Effects of arbuscular mycorrhiza on community composition and seedling recruitment in temperate forest understory

Arbuscular mycorrhizal (AM) fungal communities can influence the species composition of plant communities. This influence may result from effects of AM on seedling recruitment, although the existing evidence is limited to experimental systems. We addressed the impact of AM fungi on the plant community composition and seedling recruitment of two species – Oxalis acetosella and Prunella vulgaris – in a temperate forest understory. We established a field experiment over two years in which soil fertility (using fertilizer to enhance and sucrose to decrease fertility) and the activity of AM fungi (using fungicide) was manipulated in a factorial design. Species richness, diversity and community composition of understory plants were not influenced by soil fertility or AM fungal activity treatments. However, plant community composition was marginally significantly affected by the interaction of these treatments as the effect of AM fungal activity became evident under enhanced soil fertility. Suppression of AM fungal activity combined with decreased soil fertility increased the number of shoots of herbaceous plants. Unchanged activity of AM fungi enhanced the growth of O. acetosella seedlings under decreased soil fertility, but did not influence the growth of P. vulgaris seedlings. We conclude that the role of AM fungi in structuring plant communities depends on soil fertility. AM fungi can have a strong influence on seedling recruitment, especially for those plants that are characteristic of the habitat.     

Latitudinal variation in soil nematode communities under climate warming‐related range‐expanding and native plants

Current climate change has led to latitudinal and altitudinal range expansions of numerous species. During such range expansions, plant species are expected to experience changes in interactions with other organisms, especially with belowground biota that have a limited dispersal capacity. Nematodes form a key component of the belowground food web as they include bacterivores, fungivores, omnivores and root herbivores. However, their community composition under climate change‐driven intracontinental range‐expanding plants has been studied almost exclusively under controlled conditions, whereas little is known about actual patterns in the field. Here, we use novel molecular sequencing techniques combined with morphological quantification in order to examine nematode communities in the rhizospheres of four range‐expanding and four congeneric native species along a 2,000 km latitudinal transect from South‐Eastern to North‐Western Europe. We tested the hypotheses that latitudinal shifts in nematode community composition are stronger in range‐expanding plant species than in congeneric natives and that in their new range, range‐expanding plant species accumulate fewest root‐feeding nematodes. Our results show latitudinal variation in nematode community composition of both range expanders and native plant species, while operational taxonomic unit richness remained the same across ranges. Therefore, range‐expanding plant species face different nematode communities at higher latitudes, but this is also the case for widespread native plant species. Only one of the four range‐expanding plant species showed a stronger shift in nematode community composition than its congeneric native and accumulated fewer root‐feeding nematodes in its new range. We conclude that variation in nematode community composition with increasing latitude occurs for both range‐expanding and native plant species and that some range‐expanding plant species may become released from root‐feeding nematodes in the new range.     

Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes

Background  

We present a comprehensive technological solution for bacterial diagnostics using tmRNA as a marker molecule. A robust probe design algorithm for microbial detection microarray is implemented. The probes were evaluated for specificity and, combined with NASBA (Nucleic Acid Sequence Based Amplification) amplification, for sensitivity.     

Multi-omics approach to study the growth efficiency and amino acid metabolism in <Emphasis Type="Italic">Lactococcus lactis</Emphasis> at various specific growth rates

Background  

Lactococcus lactis is recognised as a safe (GRAS) microorganism and has hence gained interest in numerous biotechnological approaches. As it is fastidious for several amino acids, optimization of processes which involve this organism requires a thorough understanding of its metabolic regulations during multisubstrate growth.     

