic of Alzheimer's disease (AD). Thus this interaction may represent a novel target for treatment strategy against AD. In this review we summarize current findings regarding the ABAD-Abeta interaction, namely structural and biophysical data, available inhibitors and more recent data from proteomic studies.

Leiomyosarcoma of the iliac vein.

Leiomyosarcoma of the iliac vein is a very uncommon tumor. We report the case of a 55-year-old man with leiomyosarcoma of the left iliac vein. The patient had abdominal pain and hematuria. Abdominal ultrasound and computed tomography scanning demonstrated a well-defined mass in the left inguinal region, probably arising from the left iliac vein. Ultrasound-guided needle-core biopsy was consistent with a malignant growth. The patient was operated on, and a neoplastic multinodular mass attached to the posterolateral wall of the iliac vein was found. The tumor was resected en bloc, and venous reconstruction was undertaken using a saphenous vein segment. The postoperative course was uneventful, and the histologic study of the resected specimen was confirmed microscopically to be a leiomyosarcoma. No signs of recurrence or metastasis were present 29 months after complete surgical resection.

Integrated chemical exposure assessment of coastal green turtle foraging grounds on the Great Barrier Reef.

The Great Barrier Reef receives run-off from 424,000 km2 catchment area across coastal Queensland, incorporating diffuse agricultural run-off, and run-off point sources of land-based chemical pollutants from urban and industrial development. Marine biota, such as green turtles (Chelonia mydas), are exposed to these diverse chemical mixtures in their natural environments, and the long term effects on turtle and ecosystem health remain unknown. This study was part of a larger multi-disciplinary project characterising anthropogenic chemical exposures from the marine environment and turtle health. The aim of this study was to screen for a wide range of anthropogenic chemical pollutants present in the external and internal environment of green turtles, using a combination of traditional targeted chemical analyses, non-target suspect screening, and effect-based bioassay methods, while employing a case-control study design. A combination of passive (water) and grab (water, sediment) samples were investigated. Three known green turtle foraging sites were selected for sampling: two coastal 'case' sites influenced primarily by urban/industrial and agricultural activities, respectively; and a remote, offshore 'control' site. Water and sediment samples from each of the three sampling locations showed differences in chemical pollutant profiles that reflected the dominant land uses in the adjacent catchment. Targeted mass spectrometric analysis for a range of pesticides, industrial chemicals, pharmaceuticals and personal care products found the greatest detection frequency and highest concentrations in coastal samples, compared to the control. Non-target screening analysis of water showed clear differentiation in chemical profile of the urban/industrial site. In-vitro assays of sediment samples from the control site had lowest induction, compared to coastal locations, as expected. Here we present evidence that turtles foraging in coastal areas are exposed to a range of anthropogenic pollutants derived from the adjacent coastal catchment areas.

Carotid bifurcation atherosclerosis in the over-65s: a prevalence study.

AIM: The aim of this study was to determine the prevalence of carotid stenosis (CS) in the over-65 population segment residing in a catchment area (Gijón) served by the Asturias Health Service (Spain) as a necessary step in planning medical care for treating cerebrovascular disease in the elderly. METHODS: In this descriptive transversal study, 232 subjects (114 men and 118 women) randomly chosen from health card data underwent colour-flow duplex scanning of the supra-aortic trunks. RESULTS: The prevalence of CS in this sample was 21.5%. When stratified by sex and age (65-74 and >75 years of age), the CS rate was 5 points higher in the older than in the younger group, and 4 points higher among males (23.6%) than among females (19.2%). CONCLUSION: Approximately one in every 5 subjects over 65 years of age presents with CS; CS prevalence was higher in the over-75s and among males, although the differences were not statistically significant.