Prioritizing cardiovascular disease-associated variants altering NKX2-5 and TBX5 binding through an integrative computational approach.

Cardiovascular diseases (CVDs) are the leading cause of death worldwide and are heavily influenced by genetic factors. Genome-wide association studies have mapped >90% of CVD-associated variants within the noncoding genome, which can alter the function of regulatory proteins, such as transcription factors (TFs). However, due to the overwhelming number of single-nucleotide polymorphisms (SNPs) (>500,000) in genome-wide association studies, prioritizing variants for in vitro analysis remains challenging. In this work, we implemented a computational approach that considers support vector machine (SVM)-based TF binding site classification and cardiac expression quantitative trait loci (eQTL) analysis to identify and prioritize potential CVD-causing SNPs. We identified 1535 CVD-associated SNPs within TF footprints and putative cardiac enhancers plus 14,218 variants in linkage disequilibrium with genotype-dependent gene expression in cardiac tissues. Using ChIP-seq data from two cardiac TFs (NKX2-5 and TBX5) in human-induced pluripotent stem cell-derived cardiomyocytes, we trained a large-scale gapped k-mer SVM model to identify CVD-associated SNPs that altered NKX2-5 and TBX5 binding. The model was tested by scoring human heart TF genomic footprints within putative enhancers and measuring in vitro binding through electrophoretic mobility shift assay. Five variants predicted to alter NKX2-5 (rs59310144, rs6715570, and rs61872084) and TBX5 (rs7612445 and rs7790964) binding were prioritized for in vitro validation based on the magnitude of the predicted change in binding and are in cardiac tissue eQTLs. All five variants altered NKX2-5 and TBX5 DNA binding. We present a bioinformatic approach that considers tissue-specific eQTL analysis and SVM-based TF binding site classification to prioritize CVD-associated variants for in vitro analysis.

The high mobility group protein HMG20A cooperates with the histone reader PHF14 to modulate TGFß and Hippo pathways.

High mobility group (HMG) proteins are chromatin regulators with essential functions in development, cell differentiation and cell proliferation. The protein HMG20A is predicted by the AlphaFold2 software to contain three distinct structural elements, which we have functionally characterized: i) an amino-terminal, intrinsically disordered domain with transactivation activity; ii) an HMG box with higher binding affinity for double-stranded, four-way-junction DNA than for linear DNA; and iii) a long coiled-coil domain. Our proteomic study followed by a deletion analysis and structural modeling demonstrates that HMG20A forms a complex with the histone reader PHF14, via the establishment of a two-stranded alpha-helical coiled-coil structure. siRNA-mediated knockdown of either PHF14 or HMG20A in MDA-MB-231 cells causes similar defects in cell migration, invasion and homotypic cell-cell adhesion ability, but neither affects proliferation. Transcriptomic analyses demonstrate that PHF14 and HMG20A share a large subset of targets. We show that the PHF14-HMG20A complex modulates the Hippo pathway through a direct interaction with the TEAD1 transcription factor. PHF14 or HMG20A deficiency increases epithelial markers, including E-cadherin and the epithelial master regulator TP63 and impaired normal TGFß-trigged epithelial-to-mesenchymal transition. Taken together, these data indicate that PHF14 and HMG20A cooperate in regulating several pathways involved in epithelial-mesenchymal plasticity.

Impact of Empirical Antibiotic Regimens on Mortality in Neutropenic Patients with Bloodstream Infection Presenting with Septic Shock.

