Optimal metabolic strategies for microbial growth in stationary random environments.

In order to grow in any given environment, bacteria need to collect information about the medium composition and implement suitable growth strategies by adjusting their regulatory and metabolic degrees of freedom. In the standard sense, optimal strategy selection is achieved when bacteria grow at the fastest rate possible in that medium. While this view of optimality is well suited for cells that have perfect knowledge about their surroundings (e.g. nutrient levels), things are more involved in uncertain or fluctuating conditions, especially when changes occur over timescales comparable to (or faster than) those required to organize a response. Information theory however provides recipes for how cells can choose the optimal growth strategy under uncertainty about the stress levels they will face. Here we analyse the theoretically optimal scenarios for a coarse-grained, experiment-inspired model of bacterial metabolism for growth in a medium described by the (static) probability density of a single variable (the 'stress level'). We show that heterogeneity in growth rates consistently emerges as the optimal response when the environment is sufficiently complex and/or when perfect adjustment of metabolic degrees of freedom is not possible (e.g. due to limited resources). In addition, outcomes close to those achievable with unlimited resources are often attained effectively with a modest amount of fine tuning. In other terms, heterogeneous population structures in complex media may be rather robust with respect to the resources available to probe the environment and adjust reaction rates.

MicroRNAs organize intrinsic variation into stem cell states.

Pluripotent embryonic stem cells (ESCs) contain the potential to form a diverse array of cells with distinct gene expression states, namely the cells of the adult vertebrate. Classically, diversity has been attributed to cells sensing their position with respect to external morphogen gradients. However, an alternative is that diversity arises in part from cooption of fluctuations in the gene regulatory network. Here we find ESCs exhibit intrinsic heterogeneity in the absence of external gradients by forming interconverting cell states. States vary in developmental gene expression programs and display distinct activity of microRNAs (miRNAs). Notably, miRNAs act on neighborhoods of pluripotency genes to increase variation of target genes and cell states. Loss of miRNAs that vary across states reduces target variation and delays state transitions, suggesting variable miRNAs organize and propagate variation to promote state transitions. Together these findings provide insight into how a gene regulatory network can coopt variation intrinsic to cell systems to form robust gene expression states. Interactions between intrinsic heterogeneity and environmental signals may help achieve developmental outcomes.

Relationship between fitness and heterogeneity in exponentially growing microbial populations.

Despite major environmental and genetic differences, microbial metabolic networks are known to generate consistent physiological outcomes across vastly different organisms. This remarkable robustness suggests that, at least in bacteria, metabolic activity may be guided by universal principles. The constrained optimization of evolutionarily motivated objective functions, such as the growth rate, has emerged as the key theoretical assumption for the study of bacterial metabolism. While conceptually and practically useful in many situations, the idea that certain functions are optimized is hard to validate in data. Moreover, it is not always clear how optimality can be reconciled with the high degree of single-cell variability observed in experiments within microbial populations. To shed light on these issues, we develop an inverse modeling framework that connects the fitness of a population of cells (represented by the mean single-cell growth rate) to the underlying metabolic variability through the maximum entropy inference of the distribution of metabolic phenotypes from data. While no clear objective function emerges, we find that, as the medium gets richer, the fitness and inferred variability for Escherichia coli populations follow and slowly approach the theoretically optimal bound defined by minimal reduction of variability at given fitness. These results suggest that bacterial metabolism may be crucially shaped by a population-level trade-off between growth and heterogeneity.

Surgery and outcome of infective endocarditis in octogenarians: prospective data from the ESC EORP EURO-ENDO registry.

PURPOSE: High mortality and a limited performance of valvular surgery are typical features of infective endocarditis (IE) in octogenarians, even though surgical treatment is a major determinant of a successful outcome in IE. METHODS: Data from the prospective multicentre ESC EORP EURO-ENDO registry were used to assess the prognostic role of valvular surgery depending on age. RESULTS: As compared to < 80 yo patients, ≥ 80 yo had lower rates of theoretical indication for valvular surgery (49.1% vs. 60.3%, p < 0.001), of surgery performed (37.0% vs. 75.5%, p < 0.001), and a higher in-hospital (25.9% vs. 15.8%, p < 0.001) and 1-year mortality (41.3% vs. 22.2%, p < 0.001). By multivariable analysis, age per se was not predictive of 1-year mortality, but lack of surgical procedures when indicated was strongly predictive (HR 2.98 [2.43-3.66]). By propensity analysis, 304 ≥ 80 yo were matched to 608 < 80 yo patients. Propensity analysis confirmed the lower rate of indication for valvular surgery (51.3% vs. 57.2%, p = 0.031) and of surgery performed (35.3% vs. 68.4%, p < 0.0001) in ≥ 80 yo. Overall mortality remained higher in ≥ 80 yo (in-hospital: HR 1.50[1.06-2.13], p = 0.0210; 1-yr: HR 1.58[1.21-2.05], p = 0.0006), but was not different from that of < 80 yo among those who had surgery (in-hospital: 19.7% vs. 20.0%, p = 0.4236; 1-year: 27.3% vs. 25.5%, p = 0.7176). CONCLUSION: Although mortality rates are consistently higher in ≥ 80 yo patients than in < 80 yo patients in the general population, mortality of surgery in ≥ 80 yo is similar to < 80 yo after matching patients. These results confirm the importance of a better recognition of surgical indication and of an increased performance of surgery in ≥ 80 yo patients.

