Comprehensive DNA signature discovery and validation

DNA signatures are nucleotide sequences that can be used to detect the presence of an organism and to distinguish that organism from all other species. Here we describe Insignia, a new, comprehensive system for the rapid identification of signatures in the genomes of bacteria and viruses. With the availability of hundreds of complete bacterial and viral genome sequences, it is now possible to use computational methods to identify signature sequences in all of these species, and to use these signatures as the basis for diagnostic assays to detect and genotype microbes in both environmental and clinical samples. The success of such assays critically depends on the methods used to identify signatures that properly differentiate between the target genomes and the sample background. We have used Insignia to compute accurate signatures for most bacterial genomes and made them available through our Web site. A sample of these signatures has been successfully tested on a set of 46 Vibrio cholerae strains, and the results indicate that the signatures are highly sensitive for detection as well as specific for discrimination between these strains and their near relatives. Our approach, whereby the entire genomic complement of organisms are compared to identify probe targets, is a promising method for diagnostic assay development, and it provides assay designers with the flexibility to choose probes from the most relevant genes or genomic regions. The Insignia system is freely accessible via a Web interface and has been released as open source software at: http://insignia.cbcb.umd.edu.     

Influence of Atg5 Mutation in SLE Depends on Functional IL-10 Genotype

Increasing evidence supports the involvement of autophagy in the etiopathology of autoimmune diseases. Despite the identification of autophagy-related protein (Atg)-5 as one of the susceptibility loci in systemic Lupus erythematosus (SLE), the consequences of the carriage of these mutations for patients remain unclear. The present work analyzed the association of Atg5 rs573775 single nucleotide polymorphism (SNP) with SLE susceptibility, IFNα, TNFα and IL-10 serum levels, and clinical features, in 115 patients and 170 healthy individuals. Patients who where carriers of the rs573775 T* minor allele presented lower IFNα levels than those with the wild genotype, whereas the opposite result was detected for IL-10. Thus, since IL-10 production was regulated by rs1800896 polymorphisms, we evaluated the effect of this Atg5 mutation in genetically high and low IL-10 producers. Interestingly, we found that the rs573775 T* allele was a risk factor for SLE in carriers of the high IL-10 producer genotype, but not among genetically low producers. Moreover, IL-10 genotype influences SLE features in patients presenting the Atg5 mutated allele. Specifically, carriage of the rs573775 T* allele led to IL-10 upregulation, reduced IFNα and TNFα production and a low frequency of cytopenia in patients with the high IL-10 producer genotype, whereas patients with the same Atg5 allele that were low IL-10 producers presented reduced amounts of all these cytokines, had a lower prevalence of anti-dsDNA antibodies and the latest onset age. In conclusion, the Atg5 rs573775 T* allele seems to influence SLE susceptibility, cytokine production and disease features depending on other factors such as functional IL-10 genotype.     

Oncogenic ras and p53 cooperate to induce cellular senescence

Oncogenic activation of the mitogen-activated protein (MAP) kinase cascade in murine fibroblasts initiates a senescence-like cell cycle arrest that depends on the ARF/p53 tumor suppressor pathway. To investigate whether p53 is sufficient to induce senescence, we introduced a conditional murine p53 allele (p53(val135)) into p53-null mouse embryonic fibroblasts and examined cell proliferation and senescence in cells expressing p53, oncogenic Ras, or both gene products. Conditional p53 activation efficiently induced a reversible cell cycle arrest but was unable to induce features of senescence. In contrast, coexpression of oncogenic ras or activated mek1 with p53 enhanced both p53 levels and activity relative to that observed for p53 alone and produced an irreversible cell cycle arrest that displayed features of cellular senescence. p19(ARF) was required for this effect, since p53(-/-) ARF(-/-) double-null cells were unable to undergo senescence following coexpression of oncogenic Ras and p53. Although the levels of exogenous p53 achieved in ARF-null cells were relatively low, the stabilizing effects of p19(ARF) on p53 could not explain the cooperation between oncogenic Ras and p53 in promoting senescence. Hence, enforced p53 expression without oncogenic ras in p53(-/-) mdm2(-/-) double-null cells produced extremely high p53 levels but did not induce senescence. Taken together, our results indicate that oncogenic activation of the MAP kinase pathway in murine fibroblasts converts p53 into a senescence inducer through both quantitative and qualitative mechanisms.     

Pre-Training Reversible Inactivation of the Basal Amygdala (BA) Disrupts Contextual,but Not Auditory,Fear Conditioning,in Rats

The basolateral amygdala complex (BLA), including the lateral (LA), basal (BA) and accessory basal (AB) nuclei, is involved in acquisition of contextual and auditory fear conditioning. The BA is one of the main targets for hippocampal information, a brain structure critical for contextual learning, which integrates several discrete stimuli into a single configural representation. Congruent with the hodology, selective neurotoxic damage to the BA results in impairments in contextual, but not auditory, fear conditioning, similarly to the behavioral impairments found after hippocampal damage. This study evaluated the effects of muscimol-induced reversible inactivation of the BA during a simultaneous contextual and auditory fear conditioning training on later fear responses to both the context and the tone, tested separately, without muscimol administration. As compared to control rats micro-infused with vehicle, subjects micro-infused with muscimol before training exhibited, during testing without muscimol, significant reduction of freezing responses to the conditioned context, but not to the conditioned tone. Therefore, reversible inactivation of the BA during training impaired contextual, but not auditory fear conditioning, thus confirming and extending similar behavioral observations following selective neurotoxic damage to the BA and, in addition, revealing that this effect is not related to the lack of a functional BA during testing.     

