Quantification of global transcription patterns in prokaryotes using spotted microarrays

We describe an analysis, applicable to any spotted microarray dataset produced using genomic DNA as a reference, that quantifies prokaryotic levels of mRNA on a genome-wide scale. Applying this to Mycobacterium tuberculosis, we validate the technique, show a correlation between level of expression and biological importance, define the complement of invariant genes and analyze absolute levels of expression by functional class to develop ways of understanding an organism's biology without comparison to another growth condition.     

An annotated catalogue of salivary gland transcripts in the adult female mosquito, Ædes ægypti*

Background

The number of completely sequenced plastid genomes available is growing rapidly. This array of sequences presents new opportunities to perform comParative analyses. In comParative studies, it is often useful to compare across wide phylogenetic spans and, within angiosperms, to include representatives from basally diverging lineages such as the genomes reported here: Nuphar advena (from a basal-most lineage) and Ranunculus macranthus (a basal eudicot). We report these two new plastid genome sequences and make comparisons (within angiosperms, seed plants, or all photosynthetic lineages) to evaluate features such as the status of ycf15 and ycf68 as protein coding genes, the distribution of simple sequence repeats (SSRs) and longer dispersed repeats (SDR), and patterns of nucleotide composition.

Results

The Nuphar [GenBank:NC_008788] and Ranunculus [GenBank:NC_008796] plastid genomes share characteristics of gene content and organization with many other chloroplast genomes. Like other plastid genomes, these genomes are A+T-rich, except for rRNA and tRNA genes. Detailed comparisons of Nuphar with Nymphaea, another Nymphaeaceae, show that more than two-thirds of these genomes exhibit at least 95% sequence identity and that most SSRs are shared. In broader comparisons, SSRs vary among genomes in s of abundance and length and most contain repeat motifs based on A and T nucleotides.

Conclusion

SSR and SDR abundance varies by genome and, for SSRs, is proportional to genome size. Long SDRs are rare in the genomes assessed. SSRs occur less frequently than predicted and, although the majority of the repeat motifs do include A and T nucleotides, the A+T bias in SSRs is less than that predicted from the underlying genomic nucleotide composition. In codon usage third positions show an A+T bias, however variation in codon usage does not correlate with differences in A+T-richness. Thus, although plastome nucleotide composition shows "A+T richness", an A+T bias is not apparent upon more in-depth analysis, at least in these aspects. The pattern of evolution in the sequences identified as ycf15 and ycf68 is not consistent with them being protein-coding genes. In fact, these regions show no evidence of sequence conservation beyond what is normal for non-coding regions of the IR.     

Allele-specific copy number profiling by next-generation DNA sequencing

The progression and clonal development of tumors often involve amplifications and deletions of genomic DNA. Estimation of allele-specific copy number, which quantifies the number of copies of each allele at each variant loci rather than the total number of chromosome copies, is an important step in the characterization of tumor genomes and the inference of their clonal history. We describe a new method, falcon, for finding somatic allele-specific copy number changes by next generation sequencing of tumors with matched normals. falcon is based on a change-point model on a bivariate mixed Binomial process, which explicitly models the copy numbers of the two chromosome haplotypes and corrects for local allele-specific coverage biases. By using the Binomial distribution rather than a normal approximation, falcon more effectively pools evidence from sites with low coverage. A modified Bayesian information criterion is used to guide model selection for determining the number of copy number events. Falcon is evaluated on in silico spike-in data and applied to the analysis of a pre-malignant colon tumor sample and late-stage colorectal adenocarcinoma from the same individual. The allele-specific copy number estimates obtained by falcon allows us to draw detailed conclusions regarding the clonal history of the individual''s colon cancer.     

