Examining the transcriptional response in wheat Fhb1 near-isogenic lines to Fusarium graminearum infection and deoxynivalenol treatment

Citation: Hofstad, A. N., Nussbaumer, T., Akhunov, E., Shin, S., Kugler, K. G., Kistler, H. C., . . . Muehlbauer, G. J. (2016). Examining the transcriptional response in wheat Fhb1 near-isogenic lines to Fusarium graminearum infection and deoxynivalenol treatment. Plant Genome, 9(1). https://doi.org/10.3835/plantgenome2015.05.0032Fusarium head blight (FHB) is a disease caused predominantly by the fungal pathogen Fusarium graminearum that affects wheat and other small-grain cereals and can lead to severe yield loss and reduction in grain quality. Trichothecene mycotoxins, such as deoxynivalenol (DON), accumulate during infection and increase pathogen virulence and decrease grain quality. The Fhb1 locus on wheat chromosome 3BS confers Type II resistance to FHB and resistance to the spread of infection on the spike and has been associated with resistance to DON accumulation. To gain a better genetic understanding of the functional role of Fhb1 and resistance or susceptibility to FHB, we examined DON and ergosterol accumulation, FHB resistance, and the whole-genome transcriptomic response using RNA-seq in a near-isogenic line (NIL) pair carrying the resistant and susceptible alleles for Fhb1 during F. graminearum infection and DON treatment. Our results provide a gene expression atlas for the resistant and susceptible wheat–F. graminearum interaction. The DON concentration and transcriptomic results show that the rachis is a key location for conferring Type II resistance. In addition, the wheat transcriptome analysis revealed a set of Fhb1-responsive genes that may play a role in resistance and a set of DON-responsive genes that may play a role in trichothecene resistance. Transcriptomic results from the pathogen show that the F. graminearum genome responds differently to the host level of resistance. The results of this study extend our understanding of host and pathogen responses in the wheat–F. graminearum interaction. © Crop Science Society of America

Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products

Metagenomics is a valuable tool for the study of microbial communities but has been limited by the difficulty of “binning” the resulting sequences into groups corresponding to the individual species and strains that constitute the community. Moreover, there are presently no methods to track the flow of mobile DNA elements such as plasmids through communities or to determine which of these are co-localized within the same cell. We address these limitations by applying Hi-C, a technology originally designed for the study of three-dimensional genome structure in eukaryotes, to measure the cellular co-localization of DNA sequences. We leveraged Hi-C data generated from a simple synthetic metagenome sample to accurately cluster metagenome assembly contigs into groups that contain nearly complete genomes of each species. The Hi-C data also reliably associated plasmids with the chromosomes of their host and with each other. We further demonstrated that Hi-C data provides a long-range signal of strain-specific genotypes, indicating such data may be useful for high-resolution genotyping of microbial populations. Our work demonstrates that Hi-C sequencing data provide valuable information for metagenome analyses that are not currently obtainable by other methods. This metagenomic Hi-C method could facilitate future studies of the fine-scale population structure of microbes, as well as studies of how antibiotic resistance plasmids (or other genetic elements) mobilize in microbial communities. The method is not limited to microbiology; the genetic architecture of other heterogeneous populations of cells could also be studied with this technique

Comparison of the National Early Warning Score in non-elective medical and surgical patients.

BACKGROUND: The National Early Warning Score (NEWS) is used to identify deteriorating patients in hospital. NEWS is a better discriminator of outcomes than other early warning scores in acute medical admissions, but it has not been evaluated in a surgical population. The study aims were to evaluate the ability of NEWS to discriminate cardiac arrest, death and unanticipated ICU admission in patients admitted to surgical specialties, and to compare the performance of NEWS in admissions to medical and surgical specialties. METHODS: Hospitalwide data over 31 months, from adult inpatients who stayed at least one night or died on the day of admission, were analysed. The data were categorized as elective or non-elective surgical or medical admissions. The ability of NEWS to discriminate the outcomes above in these different groups was assessed using the area under the receiver operating characteristic curve (AUROC). RESULTS: There were too few outcomes to permit meaningful comparison of elective admissions, so the analysis was constrained to comparison of non-elective admissions. NEWS performed equally well, or better, for surgical as for medical patients. For death within 24 h the AUROC for surgical admissions was 0·914 (95 per cent c.i. 0·907 to 0·922), compared with 0·902 (0·898 to 0·905) for medical admissions. For the combined outcome of any of death, cardiac arrest or unanticipated ICU admission, the AUROC was 0·874 (0·868 to 0·880) for surgical admissions and 0·874 (0·871 to 0·877) for medical admissions. CONCLUSION: NEWS discriminated deterioration in non-elective surgical patients at least as well as in non-elective medical patients