AGATHE: A tool for personalized rehabilitation of cognitive functions based on simulated activities of daily living

Every year, tens of thousands of people fall victim to one of invalidating neurological pathologies. Acquired brain injury leads to cognitive impairment and heavy loss of autonomy. Rehabilitation interventions are needed to enable people to recover capacity and return to Instrumental Activities of Daily Living (iADL), such as grocery shopping. Unfortunately, the resources made available in cognitive rehabilitation are insufficient for the growing needs of victims of brain damage. The goal of the AGATHE project is to develop a tool that will provide therapists with an innovative means of dealing with cognitive rehabilitation and offer patients customized rehabilitation sessions, on the basis of simulated iADL. AGATHE fits into accessibility prospects of the tool (for everyone, everywhere and anywhere) and reduction of the cost of rehabilitation. AGATHE allows the strengthening and diversification of skills and expertise of the project's clinical and research partners as well as the opening of a new application field to the technology of the industrial partners. Initial tests of the AGATHE tool have been performed among therapists and patients after brain injury in order to validate usability issues. Perspective of efficacy trials has been identified and development projects are explored.     

Gastro-Esophageal Reflux Disease Symptoms and Demographic Factors as a Pre-Screening Tool for Barrett’s Esophagus

Background

Barrett’s esophagus (BE) occurs as consequence of reflux and is a risk factor for esophageal adenocarcinoma. The current “gold-standard” for diagnosing BE is endoscopy which remains prohibitively expensive and impractical as a population screening tool. We aimed to develop a pre-screening tool to aid decision making for diagnostic referrals.

Methodology/Principal Findings

A prospective (training) cohort of 1603 patients attending for endoscopy was used for identification of risk factors to develop a risk prediction model. Factors associated with BE in the univariate analysis were selected to develop prediction models that were validated in an independent, external cohort of 477 non-BE patients referred for endoscopy with symptoms of reflux or dyspepsia. Two prediction models were developed separately for columnar lined epithelium (CLE) of any length and using a stricter definition of intestinal metaplasia (IM) with segments ≥2 cm with areas under the ROC curves (AUC) of 0.72 (95%CI: 0.67–0.77) and 0.81 (95%CI: 0.76–0.86), respectively. The two prediction models included demographics (age, sex), symptoms (heartburn, acid reflux, chest pain, abdominal pain) and medication for “stomach” symptoms. These two models were validated in the independent cohort with AUCs of 0.61 (95%CI: 0.54–0.68) and 0.64 (95%CI: 0.52–0.77) for CLE and IM≥2 cm, respectively.

Conclusions

We have identified and validated two prediction models for CLE and IM≥2 cm. Both models have fair prediction accuracies and can select out around 20% of individuals unlikely to benefit from investigation for Barrett’s esophagus. Such prediction models have the potential to generate useful cost-savings for BE screening among the symptomatic population.     

Reliability of Trachoma Clinical Grading—Assessing Grading of Marginal Cases

Background

Clinical examination of trachoma is used to justify intervention in trachoma-endemic regions. Currently, field graders are certified by determining their concordance with experienced graders using the kappa statistic. Unfortunately, trachoma grading can be highly variable and there are cases where even expert graders disagree (borderline/marginal cases). Prior work has shown that inclusion of borderline cases tends to reduce apparent agreement, as measured by kappa. Here, we confirm those results and assess performance of trainees on these borderline cases by calculating their reliability error, a measure derived from the decomposition of the Brier score.

Methods and Findings

We trained 18 field graders using 200 conjunctival photographs from a community-randomized trial in Niger and assessed inter-grader agreement using kappa as well as reliability error. Three experienced graders scored each case for the presence or absence of trachomatous inflammation - follicular (TF) and trachomatous inflammation - intense (TI). A consensus grade for each case was defined as the one given by a majority of experienced graders. We classified cases into a unanimous subset if all 3 experienced graders gave the same grade. For both TF and TI grades, the mean kappa for trainees was higher on the unanimous subset; inclusion of borderline cases reduced apparent agreement by 15.7% for TF and 12.4% for TI. When we assessed the breakdown of the reliability error, we found that our trainees tended to over-call TF grades and under-call TI grades, especially in borderline cases.

Conclusions

The kappa statistic is widely used for certifying trachoma field graders. Exclusion of borderline cases, which even experienced graders disagree on, increases apparent agreement with the kappa statistic. Graders may agree less when exposed to the full spectrum of disease. Reliability error allows for the assessment of these borderline cases and can be used to refine an individual trainee''s grading.