Insect Transmission of Plant Pathogens

Much of biological research conducted today is multidisciplinary, partly because of the availability of ever simpler to use molecular tools and the realization that ecological systems are complex and multitrophic. Although there is a general trend toward academic specialization and cooperation, some fields still require that scientists be aware of the “bigger picture.” We consider that the study of insect-transmitted plant pathogens is one of those fields, where insect, pathogen, and plant are inseparably linked. In this triangle of interactions, researchers focus their interests on questions at the molecular and cellular to epidemiological levels. Throughout the years, plant vector entomologists have addressed a variety of important pest problems, often linking entomologists and plant pathologists for the development of improved and sustainable disease control strategies

The uncertain consequences of transferring bacterial strains between laboratories - rpoS instability as an example

Abstract\ud \ud \ud \ud Background\ud \ud Microbiological studies frequently involve exchanges of strains between laboratories and/or stock centers. The integrity of exchanged strains is vital for archival reasons and to ensure reproducible experimental results. For at least 50 years, one of the most common means of shipping bacteria was by inoculating bacterial samples in agar stabs. Long-term cultures in stabs exhibit genetic instabilities and one common instability is in rpoS. The sigma factor RpoS accumulates in response to several stresses and in the stationary phase. One consequence of RpoS accumulation is the competition with the vegetative sigma factor σ70. Under nutrient limiting conditions mutations in rpoS or in genes that regulate its expression tend to accumulate. Here, we investigate whether short-term storage and mailing of cultures in stabs results in genetic heterogeneity.\ud \ud \ud \ud Results\ud \ud We found that samples of the E. coli K-12 strain MC4100TF exchanged on three separate occasions by mail between our laboratories became heterogeneous. Reconstruction studies indicated that LB-stabs exhibited mutations previously found in GASP studies in stationary phase LB broth. At least 40% of reconstructed stocks and an equivalent proportion of actually mailed stock contained these mutations. Mutants with low RpoS levels emerged within 7 days of incubation in the stabs. Sequence analysis of ten of these segregants revealed that they harboured each of three different rpoS mutations. These mutants displayed the classical phenotypes of bacteria lacking rpoS. The genetic stability of MC4100TF was also tested in filter disks embedded in glycerol. Under these conditions, GASP mutants emerge only after a 3-week period. We also confirm that the intrinsic high RpoS level in MC4100TF is mainly due to the presence of an IS1 insertion in rssB.\ud \ud \ud \ud Conclusions\ud \ud Given that many E. coli strains contain high RpoS levels similar to MC4100TF, the integrity of such strains during transfers and storage is questionable. Variations in important collections may be due to storage-transfer related issues. These results raise important questions on the integrity of bacterial archives and transferred strains, explain variation like in the ECOR collection between laboratories and indicate a need for the development of better methods of strain transfer.We are grateful to Fundação de Amparo á Pesquisa do Estado de São Paulo (FAPESP-Brazil), who supported this study and provided a travel allowance for TF. TF was also supported by the the Australian Research Council and the US Army Research Office. We also thank K. C. Murphy and S. Kushner for respectively providing strain KM32 and plasmid pWKS130

Draft Genome Sequence of CO33, a Coffee-Infecting Isolate of Xylella fastidiosa

The draft genome sequence of Xylella fastidiosa CO33 isolate, retrieved from symptomatic leaves of coffee plant intercepted in northern Italy, is reported. The CO33 genome size is 2,681,926 bp with a GC content of 51.7%

Grapevine leafroll-associated virus 3.

