Influence of the Scalpel Finishing Technique on Marginal Gap Formation in Class II Resin Composite Restorations

OBJECTIVES

Modern adhesives and composites allow the restoration of deep defects. In such cases, the matrix technique is particularly challenging, and excess composite is a common problem. Removing such overhangs with a scalpel has already been described as a substance preserving or selective finishing technique. Clinically, restoration margins may appear as a white line after scalpel finishing, and it is unclear whether this line represents a marginal gap and/or whether scalpel finishing promotes marginal gap formation. Therefore, the aim of this study was to investigate the influence of scalpel finishing of deep Class II composite restorations on marginal gap formation.

METHODS AND MATERIALS

Standardized mesioocclusal-distal (MOD) cavities were prepared and restored in 60 human molars randomly divided into six finishing protocol groups: G1, scalpels (SC); G2, oscillating files (OF); G3, finishing strips (FS); G4, scalpels and finishing strips (SC+FS); G5, scalpels and polishing discs (SC+PD); G6, polishing discs alone (PD, controls). The groups were additionally assigned to finishing and polishing in a phantom head (groups 1-4) or hand-held setting (groups 5-6) to simulate clinical and in-vitro research conditions, respectively. After restoration, artificial aging was performed by thermocycling (5-55°C, 2500 cycles) and mechanical loading (50 newtons (N) with 500,000 cycles) prior to scanning electron microscopy analysis of proximal restoration margin quality on the mesial and distal surfaces (n=120) of each tooth. Outcomes (perfect margin, marginal gap, overhang, marginal fracture) were statistically analyzed by t-test, Mann-Whitney U test, single-factor analysis of variance, post-hoc t-test, Kruskal-Wallis test and Dunn-Bonferroni correction for multiple group comparisons. Cohen's effect size d(Cohen) was calculated to show the strength of the relationship between variables.

RESULTS

Overall, marginal quality was significantly better in the hand-held setting (SC+PD and PD) than the phantom head setting (SC, OF, FS, SC+FS). The best marginal quality was achieved with oscillating files in the phantom head setting and with scalpels plus polishing discs in the hand-held setting. Marginal gaps occurred significantly more often with scalpels, but the proportion of gaps was very low and clinically insignificant. Finishing strips were the least effective instruments for removing overhangs but performed better in combination with scalpels.

CONCLUSIONS

Scalpel finishing can effectively and gently remove overhangs from enamel. However, blades should be used with caution as they can cut the dentin and cementum. Scalpel finishing does not lead to a clinically relevant increase in marginal gaps, but should be followed by polishing, whenever possible, to eliminate any marginal fractures that might be present.

Problem of implicit assumptions about left ventricular geometry in the calculation of myocardial mass by echocardiography – a validation study with cardiac magnetic resonance

Background/Introduction

Cardiac magnetic resonance imaging (CMR) is regarded as the reference method in assessing left ventricular (LV) myocardial mass. However, 2-dimensional echocardiography (Echo) is still used due to availability and practicability.

Purpose

We sought to assess measurements of LV myocardial mass from Echo exams and validate the results with CMR on a large cohort of patients.

Methods

We analyzed 357 patients who underwent clinically indicated CMR examinations and performed a standard Echo at the same day. In Echo, the commonly used Devereux formula (CUBE) was assessed for the calculation of LV mass: 0.8 × {1.04 × [([LV end-diastolic diameter + diastolic septum-thickness + posterior wall-thickness]3 − LV end-diastolic diameter3)]} + 0.6. Mass was indexed on body surface area (g/m2). Correlation (r), regression (R2) and Bland-Altman analysis were performed in order to assess bias between the two methods. Significance was defined as a 2-tailed P value <0.05.

Results

LV myocardial mass was measured in 345 patients with CMR and Echo. The median age was 61 years [19–79], 44% were female and CMR was performed due to coronary artery diseases (45%), suspected or florid myocarditis (31%) or further diagnosis of non-ischemic heart failure (24%). LV ejection fraction (EF) ranged between 13 and 71%. We found a significant relation of measurements for myocardial mass between Echo and CMR (R2=0.6, p<0.001) (Figure 1, left). However, there was a significant proportional bias (R2=0.47, p<0.001) depending in the amount of LV mass measured (Figure 1, right). As expected, the measurement bias correlated not only with the amount of mean wall-thickness (septum & posterior wall) from Echo, but also with LV end-diastolic diameter (r=−0.55 and −0.41, p<0.001 for all). Interestingly, the amount of LV EF correlated reversely with the proportional bias (r=0.34, p<0.001).

Conclusion

The results provided by our study, highlight the problem of implicit assumptions of LV geometry in the calculation of LV myocardial mass by Echo (CUBE) compared to CMR. Furthermore, the strongly biased differences between these two measurement methods are not negligible and warrant further investigation.

Funding Acknowledgement

Type of funding sources: None.

The automatic identification of left ventricular chambers and quantification of ejection fraction using a novel artificial intelligence-based system – a validation against cardiac magnetic resonance

Background/Introduction

Cardiac magnetic resonance imaging (CMR) is regarded as the reference method in assessing left ventricular (LV) ejection fraction (EF). However, 2-dimensional echocardiography (2D-Echo) is the most frequently used technique due to availability and practicability. The interpretation of 2D-Echo examinations depends on the user's expertise and may vary between different operators. A novel vendor-independent software based on artificial intelligence (AI) performs both, automated evaluation of 2D-Echo exams and calculations of LV EF in one workflow.

Purpose

We sought to assess the ability of the AI to automatically identify appropriate LV 4- and 2-chamber views (4CV) (2CV) from 2D-Echo exams and validate the resulting EF with CMR.

Methods

We consecutively enrolled 128 patients who underwent clinically indicated CMR examinations and performed a standard 2D-Echo at the same day. The server-based AI solution recognized the optimal LV 4CV and 2CV from 2D-Echo according to quality and depth criteria and automatically performed calculation of biplane EF by endocardial borderline detection. LV EF from CMR and AI were supervised by independent cardiologists blinded to the mutual results. Pearson's correlation (R) and Bland-Altman analysis with limits of agreement (LOA) were performed in order to assess bias between the two methods. Significance was defined as a 2-tailed P value <0.05.

Results

CMR was performed and LV EF was measured in all 128 patients. The median age was 60 years [20–86], 65% were males and CMR was performed due to coronary artery diseases (33%), suspected/florid myocarditis (20%) or further diagnosis of non-ischemic heart failure (47%). Eleven cases (9%) did not pass AI's criteria due to impaired acoustic window or poor 2D-Echo images. The AI system detected either 4CV or 2CV (ratio 1.2) in 13 patients (10%), and both 4CV and 2CV in 104 patients (81% overall feasibility) with a correct classification of 100%. For these 104 patients, excellent correlation was found for AI's biplane LV EF and LV EF from CMR with r=0.91 (p<0.001) (Figure 1, left). However, the absolute mean bias between AI and CMR was 3.5% (p<0.001) and LOAs were −10.6 and +17.5% (Figure 1, right).

Conclusion

The results provided by the AI-based software showed good capabilities and a perfect classification rate to identify 4CV and 2CV. In addition, the LV EF results were excellent compared to CMR, especially since our study did not include “echocardiographically” pre-selected patients. However, differences between AI and CMR measurements are not negligible and warrant further investigation.

Funding Acknowledgement

Type of funding sources: None.

Left ventricular ejection fraction – human vs artificial intelligence: quo vadis?

Background/Introduction

Two-dimensional echocardiography (Echo) is a feasible method for assessing left ventricular (LV) ejection fraction (EF) in daily practice. However, the interpretation of Echo exams depends on the user's expertise and may vary between different operators. A novel, vendor-neutral artificial intelligence (AI) performs both, automated evaluation of Echo exams and calculations of biplane LV EF in one workflow.

Purpose

We sought to assess the ability of the AI to automatically identify appropriate LV 4- and 2-chamber views (4CV) (2CV) from routine Echo examinations and compare the resulting biplane EF with conventional hand-tracing biplane Simpson method (Human).

