Sweeps in time: leveraging the joint distribution of branch lengths

Current methods of identifying positively selected regions in the genome are limited in two key ways: the underlying models cannot account for the timing of adaptive events and the comparison between models of selective sweeps and sequence data is generally made via simple summaries of genetic diversity. Here, we develop a tractable method of describing the effect of positive selection on the genealogical histories in the surrounding genome, explicitly modeling both the timing and context of an adaptive event. In addition, our framework allows us to go beyond analyzing polymorphism data via the site frequency spectrum or summaries thereof and instead leverage information contained in patterns of linked variants. Tests on both simulations and a human data example, as well as a comparison to SweepFinder2, show that even with very small sample sizes, our analytic framework has higher power to identify old selective sweeps and to correctly infer both the time and strength of selection. Finally, we derived the marginal distribution of genealogical branch lengths at a locus affected by selection acting at a linked site. This provides a much-needed link between our analytic understanding of the effects of sweeps on sequence variation and recent advances in simulation and heuristic inference procedures that allow researchers to examine the sequence of genealogical histories along the genome.     

From microbial gene essentiality to novel antimicrobial drug targets

Background

Bacterial respiratory tract infections, mainly caused by Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis are among the leading causes of global mortality and morbidity. Increased resistance of these pathogens to existing antibiotics necessitates the search for novel targets to develop potent antimicrobials.

Result

Here, we report a proof of concept study for the reliable identification of potential drug targets in these human respiratory pathogens by combining high-density transposon mutagenesis, high-throughput sequencing, and integrative genomics. Approximately 20% of all genes in these three species were essential for growth and viability, including 128 essential and conserved genes, part of 47 metabolic pathways. By comparing these essential genes to the human genome, and a database of genes from commensal human gut microbiota, we identified and excluded potential drug targets in respiratory tract pathogens that will have off-target effects in the host, or disrupt the natural host microbiota. We propose 249 potential drug targets, 67 of which are targets for 75 FDA-approved antimicrobials and 35 other researched small molecule inhibitors. Two out of four selected novel targets were experimentally validated, proofing the concept.

Conclusion

Here we have pioneered an attempt in systematically combining the power of high-density transposon mutagenesis, high-throughput sequencing, and integrative genomics to discover potential drug targets at genome-scale. By circumventing the time-consuming and expensive laboratory screens traditionally used to select potential drug targets, our approach provides an attractive alternative that could accelerate the much needed discovery of novel antimicrobials.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-958) contains supplementary material, which is available to authorized users.     

Impact of defoliation by the biocontrol agentZygogramma bicolorataon the weed Partheniumhysterophorus in Australia

The leaf-feeding beetle Zygogrammabicolorata Pallister was introduced from Mexico intoAustralia in 1980 as a biocontrol agent for the weedParthenium hysterophorus L. (Asteraceae). Z. bicolorata became abundant in 1990, and since 1992there has been regular outbreaks resulting in thedefoliation of the weed in central Queensland. In thisstudy we evaluated the impact of defoliation by Z. bicolorata on P. hysterophorus from 1996 to1998. Z. bicolorata caused 91–100% defoliationresulting in reductions in weed density by 32–93%,plant height by 18–65%, plant biomass by 55–89%,flower production by 75–100%, soil seed-bank by13–86% and seedling emergence in the following seasonby 73–90%. At sites with continued outbreaks ofZ. bicolorata, it is expected that the existing soilseed-bank will be minimised, resulting in reduceddensity of parthenium in 6 to 7 years.     

Quantitation of cytokine-stimulated migration of endothelium and epithelium by a new assay using microcarrier beads

Recent studies have identified a group of cytokines which appear to be cell-specific regulators of mobility in nonleukocytic mammalian cells. One example is scatter factor (SF), a soluble protein(s) produced by cultured fibroblasts and vascular smooth muscle cells which causes spreading and separation ("scattering") of tight, cohesive colonies of epithelial cells. Studies of SF action have been limited because the degree of scattering is difficult to quantitate and because scattering assays cannot be used to study potential target cells that do not form tight, cohesive colonies. We developed a simple, quantitative assay of SF-stimulated mobility based on migration of target cells off microcarrier beads onto plastic culture surfaces in 24-well plates. We showed that crude and partially purified SF derived from ras-transformed 3T3 cells stimulates migration of both epithelial and vascular endothelial cells but not of producer or nonproducer fibroblasts. Scatter and migration-stimulating activities copurified on cation exchange chromatography; and the degree of stimulation was closely correlated with scattering titer regardless of SF purity. Migration of endothelial cells from beads, while extremely sensitive to SF, was not affected by serum concentration (1 to 10%), various purified growth factors, or fibronectin. Both scattering and migration from beads were blocked by cycloheximide (0.1 microgram/ml) during assay incubation, suggesting that these processes require protein synthesis. The microcarrier bead assay may be a useful quantitative tool to study the biochemical mechanisms of SF-stimulated cell migration.     

