Plants activate an immune response in defense against microbial pathogens. The first layer of immunity consists in the recognition of microbial fingerprints, called Pathogen Associated Molecular Pattern (PAMP), by a set of Pattern Recognition Receptors (PRR). In addition, the degradation products from fungi, bacteria and plant cells are recognised as Damage Associated Molecular Pattern (DAMP). The first layer of plant defence is based on Pattern Recognition Receptors (PRR) on the membrane. These receptors, either receptor kinases or receptor-like proteins (RLPs), associating with cytoplasmic kinases, recognize the presence of PAMPs, thus activating a local response named PAMP-triggered immunity (PTI), that is not strong but effective towards many pathogen species. Here we discuss and focus on Elongation Factor Tu Receptors (EFR) and flagellin sensing (FLS) receptors. In leucine-rich repeat (LRR) receptor proteins, the hydrophobic LLR domains are exposed on external membranes, providing the protein-protein interaction modules. Plants evolved this protein-protein interaction domain several times during the development of mechanisms to defend themselves from viruses, virulence factors, enzymes and effectors of bacterial and fungal pathogens. Pathogens in addition evolved proteins and enzymes that are injected in the plant cell to counterfight plant immune signaling pathways. These effectors are recognised by plant receptors sensing their presence of their cognate avirulence genes. These receptors originated from recombination during evolution and only occur in some specific tomato genotypes, instead of the widely occurring PPRs. Effector Triggered Immunity (ETI) allows a plant response to effector proteins that is more strong, but is race specific. It leads to local necrosis and apoptosis, and to the establishment of the hypersensitive response (HR). For biotrophic or hemibiotrophic pathogens, necrosis is an effective way to limit their spread, while for necrotrophic pathogens this is not efficient and sufficient way to limit their spread, since depends on the timing of infection and on the plant development phase. Pathogenic fungi strategy relies on the formation of specialised structures, or haustoria, that facilitate the nutrient uptake form plant cells. In this review, we summarize the most recent knowledge on plant pathogens and the mechanisms they evolved to circumvent plant defences among which pathogen effectors, protein decoys inactivating plant defence signals. Effectors are recognised through their binding to plant proteins by means of plant receptors, that activate the Effector Triggered Immunity (ETI). In particular, we focus on the Solanaceae, discussing general mechanisms and specific pathways that confer resistance to various pathogens. There is an arm race between plants and fungal and bacterial pathogens that has led to new protein variants and protein decoys (pseudokinases, inhibitors and sponges blocking glucanases, and Transcription Activator Like Effectors). Advances in understanding the function of pathogen effectors will provide new ways to improve plant immunity and mechanisms of defence against their pests. Finally, we present possible combinations of interventions, from gene engineering to chemical priming, acting on signaling pathways regulated by jasmonate and salicylate hormones, to increase plant resistance and activate plant defences without affecting crop yields.

Turkey ranked third place in the world for chestnut production after China and Bolivia and the country has unique chestnut populations including valuable and diverse seed propagated chestnut genotypes. In this study, chestnuts (Castanea sativa) were collected during the 2016 harvest season from Northeastern part of Turkey from promising 12 different seedling origin genotypes. Tree growth habit, nut weight, kernel ratio, kernel color, moisture, crude protein, crude fat, dietary fiber, total polyphenols, antioxidant activity and fatty acid content of fruits belongs to 12 genotypes were determined. The results showed that, the majority of genotypes had semi upright tree growth habit. The nut weight and kernel ratio were between 5.05 g (K-10) and 10.10 g (K-5) and 71.10% (K-1) and 82.44% (K-3) among genotypes. The total crude fat content ranged from 0.87% (K-7) to 2.61% (K-1) while the crude protein ranged from 4.80% (K-7) to 7.65% (K-1). The dietary fiber content made up no more than 3.61% of the remaining portion of the kernel. It was found that total polyphenols was between 1.66 and 2.70 g GAE/kg and antioxidant activity was between 5.80 and 9.07 μmol Trolox equivalent/g dry weight basis. Oleic and linoleic acid were the major fatty acids in all chestnut fruits and followed by palmitic and linolenic acid. The results showed that there was enough variations among seed propagated chestnut genotypes for most of the searched parameters and this highlights the importance of conserving the genotypes, as their high levels of heterogeneity allow them to respond to abiotic and biotic stresses and adapt to low-input farming systems.

