COPLA, a taxonomic classifier of plasmids

Background: Plasmids are mobile genetic elements, key in the dissemination of antibiotic resistance, virulence determinants and other adaptive traits in bacteria. Obtaining a robust method for plasmid classification is necessary to better understand the genetics and epidemiology of many pathogens. Until now, plasmid classification systems focused on specific traits, which limited their precision and universality. The definition of plasmid taxonomic units (PTUs), based on average nucleotide identity metrics, allows the generation of a universal plasmid classification scheme, applicable to all bacterial taxa. Here we present COPLA, a software able to assign plasmids to known and novel PTUs, based on their genomic sequence. Results: We implemented an automated pipeline able to assign a given plasmid DNA sequence to its cognate PTU, and assessed its performance using a sample of 1000 unclassified plasmids. Overall, 41% of the samples could be assigned to a previously defined PTU, a number that reached 63% in well-known taxa such as the Enterobacterales order. The remaining plasmids represent novel PTUs, indicating that a large fraction of plasmid backbones is still uncharacterized. Conclusions: COPLA is a bioinformatic tool for universal, species-independent, plasmid classification. Offered both as an automatable pipeline and an open web service, COPLA will help bacterial geneticists and clinical microbiologists to quickly classify plasmids.This work was supported by the Spanish Ministry of Science and Innovation [PID2020-117923GB-I00 to FdlC]; the Spanish Ministry of Economy, Industry and Competitiveness [DI-17-09164 to SR-S]; and USA Centers for Disease Control and Prevention [200-2019-06679 to FdlC]. The funders had no role in the design of the study, nor in the collection, analysis, and interpretation of data, nor in writing the manuscript included in this submission

Direct and indirect effects of planning density, nitrogenous fertilizer and host plant resistance on rice herbivores and their natural enemies

In rice ecosystems, seeding densities can be adjusted to compensate for lower nitrogen levels that reduce GHG emissions, or to increase farm profitability. However, density-induced changes to plant anatomy could affect herbivore-rice interactions, and alter arthropod community dynamics. We conducted an experiment that varied transplanting density (low or high), nitrogenous fertilizer (0, 60 or 150 kg added ha−1) and rice variety (resistant or susceptible to phloem-feeding insects) over two rice-growing seasons. Yields per plot increased with added nitrogen, but were not affected by variety or transplanting density. Planthopper and leafhopper densities were lower on resistant rice and in high-density field plots. Nitrogen was associated with higher densities of planthoppers, but lower densities of leafhoppers per plot. High planting densities and high nitrogen also increased rodent damage. The structure of arthropod herbivore communities was largely determined by season and transplanting density. Furthermore, two abundant planthoppers (Sogatella furcifera (Horváth) and Nilaparvata lugens (Stål)) segregated to low and high-density plots, respectively. The structure of decomposer communities was determined by season and fertilizer regime; total decomposer abundance increased in high-nitrogen plots during the dry season. Predator community structure was determined by season and total prey abundance (including decomposers) with several spider species dominating in plots with high prey abundance during the wet season. Our results indicate how rice plasticity and arthropod biodiversity promote stability and resilience in rice ecosystems. We recommend that conservation biological control, which includes a reduction or elimination of insecticides, could be promoted to attain sustainable rice production systems.info:eu-repo/semantics/publishedVersio

Response-adapted treatment with rituximab, bendamustine, mitoxantrone, and dexamethasone followed by rituximab maintenance in patients with relapsed or refractory follicular lymphoma after first-line immunochemotherapy: Results of the RBMDGELTAMO08 phase II trial

