The recent breakthroughs in the understanding of host genomics in hepatitis C.

BACKGROUND: Hepatitis C Virus (HCV) infection is spontaneously resolved in about 30% of acutely infected individuals. In those who progress to chronic hepatitis C, HCV therapy permanently eradicates infection in about 40% of cases. It has long been suspected that host genetic factors are key determinants for the control of HCV infection. DESIGN: We will review in this study four genome-wide association studies (GWAS) and two large candidate gene studies that assessed the role of host genetic variation for the natural and treatment-induced control of HCV infection. RESULTS: The studies consistently identified genetic variation in interleukin 28B (IL28B) as the strongest predictor for the control of HCV infection. Importantly, single nucleotide polymorphisms (SNPs) in IL28B strongly predicted both spontaneous and treatment-induced HCV recovery. IL28B is located on chromosome 19 and encodes interferon-λ, a type III interferon with antiviral activity, which is mediated through the JAK-STAT pathway by inducing interferon-stimulated genes. The SNPs identified in the GWAS are in high linkage disequilibrium with coding or functional non-coding SNPs that might modulate function and/or expression of IL28B. The role of the different IL28B alleles on gene expression and cytokine function has not yet been established. CONCLUSIONS: These findings provide strong genetic evidence for the influence of interferon-λ for both the natural and treatment-induced control of HCV infection, and support the further investigation of interferon-λ for the treatment of chronic hepatitis C. Furthermore, genetic testing before HCV therapy could provide important information towards an individualized HCV treatment.

Influence of early antioxidant supplements on clinical evolution and organ function in critically ill cardiac surgery, major trauma, and subarachnoid hemorrhage patients.

INTRODUCTION: Oxidative stress is involved in the development of secondary tissue damage and organ failure. Micronutrients contributing to the antioxidant (AOX) defense exhibit low plasma levels during critical illness. The aim of this study was to investigate the impact of early AOX micronutrients on clinical outcome in intensive care unit (ICU) patients with conditions characterized by oxidative stress. METHODS: We conducted a prospective, randomized, double-blind, placebo-controlled, single-center trial in patients admitted to a university hospital ICU with organ failure after complicated cardiac surgery, major trauma, or subarachnoid hemorrhage. Stratification by diagnosis was performed before randomization. The intervention was intravenous supplements for 5 days (selenium 270 microg, zinc 30 mg, vitamin C 1.1 g, and vitamin B1 100 mg) with a double-loading dose on days 1 and 2 or placebo. RESULTS: Two hundred patients were included (102 AOX and 98 placebo). While age and gender did not differ, brain injury was more severe in the AOX trauma group (P = 0.019). Organ function endpoints did not differ: incidence of acute kidney failure and sequential organ failure assessment score decrease were similar (-3.2 +/- 3.2 versus -4.2 +/- 2.3 over the course of 5 days). Plasma concentrations of selenium, zinc, and glutathione peroxidase, low on admission, increased significantly to within normal values in the AOX group. C-reactive protein decreased faster in the AOX group (P = 0.039). Infectious complications did not differ. Length of hospital stay did not differ (16.5 versus 20 days), being shorter only in surviving AOX trauma patients (-10 days; P = 0.045). CONCLUSION: The AOX intervention did not reduce early organ dysfunction but significantly reduced the inflammatory response in cardiac surgery and trauma patients, which may prove beneficial in conditions with an intense inflammation. TRIALS REGISTRATION: Clinical Trials.gov RCT Register: NCT00515736.

Mitochondrial genome evolution in fire ants (Hymenoptera: Formicidae).

BACKGROUND: Complete mitochondrial genome sequences have become important tools for the study of genome architecture, phylogeny, and molecular evolution. Despite the rapid increase in available mitogenomes, the taxonomic sampling often poorly reflects phylogenetic diversity and is often also biased to represent deeper (family-level) evolutionary relationships. RESULTS: We present the first fully sequenced ant (Hymenoptera: Formicidae) mitochondrial genomes. We sampled four mitogenomes from three species of fire ants, genus Solenopsis, which represent various evolutionary depths. Overall, ant mitogenomes appear to be typical of hymenopteran mitogenomes, displaying a general A+T-bias. The Solenopsis mitogenomes are slightly more compact than other hymentoperan mitogenomes (~15.5 kb), retaining all protein coding genes, ribosomal, and transfer RNAs. We also present evidence of recombination between the mitogenomes of the two conspecific Solenopsis mitogenomes. Finally, we discuss potential ways to improve the estimation of phylogenies using complete mitochondrial genome sequences. CONCLUSIONS: The ant mitogenome presents an important addition to the continued efforts in studying hymenopteran mitogenome architecture, evolution, and phylogenetics. We provide further evidence that the sampling across many taxonomic levels (including conspecifics and congeners) is useful and important to gain detailed insights into mitogenome evolution. We also discuss ways that may help improve the use of mitogenomes in phylogenetic analyses by accounting for non-stationary and non-homogeneous evolution among branches.