Methods

We prospectively enrolled 311 patients who underwent clinically indicated Echo exams. Biplane LV EF was manually traced online on 4CV and 2CV by cardiologists (Human). After completion of the exam, the AI-based solution recognized the optimal LV 4CV and 2CV according to quality and depth criteria and automatically performed the calculation of biplane EF by endocardial borderline detection without Human's interaction. Spearman's correlation (R) and Bland-Altman analysis with limits of agreement (LOA) were assessed for bias between the two methods. In a subgroup of 20 patients, Echo exams were automatically reanalyzed by the AI, and conventional biplane Simpson of LV EF was performed by two cardiologists blinded to the previous results to determine intraclass correlation (ICC). Significance was defined as a 2-tailed p value <0.05.

Results

311 patients (median age 72 years [19–97]; 40% female) received an Echo for valvular heart disease, ischemic and non-ischemic heart failure or other indications (39, 31, 19 and 11%). 16 cases (5%) did not pass AI's criteria due to poor Echo imaging or impaired acoustic window of patients. In 53 patients (17%) either 4CV or 2CV were recognized, but the AI system successfully identified both 4CV and 2CV in 242 patients (overall feasibility 78%). For these 242 patients, correlation between AI and Human biplane LV EF was r=0.83 (p<0.001) (Figure 1 left). The absolute mean bias between methods was 5.2% (p<0.001) and absolute LOA ranged from −9.0 to +19.4% (Figure 1 right). ICC of LV EF by Human was 0.77 (p<0.001). The AI's ability to correctly re-/classify 4CV and 2CV was 100% with an ICC of 1 for fully automated LV EF measurements.

Conclusion

The results provided by the AI-based software showed very good capability to identify 4CV and 2CV and good LV EF result compared to Human manual tracings, especially since patients were not pre-selected. However, differences between AI and Human measurements are not negligible and warrant further investigations.

Funding Acknowledgement

Type of funding sources: None.

Ψ-Footprinting approach for the identification of protein synthesis inhibitor producers

Today, one of the biggest challenges in antibiotic research is a targeted prioritization of natural compound producer strains and an efficient dereplication process to avoid undesired rediscovery of already known substances. Thereby, genome sequence-driven mining strategies are often superior to wet-lab experiments because they are generally faster and less resource-intensive. In the current study, we report on the development of a novel in silico screening approach to evaluate the genetic potential of bacterial strains to produce protein synthesis inhibitors (PSI), which was termed the protein synthesis inhibitor ('psi’) target gene footprinting approach = Ψ-footprinting. The strategy is based on the occurrence of protein synthesis associated self-resistance genes in genome sequences of natural compound producers. The screening approach was applied to 406 genome sequences of actinomycetes strains from the DSMZ strain collection, resulting in the prioritization of 15 potential PSI producer strains. For twelve of them, extract samples showed protein synthesis inhibitory properties in in vitro transcription/translation assays. For four strains, namely Saccharopolyspora flava DSM 44771, Micromonospora aurantiaca DSM 43813, Nocardioides albertanoniae DSM 25218, and Geodermatophilus nigrescens DSM 45408, the protein synthesis inhibitory substance amicoumacin was identified by HPLC-MS analysis, which proved the functionality of the in silico screening approach.

A Regulator Based "Semi-Targeted" Approach to Activate Silent Biosynthetic Gene Clusters

By culturing microorganisms under standard laboratory conditions, most biosynthetic gene clusters (BGCs) are not expressed, and thus, the products are not produced. To explore this biosynthetic potential, we developed a novel "semi-targeted" approach focusing on activating "silent" BGCs by concurrently introducing a group of regulator genes into streptomycetes of the Tübingen strain collection. We constructed integrative plasmids containing two classes of regulatory genes under the control of the constitutive promoter ermE*p (cluster situated regulators (CSR) and Streptomyces antibiotic regulatory proteins (SARPs)). These plasmids were introduced into Streptomyces sp. TÜ17, Streptomyces sp. TÜ10 and Streptomyces sp. TÜ102. Introduction of the CSRs-plasmid into strain S. sp. TÜ17 activated the production of mayamycin A. By using the individual regulator genes, we proved that Aur1P, was responsible for the activation. In strain S. sp. TÜ102, the introduction of the SARP-plasmid triggered the production of a chartreusin-like compound. Insertion of the CSRs-plasmid into strain S. sp. TÜ10 resulted in activating the warkmycin-BGC. In both recombinants, activation of the BGCs was only possible through the simultaneous expression of aur1PR3 and griR in S. sp. TÜ102 and aur1P and pntR in of S. sp. TÜ10.

OP0072 SINGLE CELL SEQUENCING REVEALS CLONALLY EXPANDED CYTOTOXIC CD4+ T CELLS IN THE JOINTS OF ACPA+ RA PATIENTS

Background:

CD4+ T cells with cytotoxic functions (CD4+ CTL) have gained attention in recent years. Accumulating evidence supports their importance in defense against human viral infections such as CMV1, EBV2, dengue3, HIV4, 5 and SARS-CoV-26. Moreover, expansion of so called CD28null cytotoxic CD4+ T cells have been reported in the blood of patients with rheumatic diseases such as rheumatoid arthritis (RA)7, myositis8 and vasculitis9 as well as in cardiovascular diseases10.

Objectives:

Here, we aimed to investigate the presence and clonal expansion of CD4+ CTL in the peripheral blood (PB) and synovial fluid (SF) of RA patients using single cell technologies.

Methods:

We assessed the expression of cytotoxic effector molecules and transcription factors in CD4+ T cells in synovial fluid (n=21) and paired peripheral blood (n=16) from ACPA- and APCA+ RA patients by multi-parameter flow cytometry. We performed single cell sequencing, in combination with 5´ TCRab sequencing, on purified CD4+ T cells from the peripheral blood (PB) and synovial fluid (SF) of ACPA+ RA patients (n=7).

Results:

Flow cytometry experiments show that Granzyme-B+ Perforin-1+ CD4+ CTL are significantly increased in the SF of ACPA+ RA patients as compared to ACPA- RA patients (p=0.0072). The presence of CD4+ CTL could be confirmed by single cell sequencing in SF of each ACPA+ RA patient tested (n=7). Moreover, we found that the adhesion G-protein coupled receptor GPR56 is selectively expressed on the recently described peripheral helper (TPH) T-cell subset11 and associates with the expression of tissue resident memory markers LAG-3, CXCR6 and CD69. In blood, we confirmed a previous report12 showing that GPR56 delineates cytotoxic CD4+ T cells. Finally, expanded TCR clones expressing cytotoxic effector molecules were identified in synovial fluid of ACPA+ RA patients and, for some patients, in their corresponding peripheral blood.

Conclusion:

We identified GPR56 as a marker of TPH cells in SF of ACPA+ RA patients that associates with tissue residency receptors. The combination of single cell sequencing and multi-parameter flow cytometry highlights the importance of CD4+ CTL in ACPA+ RA and suggests a potential therapeutic target (Figure 1).

References:

[1]Casazza J. P. et al., J Exp Med2006,203 (13), 2865-77.

[2]Landais E. et al., Blood2004,103 (4), 1408-16.

[3]Kurane I. et al. J Exp Med1989,170 (3), 763-75.

[4]Appay V. et al. J Immunol2002,168 (11), 5954-8.

[5]Juno J. A. et al. Front Immunol2017,8, 19.

[6]Meckiff B. J. et al. Cell2020,183 (5), 1340-1353 e16.

[7]Schmidt D. et al. J Clin Invest1996,97 (9), 2027-37.

[8]Fasth A. E. et al. J Immunol2009,183 (7), 4792-9.

[9]Moosig F. et al. Clin Exp Immunol1998,114 (1), 113-8.

[10]Sato K. et al. J Exp Med2006,203 (1), 239-50.

[11]Rao D. A., et al. Nature2017,542 (7639), 110-114.

[12]Peng Y. M. et al. J Leukoc Biol2011,90 (4), 735-40.

Acknowledgements:

We thank the patients who donated samples and the medical staff at the Rheumatology Clinic of Karolinska University Hospital. Julia Boström, Gloria Rostvall, and Susana Hernandez Machado are acknowledged for organizing the sampling, storage, and administration of biomaterial. This study is supported by grants from Dr. Margaretha Nilssons, the Nanna Svartz, the Ulla and Gustaf af Ugglas foundations and the Swedish association against rheumatism.

