Identification and Characterisation CRN Effectors in Phytophthora capsici Shows Modularity and Functional Diversity

Phytophthora species secrete a large array of effectors during infection of their host plants. The Crinkler (CRN) gene family encodes a ubiquitous but understudied class of effectors with possible but as of yet unknown roles in infection. To appreciate CRN effector function in Phytophthora, we devised a simple Crn gene identification and annotation pipeline to improve effector prediction rates. We predicted 84 full-length CRN coding genes and assessed CRN effector domain diversity in sequenced Oomycete genomes. These analyses revealed evidence of CRN domain innovation in Phytophthora and expansion in the Peronosporales. We performed gene expression analyses to validate and define two classes of CRN effectors, each possibly contributing to infection at different stages. CRN localisation studies revealed that P. capsici CRN effector domains target the nucleus and accumulate in specific sub-nuclear compartments. Phenotypic analyses showed that few CRN domains induce necrosis when expressed in planta and that one cell death inducing effector, enhances P. capsici virulence on Nicotiana benthamiana. These results suggest that the CRN protein family form an important class of intracellular effectors that target the host nucleus during infection. These results combined with domain expansion in hemi-biotrophic and necrotrophic pathogens, suggests specific contributions to pathogen lifestyles. This work will bolster CRN identification efforts in other sequenced oomycete species and set the stage for future functional studies towards understanding CRN effector functions.     

Potential impacts on ecosystem services of land use transitions to second‐generation bioenergy crops in GB

We present the first assessment of the impact of land use change (LUC) to second‐generation (2G) bioenergy crops on ecosystem services (ES) resolved spatially for Great Britain (GB). A systematic approach was used to assess available evidence on the impacts of LUC from arable, semi‐improved grassland or woodland/forest, to 2G bioenergy crops, for which a quantitative ‘threat matrix’ was developed. The threat matrix was used to estimate potential impacts of transitions to either Miscanthus, short‐rotation coppice (SRC, willow and poplar) or short‐rotation forestry (SRF). The ES effects were found to be largely dependent on previous land uses rather than the choice of 2G crop when assessing the technical potential of available biomass with a transition from arable crops resulting in the most positive effect on ES. Combining these data with constraint masks and available land for SRC and Miscanthus (SRF omitted from this stage due to lack of data), south‐west and north‐west England were identified as areas where Miscanthus and SRC could be grown, respectively, with favourable combinations of economic viability, carbon sequestration, high yield and positive ES benefits. This study also suggests that not all prospective planting of Miscanthus and SRC can be allocated to agricultural land class (ALC) ALC 3 and ALC 4 and suitable areas of ALC 5 are only minimally available. Beneficial impacts were found on 146 583 and 71 890 ha when planting Miscanthus or SRC, respectively, under baseline planting conditions rising to 293 247 and 91 318 ha, respectively, under 2020 planting scenarios. The results provide an insight into the interplay between land availability, original land uses, bioenergy crop type and yield in determining overall positive or negative impacts of bioenergy cropping on ecosystems services and go some way towards developing a framework for quantifying wider ES impacts of this important LUC.     

Metagenomic Investigation of Plasma in Individuals with ME/CFS Highlights the Importance of Technical Controls to Elucidate Contamination and Batch Effects

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a debilitating disease causing indefinite fatigue. ME/CFS has long been hypothesised to have an infectious cause; however, no specific infectious agent has been identified. We used metagenomics to analyse the RNA from plasma samples from 25 individuals with ME/CFS and compare their microbial content to technical controls as well as three control groups: individuals with alternatively diagnosed chronic Lyme syndrome (N = 13), systemic lupus erythematosus (N = 11), and healthy controls (N = 25). We found that the majority of sequencing reads were removed during host subtraction, thus there was very low microbial RNA content in the plasma. The effects of sample batching and contamination during sample processing proved to outweigh the effects of study group on microbial RNA content, as the few differences in bacterial or viral RNA abundance we did observe between study groups were most likely caused by contamination and batch effects. Our results highlight the importance of including negative controls in all metagenomic analyses, since there was considerable overlap between bacterial content identified in study samples and control samples. For example, Proteobacteria, Firmicutes, Actinobacteria, and Bacteriodes were found in both study samples and plasma-free negative controls. Many of the taxonomic groups we saw in our plasma-free negative control samples have previously been associated with diseases, including ME/CFS, demonstrating how incorrect conclusions may arise if controls are not used and batch effects not accounted for.     

