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Background: Developing high yielding varieties is a major challenge for breeders tackling the challenges of climate change in agriculture. The panicle (inflorescence) architecture of rice is one of the key components of yield potential and displays high inter- and intra-specific variability. The genus Oryza features two different crop species: Asian rice (Oryza sativa L.) and the African rice (O. glaberrima Steud.). One of the main morphological differences between the two independently domesticated species is the structure (or complexity) of the panicle, with O. sativa displaying a highly branched panicle, which in turn produces a larger number of grains than that of O. glaberrima. The gene regulatory network that governs intra- and interspecific panicle diversity is still under-studied., Results: To identify genetic factors linked to panicle architecture diversity in the two species, we used a set of 60 Chromosome Segment Substitution Lines (CSSLs) issued from third generation backcross (BC 3 DH) and carrying genomic segments from O. glaberrima cv. MG12 in the genetic background of O. sativa Tropical Japonica cv. Caiapó. Phenotypic data were collected for rachis and primary branch length, primary, secondary and tertiary branch number and spikelet number. A total of 15 QTLs were localized on chromosomes 1, 2, 3, 7, 11 and 12, QTLs associated with enhanced secondary and tertiary branch numbers were detected in two CSSLs. Furthermore, BC 4 F 3:5 lines carrying different combinations of substituted segments were produced to decipher the effects of the identified QTL regions on variations in panicle architecture. A detailed analysis of phenotypes versus genotypes was carried out between the two parental genomes within these regions in order to understand how O. glaberrima introgression events may lead to alterations in panicle traits., Conclusion: Our analysis led to the detection of genomic variations between O. sativa cv. Caiapó and O. glaberrima cv. MG12 in regions associated with enhanced panicle traits in specific CSSLs. These regions contain a number of key genes that regulate panicle development in O. sativa and their interspecific genomic variations may explain the phenotypic effects observed., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Background: Coagulase-negative staphylococci (CoNS) are increasingly implicated in recent patient series of spondylodiscitis, but there are no series of CoNS-spondylodiscitis available. The objective of this study was to compare the characteristics of patients with spontaneous CoNS-spondylodiscitis with those patients with Staphylococcus aureus (SA) spondylodiscitis., Methods: This was a retrospective single center study involving 147 spontaneous infectious spondylodiscitis cases observed between 2000 and 2015. The 26 cases of CoNS-spondylodiscitis (15 confirmed) were compared with 30 cases of SA-spondylodiscitis. CoNS infection was considered confirmed if the same CoNS was isolated in at least two samples at two different times., Result: Patients with CoNS-spondylodiscitis were older (70 vs. 61 years of age; p = 0.01), had associated cancer more often (15% vs. 0%; p = 0.04) and had a longer diagnostic delay (>15 days in 88% vs. 60%; p = 0.01); experienced fever less often (19% vs. 50%; p = 0.01), and had lower white blood cell (7.6 vs. 9.9G/L; p = 0.01) and polymorphonuclear leucocyte counts (5.6 vs. 7.5G/L; p = 0.04). Patients with CoNS spondylodiscitis had less pronounced inflammatory syndrome (erythrocyte sedimentation rate [ESR]: 62 vs. 81 mm at 1 h; p = 0.03; CRP: 60 vs. 147 mg/L; p = 0.0003) and less common (ESR < 30 mm: 23% vs. 0%; p = 0.01; CRP < 10 mg/L: 23% vs. 0%; p = 0.005) in comparison with patients with SA infection. The infection entry site was most often an intravascular catheter (20% vs. 3%; p = 0.008). The level of positive percutaneous needle biopsies was comparable between CoNS and SA. Two patients who died both had SA infections., Conclusion: CoNS-spondylodiscitis involved at least 10% of spontaneous spondylodiscitis cases and was more common in elderly patients, afflicted by comorbidities, and its presentation was less virulent than that of those with SA-spondylodiscitis.

