Forest ecosystem genomics and adaptation: EVOLTREE conference report

This article is a summary report of the international conference "Forest ecosystem genomics and adaptation" organized by the EVOLTREE Network of Excellence in San Lorenzo de El Escorial (Madrid), Spain, from 9 to 11 June 2010. Main achievements and results of the network are presented for the eight thematic sessions and a stakeholder session. The conference has shown that adaptive responses of trees to biotic or abiotic selection pressures can now be investigated at the gene level for traits of adaptive significance. Candidate genes have been catalogued for phenological and drought-related traits in important tree families (Salicaceae, Fagaceaea and Pinaceae), and their variation in natural populations is being explored. Genomics can now be integrated in ecological research to investigate evolutionary response to climate changes in a wide range of species. New avenues of research were also highlighted as the exploration of gene networks involved in adaptive responses and the combination of experimental and modelling approaches to disentangle components of evolutionary changes triggered by climate change. The main focus of the conference was the adaptation of trees to environmental changes. The conference was organized in eight thematic sessions ranging from genomic approaches aiming at identifying genes of adaptive significance to practical issues regarding mitigation options for combating climate change. A dialogue between scientists and end users took place in the form of an ad hoc stakeholder session. A panel of end users from various forest and policy-making institutions expressed their expectations, and the discussions with the scientists addressed the potential applications of research findings to the management of genetic resources in the context of climate changes. The conference was introduced by two keynote speakers Dr. Pierre Mathy from the European Commission, Directorate General of Research, and Dr. Allen Solomon, former National Program Leader for Global Change, US Forest Service. All the thematic sessions were introduced by high-level invited speakers from the respective fields.     

The MK5/PRAK kinase and Myc form a negative feedback loop that is disrupted during colorectal tumorigenesis

Expression of the Myc oncoprotein is downregulated in response to stress signals to allow cells to cease proliferation and escape apoptosis, but the mechanisms involved in this process are poorly understood. Cell cycle arrest in response to DNA damage requires downregulation of Myc via a p53-independent signaling pathway. Here we have used siRNA?screening of the human kinome to identify MAPKAPK5 (MK5, PRAK) as a negative regulator of Myc expression. MK5 regulates translation of Myc, since it is required for expression of miR-34b and miR-34c that bind to the 3'UTR of MYC. MK5 activates miR-34b/c expression via phosphorylation of FoxO3a, thereby promoting nuclear localization of FoxO3a and enabling it to induce miR-34b/c expression and arrest proliferation. Expression of MK5 in turn is directly activated by Myc, forming a negative feedback loop. MK5 is downregulated in colon carcinomas, arguing that this feedback loop is disrupted during colorectal tumorigenesis.     

Rapid and cost-effective screening of newly identified microsatellite loci by high-resolution melting analysis

This study describes a new method for identifying microsatellite loci that will reliably amplify and show high degree of polymorphism in a given species. Microsatellites are the most powerful codominant markers available today, but the development of novel loci remains a labour-intensive and expensive process. In de novo isolation, approaches using next generation sequencing (NGS) are gradually replacing ones using Escherichia coli libraries, resulting in unparalleled numbers of candidate loci available. We present a systematic review of published microsatellite primer notes and show that, on average, about half of all candidate loci are lost due to insufficient PCR amplification, monomorphism or multicopy status in the genome, no matter what isolation strategy is used. Thus, the screening of candidate loci remains a major step in marker development. Re-assessing capillary-electrophoresis genotyped loci via high-resolution melting analysis (HRM), we evaluate the usefulness of HRM for this step. We demonstrate its applicability in a genotyping case study and introduce a fast, HRM-based workflow for the screening of microsatellite loci. This workflow may readily be applied to NGS-based marker development and has the potential to cut the costs of traditional testing by half to three quarters.     

Application of the malaria management model to the analysis of costs and benefits of DDT versus non-DDT malaria control

Introduction

DDT is considered to be the most cost-effective insecticide for combating malaria. However, it is also the most environmentally persistent and can pose risks to human health when sprayed indoors. Therefore, the use of DDT for vector control remains controversial.

Methods

In this paper we develop a computer-based simulation model to assess some of the costs and benefits of the continued use of DDT for Indoor Residual Spraying (IRS) versus its rapid phase out. We apply the prototype model to the aggregated sub Saharan African region. For putting the question about the continued use of DDT for IRS versus its rapid phase out into perspective we calculate the same costs and benefits for alternative combinations of integrated vector management interventions.

Results

Our simulation results confirm that the current mix of integrated vector management interventions with DDT as the main insecticide is cheaper than the same mix with alternative insecticides when only direct costs are considered. However, combinations with a stronger focus on insecticide-treated bed nets and environmental management show higher levels of cost-effectiveness than interventions with a focus on IRS. Thus, this focus would also allow phasing out DDT in a cost-effective manner. Although a rapid phase out of DDT for IRS is the most expensive of the tested intervention combinations it can have important economic benefits in addition to health and environmental impacts that are difficult to assess in monetary terms. Those economic benefits captured by the model include the avoided risk of losses in agricultural exports.

Conclusions

The prototype simulation model illustrates how a computer-based scenario analysis tool can inform debates on malaria control policies in general and on the continued use of DDT for IRS versus its rapid phase out in specific. Simulation models create systematic mechanisms for analyzing alternative interventions and making informed trade offs.     

