Structural role of K224 in taniborbactam inhibition of NDM-1.

Taniborbactam (TAN; VNRX-5133) is a novel bicyclic boronic acid ß-lactamase inhibitor (BLI) being developed in combination with cefepime (FEP). TAN inhibits both serine and some metallo-ß-lactamases. Previously, the substitution R228L in VIM-24 was shown to increase activity against oxyimino-cephalosporins like FEP and ceftazidime (CAZ). We hypothesized that substitutions at K224, the homologous position in NDM-1, could impact FEP/TAN resistance. To evaluate this, a library of codon-optimized NDM K224X clones for minimum inhibitory concentration (MIC) measurements was constructed; steady-state kinetics and molecular docking simulations were next performed. Surprisingly, our investigation revealed that the addition of TAN restored FEP susceptibility only for NDM-1, as the MICs for the other 19 K224X variants remained comparable to those of FEP alone. Moreover, compared to NDM-1, all K224X variants displayed significantly lower MICs for imipenem, tebipenem, and cefiderocol (32-, 133-, and 33-fold lower, respectively). In contrast, susceptibility to CAZ was mostly unaffected. Kinetic assays with the K224I variant, the only variant with hydrolytic activity to FEP comparable to NDM-1, confirmed that the inhibitory capacity of TAN was modestly compromised (IC50 0.01 µM vs 0.14 µM for NDM-1). Lastly, structural modeling and docking simulations of TAN in NDM-1 and in the K224I variant revealed that the hydrogen bond between TAN's carboxylate with K224 is essential for the productive binding of TAN to the NDM-1 active site. In addition to the report of NDM-9 (E149K) as FEP/TAN resistant, this study demonstrates the fundamental role of single amino acid substitutions in the inhibition of NDM-1 by TAN.

Structural basis of metallo-ß-lactamase resistance to taniborbactam.

The design of inhibitors against metallo-ß-lactamases (MBLs), the largest family of carbapenemases, has been a strategic goal in designing novel antimicrobial therapies. In this regard, the development of bicyclic boronates, such as taniborbactam (TAN) and xeruborbactam, is a major achievement that may help in overcoming the threat of MBL-producing and carbapenem-resistant Gram-negative pathogens. Of concern, a recent report has shown that New Delhi MBL-9 (NDM-9) escapes the inhibitory action of TAN by a single amino acid substitution with respect to New Delhi MBL-1 (NDM-1), the most widely disseminated MBL. Here, we report a docking and computational analysis that identifies that "escape variants" against TAN can arise by disruption of the electrostatic interaction of negative charges in the active site loops of MBLs with the N-(2-aminoethyl)cyclohexylamine side chain of TAN. These changes result in non-productive binding modes of TAN that preclude reaction with the MBLs, a phenomenon that is not restricted to NDM-9. This analysis demonstrates that single amino acid substitutions in non-essential residues in MBL loops can unexpectedly elicit resistance to TAN.

Liver injury due to COVID-19 in critically ill adult patients. A retrospective study.

INTRODUCTION AND AIM: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged, causing the current pandemic of acute respiratory disease known as COVID-19. Liver injury due to COVID-19 is defined as any liver injury occurring during the course of the disease and treatment of patients with COVID-19, with or without liver disease. The incidence of elevated liver transaminases, alanine aminotransferase (ALT) and aspartate aminotransferase (AST), ranges from 2.5 to 76.3%. The aim of the present study was to describe the hepatic biochemical abnormalities, after a SARS-CoV-2-positive polymerase chain reaction (PCR) test, and the mortality rate in critically ill patients. MATERIALS AND METHODS: A retrospective study was conducted that included 70 patients seen at a private hospital in Mexico City, within the time frame of February-December 2021. Median patient age was 44.5 years (range: 37-57.2) and 43 (61.4%) of the patients were men. Liver function tests were performed on the patients at hospital admission. RESULTS: Gamma glutamyl transferase (GGT) levels were elevated (p = 0.032), as were those of AST (p = 0.011) and ALT (p = 0.021). The patients were stratified into age groups: 18-35, 36-50, and > 50 years of age. The 18 to 35-year-olds had the highest liver enzyme levels and transaminase levels were higher, the younger the patient. Due to the low mortality rate (one patient whose death did not coincide with a hepatic cause), the multivariate analysis showed an R2 association of 0.689, explained by AST, GGT, and C-reactive protein levels. CONCLUSIONS: Despite the increase in transaminases in our study population during the course of COVID-19, there was no increase in mortality. Nevertheless, hospitalized patient progression should be continuously followed.

[Liver injury due to COVID-19 in critically ill adult patients. A retrospective study]. / Lesión hepática por COVID-19 en pacientes adultos criticamente enfermos. Estudio retrospectivo.