Background: Clinical symptoms of rheumatoid arthritis (RA) improve in the course of the day, as can synovitis activity, reported via doppler ultrasound (US). The aim of the study was to establish whether the Color Doppler (CD) scores of synovitis in RA changes throughout the day., Methods: In total, 27 patients with active RA, including 14 patients receiving corticosteroids were studied. US evaluation was performed twice in each patient, at 9 a.m. (T0) and after 4 p.m. (T1) on the same day by a single radiologist and using the same instrument. Overall, 30 joints were assessed, including grey scale and CD (S0 = no flow [no detectable CD)]; S1 = mild [CD <1/3 of the synovium]; S2 = moderate [CD <2/3]; S3 = pronounced [CD >2/3])., Results: In the total population, synovitis was detected more often in the evening than in the morning (39% vs. 33%, p = 0.02). The difference remained significant only in patients without corticosteroid administration (44% vs. 37%, p = 0.04). Moreover, a greater number of CD-positive joints were likewise found (S0 vs. S1 + S2 + S3) in the evening (57% vs. 51%, p = 0.04) in patients not receiving corticosteroids (67% vs. 41%, p = 0.002). More moderate (S2) and pronounced (S3) than mild (S1) synovitis was observed at T1 vs. T0 (39% vs. 24%, p = 0.03) in patients not receiving corticosteroids. More synovitis (40% vs 36% p = 0.02) in the dominant hand were found in the evening than in the morning., Conclusion: Synovitis and CD activity increase during the day in RA patients, especially in joints of the dominant hands and in patients without corticosteroids.

Background: Erosive degenerative disc disease, also known as Modic type 1 changes, is usually characterized by low back pain with an inflammatory pain pattern, as seen in spondyloarthropathies. Intravenous pamidronate has proven to be effective in patients with ankylosing spondylitis who are refractory to nonsteroidal antiinflammatory drugs, and in painful bone diseases in general, such as Paget's disease, fibrous dysplasia or vertebral fractures. We therefore hypothesize that pamidronate would be effective in treating low back pain associated with Modic type 1 changes., Methods/design: This study, called PEPTIDE (short for the French title "Etude Prospective sur l'Efficacité et la tolérance du PamidronaTe dans les dIscopathies Degeneratives Erosives"), will be a double-blind, randomized, placebo-controlled, parallel group, phase two clinical trial. A total of 48 patients will be recruited. These patients will be randomly assigned to one of the two groups, with 24 patients in each group: one group will be given pamidronate and the other a placebo. Pamidronate will be administered at a dose of 90 mg per day for two days consecutively, and every patient, irrespective of treatment group, will be given paracetamol to maintain blinding by preventing drug-induced fever. The primary outcome measure is a between-group difference of 30 points on a 100 mm Visual Analogue Scale (VAS) at three months. Secondary outcome measures are improvement in functional status and the drug's safety. Primary and secondary outcome measures will be assessed at each visit (inclusion, at six weeks, three months, and six months). If the primary goal is not attained, the patient will be offered a rigid or semi-rigid back brace, irrespective of the treatment group., Discussion: To date, only local treatments, for example intradiscal corticosteroid therapy, lumbar arthrodesis or back braces have been studied in randomized, controlled trials, with controversial results. This trial is currently ongoing and, if conclusive, should provide physicians with an acceptable alternative to those treatments. The results should be publicly available in spring 2015., Trial Registration: ClinicalTrials.gov number, NCT01799616.

Background: Association mapping studies offer great promise to identify polymorphisms associated with phenotypes and for understanding the genetic basis of quantitative trait variation. To date, almost all association mapping studies based on structured plant populations examined the main effects of genetic factors on the trait but did not deal with interactions between genetic factors and environment. In this paper, we propose a methodological prospect of mixed linear models to analyze genotype by environment interaction effects using association mapping designs. First, we simulated datasets to assess the power of linear mixed models to detect interaction effects. This simulation was based on two association panels composed of 90 inbreds (pearl millet) and 277 inbreds (maize)., Results: Based on the simulation approach, we reported the impact of effect size, environmental variation, allele frequency, trait heritability, and sample size on the power to detect the main effects of genetic loci and diverse effect of interactions implying these loci. Interaction effects specified in the model included SNP by environment interaction, ancestry by environment interaction, SNP by ancestry interaction and three way interactions. The method was finally used on real datasets from field experiments conducted on the two considered panels. We showed two types of interactions effects contributing to genotype by environment interactions in maize: SNP by environment interaction and ancestry by environment interaction. This last interaction suggests differential response at the population level in function of the environment., Conclusions: Our results suggested the suitability of mixed models for the detection of diverse interaction effects. The need of samples larger than that commonly used in current plant association studies is strongly emphasized to ensure rigorous model selection and powerful interaction assessment. The use of ancestry interaction component brought valuable information complementary to other available approaches.