We analyzed risk factors for mortality in febrile neutropenic patients with bloodstream infections (BSI) presenting with septic shock and assessed the impact of empirical antibiotic regimens. A multicenter retrospective study (2010 to 2019) of two prospective cohorts compared BSI episodes in patients with or without septic shock. Multivariate analysis was performed to identify independent risk factors for mortality in episodes with septic shock. Of 1,563 patients with BSI, 257 (16%) presented with septic shock. Those patients with septic shock had higher mortality than those without septic shock (55% versus 15%, P < 0.001). Gram-negative bacilli caused 81% of episodes with septic shock, Gram-positive cocci caused 22%, and Candida species caused 5%. Inappropriate empirical antibiotic treatment (IEAT) was administered in 17.5% of septic shock episodes. Empirical ß-lactam combined with other active antibiotics was associated with the lowest mortality observed. When amikacin was the only active antibiotic, mortality was 90%. Addition of empirical specific Gram-positive coverage had no impact on mortality. Mortality was higher when IEAT was administered (76% versus 51%, P = 0.002). Age of >70 years (odds ratio [OR], 2.3; 95% confidence interval [CI], 1.2 to 4.7), IEAT for Candida spp. or Gram-negative bacilli (OR, 3.8; 95% CI, 1.3 to 11.1), acute kidney injury (OR, 2.6; 95% CI, 1.4 to 4.9), and amikacin as the only active antibiotic (OR, 15.2; 95% CI, 1.7 to 134.5) were independent risk factors for mortality, while the combination of ß-lactam and amikacin was protective (OR, 0.32; 95% CI, 0.18 to 0.57). Septic shock in febrile neutropenic patients with BSI is associated with extremely high mortality, especially when IEAT is administered. Combination therapy including an active ß-lactam and amikacin results in the best outcomes.

Efficient ordering of the Hadamard basis for single pixel imaging.

Single-pixel imaging is a technique that can reconstruct an image of a scene by projecting a series of spatial patterns on an object and capturing the reflected light by a single photodetector. Since the introduction of the compressed sensing method, it has been possible to use random spatial patterns and reduce its number below the Nyquist-Shannon limit to form a good quality image but with lower spatial resolution. On the other hand, Hadamard pattern based methods can reconstruct large images by increasing the acquisition measurement time. Here, we propose an efficient strategy to order the Hadamard basis patterns from higher to lower relevance, and then to reconstruct an image at very low sampling rates of at least 8%. Our proposal is based on the construction of generalized basis vectors in two dimensions and then ordering in zigzag fashion. Simulation and experimental results show that the sampling rate, image quality and computational complexity of our method are competitive to the state of the art methods.

Mid-term follow-up of balloon pulmonary angioplasty for inoperable chronic thromboembolic pulmonary hypertension: An experience in Latin America.

OBJECTIVES: To describe the characteristics of patients who undergo balloon pulmonary angioplasty (BPA) for inoperable chronic thromboembolic pulmonary hypertension (CTEPH) and report the mid-term outcomes. BACKGROUND: BPA has been recently introduced in Latin America. Mid-term results have not been published. METHODS: Prospective Chilean Registry of inoperable CTEPH patients who underwent BPA. Clinical variables were analyzed at baseline, after each procedure and at follow-up. Hemodynamic variables were recorded before and after the last BPA. RESULTS: Between August 2016 and September 2019, 22 patients (17 women), 59 ± 12.7 years, underwent 81 BPA and were followed for as long as 33.1 months (mean 17.3 ± 7.5). Mean pulmonary artery pressure decreased by 17.4% (51.1 ± 12 vs. 42.2 ± 13 mmHg, p = .001), pulmonary vascular resistance by 23.9% (766.7 ± 351 vs. 583 ± 346 dynes/s/cm-5 , p = .001), cardiac index increased by 8% (2.3 ± 0.54 vs. 2.5 ± 0.54 L/min/m2 , p = .012), N-terminal pro-B-type natriuretic peptide decreased by 73.8% (1,685 ± 1,045 vs. 441.8 ± 276 pg/dl, p = .006), and 6-min walk distance improved by 135 m (316.7 ± 94 vs. 451.1 ± 113 m, p = .001). One patient (4.5%) developed lung reperfusion injury and four patients (18.2%) had minor bleeding (hemoptysis), after the procedure. There was no mortality associated with BPA. CONCLUSIONS: Our results confirm that BPA for inoperable CTEPH is a relatively safe procedure that improves clinical and hemodynamic parameters in the mid-term. This therapy should be considered as an alternative, mainly in places where access to PAH therapy or surgery is restricted.