Intra‐specific variability and plasticity influence potential tree species distributions under climate change

Aim To assess the effect of local adaptation and phenotypic plasticity on the potential distribution of species under future climate changes. Trees may be adapted to specific climatic conditions; however, species range predictions have classically been assessed by species distribution models (SDMs) that do not account for intra‐specific genetic variability and phenotypic plasticity, because SDMs rely on the assumption that species respond homogeneously to climate change across their range, i.e. a species is equally adapted throughout its range, and all species are equally plastic. These assumptions could cause SDMs to exaggerate or underestimate species at risk under future climate change. Location The Iberian Peninsula. Methods Species distributions are predicted by integrating experimental data and modelling techniques. We incorporate plasticity and local adaptation into a SDM by calibrating models of tree survivorship with adaptive traits in provenance trials. Phenotypic plasticity was incorporated by calibrating our model with a climatic index that provides a measure of the differences between sites and provenances. Results We present a new modelling approach that is easy to implement and makes use of existing tree provenance trials to predict species distribution models under global warming. Our results indicate that the incorporation of intra‐population genetic diversity and phenotypic plasticity in SDMs significantly altered their outcome. In comparing species range predictions, the decrease in area occupancy under global warming conditions is smaller when considering our survival–adaptation model than that predicted by a ‘classical SDM’ calibrated with presence–absence data. These differences in survivorship are due to both local adaptation and plasticity. Differences due to the use of experimental data in the model calibration are also expressed in our results: we incorporate a null model that uses survival data from all provenances together. This model always predicts less reduction in area occupancy for both species than the SDM calibrated with presence–absence. Main conclusions We reaffirm the importance of considering adaptive traits when predicting species distributions and avoiding the use of occurrence data as a predictive variable. In light of these recommendations, we advise that existing predictions of future species distributions and their component populations must be reconsidered.     

Leaf temperature of soybean grown under elevated CO2 increases Aphis glycines (Hemiptera: Aphididae) population growth

Abstract Plants grown under elevated carbon dioxide (CO₂) experience physiological changes that influence their suitability as food for insects. To determine the effects of living on soybean (Glycine max Linnaeus) grown under elevated CO₂, population growth of the soybean aphid (Aphis glycines Matsumura) was determined at the SoyFACE research site at the University of Illinois, Urbana‐Champaign, Illinois, USA, grown under elevated (550 μL/L) and ambient (370 μL/L) levels of CO₂. Growth of aphid populations under elevated CO₂ was significantly greater after 1 week, with populations attaining twice the size of those on plants grown under ambient levels of CO₂. Soybean leaves grown under elevated levels of CO₂ were previously demonstrated at SoyFACE to have increased leaf temperature caused by reduced stomatal conductance. To separate the increased leaf temperature from other effects of elevated CO₂, air temperature was lowered while the CO₂ level was increased, which lowered overall leaf temperatures to those measured for leaves grown under ambient levels of CO₂. Aphid population growth on plants grown under elevated CO₂ and reduced air temperature was not significantly greater than on plants grown under ambient levels of CO₂. By increasing Glycine max leaf temperature, elevated CO₂ may increase populations of Aphis glycines and their impact on crop productivity.     

Differential elicitation of two processing proteases controls the processing pattern of the trypsin proteinase inhibitor precursor in Nicotiana attenuata

Trypsin proteinase inhibitors (TPIs) of Nicotiana attenuata are major antiherbivore defenses that increase dramatically in leaves after attack or methyl jasmonate (MeJA) elicitation. To understand the elicitation process, we characterized the proteolytic fragmentation and release of TPIs from a multidomain precursor by proteases in MeJA-elicited and unelicited plants. A set of approximately 6-kD TPI peptides was purified from leaves, and their posttranslational modifications were characterized. In MeJA-elicited plants, the diversity of TPI structures was greater than the precursor gene predicted. This elicited structural heterogeneity resulted from differential fragmentation of the linker peptide (LP) that separates the seven-domain TPI functional domains. Using an in vitro fluorescence resonance energy transfer assay and synthetic substrates derived from the LP sequence, we characterized proteases involved in both the processing of the TPI precursor and its vacuolar targeting sequence. Although both a vacuolar processing enzyme and a subtilisin-like protease were found to participate in a two-step processing of LP, only the activity of the subtilisin-like protease was significantly increased by MeJA elicitation. We propose that MeJA elicitation increases TPI precursor production and saturates the proteolytic machinery, changing the processing pattern of TPIs. To test this hypothesis, we elicited a TPI-deficient N. attenuata genotype that had been transformed with a functional NaTPI gene under control of a constitutive promoter and characterized the resulting TPIs. We found no alterations in the processing pattern predicted from the sequence: a result consistent with the saturation hypothesis.     