Ecology and evolution of social-organization: insights from fire ants and other highly eusocial insects

Social organisms exhibit conspicuous intraspecific variation in all facets of their social organization. A prominent example of such variation in the highly eusocial Hymenoptera is differences in the number of reproductive queens per colony, Differences in queen number in ants are associated with differences in a host of reproductive and social traits, including queen phenotype and breeding strategy, mode of colony reproduction, and pattern of sex allocation. We examine the causes and consequences of changes in colony queen number and associated traits using the fire ant Solenopsis invicta as a principal model. Ecological constraints on mode of colony founding may act as important selective forces causing the evolution of queen number in this and many other ants, with social organization generally perpetuated across generations by means of the social environment molding appropriate queen phenotypes and reproductive strategies. Shifts in colony queen number have profound effects on genetic structure within nests and may also influence genetic structure at higher levels (aggregations of nests or local demes) because of the association of queen number with particular mating and dispersal habits. Divergence of breeding habits between populations with different social organizations has the potential to promote genetic differentiation between these social variants. Thus, evolution of social organization can be important in generating intrinsic selective regimes that channel subsequent social evolution and in initiating the development of significant population genetic structure, including barriers to gene flow important in cladogenesis.

Evolution of glucose induced thermogenesis in obese subjects with and without diabetes: a six-year follow-up study.

The thermogenic response to a 100 g oral glucose load was measured prospectively (by indirect calorimetry) in three groups of obese subjects: (1) normal glucose tolerance (n = 12, initial weight 86.4 +/- 3.9 kg, BMI 30.4 +/- 1.1 kg/m2; (2) impaired glucose tolerance (n = 8, initial weight 105.3 +/- 7.6 kg, body mass index (BMI) 37.6 +/- 2.9 kg/m2; (3) diabetes (n = 12), initial weight 102.1 +/- 5.3 kg, BMI 36.2 +/- 2.0 kg/m2). The thermogenic response to glucose averaged 6.8 +/- 1.1 and 7.0 +/- 1.0 per cent, in the two non-diabetic obese groups respectively, and was significantly lower in the obese diabetic group (3.1 +/- 0.8 per cent). With the evolution of obesity (i.e. 6 years later), the glucose-induced thermogenesis (GIT) was significantly reduced in the non-diabetic groups (P less than 0.05) to 4.1 +/- 0.8 and 3.0 +/- 1.1 per cent respectively, and was still blunted in the diabetic group (2.1 +/- 0.7 per cent). The decrease in GIT was accompanied by a reduction in glucose tolerance and insulin response with no change in fasting plasma insulin. These effects were observed despite the fact that the body weight of the subject did not change significantly over the 6-year period. It is concluded that the decrease in GIT which accompanies the worsening of glucose tolerance and the occurrence of diabetes is a mechanism which may contribute to maintain the obesity state by a reduction of energy expenditure.

Towards a theory of the credit-risk balance sheet (II). The evolution of its structure

This article has an immediate predecessor, upon which it is based and with which readers must necessarily be familiar: Towards a Theory of the Credit-Risk Balance Sheet (Vallverdú, Somoza and Moya, 2006). The Balance Sheet is conceptualised on the basis of the duality of a credit-based transaction; it deals with its theoretical foundations, providing evidence of a causal credit-risk duality, that is, a true causal relationship; its characteristics, properties and its static and dynamic characteristics are analyzed. This article, which provides a logical continuation to the previous one, studies the evolution of the structure of the Credit-Risk Balance Sheet as a consequence of a business¿s dynamics in the credit area. Given the Credit-Risk Balance Sheet of a company at any given time, it attempts to estimate, by means of sequential analysis, its structural evolution, showing its usefulness in the management and control of credit and risk. To do this, it bases itself, with the necessary adaptations, on the by-now classic works of Palomba and Cutolo. The establishment of the corresponding transformation matrices allows one to move from an initial balance sheet structure to a final, future one, to understand its credit-risk situation trends, as well as to make possible its monitoring and control, basic elements in providing support for risk management.

Simulations in evolution. II. Relative fitness and the propagation of mutants.

In Neo-Darwinism, variation and natural selection are the two evolutionary mechanisms which propel biological evolution. Our previous article presented a histogram model [1] consisting in populations of individuals whose number changed under the influence of variation and/or fitness, the total population remaining constant. Individuals are classified into bins, and the content of each bin is calculated generation after generation by an Excel spreadsheet. Here, we apply the histogram model to a stable population with fitness F(1)=1.00 in which one or two fitter mutants emerge. In a first scenario, a single mutant emerged in the population whose fitness was greater than 1.00. The simulations ended when the original population was reduced to a single individual. The histogram model was validated by excellent agreement between its predictions and those of a classical continuous function (Eqn. 1) which predicts the number of generations needed for a favorable mutation to spread throughout a population. But in contrast to Eqn. 1, our histogram model is adaptable to more complex scenarios, as demonstrated here. In the second and third scenarios, the original population was present at time zero together with two mutants which differed from the original population by two higher and distinct fitness values. In the fourth scenario, the large original population was present at time zero together with one fitter mutant. After a number of generations, when the mutant offspring had multiplied, a second mutant was introduced whose fitness was even greater. The histogram model also allows Shannon entropy (SE) to be monitored continuously as the information content of the total population decreases or increases. The results of these simulations illustrate, in a graphically didactic manner, the influence of natural selection, operating through relative fitness, in the emergence and dominance of a fitter mutant.

