Error threshold in RNA quasispecies models with complementation

A general assumption of quasispecies models of replicons dynamics is that the fitness of a genotype is entirely determined by its sequence. However, a more biologically plausible situation is that fitness depends on the proteins that catalyze metabolic reactions, including replication. In a stirred population of replicons, such as viruses replicating and accumulating within the same cell, the association between a given genome and the proteins it encodes is not tight as it can be replicated by proteins translated from other genomes. We have investigated how this complementation phenomenon affects the error threshold in simple quasispecies mean field models. We first studied a model in which the master and the mutant genomes code for wild-type and mutant replicases, respectively. We assume that the mutant replicase has a reduced activity and that the wild-type replicase does not have increased affinity for the master genome. The whole pool of replicases can bind and replicate both genomes. We then analyze a different model considering a more extreme case of mutant genomes, the defective interfering particles (DIPs) described in many cases of viral infection. DIPs, with a higher replication rate owed to their shorter genomes, do not code for replicase, but they are able of using the replicase translated from the master genome. Our models allow to study how the probability of interaction between the genomes and the whole pool of replicases affects the error threshold. In both systems we characterize the scenario of coexistence between master and mutant genomes, providing the critical values of mutation rate, μ_c, and the critical interaction rate between master genomes and replicases, γ_c, at which the quasispecies enters into error catastrophe, a situation in which the mutant genomes dominate the population. In both cases, we showed that the error-threshold transition is given by transcritical-like bifurcations, suggesting a continuous phase transition. We have also found that the region in the parameter space (μ,γ) in which the master sequence survives is reduced when DIPs are introduced into the system.     

Expected trends and surprises in the Lateglacial and Holocene vegetation history of the Iberian Peninsula and Balearic Islands

Recent, high-resolution palaeoecological records are changing the traditional picture of post-glacial vegetation succession in the Iberian Peninsula. In addition to the influence of Lateglacial and Early Holocene climatic changes, other factors are critical in the course of vegetation development and we observe strong regional differences. The floristic composition, location and structure of glacial tree populations and communities may have been primary causes of vegetation development. Refugial populations in the Baetic cordilleras would have been a source, but not the only one, for the early Lateglacial oak expansions. From Mid to Late Holocene, inertial, resilient, and rapid responses of vegetation to climatic change are described, and regional differences in the response are stressed. The role of fire, pastoralism, agriculture, and other anthropogenic disturbances (such as mining), during the Copper, Bronze, Iberian, and Roman times, is analysed. The implications of ecological transitions in cultural changes, especially when they occur as societal collapses, are discussed.     

Novel aspects of parenchymal–mesenchymal interactions: from cell types to molecules and beyond

Mesenchymal stem or stromal cells (MSCs) were initially isolated from the bone marrow and received their name on the basis of their ability to differentiate into multiple lineages such as bone, cartilage, fat and muscle. However, more recent studies suggest that MSCs residing in perivascular compartments of the small and large blood vessels play a regulatory function supporting physiologic and pathologic responses of parenchymal cells, which define the functional representation of an organ or tissue. MSCs secrete or express factors that reach neighbouring parenchymal cells via either a paracrine effect or a direct cell‐to‐cell interaction promoting functional activity, survival and proliferation of the parenchymal cells. Previous concept of ‘epithelial–stromal’ interactions can now be widened. Given that MSC can also support hematopoietic, neuronal and other non‐epithelial parenchymal lineages, terms ‘parenchymal–stromal’ or ‘parenchymal–mesenchymal’ interactions may better describe the supportive or ‘trophic’ functions of MSC. Importantly, in many cases, MSCs specifically provide supportive microenvironment for the most primitive stem or progenitor populations and therefore can play a role as ‘stem/progenitor niche’ forming cells. So far, regulatory roles of MSCs have been reported in many tissues. In this review article, we summarize the latest studies that focused on the supportive function of MSC. This thread of research leads to a new perspective on the interactions between parenchymal and mesenchymal cells and justifies a principally novel approach for regenerative medicine based on co‐application of MSC and parenchymal cell for the most efficient tissue repair. Copyright © 2013 John Wiley & Sons, Ltd.     

Plant regeneration from callus cultures of <Emphasis Type="Italic">Maclura tinctoria</Emphasis>, an endangered woody species

Summary Some native species produce seeds with a low frequency of germination accompanied with a period of dormancy. These features make it difficult to produce new phenotypes through sexual propagation. Maclura tinctoria has been considered an endangered species due to extensive use of its wood and low frequency of seed germination. The objective of the present study is to establish an in vitro propagation system for this species. Organogenic friable callus formation from nodal segments has been obtained using woody plant medium (WPM) supplemented with 10.74 μM 1-naphthaleneacetic acid (NAA)+4.43 μM 6-benzylaminopurine (BA). Results indicate that the highest frequency of shoot formation is observed when WPM supplemented with 4.03 μM NAA+4.43 BA is used. For root formation, the use of WPM medium (pH adjusted to 7.0) supplemented with 23.62 μM indole-3-butyric acid (IBA) and 4.7gl⁻¹ activated charcoal is recommended. For acelimatization, subjecting rooted plantlets to 70%, 50%, and 30% mesh screen, each successively for a period of 7 d, has resulted in 97% plantlet survival.     

