Bioinformatic tools for DNA methylation and histone modification: A survey

Epigenetic inheritance occurs due to different mechanisms such as chromatin and histone modifications, DNA methylation and processes mediated by non-coding RNAs. It leads to changes in gene expressions and the emergence of new traits in different organisms in many diseases such as cancer. Recent advances in experimental methods led to the identification of epigenetic target sites in various organisms. Computational approaches have enabled us to analyze mass data produced by these methods. Next-generation sequencing (NGS) methods have been broadly used to identify these target sites and their patterns. By using these patterns, the emergence of diseases could be prognosticated. In this study, target site prediction tools for two major epigenetic mechanisms comprising histone modification and DNA methylation are reviewed. Publicly accessible databases are reviewed as well. Some suggestions regarding the state-of-the-art methods and databases have been made, including examining patterns of epigenetic changes that are important in epigenotypes detection.     

Coexpression of IL-5 and eotaxin-2 in mice creates an eosinophil-dependent model of respiratory inflammation with characteristics of severe asthma

Mouse models of allergen provocation and/or transgenic gene expression have provided significant insights regarding the cellular, molecular, and immune responses linked to the pathologies occurring as a result of allergic respiratory inflammation. Nonetheless, the inability to replicate the eosinophil activities occurring in patients with asthma has limited their usefulness to understand the larger role(s) of eosinophils in disease pathologies. These limitations have led us to develop an allergen-naive double transgenic mouse model that expresses IL-5 systemically from mature T cells and eotaxin-2 locally from lung epithelial cells. We show that these mice develop several pulmonary pathologies representative of severe asthma, including structural remodeling events such as epithelial desquamation and mucus hypersecretion leading to airway obstruction, subepithelial fibrosis, airway smooth muscle hyperplasia, and pathophysiological changes exemplified by exacerbated methacholine-induced airway hyperresponsiveness. More importantly, and similar to human patients, the pulmonary pathologies observed are accompanied by extensive eosinophil degranulation. Genetic ablation of all eosinophils from this double transgenic model abolished the induced pulmonary pathologies, demonstrating that these pathologies are a consequence of one or more eosinophil effector functions.     

Invertebrate cytokines: the phylogenetic emergence of interleukin-1

Cytokines are polypeptides released by activated vertebrate blood cells which have profound effects on other blood cells and which have hormone-like properties affecting other organ systems as well. In recent years a wide variety of these mediators has been isolated and characterized. Many of these molecules have subsequently been cloned and expressed in E. coli. The tremendous importance of these proteins to host immune and non-specific defense systems along with the striking similarities of their properties among different species suggested to us that cytokines may have been proteins that have been conserved through evolution. Investigations of the evolution of cytokines will help us decipher the complex cellular, humoral and molecular interactions that regulate host defenses. Studies of the invertebrates will shed light on the phylogenetic emergence of these molecules as well.     

The Origin of Species by Means of Mathematical Modelling

Darwin described biological species as groups of morphologically similar individuals. These groups of individuals can split into several subgroups due to natural selection, resulting in the emergence of new species. Some species can stay stable without the appearance of a new species, some others can disappear or evolve. Some of these evolutionary patterns were described in our previous works independently of each other. In this work we have developed a single model which allows us to reproduce the principal patterns in Darwin’s diagram. Some more complex evolutionary patterns are also observed. The relation between Darwin’s definition of species, stated above, and Mayr’s definition of species (group of individuals that can reproduce) is also discussed.     

Synthesis of bi-substrate state mimics of dihydropteroate synthase as potential inhibitors and molecular probes

The increasing emergence of resistant bacteria drives us to design and develop new antimicrobial agents. Pursuant to that goal, a new targeting approach of the dihydropteroate synthase enzyme, which serves as the site of action for the sulfonamide class of antimicrobial agents, is being explored. Using structural information, a new class of transition state mimics has been designed and synthesized that have the capacity to bind to the pterin, phosphate and para-amino binding sites. The design, synthesis and evaluation of these compounds as inhibitors of Bacillusanthracis dihydropteroate synthase is described herein. Outcomes from this work have identified the first trivalent inhibitors of dihydropteroate synthase whose activity displayed slow binding inhibition. The most active compounds in this series contained an oxidized pterin ring. The binding of these inhibitors was modeled into the dihydropteroate synthase active site and demonstrated a good correlation with the observed bioassay data, as well as provided important insight for the future design of higher affinity transition state mimics.     