Carcinome de Merket: (r)évolution [Merkel cell carcinoma: (r)evolution].

Merkel Cell Carcinoma (CCM) is an aggressive cutaneous tumor of the elderly, which has become the second cause of mortality linked to skin cancer. This has led clinicians and scientists to devote more time to the study of this rare tumor, announcing to a revolution in our understanding, diagnosis and therapy of this cancer. We present here these recent advances, which illustrate the exponential growth of knowledge in the medical field, drawing comparisons with more frequent cancers such as melanoma and squamous cell carcinoma.

The fossil record and evolution of freshwater plants: A review

Palaeobotany applied to freshwater plants is an emerging field of palaeontology. Hydrophytic plants reveal evolutionary trends of their own, clearly distinct from those of the terrestrial and marine flora. During the Precambrian, two groups stand out in the fossil record of freshwater plants: the Cyanobacteria (stromatolites) in benthic environments and the prasinophytes (leiosphaeridian acritarchs) in transitional planktonic environments. During the Palaeozoic, green algae (Chlorococcales, Zygnematales, charophytes and some extinct groups) radiated and developed the widest range of morphostructural patterns known for these groups. Between the Permian and Early Cretaceous, charophytes dominated macrophytic associations, with the consequence that over tens of millions of years, freshwater flora bypassed the dominance of vascular plants on land. During the Early Cretaceous, global extension of the freshwater environments is associated with diversification of the flora, including new charophyte families and the appearance of aquatic angiosperms and ferns for the first time. Mesozoic planktonic assemblages retained their ancestral composition that was dominated by coenobial Chlorococcales, until the appearance of freshwater dinoflagellates in the Early Cretaceous. In the Late Cretaceous, freshwater angiosperms dominated almost all macrophytic communities worldwide. The Tertiary was characterised by the diversification of additional angiosperm and aquatic fern lineages, which resulted in the first differentiation of aquatic plant biogeoprovinces. Phytoplankton also diversified during the Eocene with the development of freshwater diatoms and chrysophytes. Diatoms, which were exclusively marine during tens of millions of years, were dominant over the Chlorococcales during Neogene and in later assemblages. During the Quaternary, aquatic plant communities suffered from the effects of eutrophication, paludification and acidification, which were the result of the combined impact of glaciation and anthropogenic disturbance.

Médecine génomique et oncologie [Genomics medicine and oncology].

Progress in genomics with, in particular, high throughput next generation sequencing is revolutionizing oncology. The impact of these techniques is seen on the one hand the identification of germline mutations that predispose to a given type of cancer, allowing for a personalized care of patients or healthy carriers and, on the other hand, the characterization of all acquired somatic mutation of the tumor cell, opening the door to personalized treatment targeting the driver oncogenes. In both cases, next generation sequencing techniques allow a global approach whereby the integrality of the genome mutations is analyzed and correlated with the clinical data. The benefits on the quality of care delivered to our patients are extremely impressive.

Selection methods regulate evolution of cooperation in digital evolution.

A key, yet often neglected, component of digital evolution and evolutionary models is the 'selection method' which assigns fitness (number of offspring) to individuals based on their performance scores (efficiency in performing tasks). Here, we study with formal analysis and numerical experiments the evolution of cooperation under the five most common selection methods (proportionate, rank, truncation-proportionate, truncation-uniform and tournament). We consider related individuals engaging in a Prisoner's Dilemma game where individuals can either cooperate or defect. A cooperator pays a cost, whereas its partner receives a benefit, which affect their performance scores. These performance scores are translated into fitness by one of the five selection methods. We show that cooperation is positively associated with the relatedness between individuals under all selection methods. By contrast, the change in the performance benefit of cooperation affects the populations' average level of cooperation only under the proportionate methods. We also demonstrate that the truncation and tournament methods may introduce negative frequency-dependence and lead to the evolution of polymorphic populations. Using the example of the evolution of cooperation, we show that the choice of selection method, though it is often marginalized, can considerably affect the evolutionary dynamics.

Genomics and the origin of species.

Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isolation and of genomic properties that influence the process of speciation. Building on this work, we identify emergent trends and gaps in our understanding, propose new approaches to more fully integrate genomics into speciation research, translate speciation theory into hypotheses that are testable using genomic tools and provide an integrative definition of the field of speciation genomics.