An evaluation of the in vitro cytotoxicities of 50 chemicals by using an electrical current exclusion method versus the neutral red uptake and MTT assays

According to the 2001 National Institutes of Health guidance document on using in vitro data to estimate in vivo starting doses for acute toxicity, the performance of the electrical current exclusion method (ECE) was studied for its suitability as an in vitro cytotoxicity test. In a comparative study, two established in vitro assays based on the quantification of metabolic processes necessary for cell proliferation or organelle integrity (the MTT/WST-8 [WST-8] assay and the neutral red uptake [NRU] assay), and two cytoplasm membrane integrity assays (the trypan blue exclusion [TB] and ECE methods), were performed. IC50 values were evaluated for 50 chemicals ranging from low to high toxicity, 46 of which are listed in Halles Registry of Cytotoxicity (RC). A high correlation was found between the IC50 values obtained in this study and the IC50 data published in the RC. The assay sensitivity was highest for the ECE method, and decreased from the WST-8 assay to the NRU assay to the TB assay. The consistent results of the ECE method are based on technical standardisation, high counting rate, and the ability to combine cell viability and cell volume analysis for detection of the first signs of cell necrosis and damage of the cytoplasmic membrane caused by cytotoxic agents.     

Phage release from biofilm and planktonic Staphylococcus aureus cells

The ability of pathogenic staphylococci to form biofilms facilitates colonization and the development of chronic infections. Therapy is hampered by the high tolerance of biofilms towards antibiotic treatment and the immune system. We found evidence that lysogenic Staphylococcus aureus cells in a biofilm and in planktonic cultures spontaneously release phages into their surroundings. Phages were detected over a much longer period in biofilm cultures than in planktonic supernatants because the latter were degraded by secreted proteases. Phage release in planktonic and biofilm cultures was artificially increased by adding mitomycin C. Two morphologically distinct phages in the S. aureus strain used in this work were observed by electron microscopy. We postulate that phage-release is a frequent event in biofilms. The resulting lysis of cells in a biofilm might promote the persistence and survival of the remaining cells, as they gain a nutrient reservoir from their dead and lysed neighboring cells. This might therefore be an early differentiation and apoptotic mechanism.     

A human T-cell leukemia virus type 1 regulatory element enhances the immunogenicity of human immunodeficiency virus type 1 DNA vaccines in mice and nonhuman primates

Plasmid DNA vaccines elicit potent and protective immune responses in numerous small-animal models of infectious diseases. However, their immunogenicity in primates appears less potent. Here we investigate a novel approach that optimizes regulatory elements in the plasmid backbone to improve the immunogenicity of DNA vaccines. Among various regions analyzed, we found that the addition of a regulatory sequence from the R region of the long terminal repeat from human T-cell leukemia virus type 1 (HTLV-1) to the cytomegalovirus (CMV) enhancer/promoter increased transgene expression 5- to 10-fold and improved cellular immune responses to human immunodeficiency virus type 1 (HIV-1) antigens. In cynomolgus monkeys, DNA vaccines containing the CMV enhancer/promoter with the HTLV-1 R region (CMV/R) induced markedly higher cellular immune responses to HIV-1 Env from clades A, B, and C and to HIV-1 Gag-Pol-Nef compared with the parental DNA vaccines. These data demonstrate that optimization of specific regulatory elements can substantially improve the immunogenicity of DNA vaccines encoding multiple antigens in small animals and in nonhuman primates. This strategy could therefore be explored as a potential method to enhance DNA vaccine immunogenicity in humans.     

High molecular weight constituents from roots of Echinacea pallida: an arabinogalactan-protein and an arabinan

This investigation shows structural features of two macromolecules from roots of Echinacea pallida (Nutt.) Nutt: an arabinogalactan-protein (AGP) and an arabinan. The arabinogalactan-protein was precipitated with beta-glucosyl Yariv reagent from a high molecular weight fraction. Investigations of the neutral sugar composition revealed Gal (52.1% w/w) and Ara (38.2% w/w) in a ratio of 1.4:1, accompanied by Glc (6.9% w/w) and Rha (2.8% w/w). The content of uronic acids was 6.2%. Mild acid hydrolysis detects Ara and Glc being located at the periphery of the molecule. Linkage analyses and NMR spectroscopy revealed a backbone of the polysaccharide mainly consisting of 3-linked and 3,6-linked Galp-residues. Side chains are composed of 3,6-linked or 6-linked Galp terminating in 5-linked Araf, terminal Araf, Glcp and GlcAp. The protein part (3.9% w/w) of the AGP is rich in Hyp, Ser, Ala, Thr, Glu, Asp and Gly. The amount of Hyp was determined by a colorimetric method and found to be (0.65% (w/w) of the AGP, which is in good agreement with the result obtained by amino acid hydrolysis (0.67% w/w). The arabinan was isolated from the supernatant of the Yariv precipitation on the basis of solubility in EtOH (80%). It mainly consists of Ara (85.8%). Linkage analyses and NMR spectroscopy indicate a highly branched molecule, consisting of 3,5-linked, 5-linked and terminal Araf-residues in equal amounts.