Verification Witnesses

Over the last years, witness-based validation of verification results has become an established practice in software verification: An independent validator re-establishes verification results of a software verifier using verification witnesses, which are stored in a standardized exchange format. In addition to validation, such exchangable information about proofs and alarms found by a verifier can be shared across verification tools, and users can apply independent third-party tools to visualize and explore witnesses to help them comprehend the causes of bugs or the reasons why a given program is correct. To achieve the goal of making verification results more accessible to engineers, it is necessary to consider witnesses as first-class exchangeable objects, stored independently from the source code and checked independently from the verifier that produced them, respecting the important principle of separation of concerns. We present the conceptual principles of verification witnesses, give a description of how to use them, provide a technical specification of the exchange format for witnesses, and perform an extensive experimental study on the application of witness-based result validation, using the validators CPAchecker, UAutomizer, CPA-witness2test, and FShell-witness2test

The molecular basis of host specialization in bean pathovars of Pseudomonas syringae

Biotrophic phytopathogens are typically limited to their adapted host range. In recent decades, investigations have teased apart the general molecular basis of intraspecific variation for innate immunity of plants, typically involving receptor proteins that enable perception of pathogen-associated molecular patterns or avirulence elicitors from the pathogen as triggers for defense induction. However, general consensus concerning evolutionary and molecular factors that alter host range across closely related phytopathogen isolates has been more elusive. Here, through genome comparisons and genetic manipulations, we investigate the underlying mechanisms that structure host range across closely related strains of Pseudomonas syringae isolated from different legume hosts. Although type III secretionindependent virulence factors are conserved across these three strains, we find that the presence of two genes encoding type III effectors (hopC1 and hopM1) and the absence of another (avrB2) potentially contribute to host range differences between pathovars glycinea and phaseolicola. These findings reinforce the idea that a complex genetic basis underlies host range evolution in plant pathogens. This complexity is present even in host–microbe interactions featuring relatively little divergence among both hosts and their adapted pathogens

Genetic diversity and differentiation within and between cultivated (Vitis vinifera L. ssp. sativa) and wild (Vitis vinifera L. ssp. sylvestris) grapes

Genetic characterization of 502 diverse grape accessions including 342 cultivated (V. vinifera ssp. sativa) and 160 wild (V. vinifera ssp. sylvestris) grapes showed considerable genetic diversity among accessions. A total of 117 alleles were detected across eight SSR loci with the average of 14 alleles per locus. The genetic diversity of wild grapes was slightly lower than that observed in the cultivated grapes probably due to small populations and severe natural selection leading to drift and loss of alleles and heterozygosity in wild grapes. The distance cluster analysis (CA) supported the classical ecogeographic groups with moderate genetic differentiation among them. There was a greater affinity of Occidentalis grape to wild grape from the Caucasus than other groups. However, a number of low to moderate frequency alleles that are present in the cultivated grape are not represented in the wild grape.

Identification of mildew resistance in wild and cultivated Central Asian grape germplasm

BACKGROUND: Cultivated grapevines, Vitis vinifera subsp. sativa, evolved from their wild relative, V. vinifera subsp. sylvestris. They were domesticated in Central Asia in the absence of the powdery mildew fungus, Erysiphe necator, which is thought to have originated in North America. However, powdery mildew resistance has previously been discovered in two Central Asian cultivars and in Chinese Vitis species. RESULTS: A set of 380 unique genotypes were evaluated with data generated from 34 simple sequence repeat (SSR) markers. The set included 306 V. vinifera cultivars, 40 accessions of V. vinifera subsp. sylvestris, and 34 accessions of Vitis species from northern Pakistan, Afghanistan and China. Based on the presence of four SSR alleles previously identified as linked to the powdery mildew resistance locus, Ren1, 10 new mildew resistant genotypes were identified in the test set: eight were V. vinifera cultivars and two were V. vinifera subsp. sylvestris based on flower and seed morphology. Sequence comparison of a 620 bp region that includes the Ren1-linked allele (143 bp) of the co-segregating SSR marker SC8-0071-014, revealed that the ten newly identified genotypes have sequences that are essentially identical to the previously identified mildew resistant V. vinifera cultivars: ‘Kishmish vatkana’ and ‘Karadzhandal’. Kinship analysis determined that three of the newly identified powdery mildew resistant accessions had a relationship with ‘Kishmish vatkana’ and ‘Karadzhandal’, and that six were not related to any other accession in this study set. Clustering procedures assigned accessions into three groups: 1) Chinese species; 2) a mixed group of cultivated and wild V. vinifera; and 3) table grape cultivars, including nine of the powdery mildew resistant accessions. Gene flow was detected among the groups. CONCLUSIONS: This study provides evidence that powdery mildew resistance is present in V. vinifera subsp. sylvestris, the dioecious wild progenitor of the cultivated grape. Four first-degree parent progeny relationships were discovered among the hermaphroditic powdery mildew resistant cultivars, supporting the existence of intentional grape breeding efforts. Although several Chinese grape species are resistant to powdery mildew, no direct genetic link to the resistance found in V. vinifera could be established