Still armed after domestication? Impacts of domestication and agronomic selection on silicon defences in cereals

Plant phenotypes reflect trade‐offs between competing resource‐intensive physiological processes. A shift in resource allocation, away from anti‐herbivore defences and towards growth and reproduction, is predicted through plant domestication, such that crops are faster growing and higher yielding than their wild ancestors. These changes are hypothesized to have come at the cost of defence investment, leaving crops “disarmed by domestication”. Silicon is the principal anti‐herbivore defence in grasses, including many of our most important staple cereal crops, but the impact of domestication on silicon‐based defences is unknown. We measured the effects of both domestication and modern agronomic selection on growth rate and a suite of anti‐herbivore defences, specifically leaf toughness, silicon and phenolic concentrations. Our comparison of wild, landrace and modern cultivated cereals spanned multiple cereal species, including wheat, barley and maize, sampling eight independent domestication events and five examples of modern agronomic selection. Leaf silicon concentration showed a small, but significant, 10% reduction through domestication, but there was no effect of modern agronomic selection, and phenolic concentration was not affected by either factor. Silicon concentration correlated positively with leaf tensile strength, but negatively with foliar phenolic concentrations, suggesting a trade‐off between chemical and physical defences. Size‐standardized growth rate was independent of domestication status, and did not trade‐off with silicon or phenolic defences. However, modelling showed that relative growth rate slowed more with increasing size in plants with higher silicon levels, so that they reached a smaller final size, implying a cost of silicon‐based defence. We found the opposite pattern for phenolic‐based defence, with increasing phenolic concentrations associated with a greater plant size at maturity, and faster maximum relative growth rates. Silicon‐based defences have been reduced in cereals through domestication, consistent with our predicted costs of these defences to growth. However, modern agronomic selection has not influenced silicon defences in cereal crops and the small decrease in silicon concentration associated with domestication is unlikely to have a major effect on the ability of cereals to withstand a range of abiotic and biotic stresses. These findings have broad implications for crop protection and our understanding of plant trade‐offs

Characterization of pearl millet root architecture and anatomy reveals three types of lateral roots

Pearl millet plays an important role for food security in arid regions of Africa and India. Nevertheless, it is considered an orphan crop as it lags far behind other cereals in terms of genetic improvement efforts. Breeding pearl millet varieties with improved root traits promises to deliver benefits in water and nutrient acquisition. Here, we characterize of early pearl millet root system development using several different root phenotyping approaches that include rhizotrons and microCT. We report that early stage pearl millet root system development is characterized by a fast growing primary root that quickly colonizes deeper soil horizons. We also describe root anatomical studies that revealed 3 distinct types of lateral roots that form on both primary roots and crown roots. Finally, we detected significant variation for two root architectural traits in pearl millet inbred lines. This study provides the basis for subsequent genetic experiments to identify loci associated with interesting early root development traits in this important cereal

Evaluation and use of surveillance system data toward the identification of high-risk areas for potential cholera vaccination: a case study from Niger.