Effects of two personalized dietary strategies during a 2-year intervention in subjects with nonalcoholic fatty liver disease: A randomized trial.

BACKGROUND AND OBJECTIVES: Nonalcoholic fatty liver disease (NAFLD) management is focused on lifestyle modifications, but long-term maintenance is a challenge for many individuals. This study aimed to evaluate the long-term effects of two personalized energy-restricted dietary strategies on weight loss, metabolic and hepatic outcomes in overweight/obese subjects with NAFLD. METHODS: Ninety-eight subjects from the Fatty Liver in Obesity (FLiO) study (NCT03183193) were randomly assigned to the American Heart Association (AHA) or the FLiO dietary group in a 2-year controlled trial. Anthropometry, body composition (DXA), biochemical parameters and hepatic status (ultrasonography, Magnetic Resonance Imaging, and elastography) were assessed at baseline, 6, 12 and 24 months. RESULTS: Both the AHA and FLiO diets significantly reduced body weight at 6 (-9.7% vs -10.1%), 12 (-6.7% vs -9.6%), and 24 months (-4.8% vs -7.6%) with significant improvements in body composition, biochemical and liver determinations throughout the intervention. At the end of the follow-up, the FLiO group showed a greater decrease in ALT, liver stiffness and Fatty Liver Index, among others, compared to AHA group, although these differences were attenuated when the analyses were adjusted by weight loss percentage. The FLiO group also showed a greater increase in adiponectin compared to AHA group. CONCLUSIONS: The AHA and FLiO diets were able to improve body weight and body composition, as well as metabolic and hepatic status of participants with overweight/obesity and NAFLD within a 2-year follow-up. These findings show that both strategies are suitable alternatives for NAFLD management. However, the FLiO strategy may provide more persistent benefits in metabolic and hepatic parameters.

Antibiotic-resistant microorganisms in patients with bloodstream infection of intraabdominal origin: risk factors and impact on mortality.

BACKGROUND: Knowledge of resistance patterns is essential to choose empirical treatment. We aimed to determine the risk factors for antibiotic-resistant microorganisms (ARM) in intraabdominal infections (IAI) and their impact on mortality. METHODS: Retrospective cohort study of patients with bacteremia from IAI origin in a single hospital between January 2006 and July 2017. RESULTS: A total of 1485 episodes were recorded, including 381 (25.6%) due to ARM. Independent predictors of ARM were cirrhosis (OR 2; [95% CI 1.15-3.48]), immunosuppression (OR 1.49; 1.12-1.97), prior ceftazidime exposure (OR 3.7; 1.14-11.9), number of prior antibiotics (OR 2.33; 1.61-3.35 for 1 antibiotic), biliary manipulation (OR 1.53; 1.02-2.96), hospital-acquisition (OR 2.77; 1.89-4) and shock (OR 1.48; 1.07-2). Mortality rate of the whole cohort was 11.1%. Age (OR 1.03; 1.01-1.04), cirrhosis (OR 2.32; 1.07-4.38), urinary catheter (OR 1.99; 1.17-3.38), ultimately (OR 2.28; 1.47-3.51) or rapidly (OR 13.3; 7.12-24.9) fatal underlying disease, nosocomial infection (OR 2.76; 1.6-4.75), peritonitis (OR 1.95, 1.1-3.45), absence of fever (OR 2.17; 1.25-3.77), shock (OR 5.96; 3.89-9.13), and an ARM in non-biliary infections (OR 2.14; 1.19-3.83) were independent predictors of 30-day mortality. Source control (OR 0.24; 0.13-0.44) and 2015-2017 period (OR 0.29; 0.14-0.6) were protective. CONCLUSION: Biliary manipulation and septic shock are predictors of ARM. The presence of an ARM from a non-biliary focus is a poor-prognosis indicator. Source control continues to be of paramount importance.