Disclosure of Interests:

Alexandra Argyriou: None declared, Marc H Wadsworth II Employee of: Pfizer, Inc, Cambridge, MA 02139, United States, Adrian Lendvai: None declared, Stephen Christensen Employee of: Pfizer, Inc, Cambridge, MA 02139, United States, Aase Hensvold: None declared, Christina Gerstner: None declared, Kellie Kravarik Employee of: Pfizer, Inc, Cambridge, MA 02139, United States, Aaron Winkler Employee of: Pfizer, Inc, Cambridge, MA 02139, United States, Vivianne Malmström: None declared, Karine Chemin: None declared

POS0348 GENETIC SUSCEPTIBILITY VARIANTS FOR RHEUMATOID ARTHRITIS ARE NOT ASSOCIATED WITH EARLY REMISSION; A MULTI-COHORT STUDY

Background:

Patients who achieve remission promptly could have a specific genetic risk profile that supports regaining immune tolerance. The identification of these genes could provide novel drug targets.

Objectives:

To test the association between RA genetic risk variants with achieving remission at 6 months.

Methods:

We computed genetic risk scores (GRS) comprising of the RA susceptibility variants1 and HLA-SE status separately in 4425 patients across eight datasets from inception cohorts. Remission was defined as DAS28CRP<2.6 at 6 months. Missing DAS28CRP values in patients were imputed using predictive mean matching by MICE. We first tested whether baseline DAS28CRP changed with increasing GRS using linear regression. Next, we calculated odds ratios for GRS and HLA-SE on remission using logistic regression. Heterogeneity of the outcome between datasets was mitigated by running inverse variance meta-analysis.

Results:

Evaluation of the complete dataset, baseline clinical variables did not differ between patients achieving remission and those who did not (Table 1). Distribution of GRS was consistent between datasets. Neither GRS nor HLA-SE was associated with baseline DAS2DAS (OR1.01; 95% CI 0.99-1.04). A fixed effect meta-analysis (Figure 1.) showed no significant effect of the GRS (OR 0.99; 95% CI 0.94-1.03) or HLA-SE (OR 0.8CRP87; 95% CI 0.75-1.01) on remission at 6 months.

Table 1.

Summary of the data separated by disease activity after 6 months.

allRemission at 6 monthsNo remission at 6 monthsN4425*15582430Age, mean (sd)55.38 (13.87)5517 (14.09)55.62 (13.59)Female %68.98%65.43%70.73%ACPA+ %61.94%63.53%61.67%Baseline DAS28, mean (sd)4.76 (1.22)4.47 (1.23)5.1 (1.15)

*not all patients had 6 months data

Conclusion:

In these combined cohorts, RA genetics risk variants are not associated with early disease remission. At baseline there was no difference in genetic risk between patients achieving remission or not. Studies encompassing other genetic variants are needed to elucidate the genetics of RA remission.

References:

[1]Knevel R et al. Sci Transl Med. 2020;12(545):eaay1548.

Acknowledgements:

This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 777357, RTCure.

This project has received funding from Pfizer Inc.

Disclosure of Interests:

Samantha Jurado Zapata: None declared, Marc Maurits: None declared, Yann Abraham Employee of: Pfizer, Erik van den Akker: None declared, Anne Barton: None declared, Philip Brown: None declared, Andrew Cope: None declared, Isidoro González-Álvaro: None declared, Carl Goodyear: None declared, Annette van der Helm - van Mil: None declared, Xinli Hu Employee of: Pfizer, Thomas Huizinga: None declared, Martina Johannesson: None declared, Lars Klareskog: None declared, Dennis Lendrem: None declared, Iain McInnes: None declared, Fraser Morton: None declared, Caron Paterson: None declared, Duncan Porter: None declared, Arthur Pratt: None declared, Luis Rodriguez Rodriguez: None declared, Daniela Sieghart: None declared, Paul Studenic: None declared, Suzanne Verstappen: None declared, Leonid Padyukov: None declared, Aaron Winkler Employee of: Pfizer, John D Isaacs: None declared, Rachel Knevel Grant/research support from: Pfizer

Streptomyces dysideae sp. nov., isolated from a marine Mediterranean sponge Dysidea tupha

A Gram-stain-positive bacterium, strain RV15^T, forming an extensively branched substrate mycelium and aerial hyphae that differentiate into spiral chains of spores, was isolated from a marine sponge Dysidea tupha collected from Rovinj (Croatia). Comparison of 16S rRNA gene sequences showed that strain RV15^T is a member of the genus Streptomyces with highest sequence similarity to the type strains of Streptomyces caeruleatus (98.8 %), Streptomyces cyaneochromogenes (98.6 %) and Streptomyces shaanxiensis (98.5 %). Sequence similarities to all other Streptomyces types strains were below 98.5 %. The multilocus sequence analysis-based evolutionary distance, the average nucleotide identity value and the genome-to-genome distance of strain RV15^T and the type strain of S. caeruleatus were clearly below the species cut-off values. Strain RV15^T exhibited a quinone system composed of the major menaquinones MK-9(H₄), MK-9(H₆) and MK-9(H₂), typical for the genus Streptomyces. The polar lipid profile of strain RV15^T consisted of the predominant compounds diphosphatidylglycerol and phosphatidylethanolamine, moderate amounts of phosphatidylinositol, phosphatidylinositol mannoside, an unidentified lipid and an unidentified phospholipid. Major polyamines were spermine and spermidine. The diagnostic diaminoacid of the peptidoglycan was meso-diaminopimelic acid. The major fatty acids were iso C_16 : 0, anteiso C_17 : 1 ω9c and anteiso C_17 : 0. The results of physiological and biochemical tests allowed further phenotypic differentiation of strain RV15^T from its most-related species and hence clearly merits species status. We propose the name Streptomyces dysideae sp. nov. with the type strain RV15^T (=DSM 42110^T=LMG 27702^T).

Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia

Bacteria occupy all major ecosystems and maintain an intensive relationship to the eukaryotes, developing together into complex biomes (i.e., phycosphere and rhizosphere). Interactions between eukaryotes and bacteria range from cooperative to competitive, with the associated microorganisms affecting their host`s development, growth and health. Since the advent of non-culture dependent analytical techniques such as metagenome sequencing, consortia have been described at the phylogenetic level but rarely functionally. Multifaceted analysis of the microbial consortium of the ancient phytoplankton Botryococcus as an attractive model food web revealed that its all abundant bacterial members belong to a niche of biotin auxotrophs, essentially depending on the microalga. In addition, hydrocarbonoclastic bacteria without vitamin auxotrophies seem adversely to affect the algal cell morphology. Synthetic rearrangement of a minimal community consisting of an alga, a mutualistic and a parasitic bacteria underpins the model of a eukaryote that maintains its own mutualistic microbial community to control its surrounding biosphere. This model of coexistence, potentially useful for defense against invaders by a eukaryotic host could represent ecologically relevant interactions that cross species boundaries. Metabolic and system reconstruction is an opportunity to unravel the relationships within the consortia and provide a blueprint for the construction of mutually beneficial synthetic ecosystems.

Global transcriptome analysis of Rhizobium favelukesii LPU83 in response to acid stress

Acidic environments naturally occur worldwide and inappropriate agricultural management may also cause acidification of soils. Low soil pH values are an important barrier in the plant-rhizobia interaction. Acidic conditions disturb the establishment of the efficient rhizobia usually used as biofertilizer. This negative effect on the rhizobia-legume symbiosis is mainly due to the low acid tolerance of the bacteria. Here, we describe the identification of relevant factors in the acid tolerance of Rhizobium favelukesii using transcriptome sequencing. A total of 1924 genes were differentially expressed under acidic conditions, with ∼60% underexpressed. Rhizobium favelukesii acid response mainly includes changes in the energy metabolism and protein turnover, as well as a combination of mechanisms that may contribute to this phenotype, including GABA and histidine metabolism, cell envelope modifications and reverse proton efflux. We confirmed the acid-sensitive phenotype of a mutant in the braD gene, which showed higher expression under acid stress. Remarkably, 60% of the coding sequences encoded in the symbiotic plasmid were underexpressed and we evidenced that a strain cured for this plasmid featured an improved performance under acidic conditions. Hence, this work provides relevant information in the characterization of genes associated with tolerance or adaptation to acidic stress of R. favelukesii.