In 2008, Africa accounted for 94% of the cholera cases reported worldwide. Although the World Health Organization currently recommends the oral cholera vaccine in endemic areas for high-risk populations, its use in Sub-Saharan Africa has been limited. Here, we provide the principal results of an evaluation of the cholera surveillance system in the region of Maradi in Niger and an analysis of its data towards identifying high-risk areas for cholera

Global distribution and drivers of language extinction risk

Many of the world's languages face serious risk of extinction. Efforts to prevent this cultural loss are severely constrained by a poor understanding of the geographical patterns and drivers of extinction risk. We quantify the global distribution of language extinction risk—represented by small range and speaker population sizes and rapid declines in the number of speakers—and identify the underlying environmental and socioeconomic drivers. We show that both small range and speaker population sizes are associated with rapid declines in speaker numbers, causing 25% of existing languages to be threatened based on criteria used for species. Language range and population sizes are small in tropical and arctic regions, particularly in areas with high rainfall, high topographic heterogeneity and/or rapidly growing human populations. By contrast, recent speaker declines have mainly occurred at high latitudes and are strongly linked to high economic growth. Threatened languages are numerous in the tropics, the Himalayas and northwestern North America. These results indicate that small-population languages remaining in economically developed regions are seriously threatened by continued speaker declines. However, risks of future language losses are especially high in the tropics and in the Himalayas, as these regions harbour many small-population languages and are undergoing rapid economic growth

Female sex pheromone of the cone moth, dioryctria mendacella: Investigation of synergism between Type I and Type II pheromone components

Polyunsaturated hydrocarbons (Type II pheromone components) have been reported to be synergists for unsaturated acetates, alcohols or aldehydes (Type I components) in the sex pheromones of several species of Lepidoptera. However, there is some debate over whether the active components are the hydrocarbons themselves or more volatile degradation products. Extracts of pheromone glands of adult females of the cone moth, Dioryctria mendacella (Lepidoptera: Pyralidae), contain (Z,E)-9,11-tetradecadienyl acetate (ZE9,11-14:Ac) and at least ten times as much (Z,Z,Z,Z,Z)-3,6,9,12,15-pentacosapentaene (ZZZZZ3,6,9,12,15-25:H). The former elicits a strong electroantennogram response from males while no response could be recorded to the latter. In field trapping tests, both compounds were individually unattractive to male D. mendacella moths, but blends of the two compounds containing at least a 10:1 ratio of ZZZZZ3,6,9,12,15-25:H : ZE9,11-14:Ac were highly attractive. The relatively involatile hydrocarbon was shown to be released from the dispensers used and no significant degradation could be detected. Furthermore, blends of ZE9,11-14:Ac and analogs of ZZZZZ3,6,9,12,15-25:H with fewer carbons and/or double bonds that might be expected to produce similar degradation products to ZZZZZ3,6,9,12,15-25:H were unattractive. This indicated a specific response to the hydrocarbon itself, further substantiated by the observation that related hydrocarbons did not interfere with the activity of ZZZZZ3,6,9,12,15-25:H. Thus a three-step conversion of fish oil was used to produce a blend of unsaturated hydrocarbons containing ZZZZZ3,6,9,12,15-25:H as the major component, albeit only 30% of the total, and a blend of this material with ZE9,11-14:Ac was as attractive to male D. mendacella moths as blends with an equivalent amount of the purified material. This mixture of unsaturated hydrocarbons is much cheaper to produce than the pure pentaene, and may be useful in lures for other species using these compounds. Dioryctria mendacella is a major constraint to production of edible pine kernels throughout the Mediterranean region. Pheromone traps will provide a means to improve monitoring of seasonal flight patterns and changes in population abundance of this pest

Mobile phones carry the personal microbiome of their owners

Most people on the planet own mobile phones, and these devices are increasingly being utilized to gather data relevant to our personal health, behavior, and environment. During an educational workshop, we investigated the utility of mobile phones to gather data about the personal microbiome — the collection of microorganisms associated with the personal effects of an individual. We characterized microbial communities on smartphone touchscreens to determine whether there was significant overlap with the skin microbiome sampled directly from their owners. We found that about 22% of the bacterial taxa on participants’ fingers were also present on their own phones, as compared to 17% they shared on average with other people’s phones. When considered as a group, bacterial communities on men’s phones were significantly different from those on their fingers, while women’s were not. Yet when considered on an individual level, men and women both shared significantly more of their bacterial communities with their own phones than with anyone else’s. In fact, 82% of the OTUs were shared between a person’s index and phone when considering the dominant taxa (OTUs with more than 0.1% of the sequences in an individual’s dataset). Our results suggest that mobile phones hold untapped potential as personal microbiome sensors