INTRODUCTION AND AIM: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged, causing the current pandemic of acute respiratory disease known as COVID-19. Liver injury due to COVID-19 is defined as any liver injury occurring during the course of the disease and treatment of patients with COVID-19, with or without liver disease. The incidence of elevated liver transaminases, alanine aminotransferase (ALT) and aspartate aminotransferase (AST), ranges from 2.5 to 76.3%. The aim of the present study was to describe the hepatic biochemical abnormalities, after a SARS-CoV-2-positive polymerase chain reaction (PCR) test, and the mortality rate in critically ill patients. MATERIALS AND METHODS: A retrospective study was conducted that included 70 patients seen at a private hospital in Mexico City, within the time frame of February-December 2021. Median patient age was 44.5 years (range: 37-57.2) and 43 (61.4%) of the patients were men. Liver function tests were performed on the patients at hospital admission. RESULTS: Gamma glutamyl transferase (GGT) levels were elevated (p = 0.032), as were those of AST (p = 0.011) and ALT (p = 0.021). The patients were stratified into age groups: 18-35, 36-50, and > 50 years of age. The 18 to 35-year-olds had the highest liver enzyme levels and transaminase levels were higher, the younger the patient. Due to the low mortality rate (one patient whose death did not coincide with a hepatic cause), the multivariate analysis showed an R2 association of 0.689, explained by AST, GGT, and C-reactive protein levels. CONCLUSIONS: Despite the increase in transaminases in our study population during the course of COVID-19, there was no increase in mortality. Nevertheless, hospitalized patient progression should be continuously followed.

Structural modeling of a novel membrane-bound globin-coupled sensor in Geobacter sulfurreducens.

Globin-coupled sensors (GCS) usually consist of three domains: a sensor/globin, a linker, and a transmitter domain. The globin domain (GD), activated by ligand binding and/or redox change, induces an intramolecular signal transduction resulting in a response of the transmitter domain. Depending on the nature of the transmitter domain, GCSs can have different activities and functions, including adenylate and di-guanylate cyclase, histidine kinase activity, aerotaxis and/or oxygen sensing function. The gram-negative delta-proteobacterium Geobacter sulfurreducens expresses a protein with a GD covalently linked to a four transmembrane domain, classified, by sequence similarity, as GCS (GsGCS). While its GD is fully characterized, not so its transmembrane domain, which is rarely found in the globin superfamily. In the present work, GsGCS was characterized spectroscopically and by native ion mobility-mass spectrometry in combination with cryo-electron microscopy. Although lacking high resolution, the oligomeric state and the electron density map were valuable for further rational modeling of the full-length GsGCS structure. This model demonstrates that GsGCS forms a transmembrane domain-driven tetramer with minimal contact between the GDs and with the heme groups oriented outward. This organization makes an intramolecular signal transduction less likely. Our results, including the auto-oxidation rate and redox potential, suggest a potential role for GsGCS as redox sensor or in a membrane-bound e-/H+ transfer. As such, GsGCS might act as a player in connecting energy production to the oxidation of organic compounds and metal reduction. Database searches indicate that GDs linked to a four or seven helices transmembrane domain occur more frequently than expected.

Pediatric home confinement due to COVID-19: Somatic and anxiety spectrum consequences.

AIMS AND OBJECTIVES: We aimed to determine the impact of COVID-19 related home confinement on the paediatric population by focusing on anxiety, behavioural disturbances and somatic symptoms. BACKGROUND: To limit the spread of the COVID-19 outbreak, governments have imposed nationwide lockdowns to prevent direct contact; this has affected everyday lives and activities such as attending school classes. Such isolation may have impacted children's anxiety levels. DESIGN AND METHODS: We conducted a cross-sectional observational study using a web-based anonymous questionnaire from 22-26 April, 2020, among children (N = 2,292) in Spain. For children below 7 years of age, parents reported the children's behavioural, emotional and somatic symptoms and family environment data on a questionnaire designed by the researchers. Children over 7 years answered the Revised Children's Manifest Anxiety Scale either independently or with their parents' assistance. RESULTS: Children over 7 years, boys in particular, scored high on the anxiety spectrum. Moreover, participants who knew someone who had suffered from COVID-19 at home or whose parent was directly involved in the pandemic, obtained higher Total Anxiety scores. Significantly high values were found in all aspects of anxiety among those who feared infection or whose parents been unemployed. Of the children below 7 years, 56.3% had four or more anxiety-related symptoms, the most frequent of which were tantrums, emotional changes, restlessness and fear of being alone. The number of symptoms reported was significant when someone in the family home had been infected with COVID-19. CONCLUSIONS: The COVID-19 home confinement had a significant impact on children, causing anxiety, behavioural problems and somatic manifestations. RELEVANCE TO CLINICAL PRACTICE: Nurses play a key role in screening children who have experience confinement owing to the COVID-19 pandemic in order to detect early anxiety symptoms using tele-health. Suitable direct interventions can then be implemented or interdisciplinary manage could be started.