Disease model: hyperinsulinemia and insulin resistance. Part B--polygenic and other animal models

Deficiency of leptin or its receptor produces hyperinsulinemia with marked obesity. Paradoxically, severe insulin resistance also accompanies lipodystrophy. Animal models of these contrasting conditions have enabled us to observe the profound and complicated aspects of the underlying pathologies. In addition, conventional polygenic rodents with known genetic backgrounds, such as the spontaneously hypertensive rat and the Goto-Kakisaki rat, have also been used to investigate these abnormalities.     

Endocannabinoids and basal ganglia functionality

In recent years, our knowledge on the cannabinoid pharmacology has shown a significant rise in terms of both quantity (more compounds and more targets) and quality (more selective compounds). This allows to consider cannabinoids and related compounds as a promising new line of research for therapeutic treatment of a variety of conditions, such as brain injury, chronic pain, glaucoma, asthma, cancer and AIDS-associated effects and other pathologies. Motor disorders are another promising field for the therapeutic application of cannabinoid-related compounds, since the control of movement is one of the more relevant physiological roles of the endocannabinoid transmission in the brain. There are two pathologies, Parkinson's disease and Huntington's chorea, which are particularly interesting from a clinical point of view due to the direct relationship of endocannabinoids and their receptors with neurons that degenerate in those disorders. However, other neurological pathologies, such as Alzheimer's disease or multiple sclerosis, which are not motor disorders in origin, but present a strong alteration in the control of movement, have also been a subject of interesting research for a cannabinoid therapy. This review will summarize our current knowledge on the role of these endogenous substances in the control of movement and, in particular, on the possible therapeutic usefulness of these compounds in the treatment of motor pathologies.     

The fight against epizootics in the 21st Century

The fight against epizootics is today better organized. The tools, methods and strategies used work well and are constantly being improved, which is necessary since disease epidemiology is evolving extremely fast, dominated by a growing complexity associated to global changes and the emergence of new pathologies. The foundation of the strategy is still based on a permanent epidemiological surveillance and the immediate use of appropriate measures. Among the essential prerequisites there is the existence of effective veterinary services, for which support programmes have been developed, notably by the OIE, which is also responsible for the definition of the norms applicable in animal health. Three examples of control programmes against major epidemics are discussed here: Rinderpest (declared eradicated worldwide in 2011), Highly Pathogenic Avian Influenza (H5N1), and Foot and Mouth Disease.     

Microbial metabolic exchange--the chemotype-to-phenotype link

The function of microbial interactions is to enable microorganisms to survive by establishing a homeostasis between microbial neighbors and local environments. A microorganism can respond to environmental stimuli using metabolic exchange-the transfer of molecular factors, including small molecules and proteins. Microbial interactions not only influence the survival of the microbes but also have roles in morphological and developmental processes of the organisms themselves and their neighbors. This, in turn, shapes the entire habitat of these organisms. Here we highlight our current understanding of metabolic exchange as well as the emergence of new technologies that are allowing us to eavesdrop on microbial conversations comprising dozens to hundreds of secreted metabolites that control the behavior, survival and differentiation of members of the community. The goal of the rapidly advancing field studying multifactorial metabolic exchange is to devise a microbial 'Rosetta stone' in order to understand the language by which microbial interactions are negotiated and, ultimately, to control the outcome of these conversations.     

