Belowground DNA-based techniques: untangling the network of plant root interactions

Contains fulltext : 91591.pdf (publisher's version ) (Closed access)7 p

An update on molecular cat allergens: Fel d 1 and what else? Chapter 1: Fel d 1, the major cat allergen

Background: Cats are the major source of indoor inhalant allergens after house dust mites. The global incidence of cat allergies is rising sharply, posing a major public health problem. Ten cat allergens have been identified. The major allergen responsible for symptoms is Fel d 1, a secretoglobin and not a lipocalin, making the cat a special case among mammals. Main body: Given its clinical predominance, it is essential to have a good knowledge of this allergenic fraction, including its basic structure, to understand the new exciting diagnostic and therapeutic applications currently in development. The recent arrival of the component-resolved diagnosis, which uses molecular allergens, represents a unique opportunity to improve our understanding of the disease. Recombinant Fel d 1 is now available for in vitro diagnosis by the anti-Fel d 1 specific IgE assay. The first part of the review will seek to describe the recent advances related to Fel d 1 in terms of positive diagnosis and assessment of disease severity. In daily practice, anti-Fel d 1 IgE tend to replace those directed against the overall extract but is this attitude justified? We will look at the most recent arguments to try to answer this question. In parallel, a second revolution is taking place thanks to molecular engineering, which has allowed the development of various forms of recombinant Fel d 1 and which seeks to modify the immunomodulatory properties of the molecule and thus the clinical history of the disease via various modalities of anti-Fel d 1-specific immunotherapy. We will endeavor to give a clear and practical overview of all these trends

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research

Next-generation ARIA care pathways for rhinitis and asthma: a model for multimorbid chronic diseases

Background In all societies, the burden and cost of allergic and chronic respiratory diseases are increasing rapidly. Most economies are struggling to deliver modern health care effectively. There is a need to support the transformation of the health care system into integrated care with organizational health literacy. Main body As an example for chronic disease care, MASK (Mobile Airways Sentinel NetworK), a new project of the ARIA (Allergic Rhinitis and its Impact on Asthma) initiative, and POLLAR (Impact of Air POLLution on Asthma and Rhinitis, EIT Health), in collaboration with professional and patient organizations in the field of allergy and airway diseases, are proposing real-life ICPs centred around the patient with rhinitis, and using mHealth to monitor environmental exposure. Three aspects of care pathways are being developed: (i) Patient participation, health literacy and self-care through technology-assisted "patient activation", (ii) Implementation of care pathways by pharmacists and (iii) Next-generation guidelines assessing the recommendations of GRADE guidelines in rhinitis and asthma using real-world evidence (RWE) obtained through mobile technology. The EU and global political agendas are of great importance in supporting the digital transformation of health and care, and MASK has been recognized by DG Sante as a Good Practice in the field of digitally-enabled, integrated, person-centred care. Conclusion In 20 years, ARIA has considerably evolved from the first multimorbidity guideline in respiratory diseases to the digital transformation of health and care with a strong political involvement

Characterization of two bioluminescent Rhizobium meliloti strains constructed for field releases

Dammann-Kalinowski T, Niemann S, Keller M, Selbitschka W, Tebbe CC, Pühler A. Characterization of two bioluminescent Rhizobium meliloti strains constructed for field releases. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY. 1996;45(4):509-512.The deliberate release of genetically engineered microorganisms requires a thorough characterization of the microbes in question. For the two bioluminescent Rhizobium meliloti strains, L1 and L33 [Selbitschka et al. (1992) Mol Ecol 1:9-19; Selbitschka et al. (1995) FEMS Microbiol Ecol 16:223-232], designated for field release, the sites of genetic modifications in the chromosomes were sequenced from amplified genomic DNA. This indicated no unexpected alterations in the nucleotide sequence. The bioluminescent phenotype was stably inherited over more than 100 generations in liquid cultures. The presence of the luciferase gene in both strains did not have secondary effects on a variety of metabolic pathways as assessed by the Biolog GN system. A specific polymerase chain reaction amplification, based on the chromosomal insertion site of the luc cassette, allowed the discrimination between the two strains and thus simplifies monitoring. The RecA-deficient strain L1 showed a strongly (more than 90%) reduced ability to nodulate alfalfa in competition with its parent strain R. meliloti 2011 and its RecA(+) counterpart L33