A Phase I/II Clinical Trial to evaluate the efficacy of baricitinib to prevent respiratory insufficiency progression in onco-hematological patients affected with COVID19: A structured summary of a study protocol for a randomised controlled trial.

OBJECTIVES: Baricitinib is supposed to have a double effect on SARS-CoV2 infection. Firstly, it reduces the inflammatory response through the inhibition of the Januse-Kinase signalling transducer and activator of transcription (JAK-STAT) pathway. Moreover, it reduces the receptor mediated viral endocytosis by AP2-associated protein kinase 1 (AAK1) inhibition. We propose the use of baricinitib to prevent the progression of the respiratory insufficiency in SARS-CoV2 pneumonia in onco-haematological patients. In this phase Ib/II study, the primary objective in the safety cohort is to describe the incidence of severe adverse events associated with baricitinib administration. The primary objective of the randomized phase (baricitinib cohort versus standard of care cohort) is to evaluate the number of patients who did not require mechanical oxygen support since start of therapy until day +14 or discharge (whichever it comes first). The secondary objectives of the study (only randomized phase of the study) are represented by the comparison between the two arms of the study in terms of mortality and toxicity at day+30. Moreover, a description of the immunological related changes between the two arms of the study will be reported. TRIAL DESIGN: The trial is a phase I/II study with a safety run-in cohort (phase 1) followed by an open label phase II randomized controlled trial with an experimental arm compared to a standard of care arm. PARTICIPANTS: The study will be performed at the Institut Català d'Oncologia, a tertiary level oncological referral center in the Catalonia region (Spain). The eligibility criteria are: patients > 18 years affected by oncological diseases; ECOG performance status < 2 (Karnofsky score > 60%); a laboratory confirmed infection with SARS-CoV-2 by means of real -time PCR; radiological signs of low respiratory tract disease; absence of organ dysfunction (a total bilirubin within normal institutional limits, AST/ALT≤2.5 X institutional upper limit of normal, alkaline phosphatase ≤2.5 X institutional upper limit of normal, coagulation within normal institutional limits, creatinine clearance >30 mL/min/1.73 m2 for patients with creatinine levels above institutional normal); absence of HIV infection; no active or latent HBV or HCV infection. The exclusion criteria are: patients with oncological diseases who are not candidates to receive any active oncological treatment; hemodynamic instability at time of study enrollment; impossibility to receive oral medication; medical history of recent or active pulmonary embolism or deep venous thrombosis or patients at high-risk of suffering them (surgical intervention, immobilization); multi organ failure, rapid worsening of respiratory function with requirement of fraction of inspired oxygen (FiO2) > 50% or high-flow nasal cannula before initiation of study treatment; uncontrolled intercurrent illness (ongoing or severe active infection, symptomatic congestive heart failure, unstable angina pectoris, cardiac arrhythmia, or psychiatric illness/social situations that would limit compliance with study requirements); allergy to one or more of study treatments; pregnant or breastfeeding women; positive pregnancy test in a pre-dose examination. Patients should have the ability to understand, and the willingness to sign, a written informed consent document; the willingness to accept randomization to any assigned treatment arm; and must agree not to enroll in another study of an investigational agent prior to completion of Day +28 of study. An electronic Case Report Form in the Research Electronic Data Capture (REDCap) platform will be used to collect the data of the trial. Removal from the study will apply in case of unacceptable adverse event(s), development of an intercurrent illness, condition or procedural complication, which could interfere with the patient's continued participation and voluntary patient withdrawal from study treatment (all patients are free to withdraw from participation in this study at any time, for any reasons, specified or unspecified, and without prejudice). INTERVENTION AND COMPARATOR: Treatment will be administered on an inpatient basis. We will compare the experimental treatment with baricitinib plus the institutional standard of care compared with the standard of care alone. During the phase I, we will define the dose-limiting toxicity of baricitinib and the dose to be used in the phase 2 part of the study. The starting baricitinib dose will be an oral tablet 4 mg-once daily which can be reduced to 2 mg depending on the observed toxicity. The minimum duration of therapy will be 5 days and it can be extended to 7 days. The standard of care will include the following