Use of Pericardium for Cardiac Reconstruction Procedures in Acquired Heart Diseases-A Comprehensive Review.

BACKGROUND: Reconstruction of cardiac structures has been the goal of many surgeons even before the advent of open-heart procedures with cardiopulmonary bypass. Unsatisfactory results with synthetic materials has switched the attention to biological tissues, among which pericardium, either autologous or of animal origin, has been widely used as patch material. METHODS: We have reviewed the literature to assess the effective role of pericardial tissue in the correction of various acquired cardiac lesions. Particularly, special attention was given not only to established techniques but also to detect any peculiar and unusual application of pericardium. RESULTS: Autologous pericardium is frequently used as patch material particularly when limited valvular lesions must be corrected, while xenograft pericardium appears particularly useful in patients with endocarditis and extensive destruction of the intracardiac structures by infection and abscesses. Pericardium is an extremely versatile material owing to its pliability and strength; however, it tends to calcify in the long term when in contact with blood, although stability of the repair is maintained in most cases. CONCLUSIONS: Pericardium plays an important role in various cardiac and aortic pathologies. Tissues resistant to fibrosis and calcification to be used as patch material are the ideal solution for more successful cardiac reconstruction procedures and will hopefully be provided by the ongoing research.

Path-integral solution of MacArthur's resource-competition model for large ecosystems with random species-resources couplings.

We solve MacArthur's resource-competition model with random species-resource couplings in the "thermodynamic" limit of infinitely many species and resources using dynamical path integrals à la De Domincis. We analyze how the steady state picture changes upon modifying several parameters, including the degree of heterogeneity of metabolic strategies (encoding the preferences of species) and of maximal resource levels (carrying capacities), and discuss its stability. Ultimately, the scenario obtained by other approaches is recovered by analyzing an effective one-species-one-resource ecosystem that is fully equivalent to the original multi-species one. The technique used here can be applied for the analysis of other model ecosystems related to the version of MacArthur's model considered here.

Endothelial Progenitor Cells: An Appraisal of Relevant Data from Bench to Bedside.

The mobilization of endothelial progenitor cells (EPCs) into circulation from bone marrow is well known to be present in several clinical settings, including acute coronary syndrome, heart failure, diabetes and peripheral vascular disease. The aim of this review was to explore the current literature focusing on the great opportunity that EPCs can have in terms of regenerative medicine.

Competing endogenous RNA crosstalk at system level.

microRNAs (miRNAs) regulate gene expression at post-transcriptional level by repressing target RNA molecules. Competition to bind miRNAs tends in turn to correlate their targets, establishing effective RNA-RNA interactions that can influence expression levels, buffer fluctuations and promote signal propagation. Such a potential has been characterized mathematically for small motifs both at steady state and away from stationarity. Experimental evidence, on the other hand, suggests that competing endogenous RNA (ceRNA) crosstalk is rather weak. Extended miRNA-RNA networks could however favour the integration of many crosstalk interactions, leading to significant large-scale effects in spite of the weakness of individual links. To clarify the extent to which crosstalk is sustained by the miRNA interactome, we have studied its emergent systemic features in silico in large-scale miRNA-RNA network reconstructions. We show that, although generically weak, system-level crosstalk patterns (i) are enhanced by transcriptional heterogeneities, (ii) can achieve high-intensity even for RNAs that are not co-regulated, (iii) are robust to variability in transcription rates, and (iv) are significantly non-local, i.e. correlate weakly with miRNA-RNA interaction parameters. Furthermore, RNA levels are generically more stable when crosstalk is strongest. As some of these features appear to be encoded in the network's topology, crosstalk may functionally be favoured by natural selection. These results suggest that, besides their repressive role, miRNAs mediate a weak but resilient and context-independent network of cross-regulatory interactions that interconnect the transcriptome, stabilize expression levels and support system-level responses.