Field lysimeter investigation with luciferase-gene (luc)-tagged Sinorhizobium meliloti strains to evaluate the ecological significance of soil inoculation and a recA-mutation

Schwieger F, Dammann-Kalinowski T, Dresing U, et al. Field lysimeter investigation with luciferase-gene (luc)-tagged Sinorhizobium meliloti strains to evaluate the ecological significance of soil inoculation and a recA-mutation. SOIL BIOLOGY & BIOCHEMISTRY. 2000;32(6):859-868.The survival and vertical translocation of two isogenic, luciferase marker gene (luc)-tagged Sinorhizobum meliloti strains, L33 (RecA(+)) and L1 (RecA(-)) was studied under field conditions over a period of 2 years in a soil which was deficient in indigenous S, meliloti. Both strains were inoculated separately at the end of the growing season of 1994 onto replicate field lysimeters (diameter 32 cm) seeded with alfalfa (Medicago sativa). From an initial density of 10(6) cfu g(-1) soil in the A(p)-horizon (0-25 cm depth), populations of both strains declined during winter to 3 x 10(4) cfu g(-1) One year after the field release, a significantly increased titer of the RecA(+) strain was detected (P less than or equal to 0.05). Removal of the green parts of alfalfa from the lysimeters, 79 weeks after inoculation, resulted in a significant decline of the RecA- (2.3 x 10(3) cfu g(-1)) and a slight increase of the RecA(+) strain (9.0 x 10(3) cfu g(-1)). Throughout the whole monitoring period, marker gene-tagged cells were exclusively located in the A(p)-horizon and not below. No inoculated cells were detected in flow-through rain water (threshold of detection 10 cfu ml(-1)) even though each lysimeter was percolated with an average of 42.51 during this study. Single luciferase positive cells could be detected in the A(p)-horizons of non-inoculated lysimeters, which were located between the inoculated lysimeters using nodulation assays. Cultivation methods failed to detect these cells. The bioluminescent nodules were almost exclusively caused by strain L33 and not by L1, indicating that the RecA(-) strain was less competitive in alfalfa nodulation. Soil chemical properties and quantities of microbial populations, culturable on four different growth media, were not affected by the S. meliloti inoculations. This study demonstrates the usefulness of small scale lysimeter field releases to assess the performance and potential ecological effects of genetically modified bacterial inoculants, (C) 2000 Elsevier Science Ltd. All rights reserved

Profiling the Diversity of Microbial Communities with Single-Strand Conformation Polymorphism (SSCP).

Genetic fingerprinting techniques for microbial community analysis have evolved over the last decade into standard applications for efficient and fast differentiation of microbial communities based on their diversity. These techniques commonly analyze the diversity of PCR products amplified from extracted environmental DNA usually utilizing primers hybridizing to suspected conserved regions of the targeted genes. In comparison to the more commonly applied terminal restriction fragment length polymorphism (TRFLP) or denaturing gradient gel electrophoresis (DGGE) techniques, the here-described single-strand conformation polymorphism (SSCP) fingerprinting technique features some advantageous key characteristics. (1) Primers for the polymerase chain reaction (PCR) do only need minimal 5'-end alterations; (2) SSCP is adaptable to high throughput applications in automated sequencers; and (3) a second dimension in the SSCP gel electrophoresis can be implemented to obtain high resolution 2D gels. One central key requirement for SSCP gel electrophoresis is a tight temperature control. Gels that run at different temperatures will produce entirely different fingerprints. This can be exploited for an improved analysis of highly diverse communities by running the same template at different temperatures or by 2D-SSCP gel electrophoresis