therapies. Antibiotics will be individualized based on clinical suspicion, including the management of febrile neutropenia. Prophylaxis of thromboembolic disease will be administered to all participants. Remdesivir administration will be considered only in patients with severe pneumonia (SatO2 <94%) with less than 7 days of onset of symptoms and with supplemental oxygen requirements but not using high-flow nasal cannula, non-invasive or invasive mechanical ventilation or extracorporeal membrane oxygenation (ECMO). In the randomized phase, tocilizumab or interferon will not be allowed in the experimental arm. Tocilizumab can be used in patients in the standard of care arm at the discretion of the investigator. If it is prescribed it will be used according to the following criteria: patients who, according to his baseline clinical condition, would be an ICU tributary, interstitial pneumonia with severe respiratory failure, patients who are not on mechanical ventilation or ECMO and who are still progressing with corticoid treatment or if they are not candidates for corticosteroids. Mild ARDS (PAFI <300 mmHg) with radiological or blood gases deterioration that meets at least one of the following criteria: CRP >100mg/L D-Dimer >1,000µg/L LDH >400U/L Ferritin >700ng/ml Interleukin 6 ≥40ng/L. The use of tocilizumab is not recommended if there are AST/ALT values greater than 10 times the upper limit of normal, neutrophils <500 cells/mm3, sepsis due to other pathogens other than SARS-CoV-2, presence of comorbidity that can lead to a poor prognosis, complicated diverticulitis or intestinal perforation, ongoing skin infection. The dose will be that recommended by the Spanish Medicine Agency in patients ≥75Kg: 600mg dose whereas in patients <75kg: 400mg dose. Exceptionally, a second infusion can be assessed 12 hours after the first in those patients who experience a worsening of laboratory parameters after a first favourable response. The use of corticosteroids will be recommended in patients who have had symptoms for more than 7 days and who meet all the following criteria: need for oxygen support, non-invasive or invasive mechanical ventilation, acute respiratory failure or rapid deterioration of gas exchange, appearance or worsening of bilateral alveolar-interstitial infiltrates at the radiological level. In case of indication, it is recommended: dexamethasone 6mg/d p.o. or iv for 10 days or methylprednisolone 32mg/d orally or 30mg iv for 10 days or prednisone 40mg day p.o. for 10 days. MAIN OUTCOMES: Phase 1 part: to describe the toxicity profile of baricitinib in COVID19 oncological patients during the 5-7 day treatment period and until day +14 or discharge (whichever it comes first). Phase 2 part: to describe the number of patients in the experimental arm that will not require mechanical oxygen support compared to the standard of care arm until day +14 or discharge (whichever it comes first). RANDOMISATION: For the phase 2 of the study, the allocation ratio will be 1:1. Randomization process will be carried out electronically through the REDcap platform ( https://www.project-redcap.org/ ) BLINDING (MASKING): This is an open label study. No blinding will be performed. NUMBERS TO BE RANDOMISED (SAMPLE SIZE): The first part of the study (safety run-in cohort) will consist in the enrollment of 6 to 12 patients. In this population, we will test the toxicity of the experimental treatment. An incidence of severe adverse events grade 3-4 (graded by Common Terminology Criteria for Adverse Events v.5.0) inferior than 33% will be considered sufficient to follow with the next part of the study. The second part of the study we will perform an interim analysis of efficacy at first 64 assessed patients and a definitive one will analyze 128 assessed patients. Interim and definitive tests will be performed considering in both cases an alpha error of 0.05. We consider for the control arm this rate is expected to be 0.60 and for the experimental arm of 0.80. Considering this data, a superiority test to prove a difference of 0.20 with an overall alpha error of 0.10 and a beta error of 0.2 will be performed. Considering a 5% of dropout rate, it is expected that a total of 136 patients, 68 for each study arm, will be required to complete study accrual. TRIAL STATUS: Version 5.0. 14th October 2020 Recruitment started on the 16th of December 2020. Expected end of recruitment is June 2021. TRIAL REGISTRATION: AEMPs: 20-0356 EudraCT: 2020-001789-12, https://www.clinicaltrialsregister.eu/ctr-search/search (Not publically available as Phase I trial) Clinical trials: BARCOVID19, https://www.clinicaltrials.gov/ (In progress) FULL PROTOCOL: The full protocol is attached as an additional file, accessible from the Trials website (Additional file 1). In the interest in expediting dissemination of this material, the familiar formatting has been eliminated; this Letter serves as a summary of the key elements of the full protocol."