Background Consensus is lacking regarding the optimal salvage therapy for patients with follicular lymphoma who relapse after or are refractory to immunochemotherapy. Methods This phase II trial evaluated the efficacy and safety of response-adapted therapy with rituximab, bendamustine, mitoxantrone, and dexamethasone (RBMD) in follicular lymphoma patients who relapsed after or were refractory to first-line immunochemotherapy. Sixty patients received three treatment cycles, and depending on their response received an additional one (complete/unconfirmed complete response) or three (partial response) cycles. Patients who responded to induction received rituximab maintenance therapy for 2 years. Results Thirty-three (55%) and 42 (70%) patients achieved complete/unconfirmed complete response after three cycles and on completing induction therapy (4-6 cycles), respectively (final overall response rate, 88.3%). Median progression-free survival was 56.4 months (median follow-up, 28.3 months; 95% CI, 15.6-51.2). Overall survival was not reached. Progression-free survival did not differ between patients who received four vs six cycles (P = .6665), nor between patients who did/did not receive rituximab maintenance after first-line therapy (P = .5790). Median progression-free survival in the 10 refractory patients was 25.5 months (95% CI, 0.6-N/A) and was longer in patients who had shown progression of disease after 24 months of first-line therapy (median, 56.4 months; 95% CI, 19.8-56.4) than in those who showed early progression (median, 42.31 months; 95% CI, 24.41-NA) (P = .4258). Thirty-six (60%) patients had grade 3/4 neutropenia. Grade 3/4 febrile neutropenia and infection were recorded during induction (4/60 [6.7%] and 5/60 [8.3%] patients, respectively) and maintenance (2/43 [4.5%] and 4/43 [9.1%] patients, respectively). Conclusions This response-adapted treatment with RBMD followed by rituximab maintenance is an effective and well-tolerated salvage treatment for relapsed/refractory follicular lymphoma following first-line immunochemotherapy

Correction to: Cluster identification, selection, and description in Cluster randomized crossover trials: the PREP-IT trials

An amendment to this paper has been published and can be accessed via the original article

Aspects of brown planthopper adaptation to resistant rice varieties with the Bph3 gene

Despite over 30years of deployment, varieties with the Bph3 gene for resistance to the brown planthopper (BPH), Nilaparvata lugens (Stål) (Hemiptera: Delphacidae), are still effective in much of the Philippines. In the present study, we determined the effects of adaptation to one resistant variety, IR62 - assumed to possess the Bph3 gene - on (1) resistance against a series of varieties with similar biotypical responses (presumed to contain the same major resistance genes), and (2) a differential variety with the bph4 gene that occurs at the same chromosome position as Bph3. We also examined the effects of high soil nitrogen on the effectiveness of Bph3. Feeding, planthopper biomass, and development times were reduced in a wild BPH population when reared on IR62 compared with the susceptible standard variety TN1. However, nitrogen application increased the susceptibility of IR62. After 13 generations on IR62, BPH had adapted to the plant's resistance. Virulence of the adapted BPH against the variety 'Rathu Heenati' supports the idea that Bph3 is present in IR62. Across similar IR varieties (IR60, IR66, IR68, IR70, IR72, and IR74), feeding, planthopper biomass, and development rates were generally higher for IR62-adapted than for non-adapted BPH; however, contrary to expectations, many of these varieties were already susceptible to wild BPH. Fitness was also higher for IR62-adapted BPH on the variety 'Babawee' indicating a close relation between Bph3 and bph4. The results indicate that the conventional understanding of the genetics behind resistance in IR varieties needs to be readdressed to develop and improve deployment strategies for resistance management. © 2011 The Authors. Entomologia Experimentalis et Applicata © 2011 The Netherlands Entomological Society

Morphological variation of Aphidius ervi Haliday (Hymenoptera: Braconidae) associated with different aphid hosts