Patterning of protein-based materials

Micro- and nanopatterning of proteins on surfaces allows to develop for example high-throughput biosensors in biomedical diagnostics and in general advances the understanding of cell-material interactions in tissue engineering. Today, many techniques are available to generate protein pattern, ranging from technically simple ones, such as micro-contact printing, to highly tunable optical lithography or even technically sophisticated scanning probe lithography. Here, one focus is on the progress made in the development of protein-based materials as positive or negative photoresists allowing micro- to nanostructured scaffolds for biocompatible photonic, electronic and tissue engineering applications. The second one is on approaches, which allow a controlled spatiotemporal positioning of a single protein on surfaces, enabled by the recent developments in immobilization techniques coherent with the sensitive nature of proteins, defined protein orientation and maintenance of the protein activity at interfaces. The third one is on progress in photolithography-based methods, which allow to control the formation of protein-repellant/adhesive polymer brushes.

Interceptive use of pendulum for advance resolution of class II patient: a guided eruption plan to reduce stress on permanent teeth root

Use of the so-called distalizing mechanics is a common treatment to correct class II malocclusion. One of the first appliances made for molar distalization was the pendulum, which resulted immediately efficient. The knowledge of pendulum efficacy, in regards to distalizing treatment in adolescence, has guided the research to analyze pendulum effect in childhood: checking the pre-eruptive, natural and distal movement of upper second premolar following first upper molar distalization in order to obtain an advance resolution on Angle's Class II patient, limited treatment time, reduced periodontal inflammation and stress on permanent teeth root. A pilot study testing the possibility of a prospective study was necessary on 6 patients treated following an accurate protocol (6 months and 1-year Rx control) and 6 patient control after one year. Statistical analysis by T-Test was done. Oral hygiene controls every month were done. Second upper bicuspid vertical (1.6mm) and sagittal (2.5mm) movement mean values allow to emphasize a distal variation of tooth axis inclination of treatment group than control group, and a second upper bicuspid distal departure from "gubernaculus dentis" of second deciduous molar in treated patients. Periodontal inflammation appears inexistent on second and first upper premolar germs after the comparison between RX exam of treatment and control groups because of exploiting deciduous teeth. Besides periodontal inflammation and teeth root stress on first upper molar of treatment group, after RX analysis, results were limited compared to control groups because of the advanced orthodontic interceptive treatment during a previous stage of first upper molar root development.

Genome sequence of Bradyrhizobium yuanmingense strain P10 130, a highly efficient nitrogen-fixing bacterium that could be used for Desmodium incanum inoculation

Strain P10 130, an isolated Bradyrhizobium strain from Argentina which promotes the growth of the leguminous plant Desmodium incanum by different mechanisms was previously selected as the best candidate for D. incanum inoculation based on broader selective criteria. A close relationship between this strain and B. yuanmingense was determined by MALDI BioTyper identification and 16S rRNA gene phylogenetic analysis. This study aimed to analyse the genome sequence of B. yuanmingense P10 130 in order to deepen our knowledge regarding its plant growth-promoting traits and to establish its phylogenetic relationship with other species of Bradyrhizobium genus. The genome size of strain P10 130 was estimated to be 7.54 Mb that consisted of 65 contigs. Genome Average Nucleotide Identity (ANI) analysis revealed that B. yuanmingense CCBAU 10071 ^T was the closest strain to P10 130 with ca. 96% identity. Further analysis of the genome of B. yuanmingense P10 130 identified 20 nod/nol/NOE, 14 nif/18 fix, 5 nap/5 nor genes, which may be potentially involved in nodulation, nitrogen fixation, and denitrification process respectively. Genome sequence of B. yuanmingense P10 130 is a valuable source of information to continue the research of its potential industrial production as a biofertilizer of D. incanum.

The complexity of surface acoustic wave fields used for microfluidic applications

Using surface acoustic waves (SAW) for the agitation and manipulation of fluids and immersed particles or cells in lab-on-a-chip systems has been state of the art for several years. Basic tasks comprise fluid mixing, atomization of liquids as well as sorting and separation (or trapping) of particles and cells, e.g. in so-called acoustic tweezers. Even though the fundamental principles governing SAW excitation and propagation on anisotropic, piezoelectric substrates are well-investigated, the complexity of wave field effects including SAW diffraction, refraction and interference cannot be comprehensively simulated at this point of time with sufficient accuracy. However, the design of microfluidic actuators relies on a profound knowledge of SAW propagation, including superposition of multiple SAWs, to achieve the predestined functionality of the devices. Here, we present extensive experimental results of high-resolution analysis of the lateral distribution of the complex displacement amplitude, i.e. the wave field, alongside with the electrical S-parameters of the generating transducers. These measurements were carried out and are compared in setups utilizing travelling SAW (tSAW) excited by single interdigital transducer (IDT), standing SAW generated between two IDTs (1DsSAW, 1D acoustic tweezers) and between two pairs of IDTs (2DsSAW, 2D acoustic tweezers) with different angular alignment in respect to pure Rayleigh mode propagation directions and other practically relevant orientations. For these basic configurations, typically used to drive SAW-based microfluidics, the influence of common SAW phenomena including beam steering, coupling coefficient dispersion and diffraction on the resultant wave field is investigated. The results show how tailoring of the acoustic conditions, based on profound knowledge of the physical effects, can be achieved to finally realize a desired behavior of a SAW-based microacoustic-fluidic system.

FRI0100 COMPARISON OF PATIENTS (PTS) WITH RHEUMATOID ARTHRITIS (RA) AMONG DISEASE ACTIVITY CATEGORIES AFTER 6 MONTHS OF TREATMENT WITH A TUMOUR NECROSIS FACTOR INHIBITOR (TNFI): RESULTS FROM THE CORRONA® RA REGISTRY

Background:

Targeting remission (REM) or low disease activity (LDA) is a widely accepted treatment strategy for RA. However, there are limited data on the proportion of pts who achieve these targets, or remain in moderate (MDA) or high disease activity (HDA) following advanced therapy.

Objectives:

To estimate the proportion of RA pts in disease activity states (REM, LDA, MDA, and HDA) who were biologic-naïve at initiation and had continuous treatment with a TNFi for 6–12 months in the Corrona RA registry.

Methods:

Eligible pts were aged ≥18 years, biologic-naïve, initiated TNFi treatment between January 1, 2010 and July 31, 2019, and had continuous use of a TNFi for 6–12 months. Disease activity was defined based on Clinical Disease Activity Index (CDAI) at the visit closest to 6-month follow-up: REM, ≤2.8; LDA, >2.8–10; MDA, >10–22; and HDA, >22. Disease characteristics, disease activity measures, and pt-reported outcomes (PROs) were reported at TNFi initiation and at the 6-month follow-up visit.

Results:

2586 biologic-naïve pts who initiated a TNFi and had continuous use for 6–12 months were included. At TNFi initiation, 167 (6%) were in REM, 479 (19%) had LDA, 907 (35%) had MDA, and 1033 (40%) had HDA. After 6–12 months of treatment, 563 (21.8%) were in REM, 923 (35.7%) had LDA, 674 (26.1%) had MDA, and 426 (16.5%) had HDA. Pts with HDA/MDA at 6–12 months were more likely to have a history of hypertension (32.7% HDA; 34.0% MDA; vs 23.6% REM) and had higher mean body mass index (BMI) (30.9 HDA; 31.1 MDA; vs 29.0 REM) at baseline compared with pts in REM. Disease activity measures and PROs were worse in pts with MDA and HDA vs LDA and REM after 6–12 months (Table). Pt Global Assessment was higher than Physician Global Assessment across all groups.

Conclusion:

While 57.4% of pts who initiated a TNFi experienced a favorable outcome, >40% required additional or alternative intervention to achieve REM/LDA. Pts who remained in MDA/HDA continued to have an inadequate response to TNFi (as measured by disease activity measures and PROs) after 6–12 months of treatment compared with those who achieved REM/LDA.