Characterization of a brazilian grape germplasm collection using microsatellite markers.

Two hundred and twenty-one grapevine accessions from the Embrapa Semi-Árido, Juazeiro, Bahia, collection in Brazil were fingerprinted at seven SSR loci: VVS2, VVMD5, VVMDF7, VVMD27, VVMD31, VrZAG62, and VrZAG79

Pseudomonas syringae type III effector HopAF1 suppresses plant immunity by targeting methionine recycling to block ethylene induction

Pseudomonas syringae is a Gram-negative bacterium that uses a type III secretion system to inject type III effector (T3E) proteins into the host to cause disease in plants. Multiple P. syringae T3Es promote virulence by targeting immune system signaling pathways using diverse biochemical mechanisms. We provide evidence for a molecular function of the P. syringae T3E HopAF1. We demonstrate that the C-terminal region of HopAF1 has structural homology to deamidases. We demonstrate that an enzyme important for production of the gaseous signaling hormone ethylene is a target for HopAF1 and show that HopAF1 targets methylthioadenosine nucleosidase proteins MTN1 and MTN2 to dampen ethylene production during bacterial infection

What a Difference a Dalton Makes: Bacterial Virulence Factors Modulate Eukaryotic Host Cell Signaling Systems via Deamidation

Pathogenic bacteria commonly deploy enzymes to promote virulence. These enzymes can modulate the functions of host cell targets. While the actions of some enzymes can be very obvious (e.g., digesting plant cell walls), others have more subtle activities. Depending on the lifestyle of the bacteria, these subtle modifications can be crucially important for pathogenesis. In particular, if bacteria rely on a living host, subtle mechanisms to alter host cellular function are likely to dominate. Several bacterial virulence factors have evolved to use enzymatic deamidation as a subtle posttranslational mechanism to modify the functions of host protein targets. Deamidation is the irreversible conversion of the amino acids glutamine and asparagine to glutamic acid and aspartic acid, respectively. Interestingly, all currently characterized bacterial deamidases affect the function of the target protein by modifying a single glutamine residue in the sequence. Deamidation of target host proteins can disrupt host signaling and downstream processes by either activating or inactivating the target. Despite the subtlety of this modification, it has been shown to cause dramatic, context-dependent effects on host cells. Several crystal structures of bacterial deamidases have been solved. All are members of the papain-like superfamily and display a cysteine-based catalytic triad. However, these proteins form distinct structural subfamilies and feature combinations of modular domains of various functions. Based on the diverse pathogens that use deamidation as a mechanism to promote virulence and the recent identification of multiple deamidases, it is clear that this enzymatic activity is emerging as an important and widespread feature in bacterial pathogenesis

Pivoting the Plant Immune System from Dissection to Deployment

Diverse and rapidly evolving pathogens cause plant diseases and epidemics that threaten crop yield and food security around the world. Research over the last 25 years has led to an increasingly clear conceptual understanding of the molecular components of the plant immune system. Combined with ever-cheaper DNA-sequencing technology and the rich diversity of germ plasm manipulated for over a century by plant breeders, we now have the means to begin development of durable (long-lasting) disease resistance beyond the limits imposed by conventional breeding and in a manner that will replace costly and unsustainable chemical controls