Cytokines and growth factors cross-link heparan sulfate

The glycosaminoglycan heparan sulfate (HS), present at the surface of most cells and ubiquitous in extracellular matrix, binds many soluble extracellular signalling molecules such as chemokines and growth factors, and regulates their transport and effector functions. It is, however, unknown whether upon binding HS these proteins can affect the long-range structure of HS. To test this idea, we interrogated a supramolecular model system, in which HS chains grafted to streptavidin-functionalized oligoethylene glycol monolayers or supported lipid bilayers mimic the HS-rich pericellular or extracellular matrix, with the biophysical techniques quartz crystal microbalance (QCM-D) and fluorescence recovery after photobleaching (FRAP). We were able to control and characterize the supramolecular presentation of HS chains—their local density, orientation, conformation and lateral mobility—and their interaction with proteins. The chemokine CXCL12α (or SDF-1α) rigidified the HS film, and this effect was due to protein-mediated cross-linking of HS chains. Complementary measurements with CXCL12α mutants and the CXCL12γ isoform provided insight into the molecular mechanism underlying cross-linking. Fibroblast growth factor 2 (FGF-2), which has three HS binding sites, was also found to cross-link HS, but FGF-9, which has just one binding site, did not. Based on these data, we propose that the ability to cross-link HS is a generic feature of many cytokines and growth factors, which depends on the architecture of their HS binding sites. The ability to change matrix organization and physico-chemical properties (e.g. permeability and rigidification) implies that the functions of cytokines and growth factors may not simply be confined to the activation of cognate cellular receptors.     

Solvent-free enzymatic production of high quality cetyl esters

A solvent-free biocatalytic process for the synthesis of high quality cetyl laurate, myristate, palmitate and stearate has been optimized. This enzymatic procedure follows the fundamental principles of the Green Chemistry and lead to sustainable products, which can be labeled as natural and conform to the principal requirements for its use in high value-added goods. The four esters selected are the main components of spermaceti, a mixture of waxes very appreciated in cosmetic and pharmacy because of its physical properties and emolliency, which was formerly extracted from the head of the sperm whales. In this paper, the influence of the amount of biocatalyst, the commercially available Novozym^® 435, and the temperature were studied in an open-air batch reactor before carrying out the synthesis in a high performance vacuum reactor with dry nitrogen input to shift the equilibrium towards product formation. Under optimal conditions, conversion was higher than 98.5 %. The characterization of the enzymatic cetyl esters puts in evidence that these are ultra-pure compounds, which have similar properties to the ones obtained through the conventional industrial processes with the extra benefit of being environmentally friendly.     

Using restraints in EROS-DOCK improves model quality in pairwise and multicomponent protein docking

Protein docking algorithms aim to predict the 3D structure of a protein complex from the structures of its separated components. In the past, most docking algorithms focused on docking pairs of proteins to form dimeric complexes. However, attention is now turning towards the more difficult problem of using docking methods to predict the structures of multicomponent complexes. In both cases, however, the constituent proteins often change conformation upon complex formation, and this can cause many algorithms to fail to detect near-native binding orientations due to the high number of atomic steric clashes in the list of candidate solutions. An increasingly popular way to retain more near-native orientations is to define one or more restraints that serve to modulate or override the effect of steric clashes. Here, we present an updated version of our “EROS-DOCK” docking algorithm which has been extended to dock arbitrary dimeric and trimeric complexes, and to allow the user to define residue-residue or atom-atom interaction restraints. Our results show that using even just one residue-residue restraint in each interaction interface is sufficient to increase the number of cases with acceptable solutions within the top 10 from 51 to 121 out of 173 pairwise docking cases, and to successfully dock 8 out of 11 trimeric complexes.     

Genetic Features of Metachronous Esophageal Cancer Developed in Hodgkin’s Lymphoma or Breast Cancer Long-Term Survivors: An Exploratory Study

BackgroundDevelopment of novel therapeutic drugs and regimens for cancer treatment has led to improvements in patient long-term survival. This success has, however, been accompanied by the increased occurrence of second primary cancers. Indeed, patients who received regional radiotherapy for Hodgkin’s Lymphoma (HL) or breast cancer may develop, many years later, a solid metachronous tumor in the irradiated field. Despite extensive epidemiological studies, little information is available on the genetic changes involved in the pathogenesis of these solid therapy-related neoplasms.MethodsUsing microsatellite markers located in 7 chromosomal regions frequently deleted in sporadic esophageal cancer, we investigated loss of heterozygosity (LOH) and microsatellite instability (MSI) in 46 paired (normal and tumor) samples. Twenty samples were of esophageal carcinoma developed in HL or breast cancer long-term survivors: 14 squamous cell carcinomas (ESCC) and 6 adenocarcinomas (EADC), while 26 samples, used as control, were of sporadic esophageal cancer (15 ESCC and 11 EADC).ResultsWe found that, though the overall LOH frequency at the studied chromosomal regions was similar among metachronous and sporadic tumors, the latter exhibited a statistically different higher LOH frequency at 17q21.31 (p = 0.018). By stratifying for tumor histotype we observed that LOH at 3p24.1, 5q11.2 and 9p21.3 were more frequent in ESCC than in EADC suggesting a different role of the genetic determinants located nearby these regions in the development of the two esophageal cancer histotypes.ConclusionsAltogether, our results strengthen the genetic diversity among ESCC and EADC whether they occurred spontaneously or after therapeutic treatments. The presence of histotype-specific alterations in esophageal carcinoma arisen in HL or breast cancer long-term survivors suggests that their transformation process, though the putative different etiological origin, may retrace sporadic ESCC and EADC carcinogenesis.     