Toxicity and pharmacokinetics of insect growth regulators and other novel insecticides on pupae of Hyposoter didmator (Hymenoptera: Ichneumonidae), a parasitoid of early larval instars of lepidopteran pests

Susceptibility of the lepidopteran parasitoid Hyposoter didymator (Thunberg) to seven modern insecticides, azadirachtin, diflubenzuron, halofenozide, methoxyfenozide, pyriproxyfen, tebufenozide, and spinosad, was tested in the laboratory. Pupae were exposed to different doses of each compound by direct topical application. At the field recommended doses, methoxyfenozide and tebufenozide had no effect on H. didymator. Halofenozide had a low effect on both adult emergence and adult survival but the progeny size and parasitism capacity were not affected. Diflubenzuron was moderately toxic to the parasitoid, while azadirachtin, pyriproxyfen and spinosad were very toxic, affecting all its life parameters. In the pyriproxyfen and spinosad treatments, no progeny was obtained. As a second approach of this study, we determined the rate of penetration through the pupal cocoon and absorption in the parasitoid body as pharmacokinetic parameters important for toxicity. Most of the radioactivity was retained in the silken cocoon, indicating a low accumulation in the parasitoid body. Among all compounds tested, diflubenzuron exhibited the highest absorption in the parasitoid body, followed by pyriproxyfen. For halofenozide, methoxyfenozide and tebufenozide, low absorption (<2%) was found. In addition, we tested for the presence of molting hormone receptors in Hyposoter tissues using a monoclonal antibody 9B9. Our data suggest that the use of diflubenzuron azadirachtin, pyriproxyfen, halofenozide, and spinosad in combination with H. didymator in integrated pest management (IPM) programs should be carefully evaluated. Methoxyfenozide and tebufenozide could be considered safe for this parasitoid.     

MDR-like ABC transporter AtPGP4 is involved in auxin-mediated lateral root and root hair development

Previous data have suggested an involvement of MDR/PGP-like ABC transporters in transport of the plant hormone auxin and, recently, AtPGP1 has been demonstrated to catalyze the primary active export of auxin. Here we show that related isoform AtPGP4 is expressed predominantly during early root development. AtPGP4 loss-of-function plants reveal enhanced lateral root initiation and root hair lengths both known to be under the control of auxin. Further, atpgp4 plants show altered sensitivities toward auxin and the auxin transport inhibitor, NPA. Finally, mutant roots reveal elevated free auxin levels and reduced auxin transport capacities. These results together with yeast growth assays suggest a direct involvement of AtPGP4 in auxin transport processes controlling lateral root and root hair development.     

Empirical evidence for large‐scale human impact on intertidal aggregations,larval supply and recruitment of Pyura praeputialis around the Bay of Antofagasta,Chile

In northern Chile, Pyura praeputialis is an invasive species inhabiting rocky intertidal and subtidal habitats restricted exclusively to the Bay of Antofagasta where it forms extensive aggregations. The negative impact of Pyura gathering on mid‐intertidal abundances of this species has recently been reported at the south‐eastern end of this bay. In the present study we have increased sampling sites to cover the entire bay toward the north‐western end and the northern section, where a coastal marine reserve for the scallop fishery partially restricts shellfish gathering. Therefore, the sampling sites were chosen to represent different levels of shellfish gathering access along the northern shore of the bay. Long‐term monitoring (1999–2014) of changes in tunicate cover and the abundances of larvae and recruits at seven sites are reported. The opening of a remodelled artificial and recreational beach in 2012, on the central‐eastern shore of the bay, has increased accessibility to rocky intertidal platforms that started to be massively visited by Pyura gatherers from the summer of 2013. This allowed for the implementation of an intensive short‐term monitoring program of changes in tunicate cover and the abundances of their larvae and recruits. When gathering access was present the reduction in intertidal cover was generalized to the entire bay and followed by reductions in larvae and recruits. However, these reductions were not found in sites with more restricted gathering access. We conclude that continuous extraction by Pyura gatherers followed by reductions of conspecific larvae and recruits are the main drivers behind the reduced abundance of P. praeputialis in the entire bay of Antofagasta. Thus, if gathering is not stopped important ecosystem services provided by this tunicate in the bay may be threatened. Similar consequences may be expected if other massive and irreversible reductions in other species of the Pyura complex, that inhabit other coasts in the southern hemisphere, occur. The controversy concerning the impacts of invasive species and whether they cause negative, positive or neutral impacts to original ecosystems and fisheries is discussed.