Fast-Track Liver Transplantation: Six-year Prospective Cohort Study with an Enhanced Recovery After Surgery (ERAS) Protocol.

INTRODUCTION: Enhanced recovery after surgery (ERAS) has been shown to facilitate discharge, decrease length of stay, improve outcomes and reduce costs. We used this concept to design a comprehensive fast-track pathway (OR-to-discharge) before starting our liver transplant activity and then applied this protocol prospectively to every patient undergoing liver transplantation at our institution, monitoring the results periodically. We now report our first six years results. PATIENTS AND METHODS: Prospective cohort study of all the liver transplants performed at our institution for the first six years. Balanced general anesthesia, fluid restriction, thromboelastometry, inferior vena cava preservation and temporary portocaval shunt were strategies common to all cases. Standard immunosuppression administered included steroids, tacrolimus (delayed in the setting of renal impairment, with basiliximab induction added) and mycophenolate mofetil. Tacrolimus dosing was adjusted using a Bayesian estimation methodology. Oral intake and ambulation were started early. RESULTS: A total of 240 transplants were performed in 236 patients (191♂/45♀) over 74 months, mean age 56.3±9.6 years, raw MELD score 15.5±7.7. Predominant etiologies were alcohol (n = 136) and HCV (n = 82), with hepatocellular carcinoma present in 129 (54.7%). Nine patients received combined liver and kidney transplants. The mean operating time was 315±64 min with cold ischemia times of 279±88 min. Thirty-one patients (13.1%) were transfused in the OR (2.4±1.2 units of PRBC). Extubation was immediate (< 30 min) in all but four patients. Median ICU length of stay was 12.7 hours, and median post-transplant hospital stay was 4 days (2-76) with 30 patients (13.8%) going home by day 2, 87 (39.9%) by day 3, and 133 (61%) by day 4, defining our fast-track group. Thirty-day-readmission rate (34.9%) was significantly lower (28.6% vs. 44.7% p=0.015) in the fast-track group. Patient survival was 86.8% at 1 year and 78.6% at five years. CONCLUSION: Fast-Tracking of Liver Transplant patients is feasible and can be applied as the standard of care.

Fruit consumption and cardiometabolic risk in the PREDIMED-plus study: A cross-sectional analysis.

BACKGROUND AND AIMS: Total fruit consumption is important for cardiovascular disease prevention, but also the variety and form in which is consumed. The aim of the study was to assess the associations between total fruit, subgroups of fruits based on their color and fruit juices consumption with different cardiometabolic parameters. METHODS AND RESULTS: A total of 6633 elderly participants (aged 55-75 years) with metabolic syndrome from the PREDIMED-Plus study were included in this analysis. Fruit and fruit juice consumption was assessed using a food frequency questionnaire. Linear regression models were fitted to evaluate the association between exposure variables (total fruit, subgroups based on the color, and fruit juices) and different cardiometabolic risk factors. Individuals in the highest category of total fruit consumption (≥3 servings/d) had lower waist circumference (WC) (ß = -1.04 cm; 95%CI:-1.81, -0.26), fasting glucose levels (ß = -2.41 mg/dL; 95%CI(-4.19, -0.63) and LDL-cholesterol (ß = -4.11 mg/dL; 95%CI:-6.93, -1.36), but, unexpectedly, higher systolic blood pressure (BP) (ß = 1.84 mmHg; 95%CI: 0.37, 3.30) and diastolic BP (ß = 1.69 mmHg; 95%CI:0.83, 2.56) when compared to those in the lowest category of consumption (<1 servings/d). Participants consuming ≥1 serving/day of total fruit juice had lower WC (ß = -0.92 cm; 95%CI:-1.56, -0.27) and glucose levels (ß = -1.59 mg/dL; 95%CI:-2.95, -0.23) than those consuming <1 serving/month. The associations with cardiometabolic risk factors differed according to the color of fruits. CONCLUSION: Fruit consumption is associated with several cardiometabolic risk factors in Mediterranean elders with metabolic syndrome. The associations regarding BP levels could be attributed, at least partially, to reverse causality bias inherent to the cross-sectional design of the study.