Analysis of microbiota in cultures of the green microalga Tetraselmis suecica

ABSTRACT

Bacteria associated with microalgae strongly affect algal biomass and derived product yield and quality. Nevertheless, only a few studies have addressed the detailed phylogenetic characterization of bacterial communities associated with microalgae. In this study, the phycospheric bacterial communities associated with different Tetraselmis suecica F&M-M33 cultures, a green marine microalga with several industrial applications, were analysed using a metagenomic approach. The T. suecica F&M-M33 cultures used originated from the same ancestral microalgal non-axenic culture but were physically and geographically separated for years and maintained under different growing conditions. Despite the different history of the cultures, a ‘core’ bacterial community was identified, accounting for 70% of the total bacterial community and formed by at least 13 families. Among the ‘core’ operational taxonomic units (OTUs), 24 different genera were identified. Nevertheless, there was a high variability in the relative proportions of the taxa forming the ‘core’ community, indicating that the growing conditions and/or external contamination influence the relative abundance of these microorganisms. Our study allowed the identification of persistent taxa that may be used to deepen the knowledge of the complex relationship between T. suecica and its associated bacteria.     

Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum

Biological species may remain distinct because of genetic isolation or ecological adaptation, but these two aspects do not always coincide. To establish the nature of the species boundary within a local bacterial population, we characterized a sympatric population of the bacterium Rhizobium leguminosarum by genomic sequencing of 72 isolates. Although all strains have 16S rRNA typical of R. leguminosarum, they fall into five genospecies by the criterion of average nucleotide identity (ANI). Many genes, on plasmids as well as the chromosome, support this division: recombination of core genes has been largely within genospecies. Nevertheless, variation in ecological properties, including symbiotic host range and carbon-source utilization, cuts across these genospecies, so that none of these phenotypes is diagnostic of genospecies. This phenotypic variation is conferred by mobile genes. The genospecies meet the Mayr criteria for biological species in respect of their core genes, but do not correspond to coherent ecological groups, so periodic selection may not be effective in purging variation within them. The population structure is incompatible with traditional ‘polyphasic taxonomy′ that requires bacterial species to have both phylogenetic coherence and distinctive phenotypes. More generally, genomics has revealed that many bacterial species share adaptive modules by horizontal gene transfer, and we envisage a more consistent taxonomic framework that explicitly recognizes this. Significant phenotypes should be recognized as ‘biovars'' within species that are defined by core gene phylogeny.     

Effects of 5-Fluorouracil on Morphology,Cell Cycle,Proliferation, Apoptosis,Autophagy and ROS Production in Endothelial Cells and Cardiomyocytes

Antimetabolites are a class of effective anticancer drugs interfering in essential biochemical processes. 5-Fluorouracil (5-FU) and its prodrug Capecitabine are widely used in the treatment of several solid tumors (gastro-intestinal, gynecological, head and neck, breast carcinomas). Therapy with fluoropyrimidines is associated with a wide range of adverse effects, including diarrhea, dehydration, abdominal pain, nausea, stomatitis, and hand-foot syndrome. Among the 5-FU side effects, increasing attention is given to cardiovascular toxicities induced at different levels and intensities. Since the mechanisms related to 5-FU-induced cardiotoxicity are still unclear, we examined the effects of 5-FU on primary cell cultures of human cardiomyocytes and endothelial cells, which represent two key components of the cardiovascular system. We analyzed at the cellular and molecular level 5-FU effects on cell proliferation, cell cycle, survival and induction of apoptosis, in an experimental cardioncology approach. We observed autophagic features at the ultrastructural and molecular levels, in particular in 5-FU exposed cardiomyocytes. Reactive oxygen species (ROS) elevation characterized the endothelial response. These responses were prevented by a ROS scavenger. We found induction of a senescent phenotype on both cell types treated with 5-FU. In vivo, in a xenograft model of colon cancer, we showed that 5-FU treatment induced ultrastructural changes in the endothelium of various organs. Taken together, our data suggest that 5-FU can affect, both at the cellular and molecular levels, two key cell types of the cardiovascular system, potentially explaining some manifestations of 5-FU-induced cardiovascular toxicity.     

Human and Machine Learning in Non-Markovian Decision Making

Humans can learn under a wide variety of feedback conditions. Reinforcement learning (RL), where a series of rewarded decisions must be made, is a particularly important type of learning. Computational and behavioral studies of RL have focused mainly on Markovian decision processes, where the next state depends on only the current state and action. Little is known about non-Markovian decision making, where the next state depends on more than the current state and action. Learning is non-Markovian, for example, when there is no unique mapping between actions and feedback. We have produced a model based on spiking neurons that can handle these non-Markovian conditions by performing policy gradient descent [1]. Here, we examine the model’s performance and compare it with human learning and a Bayes optimal reference, which provides an upper-bound on performance. We find that in all cases, our population of spiking neurons model well-describes human performance.