Prognostic implications of neutrophil-lymphocyte ratio in COVID-19.

BACKGROUND: The clinical presentation of COVID-19 ranges from a mild, self-limiting disease, to multiple organ failure and death. Most severe COVID-19 cases present low lymphocytes counts and high leukocytes counts, and accumulated evidence suggests that in a subgroup of patients presenting severe COVID-19, there may be a hyperinflammatory response driving a severe hypercytokinaemia which may be, at least in part, signalling the presence of an underlying endothelial dysfunction. In this context, available data suggest a prognostic role of neutrophil-lymphocyte ratio (NLR) in various inflammatory diseases and oncological processes. Following this rationale, we hypothesized that NLR, as a marker of endothelial dysfunction, may be useful in identifying patients with a poor prognosis in hospitalized COVID-19 cases. DESIGN: A retrospective observational study performed at Hospital Universitario HM Puerta del Sur, Madrid, Spain, which included 119 patients with COVID-19 from 1 March to 31 March 2020. Patients were categorized according to WHO R&D Expert Group. RESULTS: Forty-five (12.1%) patients experienced severe acute respiratory failure requiring respiratory support. Forty-seven (12.6%) patients died. Those with worse outcomes were older (P = .002) and presented significantly higher NLR at admission (P = .001), greater increase in Peak NLR (P < .001) and higher increasing speed of NLR (P = .003) compared with follow-up patients. In a multivariable logistic regression, age, cardiovascular disease and C-reactive protein at admission and Peak NLR were significantly associated with death. CONCLUSIONS: NLR is an easily measurable, available, cost-effective and reliable parameter, which continuous monitoring could be useful for the diagnosis and treatment of COVID-19.

Identification of key sequence features required for microRNA biogenesis in plants.

MicroRNAs (miRNAs) are endogenous small RNAs of ∼21 nt that regulate multiple biological pathways in multicellular organisms. They derive from longer transcripts that harbor an imperfect stem-loop structure. In plants, the ribonuclease type III DICER-LIKE1 assisted by accessory proteins cleaves the precursor to release the mature miRNA. Numerous studies highlight the role of the precursor secondary structure during plant miRNA biogenesis; however, little is known about the relevance of the precursor sequence. Here, we analyzed the sequence composition of plant miRNA primary transcripts and found specifically located sequence biases. We show that changes in the identity of specific nucleotides can increase or abolish miRNA biogenesis. Most conspicuously, our analysis revealed that the identity of the nucleotides at unpaired positions of the precursor plays a crucial role during miRNA biogenesis in Arabidopsis.

Transcriptional regulation of MGE progenitor proliferation by PRDM16 controls cortical GABAergic interneuron production.

The mammalian cortex is populated by neurons derived from neural progenitors located throughout the embryonic telencephalon. Excitatory neurons are derived from the dorsal telencephalon, whereas inhibitory interneurons are generated in its ventral portion. The transcriptional regulator PRDM16 is expressed by radial glia, neural progenitors present in both regions; however, its mechanisms of action are still not fully understood. It is unclear whether PRDM16 plays a similar role in neurogenesis in both dorsal and ventral progenitor lineages and, if so, whether it regulates common or unique networks of genes. Here, we show that Prdm16 expression in mouse medial ganglionic eminence (MGE) progenitors is required for maintaining their proliferative capacity and for the production of proper numbers of forebrain GABAergic interneurons. PRDM16 binds to cis-regulatory elements and represses the expression of region-specific neuronal differentiation genes, thereby controlling the timing of neuronal maturation. PRDM16 regulates convergent developmental gene expression programs in the cortex and MGE, which utilize both common and region-specific sets of genes to control the proliferative capacity of neural progenitors, ensuring the generation of correct numbers of cortical neurons.

Long-Term Effectiveness of Polymerized-Type I Collagen Intra-Articular Injections in Patients with Symptomatic Knee Osteoarthritis: Clinical and Radiographic Evaluation in a Cohort Study.

OBJECTIVE: Polymerized-type I collagen (polymerized-collagen) is a downregulator of inflammation and a tissue regenerator. The aim was to evaluate the effect of intra-articular injections (IAIs) of polymerized-collagen among patients with symptomatic knee osteoarthritis (OA) in delaying or preventing joint replacement surgery. Patients and Methods. This was a cohort study of 309 patients with knee OA. Patients with mild-to-moderate disease were treated weekly with IAIs of 2 mL of polymerized-collagen for six weeks (n = 309). Follow-up was for 6-60 months. The primary endpoints included the following determinations: (1) therapeutic effect; (2) survival from total knee replacement surgery (TKR); (3) Western Ontario and McMaster University Osteoarthritis Index (WOMAC) and pain (visual analogue scale, VAS). Clinical improvement was defined as a decrease in pain exceeding 20 mm on the VAS and the achievement of at least 20% improvement from baseline with respect to the WOMAC score. Radiographic analysis was performed at baseline and 60 months. The joint space width in the medial, lateral, and patellofemoral compartments was calculated. RESULTS: Patients who received IAIs of polymerized-collagen had a statistically significant improvement in the primary criteria (p < 0.05). Kaplan-Meier survival analysis of the therapeutic effect demonstrated 98.8% survival at 60 months with TKR as the endpoint. There was no significant reduction in joint space in any compartment based on the analyzed radiographs. No serious adverse events were recorded. CONCLUSION: Polymerized-collagen increased the time to TKR by at least 60 months, modifying the disease course, improving functional disability, and decreasing pain.

Structure and function of crocodilian hemoglobins and allosteric regulation by chloride, ATP, and CO2.