De novo design of programmable inducible promoters.

Ligand-responsive allosteric transcription factors (aTF) play a vital role in genetic circuits and high-throughput screening because they transduce biochemical signals into gene expression changes. Programmable control of gene expression from aTF-regulated promoter is important because different downstream effector genes function optimally at different expression levels. However, tuning gene expression of native promoters is difficult due to complex layers of homeostatic regulation encoded within them. We engineered synthetic promoters de novo by embedding operator sites with varying affinities and radically reshaped binding preferences within a minimal, constitutive Escherichia coli promoter. Multiplexed cell-based screening of promoters for three TetR-like aTFs generated with this approach gave rich diversity of gene expression levels, dynamic ranges and ligand sensitivities and were 50- to 100-fold more active over their respective native promoters. Machine learning on our dataset revealed that relative position of the core motif and bases flanking the core motif play an important role in modulating induction response. Our generalized approach yields customizable and programmable aTF-regulated promoters for engineering cellular pathways and enables the discovery of new small molecule biosensors.

Specificity landscapes unmask submaximal binding site preferences of transcription factors.

We have developed Differential Specificity and Energy Landscape (DiSEL) analysis to comprehensively compare DNA-protein interactomes (DPIs) obtained by high-throughput experimental platforms and cutting edge computational methods. While high-affinity DNA binding sites are identified by most methods, DiSEL uncovered nuanced sequence preferences displayed by homologous transcription factors. Pairwise analysis of 726 DPIs uncovered homolog-specific differences at moderate- to low-affinity binding sites (submaximal sites). DiSEL analysis of variants of 41 transcription factors revealed that many disease-causing mutations result in allele-specific changes in binding site preferences. We focused on a set of highly homologous factors that have different biological roles but "read" DNA using identical amino acid side chains. Rather than direct readout, our results indicate that DNA noncontacting side chains allosterically contribute to sculpt distinct sequence preferences among closely related members of transcription factor families.

Estimation of the number of preventable COVID-19 deaths in relation to the restrictive measures adopted in Europe.

INTRODUCTION: In December 2019, a new coronavirus emerged in Wuhan, China, which has become a global health problem. OBJECTIVES: To estimate how many daily COVID-19 deaths per 100,000 population could have been avoided if each one of five restrictive measures had been implemented at the time the first case was diagnosed, and to estimate a multiple linear regression model predictive of the number of deaths per 100,000 population. METHODS: A simple linear regression was performed between the days elapsed since the first COVID-19 diagnosed case, implementation of each one of the five restrictive measures carried out by the 39 European studied countries, the number of hospital beds per 1,000 population (independent variables) and the number of COVID-19 deaths per 100,000 population. RESULTS: For each day elapsed from the first COVID-19 reported case to the adoption of restrictive measures, between 0.611 (p = 0.004) and 1.863 (p = 0.000) patients died per 100,000 population, depending on the implemented measure. CONCLUSIONS: Restrictive measures and social distancing, as well as promptness of their implementation, are necessary for achieving a decrease in COVID-19 infections and mortality.

INTRODUCCIÓN: En diciembre de 2019 surgió un nuevo coronavirus en Wuhan, China, que se ha convertido en un problema de salud global. OBJETIVO: Estimar cuántos fallecimientos diarios atribuibles a COVID-19 por cada 100 000 habitantes se podrían haber evitado si se hubiese llevado a cabo cada una de las cinco medidas restrictivas al momento del diagnóstico del primer caso, así como estimar un modelo de regresión lineal múltiple predictivo del número de fallecimientos por cada 100 000 habitantes. MÉTODOS: Se realizó un modelo de regresión lineal simple entre los días transcurridos desde el primer caso diagnosticado de COVID-19, la implantación de cada una de las cinco medidas llevadas a cabo por los 39 países europeos estudiados, el número de camas hospitalarias por 1000 habitantes (variables independientes) y el número de fallecimientos por COVID-19 por 100 000 habitantes. RESULTADOS: Por cada día transcurrido desde el primer caso notificado de COVID-19 hasta la adopción de las medidas restrictivas, fallecieron entre 0.611 (p = 0.004) y 1.863 (p = 0.000) pacientes por cada 100 000 habitantes, dependiendo de la medida implementada. CONCLUSIONES: Las medidas restrictivas y el distanciamiento social, así como la celeridad de su instauración, son necesarios para lograr el descenso del número de contagios de COVID-19 y su mortalidad.