Major characteristics of the cellulolytic system of Clostridium thermocellum coincide with those of the purified cellulosome

The properties of the cellulosome (a cellulose-binding, multiple cellulase-containing protein complex isolated from Clostridium thermocellum) have been compared with the previously reported characteristics for crude cellulase [see 1,4-(1,3;1,4)-β-d-glucan 4-glucanohydrolase, EC 3.2.1.4] preparations. Similar to the crude enzyme system, true cellulolytic activity was demonstrated for the purified cellulosome on the basis of extensive solubilization of microcrystalline cellulose. The cellulolytic activity of the purified cellulosome was enhanced both by calcium ions and by thiols, and was inhibited by cellobiose (the major end product of the cellulosome-mediated cellulose degradation). In addition, at low ionic strength, cellulose-adsorbed cellulosome was detached intact from the cellulose matrix. Using controlled conditions, maximum enzymatic activity was shown to correspond to suboptimal conditions of cellulosome adsorption to cellulose. The results suggest that previous data accumulated for the crude cellulase system in C. thermocellum essentially reflect the contribution of the cellulosome.     

Effect of increased temperature in apical regions of maize ears on starch-synthesis enzymes and accumulation of sugars and starch

Apical florets of maize (Zea mays L.) ears differentiate later than basal florets and form kernels which have lower dry matter accumulation rates. The purpose of this study was to determine whether increasing the temperature of apical kernels during the dry matter accumulation period would alter the difference in growth rate between apical and basal kernels. Apical regions of field-grown maize (cultivar Cornell 175) ears were heated to 25 ± 3°C from 7 days after pollination to maturity (tip-heated ears) and compared with unheated ears (control). In controls, apical-kernel endosperm had 24% smaller dry weight at maturity, lower concentration of sucrose, and lower activity of ADP-Glc starch synthase than basal-kernel endosperm, whereas ADP-Glc-pyrophosphorylase (ADPG-PPase) activities were similar. In tip-heated ears apical-kernel endosperm had the same growth rate and final weight as basal-kernel endosperm and apical kernels had higher sucrose concentrations, higher ADP-Glc starch synthase activity, and similar ADPG-PPase activity. Total grain weight per ear was not increased by tip-heating because the increase in size of apical kernels was partially offset by a slight decrease in size of the basal- and middle-position kernels. Tip-heating hastened some of the developmental events in apical kernels. ADPG-PPase and ADP-Glc starch synthase activities reached peak levels and starch concentration began rising earlier in apical kernels. However, tip-heating did not shorten the period of starch accumulation in apical kernels. The results indicate that the lower growth rate and smaller size of apical kernels are not solely determined by differences in prepollination floret development.     

The beneficial effect of reduced elongation growth on submergence tolerance of rice

Adverse effects of elongation growth on tolerance to completesubmergence for up to 14 d were evaluated in rice seedlingsof cultivars which differed in submergence tolerance. Thereis a good negative correlation between per cent survival andelongation growth of genotypes during complete submergence (r= – 0.81). When elongation growth underwater is minimizedby application of a gibberellin biosynthesis inhibitor, percent survival increases by as much as 50 times for one cultivar.These effects are likely related to elongation growth since(i) addition of gibberellin had the opposite effect by reducingsurvival, and (ii) when the elongation inhibitor and gibberellinwere added together, there was no effect on elongation growthand the per cent survival did not change. A GA-deficient mutantof rice which had little elongation ability during submergenceshowed a high level of submergence tolerance when plants weresubmerged at equal initial dry weights and carbohydrate levelsrelative to a submergence-tolerant cultivar. These results areconsistent with the hypothesis that elongation growth competeswith maintenance processes for energy and hence reduces survivalduring submergence. The impact of these findings is that inenvironments where elongation ability is not required, thereis a potential to increase submergence tolerance of agriculturallyimportant cultivars by selecting for least elongation, at leastduring periods of complete submergence. Furthermore, this trade-offbetween stimulated elongation growth and submergence tolerancewill have important ecological consequences for the distributionof plant species in different flood-prone environments. Key words: Gibberellin, growth, Oryza sativa, rice, submergence     

Identification of a dihydrophaseic Acid aldopyranoside from soybean tissue

A previously unidentified abscisic acid metabolite has been isolated and characterized. (±)-[2-¹⁴C]Abscisic acid was incubated in intact soybean leaves and pods; the radiolabeled metabolite was purified by high performance liquid chromatography with on-line scintillation spectrometry detection. Gas chromatography-mass spectrometry was used to obtain spectra of the acetylated and methyl esterified derivatives. The data were consistent with a proposed dihydrophaseic acid-aldopyranoside identity. Conjugation through the 4′-hydroxyl of dihydrophaseic acid is suggested.     

Enzymes of the coelacanth Latimeria chalumnae evidenced by starch gel electrophoresis

Synopsis The coelacanth, Latimeria chalumnae, is often referred to as a living relic. The opportunity to examine its biochemical molecular structure was sought in an effort to define the degree of its genetic variability. The coelacanth is thought to live only in a small area around the Comoro Islands in the Western Indian Ocean. The scenario presented suggests that the coelacanth may have lost genetic variability as a result of genetic drift within a small population. The narrow geographic range of the coelacanth suggests adjustment to a relatively limited environment. The loss of specific alleles through genetic drift can reduce the ability of a fish population to adapt to changes in environmental conditions. The coelacanth needs strong conservation measures to be taken to curtail the capture of specimens and for the protection of its limited natural habitat.