Canonical Wnt signaling: high-throughput RNAi widens the path

The canonical Wnt signaling pathway is highly conserved in evolution, widely used throughout animal development, and frequently hyperactive in cancer. Although Wnt signaling has been the subject of extensive genetic analysis in the past, some 200 genes have now been identified as candidate modulators of this pathway by a recent study using high-throughput RNAi screening.     

Down under the southeastern Pacific: marine non-indigenous species in Chile

This article presents the first compilation of marine non-indigenous species (NIS) of algae and macro-invertebrates invading Chilean waters. A total of 32 cosmopolitan and non-cosmopolitan species are reported. Among them there are six species considered as extending their southern range of distribution in connection with El Niño events. The article highlights negative and positive impacts caused by marine NIS invasions. Among the first are Codium fragile var. tomentosoide, considered as a pest in Gracilaria chilensis aquaculture facilities in northern Chile, and Ciona intestinalis, a pest in scallop aquaculture installations. Among the second are bio-engineers species, such as the ascidian Pyura praeputialis and the sea grass Heterozostera tasmanica, which have caused an increase in local biodiversity and enhancement of nursery grounds via the creation of new habitats. Further more, invaders such as the algae Mastocarpus papillosus, Porphyra linearis and P. pseudolinearis represent new exploitable resources, extracted by coastal food gatherers along the coast (M. papillosus) or potential species to develop aquaculture. Additional information is presented on the anemone Anemonia alicemartinae, which appears to be a native species (?), having shown in the past 40–50 years, a geographical southward range extension of approximately 1900 km. The number of NIS reported for Chile is compared with those published for the southwestern Atlantic, South Africa, North America (Atlantic and Pacific coasts) and New Zealand. It is suggested that probably the low number of Chilean NIS is due to the fact that the Chilean coasts are environmentally less stressed than other coasts in the world, due to the scarcity of estuaries, gulfs, enclosed bays, lagoons and low human populations. These kinds of sheltered areas have been suggested as centers for bio-invasions, due to the high rate of human-mediated transfer and increase of pollutants. Furthermore, none of NIS reported from Chile show a fast geographical expansion rate (exception of A. alicemartinae), nor invading strategies such as those described for marine NIS in other latitudes, where notorious ecological unbalances following invasions have been observed. An alternative hypothesis is that the low number of marine NIS invading Chile is underestimated, since the modern list of species generated through specific taxonomically intensive port and harbor surveys is still lacking. Fifteen species (five invertebrate and 10 fish) have been deliberately imported to Chile for aquaculture. The invertebrates appear to be controlled within aquaculture facilities and have not established naturalized populations or caused direct ecological impacts on local communities. On the contrary, several millions of salmoniforms (and rainbow trout) have escaped from farming facilities in southern Chile and established naturalized populations. Studies on ecological impacts are lacking. These escapees are also playing a role in the enhancement of artisanal and sport fishery activities.     

Metabolic effect of telmisartan and losartan in hypertensive patients with metabolic syndrome

Background

Metabolic syndrome is a cluster of common cardiovascular risk factors that includes hypertension and insulin resistance. Hypertension and diabetes mellitus are frequent comorbidities and, like metabolic syndrome, increase the risk of cardiovascular events. Telmisartan, an antihypertensive agent with evidence of partial peroxisome proliferator-activated receptor activity-gamma (PPARγ) activity, may improve insulin sensitivity and lipid profile in patients with metabolic syndrome.

Methods

In a double-blind, parallel-group, randomized study, patients with World Health Organization criteria for metabolic syndrome received once-daily doses of telmisartan (80 mg, n = 20) or losartan (50 mg, n = 20) for 3 months. At baseline and end of treatment, fasting and postprandial plasma glucose, insulin sensitivity, glycosylated haemoglobin (HBA_1c) and 24-hour mean systolic and diastolic blood pressures were determined.

Results

Telmisartan, but not losartan, significantly (p < 0.05) reduced free plasma glucose, free plasma insulin, homeostasis model assessment of insulin resistance and HbA_ic. Following treatment, plasma glucose and insulin were reduced during the oral glucose tolerance test by telmisartan, but not by losartan. Telmisartan also significantly reduced 24-hour mean systolic blood pressure (p < 0.05) and diastolic blood pressure (p < 0.05) compared with losartan.

Conclusion

As well as providing superior 24-hour blood pressure control, telmisartan, unlike losartan, displayed insulin-sensitizing activity, which may be explained by its partial PPARγ activity.