Estimation of the number of preventable COVID-19 deaths in relation to the restrictive measures adopted in America.

INTRODUCTION: In America, the United States was particularly affected by the COVID-19 pandemic. OBJECTIVES: To estimate how many daily COVID-19 deaths per 100,000 population would have been avoided if each one of five restrictive measures had been implemented at the time of diagnosis and to estimate a multiple linear regression model predictive of the number of deaths per 100,000 population based on the measures adopted by the countries. METHODS: A simple linear regression was performed between the days elapsed since the first COVID-19 diagnosed case and the implementation of each one of the five restrictive measures by the 27 American countries studied and the number of COVID-19 deaths per 100,000 population. RESULTS: For each day between the first COVID-19 reported case and the adoption of restrictive measures, between 0.250 (p = 0.021) and 0.600 (p = 0.001) patients per 100,000 population died, depending on the measure in question. CONCLUSIONS: Adoption of restrictive measures and social distancing are necessary for reducing the number of people infected with COVID-19 and their mortality. In addition, promptness of their establishment is essential in order to reduce the number of deaths.

INTRODUCCIÓN: En América, Estados Unidos se vio particularmente afectado por la pandemia de COVID-19. OBJETIVOS: Estimar cuántas muertes diarias por COVID-19 por 100 000 habitantes se hubiesen evitado si cada una de las cinco medidas restrictivas se hubiera implementado en el momento del diagnóstico, así como estimar un modelo de regresión lineal múltiple predictivo del número de muertes por 100 000 habitantes basado en las medidas adoptadas por los países. MÉTODOS: Se realizó una regresión lineal simple entre los días transcurridos desde el primer caso diagnosticado de COVID-19 y la implantación de cada una de las cinco medidas restrictivas llevadas a cabo por los 27 países americanos estudiados y el número de muertes por COVID-19 por cada 100 000 habitantes. RESULTADOS: Por cada día entre el primer caso reportado de COVID-19 y la adopción de medidas restrictivas, fallecieron entre 0.250 (p = 0.021) y 0.600 (p = 0.001) pacientes por cada 100 000 habitantes, dependiendo de la medida en cuestión. CONCLUSIONES: La adopción de medidas restrictivas y la distancia social son necesarias para reducir el número de personas infectadas con COVID-19 y su mortalidad; además, la velocidad de su establecimiento es esencial para reducir el número de muertes.

A Laser-Activated Membrane Introduction Mass Spectrometry Study of Proton Spillover Promoted Alkane Dehydrogenation.

Operando high-throughput evaluation of heterogeneous catalysts by laser-activated membrane introduction mass spectrometry (LAMIMS) elucidates the Pt loading dependence of methylcyclohexane dehydrogenation on platinized γ-alumina beads. A CO2 marking laser rapidly and sequentially heats catalyst beads positioned on a heat-dissipating carbon paper support that overlays a silicone membrane, separating the bead library reaction zone from a quadrupole mass analyzer. The toluene m/z peak varies logarithmically with Pt loading, suggesting that reactivity includes factors that are negatively correlated to Pt loading. These factors may include the Pt/γ-Al2O3 surface interfacial region as one component of a heterogeneous catalytically active surface area/mass. This work demonstrates LAMIMS as a broadly applicable high-throughput operando screening method for heterogeneous catalysts.

Association between dairy product consumption and hyperuricemia in an elderly population with metabolic syndrome.

