Fine mapping of Co-x,an anthracnose resistance gene to a highly virulent strain of Colletotrichum lindemuthianum in common bean

Key message

The Co - x anthracnose R gene of common bean was fine-mapped into a 58 kb region at one end of chromosome 1, where no canonical NB-LRR-encoding genes are present in G19833 genome sequence.

Abstract

Anthracnose, caused by the phytopathogenic fungus Colletotrichum lindemuthianum, is one of the most damaging diseases of common bean, Phaseolus vulgaris. Various resistance (R) genes, named Co-, conferring race-specific resistance to different strains of C. lindemuthianum have been identified. The Andean cultivar JaloEEP558 was reported to carry Co-x on chromosome 1, conferring resistance to the highly virulent strain 100. To fine map Co-x, 181 recombinant inbred lines derived from the cross between JaloEEP558 and BAT93 were genotyped with polymerase chain reaction (PCR)-based markers developed using the genome sequence of the Andean genotype G19833. Analysis of RILs carrying key recombination events positioned Co-x at one end of chromosome 1 to a 58 kb region of the G19833 genome sequence. Annotation of this target region revealed eight genes: three phosphoinositide-specific phospholipases C (PI-PLC), one zinc finger protein and four kinases, suggesting that Co-x is not a classical nucleotide-binding leucine-rich encoding gene. In addition, we identified and characterized the seven members of common bean PI-PLC gene family distributed into two clusters located at the ends of chromosomes 1 and 8. Co-x is not a member of Co-1 allelic series since these two genes are separated by at least 190 kb. Comparative analysis between soybean and common bean revealed that the Co-x syntenic region, located at one end of Glycine max chromosome 18, carries Rhg1, a major QTL contributing to soybean cyst nematode resistance. The PCR-based markers generated in this study should be useful in marker-assisted selection for pyramiding Co-x with other R genes.     

Risk Factors for Death in 632 Patients with Sickle Cell Disease in the United States and United Kingdom

Background

The role of pulmonary hypertension as a cause of mortality in sickle cell disease (SCD) is controversial.

Methods and Results

We evaluated the relationship between an elevated estimated pulmonary artery systolic pressure and mortality in patients with SCD. We followed patients from the walk-PHaSST screening cohort for a median of 29 months. A tricuspid regurgitation velocity (TRV)≥3.0 m/s cuttof, which has a 67–75% positive predictive value for mean pulmonary artery pressure ≥25 mm Hg was used. Among 572 subjects, 11.2% had TRV≥3.0 m/sec. Among 582 with a measured NT-proBNP, 24.1% had values ≥160 pg/mL. Of 22 deaths during follow-up, 50% had a TRV≥3.0 m/sec. At 24 months the cumulative survival was 83% with TRV≥3.0 m/sec and 98% with TRV<3.0 m/sec (p<0.0001). The hazard ratios for death were 11.1 (95% CI 4.1–30.1; p<0.0001) for TRV≥3.0 m/sec, 4.6 (1.8–11.3; p = 0.001) for NT-proBNP≥160 pg/mL, and 14.9 (5.5–39.9; p<0.0001) for both TRV≥3.0 m/sec and NT-proBNP≥160 pg/mL. Age >47 years, male gender, chronic transfusions, WHO class III–IV, increased hemolytic markers, ferritin and creatinine were also associated with increased risk of death.

Conclusions

A TRV≥3.0 m/sec occurs in approximately 10% of individuals and has the highest risk for death of any measured variable.

The study is registered in ClinicalTrials.gov with identifier

{"type":"clinical-trial","attrs":{"text":"NCT00492531","term_id":"NCT00492531"}}NCT00492531     

Nonlinear scaling of foraging contacts with rodent population density

Density‐dependent shifts in population processes like territoriality, reproduction, dispersal, and parasite transmission are driven by changes in contacts between individuals. Despite this, surprisingly little is known about how contacts change with density, and thus the mechanisms driving density‐dependent processes. A simple linear contact–density function is often assumed, but this is not based on a sound basis of empirical data. We addressed this question using a replicated, semi‐natural experiment in which we measured contacts at feeding stations between multimammate mice, Mastomys natalensis, across ten distinct, linearly increasing densities between 10 and 272 animals/ha. Unexpectedly, unique contacts increased not linearly but sigmoidally with density, which we attribute to the species’ scramble competition mating system, small‐scale dominance/avoidance and absence of territoriality. These results provide new insights into how species’ characteristics can relate to density‐dependent changes in contacts, and the unexpected shape of the contact–density function warrants that density‐dependence in ecological models, such as parasite transmission models, must be parameterized with care.     

Comparative maps of motion and assembly of filamentous actin and myosin II in migrating cells

To understand the mechanism of cell migration, one needs to know how the parts of the motile machinery of the cell are assembled and how they move with respect to each other. Actin and myosin II are thought to be the major structural and force-generating components of this machinery (Mitchison and Cramer, 1996; Parent, 2004). The movement of myosin II along actin filaments is thought to generate contractile force contributing to cell translocation, but the relative motion of the two proteins has not been investigated. We use fluorescence speckle and conventional fluorescence microscopy, image analysis, and computer tracking techniques to generate comparative velocity and assembly maps of actin and myosin II over the entire cell in a simple model system of persistently migrating fish epidermal keratocytes. The results demonstrate contrasting polarized assembly patterns of the two components, indicate force generation at the lamellipodium-cell body transition zone, and suggest a mechanism of anisotropic network contraction via sliding of myosin II assemblies along divergent actin filaments.     