Numb proteins specify asymmetric cell fates via an endocytosis- and proteasome-independent pathway

Numb proteins are evolutionarily conserved signaling molecules that make the daughter cells different after asymmetric divisions by segregating to only one daughter. They contain distinct binding motifs for alpha-adaptin (alpha-Ada) and proteins with Eps15 homology (EH) domains, which regulate endocytosis, and for E3 ubiquitin ligases, which target proteins for proteasome-mediated degradation. In Drosophila melanogaster, Numb acts by inhibiting Notch activity to cause a bias in Notch-mediated cell-cell communication. These findings have led to the hypothesis that Numb modulates Notch signaling by using endocytosis and proteasomes to directly reduce Notch protein levels at the cell surface. Here we show that two Drosophila EH proteins, Eps15 homologue 1 (EH1) and the dynamin-associated 160-kDa protein (Dap160), negatively regulate Notch signaling. However, neither elimination of the binding motifs for endocytic proteins nor simultaneous reduction of proteasome activity affects the activity of Numb proteins. Our findings indicate that an endocytosis- and proteasome-independent pathway may mediate Numb signaling in asymmetric cell fate specification.     

The role of penicillin amidases in nature and in industry

Penicillin amidase (PA) is the enzyme used commercially for the production of semisynthetic penicillins. During the past decade, a detailed picture of the structure and regulation of the gene encoding this enzyme has emerged, revealing a variety of interesting features that are unique among microorganisms. Clues to the biological role of this enzyme have been provided, as well as new strategies for the commercial production and utilization of PA.     

Life-stage-specific differences in exploitation of food mixtures: diet mixing enhances copepod egg production but not juvenile development

Development, egg production and hatching success of the calanoidcopepods Temora longicornis and Pseudocalanus elongatus weremeasured in food mixtures to test their ability to obtain acomplete nutrition by combining different nutritionally poorfood species. In all the food mixtures used, the copepods failedto moult past the first copepodite stage, and the mortalitywas high. In sharp contrast, mixing two nutritionally poor foodspecies often resulted in egg production which was not significantlydifferent from nutritionally high quality food, although hatchingsuccess in many mixtures was low. Whereas egg production wassignificantly correlated with particulate organic nitrogen inthe diet, and independent of the highly unsaturated fatty acids(HUFAs), eicosapentaenoic acid (EPA) and docosahexaenoic acid(DHA), hatching increased with increasing DHA and EPA concentration.Growth and juvenile mortality were, however, independent ofeither nitrogen or HUFAs in the diet. Our results show thatadult copepods are effective in combining their nutrition fromseveral food sources, whereas juveniles are not. We suggestthat there are species- and life-stage-specific differencesin nutritional requirements and/or in the ability to digestand/or assimilate essential nutrients from food mixtures, whichmay significantly contribute to the success of copepod populationsin nature.     

In vitro assembly into virus-like particles is an intrinsic quality of Pichia pastoris derived HCV core protein

Different variants of hepatitis C virus core protein (HCcAg) have proved to self-assemble in vitro into virus-like particles (VLPs). However, difficulties in obtaining purified mature HCcAg have limited these studies. In this study, a high degree of monomeric HCcAg purification was accomplished using chromatographic procedures under denaturing conditions. Size exclusion chromatography and sucrose density gradient centrifugation of renatured HCcAg (in the absence of structured RNA) under reducing conditions suggested that it assembled into empty capsids. The electron microscopy analysis of renatured HCcAg showed the presence of spherical VLPs with irregular shapes and an average diameter of 35nm. Data indicated that HCcAg monomers assembled in vitro into VLPs in the absence of structured RNA, suggesting that recombinant HCcAg used in this work contains all the information necessary for the assembly process. However, they also suggest that some cellular factors might be required for the proper in vitro assembly of capsids.     

β-catenin confers resistance to PI3K and AKT inhibitors and subverts FOXO3a to promote metastasis in colon cancer

The Wnt–β-catenin and PI3K-AKT-FOXO3a pathways have a central role in cancer. AKT phosporylates FOXO3a, relocating it from the cell nucleus to the cytoplasm, an effect that is reversed by PI3K and AKT inhibitors. Simultaneous hyperactivation of the Wnt–β-catenin pathway and inhibition of PI3K-AKT signaling promote nuclear accumulation of β-catenin and FOXO3a, respectively, promoting cell scattering and metastasis by regulating a defined set of target genes. Indeed, the anti-tumoral AKT inhibitor API-2 promotes nuclear FOXO3a accumulation and metastasis of cells with high nuclear β-catenin content. Nuclear β-catenin confers resistance to the FOXO3a-mediated apoptosis induced by PI3K and AKT inhibitors in patient-derived primary cultures and in corresponding xenograft tumors in mice. This resistance is reversed by XAV-939, an inhibitor of Wnt–β-catenin signaling. In the presence of high nuclear β-catenin content, activation of FOXO3a by PI3K or AKT inhibitors makes it behave as a metastasis inductor rather than a proapoptotic tumor suppressor. We show that it is possible to evaluate the β-catenin status of patients' carcinomas and the response of patient-derived cells to target-directed drugs that accumulate FOXO3a in the nucleus before deciding on a course of treatment. We propose that this evaluation could be essential to the provision of a safer and more effective personalized treatment.