BACKGROUND AND AIMS: The prevalence of hyperuricemia has increased substantially in recent decades. It has been suggested that it is an independent risk factor for weight gain, hypertension, hypertriglyceridemia, metabolic syndrome (MetS), and cardiovascular disease. Results from epidemiological studies conducted in different study populations have suggested that high consumption of dairy products is associated with a lower risk of developing hyperuricemia. However, this association is still unclear. The aim of the present study is to explore the association of the consumption of total dairy products and their subtypes with the risk of hyperuricemia in an elderly Mediterranean population with MetS. METHODS AND RESULTS: Baseline cross-sectional analyses were conducted on 6329 men/women (mean age 65 years) with overweight/obesity and MetS from the PREDIMED-Plus cohort. Dairy consumption was assessed using a food frequency questionnaire. Multivariable-adjusted Cox regressions were fitted to analyze the association of quartiles of consumption of total dairy products and their subtypes with the prevalence of hyperuricemia. Participants in the upper quartile of the consumption of total dairy products (multiadjusted prevalence ratio (PR) = 0.84; 95% CI: 0.75-0.94; P-trend 0.02), low-fat dairy products (PR = 0.79; 95% CI: 0.70-0.89; P-trend <0.001), total milk (PR = 0.81; 95% CI: 0.73-0.90; P-trend<0.001), low-fat milk (PR = 0.80; 95% CI: 0.72-0.89; P-trend<0.001, respectively), low-fat yogurt (PR = 0.89; 95% CI: 0.80-0.98; P-trend 0.051), and cheese (PR = 0.86; 95% CI: 0.77-0.96; P-trend 0.003) presented a lower prevalence of hyperuricemia. Whole-fat dairy, fermented dairy, and yogurt consumption were not associated with hyperuricemia. CONCLUSIONS: High consumption of total dairy products, total milk, low-fat dairy products, low-fat milk, low-fat yogurt, and cheese is associated with a lower risk of hyperuricemia.

Flexibility and structure of flanking DNA impact transcription factor affinity for its core motif.

Spatial and temporal expression of genes is essential for maintaining phenotype integrity. Transcription factors (TFs) modulate expression patterns by binding to specific DNA sequences in the genome. Along with the core binding motif, the flanking sequence context can play a role in DNA-TF recognition. Here, we employ high-throughput in vitro and in silico analyses to understand the influence of sequences flanking the cognate sites in binding of three most prevalent eukaryotic TF families (zinc finger, homeodomain and bZIP). In vitro binding preferences of each TF toward the entire DNA sequence space were correlated with a wide range of DNA structural parameters, including DNA flexibility. Results demonstrate that conformational plasticity of flanking regions modulates binding affinity of certain TF families. DNA duplex stability and minor groove width also play an important role in DNA-TF recognition but differ in how exactly they influence the binding in each specific case. Our analyses further reveal that the structural features of preferred flanking sequences are not universal, as similar DNA-binding folds can employ distinct DNA recognition modes.

Current nutritional status assessment tools for metabolic care and clinical nutrition.

PURPOSE OF REVIEW: The aim of this report is to critically review existing questionnaires and tools to assess nutritional status in different populations and pathological conditions. RECENT FINDINGS: A total of 16 instruments to evaluate nutritional status were recorded, which were based on anthropometrical determinations, biochemical markers, clinical examinations and subjective questionnaires, depending on the nutritional assessment focus, involving different concepts: screening of the risk, diagnosis and severity of malnutrition, as well as the consequences of undernutrition or overnutrition. SUMMARY: A variety of questionnaires, equations and tools were found with ability to assess nutritional status for metabolic care or clinical nutrition purposes, but apparently there is no optimal, universal and reliable nutritional status screening system for all metabolic conditions. Novel assessment instruments should provide high sensibility and specificity, be precise and reliable as well as inexpensive and simple, in order to avoid the additional burden of excessive loads of costs, work and time while dynamically overcoming the influence of disease diversity.

Synthetic genome readers target clustered binding sites across diverse chromatin states.