Durability of the Mitroflow Pericardial Prosthesis: Influence of Patient-Prosthesis Mismatch and New Anticalcification Treatment.

BACKGROUND: The Mitroflow pericardial bioprosthesis (MPB) has been recently associated with a high incidence of early structural failures, questioning its validity as cardiac valve substitute. We have therefore reviewed our experience with this device. MATERIALS AND METHODS: A total of 398 patients with a mean age of 75 ± 7 years (58% above the age of 75 years) had aortic valve replacement with a Mitroflow prosthesis (2005-2015). Most patients had calcific aortic stenosis (86%) and were in sinus rhythm (89%). Mean EuroSCORE II was 5.5 ± 6.2. Mean follow-up was 4 ± 2 years (range: 4 months to 10 years), which was 100% complete. RESULTS: Hospital mortality was 6.5%; at discharge, 25% of patients had a moderate patient-prosthesis mismatch and none had a severe mismatch. Cumulative incidence of structural valve deterioration in the entire series was 2% (95% confidence interval [CI]: 1-4) at 5 years and 7% (95% CI: 4-14) at 8 years. Significant factors influencing MPB durability were age ≤ 65 years (p < 0.001) and the presence of patient-prosthesis mismatch (p = 0.01). No cases of structural valve deterioration were observed in patients with the new prosthetic model incorporating an anticalcification treatment the first 4 years of follow-up. CONCLUSIONS: The Mitroflow prosthesis has shown satisfactory results in the first decade of use. Durability appears adversely influenced by patient age and patient-prosthesis mismatch. Thus, a careful valve size selection and implantation in patients >65 years of age appears to be associated with excellent valve durability in the aortic position. Whether the new anticalcification treatment will provide a more durable prosthesis must be verified at a longer follow-up.

Acute aortic dissection and pregnancy: Review and meta-analysis of incidence, presentation, and pathologic substrates.

OBJECTIVES: Pregnancy has been recognized as a predisposing factor for acute aortic dissection (AAD) although its occurrence is quite rare. Currently, no trial and few prospective studies exist about this catastrophic event. The present review and meta-analysis aims to update information on clinical presentation, potential risk factors, treatment, and outcome of acute dissection during pregnancy and puerperium. METHODS: A comprehensive search of three databases was performed to identify all patients reported in articles published from January 1987. A proportional single-arm meta-analysis with random-effects model was used to pool these variables: risk factors, pregnancy/postpartum occurrence, surgical characteristics, and outcomes. RESULTS: A total of 11 reports and 85 patients with pregnancy-related AAD were available for this study. The prevalence of connective tissue disorders was 62%, Marfan syndrome being the most common. Out of 76 patients, 46 (61%) had dissection during pregnancy and 30 (39%) during puerperium; 40% of events occurred in primigravidae and 60% in multigravidae. Type A and type B dissection occurred in 67% vs 33% of patients. Surgery was performed in 73% of cases with a maternal and fetal mortality of 23% and 27%, respectively. CONCLUSIONS: Throughout pregnancy, AAD is quite rare but fatal, especially in Marfan and Loeys-Dietz syndromes, while isolated bicuspid aortic valve is not a risk factor. Even in Marfan syndrome, pathogenesis and evolution of the disease are still unclear. Occurrence of dissection also during puerperium indicates the need for continuous counselling and aortic size monitoring in women at-risk.

Cell differentiation in cardiac myxomas: confocal microscopy and gene expression analysis after laser capture microdissection.

Cardiac myxomas are rare tumors with a heterogeneous cell population including properly neoplastic (lepidic), endothelial and smooth muscle cells. The assessment of neoplastic (lepidic) cell differentiation pattern is rather difficult using conventional light microscopy immunohistochemistry and/or whole tissue extracts for mRNA analyses. In a preliminary study, we investigated 20 formalin-fixed and paraffin-embedded cardiac myxomas by means of conventional immunohistochemistry; in 10/20 cases, cell differentiation was also analyzed by real-time RT-PCR after laser capture microdissection of the neoplastic cells, whereas calretinin and endothelial antigen CD31 immunoreactivity was localized in 4/10 cases by double immunofluorescence confocal microscopy. Gene expression analyses of α-smooth muscle actin, endothelial CD31 antigen, alpha-cardiac actin, matrix metalloprotease-2 (MMP2) and tissue inhibitor of matrix metalloprotease-1 (TIMP1) was performed on cDNA obtained from either microdissected neoplastic cells or whole tumor sections. We found very little or absent CD31 and α-Smooth Muscle Actin expression in the microdissected cells as compared to the whole tumors, whereas TIMP1 and MMP2 genes were highly expressed in both ones, greater levels being found in patients with embolic phenomena. α-Cardiac Actin was not detected. Confocal microscopy disclosed two different signals corresponding to calretinin-positive myxoma cells and to endothelial CD31-positive cells, respectively. In conclusion, the neoplastic (lepidic) cells showed a distinct gene expression pattern and no consistent overlapping with endothelial and smooth muscle cells or cardiac myocytes; the expression of TIMP1 and MMP2 might be related to clinical presentation; larger series studies using also systematic transcriptome analysis might be useful to confirm the present results.