Grapevine leafroll disease (GLD) is one of the most important grapevine viral diseases affecting grapevines worldwide. The impact on vine health, crop yield, and quality is difficult to assess due to a high number of variables, but significant economic losses are consistently reported over the lifespan of a vineyard if intervention strategies are not implemented. Several viruses from the family Closteroviridae are associated with GLD. However, Grapevine leafroll-associated virus 3 (GLRaV-3), the type species for the genus Ampelovirus, is regarded as the most important causative agent. Here we provide a general overview on various aspects of GLRaV-3, with an emphasis on the latest advances in the characterization of the genome. The full genome of several isolates have recently been sequenced and annotated, revealing the existence of several genetic variants. The classification of these variants, based on their genome sequence, will be discussed and a guideline is presented to facilitate future comparative studies. The characterization of sgRNAs produced during the infection cycle of GLRaV-3 has given some insight into the replication strategy and the putative functionality of the ORFs. The latest nucleotide sequence based molecular diagnostic techniques were shown to be more sensitive than conventional serological assays and although ELISA is not as sensitive it remains valuable for high-throughput screening and complementary to molecular diagnostics. The application of next-generation sequencing is proving to be a valuable tool to study the complexity of viral infection as well as plant pathogen interaction. Next-generation sequencing data can provide information regarding disease complexes, variants of viral species, and abundance of particular viruses. This information can be used to develop more accurate diagnostic assays. Reliable virus screening in support of robust grapevine certification programs remains the cornerstone of GLD management

AVOCADO: A Virtual Observatory Census to Address Dwarfs Origins

Dwarf galaxies are by far the most abundant of all galaxy types, yet their properties are still poorly understood -especially due to the observational challenge that their intrinsic faintness represents. AVOCADO aims at establishing firm conclusions on their formation and evolution by constructing a homogeneous, multiwavelength dataset for a statistically significant sample of several thousand nearby dwarfs (-18 < Mi < -14). Using public data and Virtual Observatory tools, we have built GALEX+SDSS+2MASS spectral energy distributions that are fitted by a library of single stellar population models. Star formation rates, stellar masses, ages and metallicities are further complemented with structural parameters that can be used to classify them morphologically. This unique dataset, coupled with a detailed characterization of each dwar's environment, allows for a fully comprehensive investigation of their origins and to track the (potential) evolutionary paths between the different dwarf types.Comment: 4 pages, 1 figure. To appear in the proceedings of IAU Symposium 277, "Tracing the Ancestry of Galaxies on the Land of our Ancestors", Carignan, Freeman, and Combes, ed

Occurrence of Grapevine Leafroll-Associated Virus Complex in Napa Valley

Grapevine leafroll disease (GLD) is caused by a complex of several virus species (grapevine leafroll-associated viruses, GLRaV) in the family Closteroviridae. Because of its increasing importance, it is critical to determine which species of GLRaV is predominant in each region where this disease is occurring. A structured sampling design, utilizing a combination of RT-PCR based testing and sequencing methods, was used to survey GLRaVs in Napa Valley (California, USA) vineyards (n = 36). Of the 216 samples tested for GLRaV-1, -2, -3, -4, -5, and -9, 62% (n = 134) were GLRaV positive. Of the positives, 81% (n = 109) were single infections with GLRaV-3, followed by GLRaV-2 (4%, n = 5), while the remaining samples (15%, n = 20) were mixed infections of GLRaV-3 with GLRaV-1, 2, 4, or 9. Additionally, 468 samples were tested for genetic variants of GLRaV-3, and of the 65% (n = 306) of samples positive for GLRaV-3, 22% were infected with multiple GLRaV-3 variants. Phylogenetic analysis utilizing sequence data from the single infection GLRaV-3 samples produced seven well-supported GLRaV-3 variants, of which three represented 71% of all GLRaV-3 positive samples in Napa Valley. Furthermore, two novel variants, which grouped with a divergent isolate from New Zealand (NZ-1), were identified, and these variants comprised 6% of all positive GLRaV-3 samples. Spatial analyses showed that GLRaV-3a, 3b, and 3c were not homogeneously distributed across Napa Valley. Overall, 86% of all blocks (n = 31) were positive for GLRaVs and 90% of positive blocks (n = 28) had two or more GLRaV-3 variants, suggesting complex disease dynamics that might include multiple insect-mediated introduction events

Wave runup video detection using the Radon Transform

A new method of runup detection from video imagery is introduced and validated at an energetic dissipative beach. The instantaneous waterline is detected from uprush and backwash by using the Radon Transform (RT). The method is compared to conventional color contrast method from RGB images and LiDAR measurements. In our observations, the RT shows better detection skill even for adverse conditions, such as those present on flat dissipative swash zones where contrast is reduced. Because the RT is a proxy of deeper waterline (similar to 0.1 m) it is less sensitive to lack of contrast due to sand saturation. Moreover, since it is based on motion detection, it is less sensitive to changes in lighting conditions. Overall, the RT offers an attractive alternative for long term automated detection of the runup