Hemoglobins (Hbs) of crocodilians are reportedly characterized by unique mechanisms of allosteric regulatory control, but there are conflicting reports regarding the importance of different effectors, such as chloride ions, organic phosphates, and CO2. Progress in understanding the unusual properties of crocodilian Hbs has also been hindered by a dearth of structural information. Here, we present the first comparative analysis of blood properties and Hb structure and function in a phylogenetically diverse set of crocodilian species. We examine mechanisms of allosteric regulation in the Hbs of 13 crocodilian species belonging to the families Crocodylidae and Alligatoridae. We also report new amino acid sequences for the α- and ß-globins of these taxa, which, in combination with structural analyses, provide insights into molecular mechanisms of allosteric regulation. All crocodilian Hbs exhibited a remarkably strong sensitivity to CO2, which would permit effective O2 unloading to tissues in response to an increase in metabolism during intense activity and diving. Although the Hbs of all crocodilians exhibit similar intrinsic O2-affinities, there is considerable variation in sensitivity to Cl- ions and ATP, which appears to be at least partly attributable to variation in the extent of NH2-terminal acetylation. Whereas chloride appears to be a potent allosteric effector of all crocodile Hbs, ATP has a strong, chloride-independent effect on Hb-O2 affinity only in caimans. Modeling suggests that allosteric ATP binding has a somewhat different structural basis in crocodilian and mammalian Hbs.

Conformational and Reaction Dynamic Coupling in Histidine Kinases: Insights from Hybrid QM/MM Simulations.

Histidine kinases (HK) of bacterial two-component systems represent a hallmark of allosterism in proteins, being able to detect a signal through the sensor domain and transmit this information through the protein matrix to the kinase domain which, once active, autophosphorylates a specific histidine residue. Inactive-to-active transition results in a large conformational change that moves the kinase on top of the histidine. In the present work, we use several molecular simulation techniques (Molecular Dynamics, Hybrid QM/MM, and constant pH molecular dynamics) to study the activation and autophosphorylation reactions in L. plantarum WalK, a cis-acting HK. In agreement with previous results, we show that the chemical step requires tight coupling with the conformational step in order to maintain the histidine phosphoacceptor in the correct tautomeric state, with a reactive δ-nitrogen. During the conformational transition, the kinase domain is never released and walks along the HK helix axis, breaking and forming several conserved residue-based contacts. The phosphate transfer reaction is concerted in the transition state region and is catalyzed through the stabilization of the negative developing charge of transferring phosphate along the reaction.

Study of the role of Mg2+ in dsRNA processing mechanism by bacterial RNase III through QM/MM simulations.

The ribonuclease III (RNase III) cleaves dsRNA in specific positions generating mature RNAs. RNase III enzymes play important roles in RNA processing, post-transcriptional gene expression, and defense against viral infection. The enzyme's active site contains Mg2+ ions bound by a network of acidic residues and water molecules, but there is a lack of information about their specific roles. In this work, multiple steered molecular dynamics simulations at QM/MM level were performed to explore the hydrolysis reaction carried out by the enzyme. Free energy profiles modifying the features of the active site are obtained and the role of Mg2+ ions, the solvent molecules and the residues of the active site are discussed in detail. Our results show that Mg2+ ions carry out different roles in the hydrolysis process positioning the substrate for the attack from a coordinated nucleophile and activating it to perform hydrolysis reaction, cleaving the dsRNA backbone in a SN2 substitution. In addition, water molecules present in the active site lower the energy barrier of the process. RNase III hydrolyzes dsRNA to generate mature RNAs. For this purpose, its active site contains Mg2+ which has an important role during the reaction. Results show that the Mg2+ activates the solvent molecule that produces the nucleophilic attack and the surrounding waters contribute significantly to the hydrolysis process.

[Asociación de la composición corporal total con la fuerza del tronco, el dolor y la discapacidad en pacientes con espondiloartrosis lumbar]. / The association of total body composition with trunk strength, pain and disability in patients with lumbar osteoarthritis.