Phylogenetic trees illustrate the evolutionary history of genes and species. Although genes evolve along with the species they belong to, a species tree and gene tree are often not identical. The reasons for this are the evolutionary events at the gene level, like duplication or transfer. These differences are handled by phylogenetic reconciliation, which formally is a mapping between a gene tree nodes and a species tree nodes and branches. We investigate models of reconciliation with gene transfers replacing existing genes, which is a biologically important event, but has never been included in the reconciliation models. The problem is close to the dated version of the classical subtree prune and regraft (SPR) distance problem, where a pruned subtree has to be regrafted only on a branch closer to the root. We prove that the reconciliation problem including transfer with replacement is NP-hard, and that, if speciations and transfers with replacement are the only allowed evolutionary events, it is fixed-parameter tractable with respect to the reconciliation’s weight. We prove that the results extend to the dated SPR problem.

Most estimates for penalised linear regression can be viewed as posterior modes for an appropriate choice of prior distribution. Bayesian shrinkage methods, particularly the horseshoe estimator, have recently attracted a great deal of attention in the problem of estimating sparse, high-dimensional linear models. This paper extends these ideas, and presents a Bayesian grouped model with continuous global-local shrinkage priors to handle complex group hierarchies that include overlapping and multilevel group structures. As the posterior mean is never a sparse estimate of the linear model coefficients, we extend the recently proposed decoupled shrinkage and selection (DSS) technique to the problem of selecting groups of variables from posterior samples. To choose a final, sparse model, we also adapt generalised information criteria approaches to the DSS framework. To ensure that sparse groups, in which only a few predictors are active, can be effectively identified, we provide an alternative degrees of freedom estimator for sparse Bayesian linear models that takes into account the effects of shrinkage on the model coefficients. Simulations and real data analysis using our proposed method show promising performance in terms of correct identification of active and inactive groups, and prediction, in comparison with a Bayesian grouped slab-and-spike approach.

Humans show impaired recognition of faces that are presented upside down, a phenomenon termed face inversion effect, which is thought to reflect the special relevance of faces for humans. Here, we investigated whether a phylogenetically distantly related avian species, the carrion crow, with similar socio-cognitive abilities to human and non-human primates, exhibits a face inversion effect. In a delayed matching-to-sample task, two crows had to differentiate profiles of crow faces as well as matched controls, presented both upright and inverted. Because crows can discriminate humans based on their faces, we also assessed the face inversion effect using human faces. Both crows performed better with crow faces than with human faces and performed worse when responding to inverted pictures in general compared to upright pictures. However, neither of the crows showed a face inversion effect. For comparative reasons, the tests were repeated with human subjects. As expected, humans showed a face-specific inversion effect. Therefore, we did not find any evidence that crows—like humans—process faces as a special visual stimulus. Instead, individual recognition in crows may be based on cues other than a conspecific’s facial profile, such as their body, or on processing of local features rather than holistic processing.

Humans show impaired recognition of faces that are presented upside down, a phenomenon termed face inversion effect, which is thought to reflect the special relevance of faces for humans. Here, we investigated whether a phylogenetically distantly related avian species, the carrion crow, with similar socio-cognitive abilities to human and non-human primates, exhibits a face inversion effect. In a delayed matching-to-sample task, two crows had to differentiate profiles of crow faces as well as matched controls, presented both upright and inverted. Because crows can discriminate humans based on their faces, we also assessed the face inversion effect using human faces. Both crows performed better with crow faces than with human faces and performed worse when responding to inverted pictures in general compared to upright pictures. However, neither of the crows showed a face inversion effect. For comparative reasons, the tests were repeated with human subjects. As expected, humans showed a face-specific inversion effect. Therefore, we did not find any evidence that crows—like humans—process faces as a special visual stimulus. Instead, individual recognition in crows may be based on cues other than a conspecific’s facial profile, such as their body, or on processing of local features rather than holistic processing.