Analysis of histological frequency and pediatric cancer in Rondônia, Western Amazonia (Brazil)

Objective:Describe the histological and cancer frequency in children and adolescents attended at the Hospital de Base Dr. Ary Pinheiro and the Hospital de Barretos / Rondônia, Western Amazonia, in the years 2014 and 2015. Method: This is a descriptive, quantitative and transverse study. We used a structured instrument containing a series of variables, such as gender, age, histological types, more frequent neoplasms, lymphomas, leukemias, among others. We asked The Comitê de Ética em Pesquisa em Seres Humanos (Research Ethics Committee) to dispense the Informed Consent Form because the study did not require intervention on the patient or collection of biological material, and no possibility of constraints on patients and their relatives. Results: From 75 cases, 32 (42.7%) were female and 43 (57.3%) were male. Regarding the distribution of patients according to the age group, 21 (28.0%) were younger than 4 years, 12 (16.0%), 5 to 9 years, 17 (22.6%) from 10 to 14 and 25 (33.4%) from 15 to 19. The most frequent histological types by gender were leukemias of myeloproliferative diseases and myelodysplastic diseases with 30% and 50% new cases in the period, followed by lymphomas and reticuloendothelial neoplasms with 16.65% and 20, 0% of the histological types in the period. Leukemia in the hematopoietic and reticuloendothelial system (C42) is the most frequent cancer in both, female and male gender, with 47.5% of cancers in the biennium. The second group of cancers in children from 0 to 19 years old and location of the primary tumor is the encephalon carcinoma (C71), with 11.25% of the new cases. Conclusions: The results presented with their proper nuances are in agreement with the data of studies carried out in Brazil and in other countries

Charge asymmetries of top quarks at hadron colliders revisited

A sizeable difference in the differential production cross section of top- compared to antitop-quark production, denoted charge asymmetry, has been observed at the Tevatron. The experimental results seem to exceed the theory predictions based on the Standard Model by a significant amount and have triggered a large number of suggestions for "new physics". In the present paper the Standard Model predictions for Tevatron and LHC experiments are revisited. This includes a reanalysis of electromagnetic as well as weak corrections, leading to a shift of the asymmetry by roughly a factor 1.1 when compared to the results of the first papers on this subject. The impact of cuts on the transverse momentum of the top-antitop system is studied. Restricting the ttbar system to a transverse momentum less than 20 GeV leads to an enhancement of the asymmetries by factors between 1.3 and 1.5, indicating the importance of an improved understanding of the $t\bar t$-momentum distribution. Predictions for similar measurements at the LHC are presented, demonstrating the sensitivity of the large rapidity region both to the Standard Model contribution and effects from "new physics".Comment: 23 pages. Final version to appear in JHE

Androgen responsive intronic non-coding RNAs

BACKGROUND: Transcription of large numbers of non-coding RNAs originating from intronic regions of human genes has been recently reported, but mechanisms governing their biosynthesis and biological functions are largely unknown. In this work, we evaluated the existence of a common mechanism of transcription regulation shared by protein-coding mRNAs and intronic RNAs by measuring the effect of androgen on the transcriptional profile of a prostate cancer cell line. RESULTS: Using a custom-built cDNA microarray enriched in intronic transcribed sequences, we found 39 intronic non-coding RNAs for which levels were significantly regulated by androgen exposure. Orientation-specific reverse transcription-PCR indicated that 10 of the 13 were transcribed in the antisense direction. These transcripts are long (0.5–5 kb), unspliced and apparently do not code for proteins. Interestingly, we found that the relative levels of androgen-regulated intronic transcripts could be correlated with the levels of the corresponding protein-coding gene (asGAS6 and asDNAJC3) or with the alternative usage of exons (asKDELR2 and asITGA6) in the corresponding protein-coding transcripts. Binding of the androgen receptor to a putative regulatory region upstream from asMYO5A, an androgen-regulated antisense intronic transcript, was confirmed by chromatin immunoprecipitation. CONCLUSION: Altogether, these results indicate that at least a fraction of naturally transcribed intronic non-coding RNAs may be regulated by common physiological signals such as hormones, and further corroborate the notion that the intronic complement of the transcriptome play functional roles in the human gene-expression program