In silico analyses of Fsf1 sequences, a new group of fungal proteins orthologous to the metazoan sideroblastic anemia-related sideroflexin family

Sideroblastic anemias are pathologies observed in metazoan species characterized by accumulation of iron in the mitochondria (sideroblasts), defective erythropoiesis, and iron overload. Some genes have been associated with sideroblastic anemia, e.g. delta-aminolevulinic acid synthase gene (e-ALAS2). Recently, a new sideroblastic-associated protein family was discovered in metazoans and termed sideroflexin (Sfxn). The metazoan Sfxn family comprises five groups of paralogous proteins, present in mitochondria and whose functions are unknown. Using an in silico approach, we have identified and characterized new sideroflexin sequences from the genomes of different fungal species. An in-depth phylogenetic analysis of these new fungal Sfxn sequences (termed Fsf1p) showed that they form a distinct clade within the metazoan Sfxn family. Hydrophobic cluster analysis and transmembrane topological mapping allowed us to compare conserved regions among Fsf1 and Sfxn proteins. The results indicate that Fsf1 probably belongs to an ancient, mitochondrial group of proteins, necessary to maintain the homeostasis of iron within this organelle.     

Protein folding in the post-genomic era

Protein folding is a topic of fundamental interest since it concerns the mechanisms by which the genetic message is translated into the three-dimensional and functional structure of proteins. In these post-genomic times, the knowledge of the fundamental principles are required in the exploitation of the information contained in the increasing number of sequenced genomes. Protein folding also has practical applications in the understanding of different pathologies and the development of novel therapeutics to prevent diseases associated with protein misfolding and aggregation. Significant advances have been made ranging from the Anfinsen postulate to the "new view" which describes the folding process in terms of an energy landscape. These new insights arise from both theoretical and experimental studies. The problem of folding in the cellular environment is briefly discussed. The modern view of misfolding and aggregation processes that are involved in several pathologies such as prion and Alzheimer diseases. Several approaches of structure prediction, which is a very active field of research, are described.     

The brain under the knife: serial sectioning and the development of late nineteenth-century neuroanatomy

Major changes took place during the last quarter of the nineteenth century in the ways that the brain tissue was maintained, manipulated and studied, and, consequently, in the ways that its structure, functions and pathologies were seen and represented in neurological literature. The paper exemplifies these changes by comparing German neuroanatomy in the 1860s and early 1870s (represented above all by Theodor Meynert) with the turn-of-the-century view of the brain (represented by Constantin von Monakow and others). It argues for the crucial importance of a method--serial sectioning--to the emergence of the new view of the brain. Serial sectioning in turn owes its existence to the new techniques in staining and sectioning that were introduced in the 1870s and 1880s. In particular, the paper highlights the role of a cutting device, the microtome, in enabling serial sectioning and in thereby contributing to the emergence of a new view of the brain.     

Synthetic flavonoids with antimicrobial activity: a review

The emergence of drug-resistant microbes left us with a great need for new antimicrobial agents. Flavonoids, with their wide range of biological activities, are good candidates in this respect. Although naturally occurring flavonoids are the most studied ones, semi-synthetic or synthetic flavonoids have proven to have great potential, inhibiting and even killing microbes at concentrations below 1 μg ml⁻¹. The substitution pattern of these flavonoids often includes hydroxy groups, halogens or other heteroatomic rings, such as pyridine, piperidine or 1,3-dithiolium cations. However, the great variety in substituents makes it difficult to draw any definitive conclusion regarding their structure–activity relationship.     

The emergence of molecular profiling and omics techniques in seagrass biology; furthering our understanding of seagrasses

Seagrass meadows are disappearing at alarming rates as a result of increasing coastal development and climate change. The emergence of omics and molecular profiling techniques in seagrass research is timely, providing a new opportunity to address such global issues. Whilst these applications have transformed terrestrial plant research, they have only emerged in seagrass research within the past decade; In this time frame we have observed a significant increase in the number of publications in this nascent field, and as of this year the first genome of a seagrass species has been sequenced. In this review, we focus on the development of omics and molecular profiling and the utilization of molecular markers in the field of seagrass biology. We highlight the advances, merits and pitfalls associated with such technology, and importantly we identify and address the knowledge gaps, which to this day prevent us from understanding seagrasses in a holistic manner. By utilizing the powers of omics and molecular profiling technologies in integrated strategies, we will gain a better understanding of how these unique plants function at the molecular level and how they respond to on-going disturbance and climate change events.     