Targeting the genome with sequence-specific DNA-binding molecules is a major goal at the interface of chemistry, biology, and precision medicine. Polyamides, composed of N-methylpyrrole and N-methylimidazole monomers, are a class of synthetic molecules that can be rationally designed to "read" specific DNA sequences. However, the impact of different chromatin states on polyamide binding in live cells remains an unresolved question that impedes their deployment in vivo. Here, we use cross-linking of small molecules to isolate chromatin coupled to sequencing to map the binding of two bioactive and structurally distinct polyamides to genomes directly within live H1 human embryonic stem cells. This genome-wide view from live cells reveals that polyamide-based synthetic genome readers bind cognate sites that span a range of binding affinities. Polyamides can access cognate sites within repressive heterochromatin. The occupancy patterns suggest that polyamides could be harnessed to target loci within regions of the genome that are inaccessible to other DNA-targeting molecules.

Maresin 1 improves insulin sensitivity and attenuates adipose tissue inflammation in ob/ob and diet-induced obese mice.

The beneficial actions of n-3 fatty acids on obesity-induced insulin resistance and inflammation have been related to the synthesis of specialized proresolving lipid mediators (SPMs) like resolvins. The aim of this study was to evaluate the ability of one of these SPMs, maresin 1 (MaR1), to reverse adipose tissue inflammation and/or insulin resistance in two models of obesity: diet-induced obese (DIO) mice and genetic (ob/ob) obese mice. In DIO mice, MaR1 (2 µg/kg; 10 d) reduced F4/80-positive cells and expression of the proinflammatory M1 macrophage phenotype marker Cd11c in white adipose tissue (WAT). Moreover, MaR1 decreased Mcp-1, Tnf-α, and Il-1ß expression, upregulated adiponectin and Glut-4, and increased Akt phosphorylation in WAT. MaR1 administration (2 µg/kg; 20 d) to ob/ob mice did not modify macrophage recruitment but increased the M2 macrophage markers Cd163 and Il-10. MaR1 reduced Mcp-1, Tnf-α, Il-1ß, and Dpp-4 and increased adiponectin gene expression in WAT. MaR1 treatment also improved the insulin tolerance test of ob/ob mice and increased Akt and AMPK phosphorylation in WAT. These data suggest that treatment with MaR1 can counteract the dysfunctional inflamed WAT and could be useful to improve insulin sensitivity in murine models of obesity.-Martínez-Fernández, L., González-Muniesa, P., Laiglesia, L. M., Sáinz, N., Prieto-Hontoria, P. L., Escoté, X., Odriozola, L., Corrales, F. J., Arbones-Mainar, J. M., Martínez, J. A., Moreno-Aliaga, M. J. Maresin 1 improves insulin sensitivity and attenuates adipose tissue inflammation in ob/ob and diet-induced obese mice.

Analysis of the relationship between coexpression domains and chromatin 3D organization.

Gene order is not random in eukaryotic chromosomes, and co-regulated genes tend to be clustered. The mechanisms that determine co-regulation of large regions of the genome and its connection with chromatin three-dimensional (3D) organization are still unclear however. Here we have adapted a recently described method for identifying chromatin topologically associating domains (TADs) to identify coexpression domains (which we term "CODs"). Using human normal breast and breast cancer RNA-seq data, we have identified approximately 500 CODs. CODs in the normal and breast cancer genomes share similar characteristics but differ in their gene composition. COD genes have a greater tendency to be coexpressed with genes that reside in other CODs than with non-COD genes. Such inter-COD coexpression is maintained over large chromosomal distances in the normal genome but is partially lost in the cancer genome. Analyzing the relationship between CODs and chromatin 3D organization using Hi-C contact data, we find that CODs do not correspond to TADs. In fact, intra-TAD gene coexpression is the same as random for most chromosomes. However, the contact profile is similar between gene pairs that reside either in the same COD or in coexpressed CODs. These data indicate that co-regulated genes in the genome present similar patterns of contacts irrespective of the frequency of physical chromatin contacts between them.