Translating ceRNA Susceptibilities into Correlation Functions.

Competition to bind microRNAs induces an effective positive cross talk between their targets, which are therefore known as "competing endogenous RNAs" (ceRNAs). Although such an effect is known to play a significant role in specific situations, estimating its strength from data and experimentally in physiological conditions appears to be far from simple. Here, we show that the susceptibility of ceRNAs to different types of perturbations affecting their competitors (and hence their tendency to cross talk) can be encoded in quantities as intuitive and as simple to measure as correlation functions. This scenario is confirmed by extensive numerical simulations and validated by re-analyzing phosphatase and tensin homolog's cross-talk pattern from The Cancer Genome Atlas breast cancer database. These results clarify the links between different quantities used to estimate the intensity of ceRNA cross talk and provide, to our knowledge, new keys to analyze transcriptional data sets and effectively probe ceRNA networks in silico.

Independent channels for miRNA biosynthesis ensure efficient static and dynamic control in the regulation of the early stages of myogenesis.

Motivated by recent experimental work, we define and study a deterministic model of the complex miRNA-based regulatory circuit that putatively controls the early stage of myogenesis in human. We aim in particular at a quantitative understanding of (i) the roles played by the separate and independent miRNA biosynthesis channels (one involving a miRNA-decoy system regulated by an exogenous controller, the other given by transcription from a distinct genomic locus) that appear to be crucial for the differentiation program, and of (ii) how competition to bind miRNAs can efficiently control molecular levels in such an interconnected architecture. We show that optimal static control via the miRNA-decoy system constrains kinetic parameters in narrow ranges where the channels are tightly cross-linked. On the other hand, the alternative locus for miRNA transcription can ensure that the fast concentration shifts required by the differentiation program are achieved, specifically via non-linear response of the target to even modest surges in the miRNA transcription rate. While static, competition-mediated regulation can be achieved by the miRNA-decoy system alone, both channels are essential for the circuit's overall functionality, suggesting that that this type of joint control may represent a minimal optimal architecture in different contexts.

Probing the Limits to MicroRNA-Mediated Control of Gene Expression.

According to the 'ceRNA hypothesis', microRNAs (miRNAs) may act as mediators of an effective positive interaction between long coding or non-coding RNA molecules, carrying significant potential implications for a variety of biological processes. Here, inspired by recent work providing a quantitative description of small regulatory elements as information-conveying channels, we characterize the effectiveness of miRNA-mediated regulation in terms of the optimal information flow achievable between modulator (transcription factors) and target nodes (long RNAs). Our findings show that, while a sufficiently large degree of target derepression is needed to activate miRNA-mediated transmission, (a) in case of differential mechanisms of complex processing and/or transcriptional capabilities, regulation by a post-transcriptional miRNA-channel can outperform that achieved through direct transcriptional control; moreover, (b) in the presence of large populations of weakly interacting miRNA molecules the extra noise coming from titration disappears, allowing the miRNA-channel to process information as effectively as the direct channel. These observations establish the limits of miRNA-mediated post-transcriptional cross-talk and suggest that, besides providing a degree of noise buffering, this type of control may be effectively employed in cells both as a failsafe mechanism and as a preferential fine tuner of gene expression, pointing to the specific situations in which each of these functionalities is maximized.

Constrained Allocation Flux Balance Analysis.

New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement Flux Balance Analysis. We introduce here Constrained Allocation Flux Balance Analysis, CAFBA, in which the biosynthetic costs associated to growth are accounted for in an effective way through a single additional genome-wide constraint. Its roots lie in the experimentally observed pattern of proteome allocation for metabolic functions, allowing to bridge regulation and metabolism in a transparent way under the principle of growth-rate maximization. We provide a simple method to solve CAFBA efficiently and propose an "ensemble averaging" procedure to account for unknown protein costs. Applying this approach to modeling E. coli metabolism, we find that, as the growth rate increases, CAFBA solutions cross over from respiratory, growth-yield maximizing states (preferred at slow growth) to fermentative states with carbon overflow (preferred at fast growth). In addition, CAFBA allows for quantitatively accurate predictions on the rate of acetate excretion and growth yield based on only 3 parameters determined by empirical growth laws.