Winter circulation weather types and hospital admissions for respiratory diseases in Galicia,Spain

The link between various pathologies and atmospheric conditions has been a constant topic of study over recent decades in many places across the world; knowing more about it enables us to pre-empt the worsening of certain diseases, thereby optimizing medical resources. This study looked specifically at the connections in winter between respiratory diseases and types of atmospheric weather conditions (Circulation Weather Types, CWT) in Galicia, a region in the north-western corner of the Iberian Peninsula. To do this, the study used hospital admission data associated with these pathologies as well as an automatic classification of weather types. The main result obtained was that weather types giving rise to an increase in admissions due to these diseases are those associated with cold, dry weather, such as those in the east and south-east, or anticyclonic types. A second peak was associated with humid, hotter weather, generally linked to south-west weather types. In the future, this result may help to forecast the increase in respiratory pathologies in the region some days in advance.     

Antibiotic use in humans and bacterial resistance.

As with any public health problem, the evolution of antibacterial resistance must be viewed from a perspective of risk, and analysed in terms of probabilities within the populations. It is necessary to be able to predict the risk of antibacterial resistance, in the future, and two main strategies have recently been developed in mathematical models that may help to evaluate these risks. It is also important to understand how antibiotics are used and how their use affects the evolution of antibacterial resistance. Understanding the epidemiology of antibacterial resistance will enable us to develop preventive strategies to limit existing resistance and to avoid the emergence of new strains of resistant bacteria.     

Fiber-reinforced computational model of the aortic root incorporating thoracic aorta and coronary structures

Cardiovascular diseases are still the leading causes of death in the developed world. The decline in the mortality associated with circulatory system diseases is accredited to development of new diagnostic and prognostic tools. It is well known that there is an inter relationship between the aortic valve impairment and pathologies of the aorta and coronary vessels. However, due to the limitations of the current tools, the possible link is not fully elucidated. Following our previous model of the aortic root including the coronaries, in this study, we have further developed the global aspect of the model by incorporating the anatomical structure of the thoracic aorta. This model is different from all the previous studies in the sense that inclusion of the coronary structures and thoracic aorta into the natural aortic valve introduces the notion of globality into the model enabling us to explore the possible link between the regional pathologies. The developed model was first validated using the available data in the literature under physiological conditions. Then, to provide a support for the possible association between the localized cardiovascular pathologies and global variations in hemodynamic conditions, we simulated the model for two pathological conditions including moderate and severe aortic valve stenoses. The findings revealed that malformations of the aortic valve are associated with development of low wall shear stress regions and helical blood flow in thoracic aorta that are considered major contributors to aortic pathologies.     

A randomized,double-blind,placebo-controlled phase 2 study evaluating the efficacy and safety of romiplostim treatment of patients with low or intermediate-1 risk myelodysplastic syndrome receiving lenalidomide

Mitochondria are the most complex and the most important organelles of eukaryotic cells, which are involved in many cellular processes, including energy metabolism, apoptosis, and aging. And mitochondria have been identified as the "hot spot" by researchers for exploring relevant associated dysfunctions in many fields. The emergence of comparative proteomics enables us to have a close look at the mitochondrial proteome in a comprehensive and effective manner under various conditions and cellular circumstances. Two-dimensional electrophoresis combined with mass spectrometry is still the most popular techniques to study comparative mitochondrial proteomics. Furthermore, many new techniques, such as ICAT, MudPIT, and SILAC, equip researchers with more flexibilities inselecting proper methods. This article also reviews the recent development of comparative mitochondrial proteomics on diverse human diseases. And the results of mitochondrial proteomics enhance a better understanding of the pathogenesis associated with mitochondria and provide promising therapeutic targets.