INTRODUCCIÓN: Las alteraciones en la composición corporal total podrían influir sobre la fuerza, el dolor y la discapacidad en pacientes con espondiloartrosis lumbar. OBJETIVO: Analizar la asociación de la composición corporal total con la fuerza muscular del tronco, el dolor y la discapacidad en pacientes con espondiloartrosis lumbar. MÉTODO: Estudio piloto en mayores de 50 años con dolor crónico de espalda baja y espondiloartrosis lumbar. Se excluyeron pacientes con diabetes mellitus, depresión, ansiedad, artropatías inflamatorias, fracturas vertebrales, escoliosis, cirugías de columna, cardiopatías, hipertensión arterial, radiculopatía o claudicación neurogénica. Se recolectaron datos sobre tiempo de evolución, composición corporal (masa grasa y muscular total), fuerza del tronco (isocinesia), dolor (escala numérica verbal) y discapacidad (Roland Morris). Análisis estadístico con U de Mann-Whitney y correlaciones de Spearman. RESULTADOS: 27 pacientes (18 mujeres y 9 hombres) con edad de 58.59 ± 6.98 años. La masa muscular total se asoció con el dolor (rho: -0.63, p = 0.001) y con la fuerza del tronco (flexores rho: -0.42, p = 0.02; extensores rho: -0.50, p = 0.007), sin correlación con la discapacidad. No se encontró correlación de la masa grasa con ninguna de las variables. CONCLUSIÓN: La disminución de la masa muscular se asocia con el dolor, pero no con la discapacidad, en pacientes con espondiloartrosis lumbar. BACKGROUND: Variations in body composition among patients with lumbar osteoarthritis may influence pain and disability and muscle strength. OBJECTIVE: To analyze the relationship between body composition with pain, disability and muscle strength, in patients with lumbar osteoarthritis. METHODS: Pilot study in patients older than 50 years of age, with chronic low back pain and lumbar osteoarthritis, who agreed to participate through informed consent. We excluded patients with diabetes mellitus, depression, anxiety, inflammatory arthropathies, vertebral fractures, idiopathic scoliosis, spinal surgery, heart disease or hypertension, radiculopathy or neurogenic claudication. Data on evolution time, body composition (total body fat and muscle mass), trunk strength, pain (numerical rating scale), and disability (Roland Morris questionnaire) were collected. Mann-Whitney U-test and Spearman correlations were performed. RESULTS: 27 patients (18 women and 9 men) aged 58.59 ± 6.98 years. Negative correlations between muscle mass with pain (rho: −0.63, p = 0.001) and strength (flexors rho: −0.42, p = 0.02; extensors rho: −0.50, p = 0.007) were found, without correlation with disability. No correlations of fat mass with pain or disability were found. CONCLUSION: Decreased of muscle mass were associated with higher pain scores without influencing the disability in patients with lumbar osteoarthritis..

Impact of inkjet printed ZnO electron transport layer on the characteristics of polymer solar cells.

In this paper, we demonstrate that zinc oxide (ZnO) layers deposited by inkjet printing (IJP) can be successfully applied to the low-temperature fabrication of efficient inverted polymer solar cells (i-PSCs). The effects of ZnO layers deposited by IJP as electron transport layer (ETL) on the performance of i-PSCs based on PTB7-Th:PC70BM active layers are investigated. The morphology of the ZnO-IJP layers was analysed by AFM, and compared to that of ZnO layers deposited by different techniques. The study shows that the morphology of the ZnO underlayer has a dramatic effect on the band structure and non-geminate recombination kinetics of the active layer deposited on top of it. Charge carrier and transient photovoltage measurements show that non-geminate recombination is governed by deep trap states in devices made from ZnO-IJP while trapping is less significant for other types of ZnO. The power conversion efficiency of the devices made from ZnO-IJP is mostly limited by their slightly lower J SC, resulting from non-optimum photon conversion efficiency in the visible part of the solar spectrum. Despite these minor limitations their J-V characteristics compare very favourably with that of devices made from ZnO layer deposited using different techniques.

Crystal Structure of the Metallo-ß-Lactamase GOB in the Periplasmic Dizinc Form Reveals an Unusual Metal Site.

Metallo-beta-lactamases (MBLs) are broad-spectrum, Zn(II)-dependent lactamases able to confer resistance to virtually every ß-lactam antibiotic currently available. The large diversity of active-site structures and metal content among MBLs from different sources has limited the design of a pan-MBL inhibitor. GOB-18 is a divergent MBL from subclass B3 that is expressed by the opportunistic Gram-negative pathogen Elizabethkingia meningoseptica This MBL is atypical, since several residues conserved in B3 enzymes (such as a metal ligand His) are substituted in GOB enzymes. Here, we report the crystal structure of the periplasmic di-Zn(II) form of GOB-18. This enzyme displays a unique active-site structure, with residue Gln116 coordinating the Zn1 ion through its terminal amide moiety, replacing a ubiquitous His residue. This situation contrasts with that of B2 MBLs, where an equivalent His116Asn substitution leads to a di-Zn(II) inactive species. Instead, both the mono- and di-Zn(II) forms of GOB-18 are active against penicillins, cephalosporins, and carbapenems. In silico docking and molecular dynamics simulations indicate that residue Met221 is not involved in substrate binding, in contrast to Ser221, which otherwise is conserved in most B3 enzymes. These distinctive features are conserved in recently reported GOB orthologues in environmental bacteria. These findings provide valuable information for inhibitor design and also posit that GOB enzymes have alternative functions.

dsRNA-protein interactions studied by molecular dynamics techniques. Unravelling dsRNA recognition by DCL1.