Background: The script concordance test (SCT) is a method for assessing clinical reasoning of medical students by placing them in a context of uncertainty such as they will encounter in their future daily practice. Script concordance testing is going to be included as part of the computer-based national ranking examination (iNRE).This study was designed to create a script concordance test in rheumatology and use it for DCEM3 (fifth year) medical students administered via the online platform of the Clermont-Ferrand medical school., Methods: Our SCT for rheumatology teaching was constructed by a panel of 19 experts in rheumatology (6 hospital-based and 13 community-based). One hundred seventy-nine DCEM3 (fifth year) medical students were invited to take the test. Scores were computed using the scoring key available on the University of Montreal website. Reliability of the test was estimated by the Cronbach alpha coefficient for internal consistency., Results: The test comprised 60 questions. Among the 26 students who took the test (26/179: 14.5%), 15 completed it in its entirety. The reference panel of rheumatologists obtained a mean score of 76.6 and the 15 students had a mean score of 61.5 (p = 0.001). The Cronbach alpha value was 0.82., Conclusions: An online SCT can be used as an assessment tool for medical students in rheumatology. This study also highlights the active participation of community-based rheumatologists, who accounted for the majority of the 19 experts in the reference panel.A script concordance test in rheumatology for 5th year medical students.

Background: Clonal propagation is a particular reproductive system found in both the plant and animal kingdoms, from human parasites to clonally propagated crops. Clonal diversity provides information about plant and animal evolutionary history, i.e. how clones spread, or the age of a particular clone. In plants, this could provide valuable information about agrobiodiversity dynamics and more broadly about the evolutionary history of a particular crop. We studied the evolutionary history of yam, Dioscorea rotundata. In Africa, Yam is cultivated by tuber clonal propagation., Results: We used 12 microsatellite markers to identify intra-clonal diversity in yam varieties. We then used this diversity to assess the relative ages of clones. Using simulations, we assessed how Approximate Bayesian Computation could use clonal diversity to estimate the age of a clone depending on the size of the sample, the number of independent samples and the number of markers. We then applied this approach to our particular dataset and showed that the relative ages of varieties could be estimated, and that each variety could be ranked by age., Conclusions: We give a first estimation of clone age in an approximate Bayesian framework. However the precise estimation of clone age depends on the precision of the mutation rate. We provide useful information on agrobiodiversity dynamics and suggest recurrent creation of varietal diversity in a clonally propagated crop.

Background: In the past few years, functional genomics information has been rapidly accumulating on Rubiaceae species and especially on those belonging to the Coffea genus (coffee trees). An increasing number of expressed sequence tag (EST) data and EST- or genomic-derived microsatellite markers have been generated, together with Conserved Ortholog Set (COS) markers. This considerably facilitates comparative genomics or map-based genetic studies through the common use of orthologous loci across different species. Similar genomic information is available for e.g. tomato or potato, members of the Solanaceae family. Since both Rubiaceae and Solanaceae belong to the Euasterids I (lamiids) integration of information on genetic markers would be possible and lead to more efficient analyses and discovery of key loci involved in important traits such as fruit development, quality, and maturation, or adaptation. Our goal was to develop a comprehensive web data source for integrated information on validated orthologous markers in Rubiaceae., Description: MoccaDB is an online MySQL-PHP driven relational database that houses annotated and/or mapped microsatellite markers in Rubiaceae. In its current release, the database stores 638 markers that have been defined on 259 ESTs and 379 genomic sequences. Marker information was retrieved from 11 published works, and completed with original data on 132 microsatellite markers validated in our laboratory. DNA sequences were derived from three Coffea species/hybrids. Microsatellite markers were checked for similarity, in vitro tested for cross-amplification and diversity/polymorphism status in up to 38 Rubiaceae species belonging to the Cinchonoideae and Rubioideae subfamilies. Functional annotation was provided and some markers associated with described metabolic pathways were also integrated. Users can search the database for marker, sequence, map or diversity information through multi-option query forms. The retrieved data can be browsed and downloaded, along with protocols used, using a standard web browser. MoccaDB also integrates bioinformatics tools (CMap viewer and local BLAST) and hyperlinks to related external data sources (NCBI GenBank and PubMed, SOL Genomic Network database)., Conclusion: We believe that MoccaDB will be extremely useful for all researchers working in the areas of comparative and functional genomics and molecular evolution, in general, and population analysis and association mapping of Rubiaceae and Solanaceae species, in particular.