Table

Summary of disease activity measures and PROs in previously biologic-naïve pts at the 6–12-month follow-up visit, stratified by disease activity category at the 6–12-month follow-up visit

Characteristics at 6–12 months, mean (standard deviation)Disease activity category at 6–12 monthsREM (n=563)LDA (n=923)MDA (n=674)HDA (n=426)CDAI1.2 (0.8)6.2 (2.1)15.4 (3.4)32.7 (9.2)Tender joint count (28)0.1 (0.3)1.0 (1.3)4.3 (3.3)13.4 (7.0)Swollen joint count (28)0.1 (0.3)1.1 (1.6)4.0 (3.6)9.1 (5.9)C-reactive protein6.4 (22.7)7.0 (10.6)11.1 (19.9)12.6 (22.1)Modified health assessment questionnaire0.1 (0.2)0.3 (0.4)0.5 (0.5)0.8 (0.5)Pt global assessment6.6 (6.8)28.6 (20.9)43.7 (25.7)58.0 (22.7)Physician global assessment3.6 (4.3)12.1 (10.4)27.4 (15.9)44.9 (19.8)Pt pain assessment8.7 (11.0)30.3 (23.5)46.1 (27.0)59.9 (24.4)Pt fatigue assessment15.7 (19.2)34.5 (26.6)48.3 (28.0)59.4 (27.5)Morning stiffness (min)16.5 (36.5)55.4 (146.3)96.9 (197.5)143.6 (260.0)

Disclosure of Interests:

Joel M Kremer Shareholder of: May own stocks and opinions, Grant/research support from: Research and consulting fees from AbbVie Inc., Consultant of: AbbVie, Amgen, BMS, Genentech, Inc., Gilead, GSK, Lilly, Pfizer, Regeneron and Sanofi, Employee of: Corrona, LLC employee, Anne Winkler Consultant of: AbbVie, Pfizer, and Novratis, Speakers bureau: AbbVie, Janssen, Sanofi, Genentech, Celgene, Eli Lilly, and Novartis., Laura Anatale-Tardiff Employee of: Corrona, LLC employee, Robert McLean Employee of: Corrona, LLC, Ying Shan Employee of: Corrona, LLC employee, Page Moore Employee of: Corrona, LLC employee, Namita Tundia Shareholder of: May own stocks and options, Employee of: AbbVie employee, Jessica Suboticki Shareholder of: AbbVie Inc., Employee of: AbbVie Inc., John Tesser Consultant of: Sanofi/Regeneron, Speakers bureau: Sanofi/Regeneron

THU0032 MODIFIED PEPTIDES AS A NOVEL IMMUNOTHERAPY FOR RHEUMATOID ARTHRITIS

Background:

Rheumatoid arthritis (RA) is a highly prevalent and severe systemic autoimmune disease associated with permanent disability and strong socio-economic burdens. Currently, there is no therapeutic treatment and RA patients rely on lifelong, costly treatments. Imcyse develops modified peptides eliciting antigen specific cytolytic CD4 T cells (cCD4+) that induce apoptosis of antigen presenting cells (APC) in a contact dependent manner. cCD4+ also induce apoptosis of autoantigen-specific bystander T-cells, activated by the same APC thus eliminating the risk of general immunosuppression. Peptides consist of MHC class II T cell epitopes of a target autoantigen modified in their flanking region by the addition of an amino acid sequence containing a thiol-disulphide oxidoreductase active motif1.

Objectives:

The goal of this study was to synthesize modified peptides from a target RA autoantigen and test their potency to generatein vitrospecific and cytolytic CD4+ T cells from RA patients.

Methods:

We designed modified peptides from a target RA autoantigen after in silico and in vitro assessment to identify MHC II core binding region, HLA class II binding capacities and physiochemical properties.

CD4+ T cells were purified from PBMC of a newly diagnosed seropositive RA patient and co-cultured with autologous APC in the presence of the modified peptide. The CD4+ T cells were restimulated periodically. Peptide’s ability to generate specific CD4+ T cells was evaluated by flow cytometric analysis of the expression of surface activation marker CD154 (CD40L). The peptide specific CD4+ T cell lines were sorted based on their surface CD154 expression. Their pro-apoptotic activity was assessed after overnight (O/N) co-culture of CD4+ T cells with fluorescent tracer labelled autologous lymphoblastoid cells lines (LCL). Flow cytometry quantification of LCL apoptosis was measured by annexin V staining. MHC II restriction of CD4+ T cells was demonstrated by the addition of blocking antibodies against HLA-DR, DP or DQ molecules.

Results:

CD4+ T cells were in vitro expanded after six consecutive stimulations with the peptide. We investigated their specificity by flow cytometry and showed that 69% of CD4+ T cells that were stimulated O/N in the presence of the peptide expressed the activation marker CD154 versus 29% of CD4+ T cells that were stimulated in its absence. These cells were sorted based on CD154 expression following specific stimulation. Cell enrichment was then assessed by flow cytometric analysis. Data showed that more than 91% (background 3%) were peptide specific based on CD154 expression.

After co-culture of CD4+ T cells with LCL, in independent experiments, Annexin V binding was detected on peptide loaded LCL, ranging from 69% to 89%, while when LCL were kept unloaded these values were between 30% and 55%, respectively, indicating that when specifically activated, these CD4+ T cells had pro-apoptotic activity. When both the peptide and blocking antibodies against HLA-DR, DP or DQ molecules added in the co-culture the pro-apoptotic activity was inhibited by 68%, 20% and 25%, respectively.

Conclusion:

The preliminary but very promising data show that our modified peptide generates peptide-specific CD4+ T cells with lytic properties that lyse target APC in an HLA class II specific manner. Our plan is to show that these CD4+ T cells can also induce apoptosis in bystander T cells and to further validate our results in additional RA donors.

References:

[1]Carlier, V. A., Vanderelst, L., Janssens, W. & Jacquemin, M. G. Increased Synapse Formation Obtained by T Cell Epitopes Containing a CxxC Motif in Flanking Residues Convert CD4 + T Cells into Cytolytic Effectors.7, (2012).

Disclosure of Interests:

Eleni Araklioti Grant/research support from: This work was supported by Pfizer Inc. and by Walloon Region, Ludivine Herman Grant/research support from: This work was supported by Pfizer Inc. and by Walloon Region, Ngoc Quynh Nhu Nguyen Grant/research support from: This work was supported by Pfizer Inc. and by Walloon Region, Roxana Roohi Ahangarani Grant/research support from: This work was supported by Pfizer Inc. and by Walloon Region, Milos Erak Grant/research support from: This work was supported by Pfizer Inc. and by Walloon Region, Bernard Lauwerys: None declared, Patrick Durez Speakers bureau: AbbVie, Bristol-Myers Squibb, Celltrion, Eli Lilly, Pfizer, Sanofi, Vincent Geenen: None declared, Aaron Winkler Shareholder of: Shareholder of Pfizer, Inc, Employee of: Full time employee of Pfizer, Inc, Marcelle Van Mechelen Grant/research support from: This work was supported by Pfizer Inc. and by Walloon Region, Luc Vander Elst Grant/research support from: This work was supported by Pfizer Inc. and by Walloon Region, Vincent Carlier Grant/research support from: This work was supported by Pfizer Inc. and by Walloon Region

Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics

The genus Pseudomonas comprises many known plant-associated microbes with plant growth promotion and disease suppression properties. Genome-based studies allow the prediction of the underlying mechanisms using genome mining tools and the analysis of the genes unique for a strain by implementing comparative genomics. Here, we provide the genome sequence of the strain Pseudomonas brassicacearum 3Re2-7, formerly known as P. trivialis and P. reactans, elucidate its revised taxonomic classification, experimentally verify the gene predictions by transcriptome sequencing, describe its genetic biocontrol potential and contextualize it to other known Pseudomonas biocontrol agents. The P. brassicacearum 3Re2-7 genome comprises a circular chromosome with a size of 6,738,544 bp and a GC-content of 60.83%. 6267 genes were annotated, of which 6113 were shown to be transcribed in rich medium and/or in the presence of Rhizoctonia solani. Genome mining identified genes related to biocontrol traits such as secondary metabolite and siderophore biosynthesis, plant growth promotion, inorganic phosphate solubilization, biosynthesis of lipo- and exopolysaccharides, exoproteases, volatiles and detoxification. Core genome analysis revealed, that the 3Re2-7 genome exhibits a high collinearity with the representative genome for the species, P. brassicacearum subsp. brassicacearum NFM421. Comparative genomics allowed the identification of 105 specific genes and revealed gene clusters that might encode specialized biocontrol mechanisms of strain 3Re2-7. Moreover, we captured the transcriptome of P. brassicacearum 3Re2-7, confirming the transcription of the predicted biocontrol-related genes. The gene clusters coding for 2,4-diacetylphloroglucinol (phlABCDEFGH) and hydrogen cyanide (hcnABC) were shown to be highly transcribed. Further genes predicted to encode putative alginate production enzymes, a pyrroloquinoline quinone precursor peptide PqqA and a matrixin family metalloprotease were also found to be highly transcribed. With this study, we provide a basis to further characterize the mechanisms for biocontrol in Pseudomonas species, towards a sustainable and safe application of P. brassicacearum biocontrol agents.