Double stranded RNA (dsRNA) participates in several biological processes, where RNA molecules acquire secondary structure inside the cell through base complementarity. The double stranded RNA binding domain (dsRBD) is one of the main protein folds that is able to recognize and bind to dsRNA regions. The N-terminal dsRBD of DCL1 in Arabidopsis thaliana (DCL1-1), in contrast to other studied dsRBDs, lacks a stable structure, behaving as an intrinsically disordered protein. DCL1-1 does however recognize dsRNA by acquiring a canonical fold in the presence of its substrate. Here we present a detailed modeling and molecular dynamics study of dsRNA recognition by DCL1-1. We found that DCL1-1 forms stable complexes with different RNAs and we characterized the residues involved in binding. Although the domain shows a binding loop substantially shorter than other homologs, it can still interact with the dsRNA and results in bending of the dsRNA A-type helix. Furthermore, we found that R8, a non-conserved residue located in the first dsRNA binding region, recognizes preferentially mismatched base pairs. We discuss our findings in the context of the function of DCL1-1 within the microRNA processing complex.

Guías alimentarias para la población española (SENC, diciembre 2016); la nueva pirámide de la alimentación saludable / No disponible

Objetivo: La Sociedad Española de Nutrición Comunitaria (SENC) planteó en 1994 una guía alimentaria para la población española, renovada en 2001. Se presenta una nueva edición actualizada basada en la mejor evidencia científica disponible. Métodos: Desde un enfoque de salud en todas las políticas se convocó un grupo de expertos en nutrición y salud pública vinculados con la SENC para revisar la evidencia sobre dieta-salud, ingesta nutricional y consumo alimentario en la población española, hábitos de preparación y consumo de alimentos, factores determinantes e impacto de la dieta en la sostenibilidad medioambiental. Se han considerado revisiones sistemáticas existentes, actualizaciones, informes, metaanálisis y estudios recientes de calidad. El grupo colaborativo contribuyó a la elaboración del documento de trabajo y diseño del icono gráfico posteriormente sometidos a consulta, discusión y evaluación cualitativa con especial relevancia a través del Grupo Consultor de las Guías SENC-diciembre 2016. Resultados: Las nuevas recomendaciones y su representación gráfica subrayan como consideraciones básicas practicar actividad física, equilibrio emocional, balance energético para mantener el peso corporal adecuado, procedimientos culinarios saludables e ingesta adecuada de agua. Las recomendaciones promueven una alimentación equilibrada, variada y moderada que incluye cereales de grano entero, frutas, verduras, legumbres, cantidades variables de lácteos y alterna el consumo de pescados, huevos y carnes magras, junto con el uso preferente de aceite de oliva virgen extra como grasa culinaria. Refuerzan el interés por una dieta saludable, solidaria, sostenible, con productos de temporada, de cercanía, eje de convivialidad, dedicando el tiempo suficiente y animan a valorar la información del etiquetado nutricional. Conclusiones: El análisis de la evidencia disponible y de la información actualizada sobre el consumo alimentario en España pone de manifiesto la necesidad de reforzar e implementar las recomendaciones recogidas en este documento para conseguir progresivamente un mayor grado de adherencia (AU)

Objective: The Spanish Society of Community Nutrition (SENC) designed in 1994 a food guide for the Spanish population, updated in 2001. This report presents a new updated edition based on the best scientific evidence available. Methods: From a health in all policies approach, a group of experts in nutrition and public health associated with SENC was convened to review the evidence on diet-health, nutrition intake and food consumption in the Spanish population, as well as food preparation and consumption habits, determinants and impact of diet on environmental sustainability. Existing systematic reviews, updates, reports, meta-analysis and the latest quality studies have been considered. The collaborative group contributed to draft the document and design the graphic icon, then subject of a consultation process, discussion and qualitative evaluation, particularly relevant through the Advisory Group for the SENC-December 2016 Dietary Guidelines. Results: The new recommendations and its graphical representation highlights as basic considerations the practice of physical activity, emotional balance, energy balance to maintain body weight at adequate levels, healthy cooking procedures and adequate water intake. The recommendations promote a balanced, varied and moderate diet that includes whole grains, fruits, vegetables, legumes, varying amounts of dairy and alternating consumption of fish, eggs and lean meats, along with the preferential use of extra virgin olive oil for cooking and seasoning. Reinforce the interest in a healthy, sympathetic, supportive, sustainable diet, based on seasonal and local products, axis for conviviality, devoting adequate time and encourage the use of nutrition labelling information. Conclusions: The analysis of the evidence available and updated information on food consumption in Spain highlights the need to strengthen and implement the recommendations contained in this document to progressively achieve a greater adherence (AU)