Micro-RNA-21 (biomarker) and global longitudinal strain (functional marker) in detection of myocardial fibrotic burden in severe aortic valve stenosis: a pilot study.

AIMS: Myocardial fibrosis (MF) is a deleterious consequence of aortic valve stenosis (AVS). Global longitudinal strain (GLS) is a novel left ventricular (LV) functional parameter potentially useful to non-invasively estimate MF. MicroRNAs (miRNAs) are non-coding small ribonucleic acids (RNA) modulating genes function, mainly through RNA degradation. miRNA-21 is a biomarker associated with MF in pressure overload. The aim of the present study was to find an integrated algorithm for detection of MF using a combined approach with both bio- and functional markers. METHODS: Thirty-six patients (75.2 ± 8 y.o.; 63 % Female) with severe AVS and preserved LV ejection fraction (EF), candidate to surgical aortic valve replacement (sAVR) were enrolled. Clinical, bio-humoral evaluation (including plasmatic miRNA-21 collected using specific tubes, PAXgene, for stabilization of peripheral RNA) and a complete echocardiographic study, including GLS and septal strain, were performed before sAVR. Twenty-eight of those patients underwent sAVR and, in 23 of them, an inter-ventricular septum biopsy was performed. Tissues were fixed in formalin and embedded in paraffin. Sections were stained with Hematoxylin and Eosin for histological evaluation and with histochemical Masson trichrome for collagen fibers. The different components were calculated and expressed as micrometers(2). To evaluate tissue miRNA components, sections 2-µm thick were cut using a microtome blade for each slide. Regression analysis was performed to test association between dependent variable and various predictors included in the model. RESULTS: Despite a preserved EF (66 ± 11 %), patients presented altered myocardial deformation parameters (GLS -14,02 ± 3.8 %; septal longitudinal strain, SSL -9.63 ± 2.9 %; septal longitudinal strain rate, SL-Sr -0.58 ± 0.17 1/s; Septal Longitudinal early-diastolic strain rate, SL-SrE 0.62 ± 0.32 1/s). The extent of MF showed an inverse association with both GLS and septal longitudinal deformation indices (GLS: R(2) = 0.30; p = 0.02; SSL: R(2) = 0.36; p = 0.01; SL-Sr: R(2) = 0.39; p < 0.001; SL-SrE: R(2) = 0.35; p = 0.001). miRNA-21 was mainly expressed in fibrous tissue (p < 0.0001). A significant association between MF and plasmatic miRNA-21, alone and weighted for measures of structural (LVMi R(2) = 0.50; p = 0.0005) and functional (SSL R(2) = 0.35; p = 0.006) remodeling, was found. CONCLUSIONS: In AVS, MF is associated with alterations of regional and global strain. Plasmatic miRNA-21 is directly related to MF and associated with LV structural and functional impairment.

RNA-based regulation: dynamics and response to perturbations of competing RNAs.

The observation that, through a titration mechanism, microRNAs (miRNAs) can act as mediators of effective interactions among their common targets (competing endogenous RNAs or ceRNAs) has brought forward the idea (i.e., the ceRNA hypothesis) that RNAs can regulate each other in extended cross-talk networks. Such an ability might play a major role in posttranscriptional regulation to shape a cell's protein repertoire. Recent work focusing on the emergent properties of the cross-talk networks has emphasized the high flexibility and selectivity that may be achieved at stationarity. On the other hand, dynamical aspects, possibly crucial on the relevant timescales, are far less clear. We have carried out a dynamical study of the ceRNA hypothesis on a model of posttranscriptional regulation. Sensitivity analysis shows that ceRNA cross-talk is dynamically extended, i.e., it may take place on timescales shorter than those required to achieve stationarity even in cases where no cross-talk occurs in the steady state, and is possibly amplified. In addition, in the case of large, transfection-like perturbations, the system may develop a strongly nonlinear, threshold response. Finally, we show that the ceRNA effect provides a very efficient way for a cell to achieve fast positive shifts in the level of a ceRNA when necessary. These results indicate that competition for miRNAs may indeed provide an elementary mechanism to achieve system-level regulatory effects on the transcriptome over physiologically relevant timescales.