A comprehensive analysis of the Lactuca sativa, L. transcriptome during different stages of the compatible interaction with Rhizoctonia solani

The leafy green vegetable Lactuca sativa, L. is susceptible to the soil-born fungus Rhizoctonia solani AG1-IB. In a previous study, we reported on the transcriptional response of R. solani AG1-IB (isolate 7/3/14) during the interspecies interaction with L. sativa cv. Tizian by means of RNA sequencing. Here we present the L. sativa transcriptome and metabolome from the same experimental approach. Three distinct interaction zones were sampled and compared to a blank (non-inoculated) sample: symptomless zone 1, zone 2 showing light brown discoloration, and a dark brown zone 3 characterized by necrotic lesions. Throughout the interaction, we observed a massive reprogramming of the L. sativa transcriptome, with 9231 unique genes matching the threshold criteria for differential expression. The lettuce transcriptome of the light brown zone 2 presents the most dissimilar profile compared to the uninoculated zone 4, marking the main stage of interaction. Transcripts putatively encoding several essential proteins that are involved in maintaining jasmonic acid and auxin homeostasis were found to be negatively regulated. These and other indicator transcripts mark a potentially inadequate defence response, leading to a compatible interaction. KEGG pathway mapping and GC-MS metabolome data revealed large changes in amino acid, lignin and hemicellulose related pathways and related metabolites.

Harvest of the Oleaginous Microalgae Scenedesmus obtusiusculus by Flocculation From Culture Based on Natural Water Sources

Harvest and dewatering poses a significant economical burden for industrial algae biomass production. To mitigate these effects, energy efficient techniques for these process steps have to be developed. Flocculation of the microalgae Scenedesmus obtusiusculus in salt based medium was induced by pH-shift and alternatively by addition of two biological flocculants, chitosan, and the commercial tannin CFL-PT. This is the first time that CFL-PT is used as an algae flocculant particularly focusing on harvesting of halophilic strains. The method was characterized and subsequently optimized. In comparison to biological flocculants, induction by pH shift is far cheaper, but due to buffering effects of the brackish cultivation medium infeasible amounts of base are required to raise the pH-value. tannin appears to be superior compared to chitosan not only in the absence of algae organic matter (AOM), but tannin-based harvest is also more robust regarding culture pH in presence of AOM. A higher flocculant-demand for modified tannin compared to chitosan is offset by the lower price. Given the employed strain and cultivation conditions, cultivation time had no pronounced effect on flocculation efficiencies (FE) while algae zeta-potential and bacterial communities also remained stable.

Binning enables efficient host genome reconstruction in cnidarian holobionts

Background

Many cnidarians, including stony corals, engage in complex symbiotic associations, comprising the eukaryotic host, photosynthetic algae, and highly diverse microbial communities—together referred to as holobiont. This taxonomic complexity makes sequencing and assembling coral host genomes extremely challenging. Therefore, previous cnidarian genomic projects were based on symbiont-free tissue samples. However, this approach may not be applicable to the majority of cnidarian species for ecological reasons. We therefore evaluated the performance of an alternative method based on sequence binning for reconstructing the genome of the stony coral Porites rus from a hologenomic sample and compared it to traditional approaches.

Results

Our results demonstrate that binning performs well for hologenomic data, producing sufficient reads for assembling the draft genome of P. rus. An assembly evaluation based on operational criteria showed results that were comparable to symbiont-free approaches in terms of completeness and usefulness, despite a high degree of fragmentation in our assembly. In addition, we found that binning provides sufficient data for exploratory k-mer estimation of genomic features, such as genome size and heterozygosity.

Conclusions

Binning constitutes a powerful approach for disentangling taxonomically complex coral hologenomes. Considering the recent decline of coral reefs on the one hand and previous limitations to coral genome sequencing on the other hand, binning may facilitate rapid and reliable genome assembly. This study also provides an important milestone in advancing binning from the metagenomic to the hologenomic and from the prokaryotic to the eukaryotic level.

Oil type and temperature dependent biodegradation dynamics - Combining chemical and microbial community data through multivariate analysis

BACKGROUND

This study investigates a comparative multivariate approach for studying the biodegradation of chemically dispersed oil. The rationale for this approach lies in the inherent complexity of the data and challenges associated with comparing multiple experiments with inconsistent sampling points, with respect to inferring correlations and visualizing multiple datasets with numerous variables. We aim to identify novel correlations among microbial community composition, the chemical change of individual petroleum hydrocarbons, oil type and temperature by creating modelled datasets from inconsistent sampling time points. Four different incubation experiments were conducted with freshly collected Norwegian seawater and either Grane and Troll oil dispersed with Corexit 9500. Incubations were conducted at two different temperatures (5 °C and 13 °C) over a period of 64 days.

RESULTS

PCA analysis of modelled chemical datasets and calculated half-lives revealed differences in the biodegradation of individual hydrocarbons among temperatures and oil types. At 5 °C, most n-alkanes biodegraded faster in heavy Grane oil compared to light Troll oil. PCA analysis of modelled microbial community datasets reveal differences between temperature and oil type, especially at low temperature. For both oils, Colwelliaceae and Oceanospirillaceae were more prominent in the colder incubation (5 °C) than the warmer (13 °C). Overall, Colwelliaceae, Oceanospirillaceae, Flavobacteriaceae, Rhodobacteraceae, Alteromonadaceae and Piscirickettsiaceae consistently dominated the microbial community at both temperatures and in both oil types. Other families known to include oil-degrading bacteria were also identified, such as Alcanivoracaceae, Methylophilaceae, Sphingomonadaceae and Erythrobacteraceae, but they were all present in dispersed oil incubations at a low abundance (< 1%).

CONCLUSIONS

In the current study, our goal was to introduce a comparative multivariate approach for studying the biodegradation of dispersed oil, including curve-fitted models of datasets for a greater data resolution and comparability. By applying these approaches, we have shown how different temperatures and oil types influence the biodegradation of oil in incubations with inconsistent sampling points. Clustering analysis revealed further how temperature and oil type influence single compound depletion and microbial community composition. Finally, correlation analysis of degraders community, with single compound data, revealed complexity beneath usual abundance cut-offs used for microbial community data in biodegradation studies.

Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing

An animals' body is densely populated with bacteria. Although a large number of investigations on physiological microbial colonisation have emerged in recent years, our understanding of the composition, ecology and function of the microbiota remains incomplete. Here, we investigated whether songbirds have an individual-specific skin microbiome that is similar across different body regions. We collected skin microbe samples from three different bird species (Taeniopygia gutatta, Lonchura striata domestica and Stagonopleura gutatta) at two body locations (neck region, preen gland area). To characterise the skin microbes and compare the bacterial composition, we used high-throughput 16S rRNA amplicon sequencing. This method proved suitable for identifying the skin microbiome of birds, even though the bacterial load on the skin appeared to be relatively low. We found that across all species, the two evaluated skin areas of each individual harboured very similar microbial communities, indicative of an individual-specific skin microbiome. Despite experiencing the same environmental conditions and consuming the same diet, significant differences in the skin microbe composition were identified among the three species. The bird species differed both quantitatively and qualitatively regarding the observed bacterial taxa. Although each species harboured its own unique set of skin microbes, we identified a core skin microbiome among the studied species. As microbes are known to influence the host's body odour, our findings of an individual-specific skin microbiome might suggest that the skin microbiome in birds is involved in the odour production and could encode information on the host's genotype.

Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species

BACKGROUND

Genome mining tools have enabled us to predict biosynthetic gene clusters that might encode compounds with valuable functions for industrial and medical applications. With the continuously increasing number of genomes sequenced, we are confronted with an overwhelming number of predicted clusters. In order to guide the effective prioritization of biosynthetic gene clusters towards finding the most promising compounds, knowledge about diversity, phylogenetic relationships and distribution patterns of biosynthetic gene clusters is necessary.