Observations on the length of the intestinal tract of African <Emphasis Type="Italic">Loxodonta africana</Emphasis> (Blumenbach 1797) and Asian elephants <Emphasis Type="Italic">Elephas maximus</Emphasis> (Linné 1735)

The digestive tract of elephants is surprisingly short compared to other herbivorous mammals. However, measurements relating the length of the intestine to the body mass of the respective individual are rare. In this study, we report such data for an African elephant and an Asian elephant. Our data support the hypothesis that Asian elephants have a longer intestinal tract than their African counterparts. These findings are in accord with the observation of longer retention times and higher digestion coefficients in Asian as compared to African elephants. This difference between the species could be the reflection of slightly different ecological niches, with Asian elephants adapted to a natural diet with a higher proportion of grass.     

Fluorescent ornamentation in the Rhinoceros Auklet Cerorhinca monocerata

Avian species have developed a range of markers for transmitting information, among them ornamented plumage, behavioural patterns and conspicuous bill structures. Members of the marine subfamily Fraterculinae have some of the most visibly noticeable ornaments among seabirds, and some species have been recently found to possess fluorescent properties in seasonally acquired bill plates. We examined a member of this subfamily, the Rhinoceros Auklet Cerorhinca monocerata, for fluorescence in the upper and lower mandibles as well as the namesake horn grown in preparation for mate selection. Fluorescence was noted primarily in the horn of adults, with greater variation present among individuals than between the sexes.     

Development and proliferation of Trypanosoma musculi in the presence of adherent splenic cells

The development and proliferation of Trypanosoma musculi parasites were studied in vitro in the presence of adherent splenic cells. The parasites grew and proliferated only when attached by their flagellar tips to adherent splenic cells. Analyses of excretory-secretory products of the adherent cells-parasites did not indicate any detectable soluble growth factor that might be responsible for the growth of these trypanosomes. During the proliferation, the kinetoplast migrated toward the nucleus, and once in the vicinity of the nucleus, nuclear division was triggered. The nucleus and kinetoplast divided at the same time Trypanosoma musculi parasites started dividing from their flagellar ends, and daughter cells were formed within 48 hr. In the absence of adherent splenic cells in vitro, the parasites were transformed into round nonviable forms.     

AL-12182, a novel 11-oxa prostaglandin analog with topical ocular hypotensive activity in the monkey

A series of 11-oxa prostaglandin analogs was evaluated for FP receptor binding and activation. Several compounds having aryloxy-terminated lower chains were found to be potent agonists. Topical ocular dosing of AL-12182, the isopropyl ester prodrug of the potent agonist 13, lowered intraocular pressure in the monkey by 40% accompanied by minimal conjunctival hyperemia in the rabbit. AL-12182 was synthesized on multigram scale starting with D-sorbitol.     

Ontology for genome comparison and genomic rearrangements

We present an ontology for describing genomes, genome comparisons, their evolution and biological function. This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution. It provides a framework for communication about comparative genomics, and a basis upon which further automated analysis can be built. The nomenclature defined by the ontology will foster clearer communication between biologists, and also standardize terms used by data publishers in the results of analysis programs. The overriding aim of this ontology is the facilitation of consistent annotation of genomes through computational methods, rather than human annotators. To this end, the ontology includes definitions that support computer analysis and automated transfer of annotations between genomes, rather than relying upon human mediation.     

Arizonasaurus and its implications for archosaur divergence

The Moenkopi Formation has yielded partial and isolated remains of important archosaurs including rauisuchian skull fragments and isolated poposaur centra and pelvic girdle elements. A recently discovered skeleton referable to Arizonasaurus babbitti shows that most of these archosaurian remains belong to one taxon. Characteristics of the skeleton of Arizonasaurus show that it belongs to a poorly known group of Middle Triassic (240-230 Myr ago) archosaurs called the ctenosauriscids, and that ctenosauriscids are or are closely related to poposaurs. Furthermore, many characteristics of Arizonasaurus provide evidence that poposaurids and ctenosauriscids are derived rauisuchians. The presence of a poposaurid in the early Middle Triassic suggests that the divergence of birds and crocodiles occurred earlier than previously thought. Middle Triassic ctenosauriscids also allow the correlation of Triassic faunas in Europe, Asia, North America and Africa. The Moenkopi Formation fauna represents a transitional fauna between Early and Late Triassic faunas.