Over-expression and refolding of MAP kinase phosphatase 3

MAP kinase phosphatase 3 (MKP3, also known as DUSP6 and PYST1) is involved in extracellular signal receptor kinase (ERK) regulation and functions as a specific phosphatase to the activated (phosphorylated) forms of ERK1 and ERK2. MKP3 displays allosteric activation, which aids in tightly regulating its function to ERK substrates, but not other related MAPKs. Due to MKP3's specificity for the ERK signaling pathway, the development of specific activators or inhibitors to the enzyme have been suggested in order to expressly influence the ERK1 and ERK2 pathways. To produce the high yields of MKP3 protein necessary for physico-chemical characterization of MKP3 and for high throughput screening of its small-molecule activators and inhibitors, we have cloned, purified and, and identified refolding conditions suitable for producing full-length, human MKP3 from Escherichia coli inclusion bodies. Furthermore, we demonstrate the use of a 96-well plate format refolding assay in which the ERK-induced activity of MKP3 is simulated by 33% DMSO. The assay allowed for rapid detection of MKP3's function following a refolding screen in the absence of ERK and thus provides quick and inexpensive testing of MKP3 activity. Following screening, the refolded product was confirmed to be correctly folded by steady-state kinetic analysis and by the CD spectroscopy-determined secondary structure content. CD data were consistent with 36% helix and 14% sheet, which compared to an expected 32.9% helix and 12.4% sheet. These data indicated that MKP3 was properly folded, making it a suitable protein for use in functional studies.     

Bayesian multisensory integration and cross-modal spatial links.

Our perception of the word is the result of combining information between several senses, such as vision, audition and proprioception. These sensory modalities use widely different frames of reference to represent the properties and locations of object. Moreover, multisensory cues come with different degrees of reliability, and the reliability of a given cue can change in different contexts. The Bayesian framework--which we describe in this review--provides an optimal solution to deal with this issue of combining cues that are not equally reliable. However, this approach does not address the issue of frames of references. We show that this problem can be solved by creating cross-modal spatial links in basis function networks. Finally, we show how the basis function approach can be combined with the Bayesian framework to yield networks that can perform optimal multisensory combination. On the basis of this theory, we argue that multisensory integration is a dialogue between sensory modalities rather that the convergence of all sensory information onto a supra-modal area.     

No short‐ or long‐term effects of geolocator attachment detected in Pied Flycatchers Ficedula hypoleuca

Tracking small passerines using miniaturized location tags is a rapidly expanding field of study. In a 1‐year study, we tested whether there were any short‐ or longer‐term effects of fitting geolocators weighing 3% of body mass on male Pied Flycatchers Ficedula hypoleuca. In the deployment year, we compared adult provisioning rates to nestlings, nestling growth and nest success between nesting attempts in which adult males were fitted with a geolocator, with control nests where males had the same capture history but were not tagged. We found no difference between treatments in provisioning effort by males or their associated female 2 days after geolocator fitting, in terms of nestling growth, subsequent brood reduction or nest success. Return rate, arrival date on territories, nest timing and breeding parameters were compared between tagged and untagged males in the following breeding season. We found no difference in return rate or arrival date, and no difference in nest timing, fecundity or outcome. Our study suggests that fitting lightweight tags to small passerines need not affect behaviour, breeding or apparent between‐year survival. However, tagging new species should still require assessment and comparison with well‐matched control cohorts, and it should be recognized that tag effects could vary between years and populations, mediated by environmental conditions.     

Meta-Fish-Lib: A generalised,dynamic DNA reference library pipeline for metabarcoding of fishes

The accuracy and reliability of DNA metabarcoding analyses depend on the breadth and quality of the reference libraries that underpin them. However, there are limited options available to obtain and curate the huge volumes of sequence data that are available on public repositories such as NCBI and BOLD. Here, we provide a pipeline to download, clean and annotate mitochondrial DNA sequence data for a given list of fish species. Features of this pipeline include (a) support for multiple metabarcode markers; (b) searches on species synonyms and taxonomic name validation; (c) phylogeny assisted quality control for identification and removal of misannotated sequences; (d) automatically generated coverage reports for each new GenBank release update; and (e) citable, versioned DOIs. As an example we provide a ready-to-use curated reference library for the marine and freshwater fishes of the U.K. To augment this reference library for environmental DNA metabarcoding specifically, we generated 241 new MiFish-12S sequences for 88 U.K. marine species, and make available new primer sets useful for sequencing these. This brings the coverage of common U.K. species for the MiFish-12S fragment to 93%, opening new avenues for scaling up fish metabarcoding across wide spatial gradients. The Meta-Fish-Lib reference library and pipeline is hosted at https://github.com/genner-lab/meta-fish-lib .