RESULTS

Here, we provide a comprehensive analysis of the model actinobacterial genus Amycolatopsis and its potential for the production of secondary metabolites. A phylogenetic characterization, together with a pan-genome analysis showed that within this highly diverse genus, four major lineages could be distinguished which differed in their potential to produce secondary metabolites. Furthermore, we were able to distinguish gene cluster families whose distribution correlated with phylogeny, indicating that vertical gene transfer plays a major role in the evolution of secondary metabolite gene clusters. Still, the vast majority of the diverse biosynthetic gene clusters were derived from clusters unique to the genus, and also unique in comparison to a database of known compounds. Our study on the locations of biosynthetic gene clusters in the genomes of Amycolatopsis' strains showed that clusters acquired by horizontal gene transfer tend to be incorporated into non-conserved regions of the genome thereby allowing us to distinguish core and hypervariable regions in Amycolatopsis genomes.

CONCLUSIONS

Using a comparative genomics approach, it was possible to determine the potential of the genus Amycolatopsis to produce a huge diversity of secondary metabolites. Furthermore, the analysis demonstrates that horizontal and vertical gene transfer play an important role in the acquisition and maintenance of valuable secondary metabolites. Our results cast light on the interconnections between secondary metabolite gene clusters and provide a way to prioritize biosynthetic pathways in the search and discovery of novel compounds.

On the Enigma of Glutathione-Dependent Styrene Degradation in Gordonia rubripertincta CWB2

Among bacteria, only a single styrene-specific degradation pathway has been reported so far. It comprises the activity of styrene monooxygenase, styrene oxide isomerase, and phenylacetaldehyde dehydrogenase, yielding phenylacetic acid as the central metabolite. The alternative route comprises ring-hydroxylating enzymes and yields vinyl catechol as central metabolite, which undergoes meta-cleavage. This was reported to be unspecific and also allows the degradation of benzene derivatives. However, some bacteria had been described to degrade styrene but do not employ one of those routes or only parts of them. Here, we describe a novel "hybrid" degradation pathway for styrene located on a plasmid of foreign origin. As putatively also unspecific, it allows metabolizing chemically analogous compounds (e.g., halogenated and/or alkylated styrene derivatives). Gordonia rubripertincta CWB2 was isolated with styrene as the sole source of carbon and energy. It employs an assembled route of the styrene side-chain degradation and isoprene degradation pathways that also funnels into phenylacetic acid as the central metabolite. Metabolites, enzyme activity, genome, transcriptome, and proteome data reinforce this observation and allow us to understand this biotechnologically relevant pathway, which can be used for the production of ibuprofen.IMPORTANCE The degradation of xenobiotics by bacteria is not only important for bioremediation but also because the involved enzymes are potential catalysts in biotechnological applications. This study reveals a novel degradation pathway for the hazardous organic compound styrene in Gordonia rubripertincta CWB2. This study provides an impressive illustration of horizontal gene transfer, which enables novel metabolic capabilities. This study presents glutathione-dependent styrene metabolization in an (actino-)bacterium. Further, the genomic background of the ability of strain CWB2 to produce ibuprofen is demonstrated.

Microbial communities in seawater from an Arctic and a temperate Norwegian fjord and their potentials for biodegradation of chemically dispersed oil at low seawater temperatures

Biodegradation of chemically dispersed oil at low temperature (0-2 °C) was compared in natural seawater from Arctic (Svalbard) and a temperate (Norway) fjords. The oil was premixed with a dispersant (Corexit 9500) and small-droplet oil dispersions prepared. Faster biotransformation of n-alkanes in the Arctic than in the temperate seawater were associated with the initially higher abundance of the alkane-degrading genus Oleispira in the Arctic than the temperate seawater. Comparable transformation of aromatic hydrocarbons was further associated with the late emergences Cycloclasticus in both seawater sources. The results showed that chemically dispersed oil may be rapidly biodegraded by microbial communities in Arctic seawater. Compared to oil biodegradation studies at higher seawater temperatures, longer lag-periods were experienced here, and may be attributed to both microbial and oil properties at these low seawater temperatures.

Biodegradation of dispersed oil in seawater is not inhibited by a commercial oil spill dispersant

Chemical dispersants are well-established as oil spill response tools. Several studies have emphasized their positive effects on oil biodegradation, but recent studies have claimed that dispersants may actually inhibit the oil biodegradation process. In this study, biodegradation of oil dispersions in natural seawater at low temperature (5°C) was compared, using oil without dispersant, and oil premixed with different concentrations of Slickgone NS, a widely used oil spill dispersant in Europe. Saturates (nC10-nC36 alkanes), naphthalenes and 2- to 5-ring polycyclic aromatic hydrocarbons (PAH) were biotransformed at comparable rates in all dispersions, both with and without dispersant. Microbial communities differed primarily between samples with or without oil, and they were not significantly affected by increasing dispersant concentrations. Our data therefore showed that a common oil spill dispersant did not inhibit biodegradation of oil at dispersant concentrations relevant for response operations.

Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome

Lettuce (Lactuca sativa, L.) is an important annual plant of the family Asteraceae (Compositae). The commercial lettuce cultivar Tizian has been used in various scientific studies investigating the interaction of the plant with phytopathogens or biological control agents. Here, we present the de novo draft genome sequencing and gene prediction for this specific cultivar derived from transcriptome sequence data. The assembled scaffolds amount to a size of 2.22 Gb. Based on RNAseq data, 31,112 transcript isoforms were identified. Functional predictions for these transcripts were determined within the GenDBE annotation platform. Comparison with the cv. Salinas reference genome revealed a high degree of sequence similarity on genome and transcriptome levels, with an average amino acid identity of 99%. Furthermore, it was observed that two large regions are either missing or are highly divergent within the cv. Tizian genome compared to cv. Salinas. One of these regions covers the major resistance complex 1 region of cv. Salinas. The cv. Tizian draft genome sequence provides a valuable resource for future functional and transcriptome analyses focused on this lettuce cultivar.

Schistocytic anaemia, severe thrombocytopenia, and renal dysfunction: thrombotic microangiopathy due to severe acquired ADAMTS-13 deficiency

We present the case of a woman (age: 64 years) with acute thrombotic microangiopathy due to severe acquired ADAMTS-13 (von Willebrand factor-cleaving protease) deficiency. She was successfully treated with plasma exchange therapy and glucocorticosteroids. She relapsed seven months later, and splenectomy led to lasting remission.

Pathomechanisms of thrombotic thrombocytopenic purpura, especially the role of ADAMTS-13, are discussed and therapeutic measures outlined.

Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation

BACKGROUND

Oleaginous microalgae are promising production hosts for the sustainable generation of lipid-based bioproducts and as bioenergy carriers such as biodiesel. Transcriptomics of the lipid accumulation phase, triggered efficiently by nitrogen starvation, is a valuable approach for the identification of gene targets for metabolic engineering.

RESULTS

An explorative analysis of the detailed transcriptional response to different stages of nitrogen availability was performed in the oleaginous green alga Monoraphidium neglectum. Transcript data were correlated with metabolic data for cellular contents of starch and of different lipid fractions. A pronounced transcriptional down-regulation of photosynthesis became apparent in response to nitrogen starvation, whereas glucose catabolism was found to be up-regulated. An in-depth reconstruction and analysis of the pathways for glycerolipid, central carbon, and starch metabolism revealed that distinct transcriptional changes were generally found only for specific steps within a metabolic pathway. In addition to pathway analyses, the transcript data were also used to refine the current genome annotation. The transcriptome data were integrated into a database and complemented with data for other microalgae which were also subjected to nitrogen starvation. It is available at https://tdbmn.cebitec.uni-bielefeld.de.

CONCLUSIONS

Based on the transcriptional responses to different stages of nitrogen availability, a model for triacylglycerol and lipid hyperaccumulation is proposed, which involves transcriptional induction of thioesterases, differential regulation of lipases, and a re-routing of the central carbon metabolism. Over-expression of distinct thioesterases was identified to be a potential strategy to increase the oleaginous phenotype of M. neglectum, and furthermore specific lipases were identified as potential targets for future metabolic engineering approaches.