Background Parasitoids are frequently used in biological control due to the fact that they are considered host specific and highly efficient at attacking their hosts. As they spend a significant part of their life cycle within their hosts, feeding habits and life history of their host can promote specialization via host-race formation (sequential radiation). The specialized host races from different hosts can vary morphologically, behaviorally and genetically. However, these variations are sometimes inconspicuous and require more powerful tools in order to detect variation such as geometric morphometrics analysis. Methods We examined Aphidius ervi, an important introduced biological control agent in Chile associated with a great number of aphid species, which are exploiting different plant hosts and habitats. Several combinations (biotypes) of parasitoids with various aphid/host plant combinations were analyzed in order to obtain measures of forewing shape and size. To show the differences among defined biotypes, we chose 13 specific landmarks on each individual parasitoid wing. The analysis of allometric variation calculated in wing shape and size over centroid size (CS), revealed the allometric changes among biotypes collected from different hosts. To show all differences in shape of forewings, we made seven biotype pairs using an outline-based geometric morphometrics comparison. Results The biotype A. pis_pea (Acyrthosiphon pisum on pea) was the extreme wing size in this study compared to the other analyzed biotypes. Aphid hosts have a significant influence in the morphological differentiation of the parasitoid forewing, splitting biotypes in two groups. The first group consisted of biotypes connected with Acyrthosiphon pisum on legumes, while the second group is composed of biotypes connected with aphids attacking cereals, with the exception of the R. pad_wheat (Rhopalosiphum padi on wheat) biotype. There was no significant effect of plant species on parasitoid wing size and shape. Discussion Although previous studies have suggested that the genotype of parasitoids is of greater significance for the morphological variations of size and shape of wings, this study indicates that the aphid host on which A. ervi develops is the main factor to alter the structure of parasitoid forewings. Bigger aphid hosts implied longer and broader forewings of A. ervi

Direct and Indirect Effects of Planting Density, Nitrogenous Fertilizer and Host Plant Resistance on Rice Herbivores and Their Natural Enemies

In rice ecosystems, seeding densities can be adjusted to compensate for lower nitrogen levels that reduce GHG emissions, or to increase farm profitability. However, density-induced changes to plant anatomy could affect herbivore-rice interactions, and alter arthropod community dynamics. We conducted an experiment that varied transplanting density (low or high), nitrogenous fertilizer (0, 60 or 150 kg added ha−1) and rice variety (resistant or susceptible to phloem-feeding insects) over two rice-growing seasons. Yields per plot increased with added nitrogen, but were not affected by variety or transplanting density. Planthopper and leafhopper densities were lower on resistant rice and in high-density field plots. Nitrogen was associated with higher densities of planthoppers, but lower densities of leafhoppers per plot. High planting densities and high nitrogen also increased rodent damage. The structure of arthropod herbivore communities was largely determined by season and transplanting density. Furthermore, two abundant planthoppers (Sogatella furcifera (Horváth) and Nilaparvata lugens (Stål)) segregated to low and high-density plots, respectively. The structure of decomposer communities was determined by season and fertilizer regime; total decomposer abundance increased in high-nitrogen plots during the dry season. Predator community structure was determined by season and total prey abundance (including decomposers) with several spider species dominating in plots with high prey abundance during the wet season. Our results indicate how rice plasticity and arthropod biodiversity promote stability and resilience in rice ecosystems. We recommend that conservation biological control, which includes a reduction or elimination of insecticides, could be promoted to attain sustainable rice production systems

Direct and Indirect Effects of Planting Density, Nitrogenous Fertilizer and Host Plant Resistance on Rice Herbivores and Their Natural Enemies

In rice ecosystems, seeding densities can be adjusted to compensate for lower nitrogen levels that reduce GHG emissions, or to increase farm profitability. However, density-induced changes to plant anatomy could affect herbivore-rice interactions, and alter arthropod community dynamics. We conducted an experiment that varied transplanting density (low or high), nitrogenous fertilizer (0, 60 or 150 kg added ha−1) and rice variety (resistant or susceptible to phloem-feeding insects) over two rice-growing seasons. Yields per plot increased with added nitrogen, but were not affected by variety or transplanting density. Planthopper and leafhopper densities were lower on resistant rice and in high-density field plots. Nitrogen was associated with higher densities of planthoppers, but lower densities of leafhoppers per plot. High planting densities and high nitrogen also increased rodent damage. The structure of arthropod herbivore communities was largely determined by season and transplanting density. Furthermore, two abundant planthoppers (Sogatella furcifera (Horváth) and Nilaparvata lugens (Stål)) segregated to low and high-density plots, respectively. The structure of decomposer communities was determined by season and fertilizer regime; total decomposer abundance increased in high-nitrogen plots during the dry season. Predator community structure was determined by season and total prey abundance (including decomposers) with several spider species dominating in plots with high prey abundance during the wet season. Our results indicate how rice plasticity and arthropod biodiversity promote stability and resilience in rice ecosystems. We recommend that conservation biological control, which includes a reduction or elimination of insecticides, could be promoted to attain sustainable rice production systems