Linking secondary metabolites to biosynthesis genes in the fungal endophyte Cyanodermella asteris: The anti-cancer bisanthraquinone skyrin

Fungal aromatic polyketides display a very diverse and widespread group of natural products. Due to their excellent light absorption properties and widely studied biological activities, they offer numerous application for food, textile and pharmaceutical industry. The biosynthetic pathways of fungal aromatic polyketides usually involve a set of successive enzymes, in which a non-reductive polyketide synthase iteratively catalyzes the essential assembly of simple building blocks into (often polycyclic) aromatic compounds. However, only a limited number of such pathways have been described so far and further elucidation of the individual biosynthetic steps is needed to fully exploit the biotechnological and medicinal potential of these compounds. Here, we identified the bisanthraquinone skyrin as the main pigment of the fungus Cyanodermella asteris, an endophyte that has recently been isolated from the traditional Chinese medicinal plant Aster tataricus. The genome of C. asteris was sequenced, assembled and annotated, which enables first insights into a genome from a non-lichenized member of the class Lecanoromycetes. Genetic and in silico analyses led to the identification of a gene cluster of five genes suggested to encode the enzymatic pathway for skyrin. Our study is a starting point for rational pathway engineering in order to drive the production towards higher yields or more active derivatives. Moreover, our investigations revealed a large potential of secondary metabolite production in C. asteris as well as in all Lecanoromycetes of which genomes were available. These findings convincingly emphasize that Lecanoromycetes are prolific producers of secondary metabolites.

The Rhizoctonia solani AG1-IB (isolate 7/3/14) transcriptome during interaction with the host plant lettuce (Lactuca sativa L.)

The necrotrophic pathogen Rhizoctonia solani is one of the most economically important soil-borne pathogens of crop plants. Isolates of R. solani AG1-IB are the major pathogens responsible for bottom-rot of lettuce (Lactuca sativa L.) and are also responsible for diseases in other plant species. Currently, there is lack of information regarding the molecular responses in R. solani during the pathogenic interaction between the necrotrophic soil-borne pathogen and its host plant. The genome of R. solani AG1-IB (isolate 7/3/14) was recently established to obtain insights into its putative pathogenicity determinants. In this study, the transcriptional activity of R. solani AG1-IB was followed during the course of its pathogenic interaction with the host plant lettuce under controlled conditions. Based on visual observations, three distinct pathogen-host interaction zones on lettuce leaves were defined which covered different phases of disease progression on tissue inoculated with the AG1-IB (isolate 7/3/14). The zones were defined as: Zone 1-symptomless, Zone 2-light brown discoloration, and Zone 3-dark brown, necrotic lesions. Differences in R. solani hyphae structure in these three zones were investigated by microscopic observation. Transcriptional activity within these three interaction zones was used to represent the course of R. solani disease progression applying high-throughput RNA sequencing (RNA-Seq) analysis of samples collected from each Zone. The resulting three transcriptome data sets were analyzed for their highest expressed genes and for differentially transcribed genes between the respective interaction zones. Among the highest expressed genes was a group of not previously described genes which were transcribed exclusively during early stages of interaction, in Zones 1 and 2. Previously described importance of up-regulation in R. solani agglutinin genes during disease progression could be further confirmed; here, the corresponding genes exhibited extremely high transcription levels. Most differentially higher expressed transcripts were found within Zone 2. In Zone 3, the zone with the strongest degree of interaction, gene transcripts indicative of apoptotic activity were highly abundant. The transcriptome data presented in this work support previous models of the disease and interaction cycle of R. solani and lettuce and may influence effective techniques for control of this pathogen.

A Mitochondrial Autonomously Replicating Sequence from Pichia pastoris for Uniform High Level Recombinant Protein Production

Pichia pastoris is a non-conventional methylotrophic yeast that is widely used for recombinant protein production, typically by stably integrating the target gene into the genome as part of an expression cassette. However, the comparatively high clonal variability associated with this approach usually necessitates a time intense screening step in order to find strains with the desired productivity. Some of the factors causing this clonal variability can be overcome using episomal vectors containing an autonomously replicating sequence (ARS). Here, we report on the discovery, characterization, and application of a fragment of mitochondrial DNA from P. pastoris for use as an ARS. First encountered as an off-target event in an experiment aiming for genomic integration, the newly created circular plasmid named “pMito” consists of the expression cassette and a fragment of mitochondrial DNA. Multiple matches to known ARS consensus sequence motifs, but no exact match to known chromosomal ARS from P. pastoris were detected on the fragment, indicating the presence of a novel ARS element. Different variants of pMito were successfully used for transformation and their productivity characteristics were assayed. All analyzed clones displayed a highly uniform expression level, exceeding by up to fourfold that of a reference with a single copy integrated in its genome. Expressed GFP could be localized exclusively to the cytoplasm via super-resolution fluorescence microscopy, indicating that pMito is present in the nucleus. While expression levels were homogenous among pMito clones, an apparent upper limit of expression was visible that could not be explained based on the gene dosage. Further investigation is necessary to fully understand the bottle-neck hindering this and other ARS vectors in P. pastoris from reaching their full capability. Lastly, we could demonstrate that the mitochondrial ARS from P. pastoris is also suitable for episomal vector transformation in Saccharomyces cerevisiae, widening the potential for biotechnological application. pMito displayed strong potential to reduce clonal variability in experiments targeting recombinant protein production. These findings also showcase the as of yet largely untapped potential of mitochondrial ARS from different yeasts for biotechnological applications.

[Phonemic balance of the Freiburg monosyllabic speech test]

BACKGROUND

ISO 8253-3 [4] describes the requirements for speech tests with respect to their phonemic balance. The fulfillment of these requirements by the Freiburg monosyllabic speech test were examined.

METHODS

The Freiburg monosyllables were phonologically transcribed and analyzed with respect to their structural types, vowels and consonants, as well as phonological classes, and compared to reference values.

RESULTS

The phonemic distribution of the Freiburg monosyllables differs slightly from the reference values for the German language. The differences are presumably related to the restriction to monosyllabic substantives. Most test lists (except for 12) contain similar proportions of different phonem classes for vowel and consonants according to Hahlbrock and ISO 8253-3 [4].

CONCLUSION

The deviations of test lists 5, 11, and 15 in a study for perceptual equivalence cannot be explained by phonemic imbalance in comparison to other test lists. Only the lower recognition rates for test list 12 might be explained by its deviant phonemic distribution.

[Test-retest reliability of the Freiburg monosyllabic speech test]

BACKGROUND

ISO 8253-3 describes the requirements for speech tests used in audiology. One aspect is the test-retest reliability, which was here examined for the Freiburg monosyllabic speech test.

METHODS

Speech recognition scores were examined for 30 listeners with normal hearing ability. All 20 lists of the Freiburg monosyllabic speech test were tested at four different presentation levels. The retest was carried out 7-9 months later.

RESULTS

The test-retest reliability of the Freiburg monosyllabic speech test in this study is between 13 percentage points for a speech recognition score of 95 %, and 24 percentage points for a speech recognition score of 39 %. The measurement accuracy can be estimated using binomial distribution.

CONCLUSION

The reproducibility of the results is limited by the small number of test items (20 words) in each list. This does not fulfill the requirements for speech tests in diagnostics and rehabilitation. An improvement of the test-retest reliability can be achieved using several test lists.

[Evaluation of the perceptual equivalence of test lists in the Freiburg monosyllabic speech test]

BACKGROUND

In the past, the perceptual balance of test lists for the Freiburg monosyllabic speech test (FBE) was frequently evaluated without producing consistent results. Until now, the studies used very diverse methods and did not accurately follow the standardized specifications. In this study, therefore, the perceptual equivalence of test lists was verified with a large group of participants according to the standard ISO EN 8253-3.

METHODS

A total of 160  suitable otologically normal subjects were recruited at two institutions, each of whom listened to all test lists of the FBE using predefined measurement conditions. The subjects were divided in three groups depending on the transducer used for test list presentation (headphones "HDA 200" and "TDH 39", as well as free-field loudspeaker, "FF"). Lists that deviated were identified using the approaches specified in the standard.

RESULTS

The reference curve for FBE was not met by any group. While the "HDA 200" group indicated 4.6 dB lower thresholds, results for the "TDH 39" and "FF" groups showed 1.2 and 2.5 dB higher thresholds, respectively. For an average speech recognition score of 44.3 %, test lists 5, 11, 12, and 15 lay outside the calculated tolerance range of 4.5 to -4.4 percent points. The same lists also deviated when calculating discrimination functions and therefore do not fulfill the criteria for perceptual equivalence.

DISCUSSION

In the future, lists identified as deviating from the norm should not be used. The results of this study only partly agree with results from former studies.