Proceedings of the inaugural Dark Genome Symposium: November 2022

In November 2022 the first Dark Genome Symposium was held in Boston, USA. The meeting was hosted by Rome Therapeutics and Enara Bio, two biotechnology companies working on translating our growing understanding of this vast genetic landscape into therapies for human disease. The spirit and ambition of the meeting was one of shared knowledge, looking to strengthen the network of researchers engaged in the field. The meeting opened with a welcome from Rosana Kapeller and Kevin Pojasek followed by a first session of field defining talks from key academics in the space. A series of panels, bringing together academia and industry views, were then convened covering a wide range of pertinent topics. Finally, Richard Young and David Ting gave their views on the future direction and promise for patient impact inherent in the growing understanding of the Dark Genome.

Preprint Highlight: Constriction forces imposed by basement membranes regulate developmental cell migration

Extracellular matrix (ECM) stiffness affects many processes of ECM-associated cells, such as migration and differentiation. Whether ECM mechanical properties also affect distant cell populations remains largely unexplored. This preprint studies migration of border cells within Drosophila ovarian follicles as a model system. Border cells migrate toward the center of the follicle by moving between nurse cells, which are surrounded by follicle cells that are themselves encased by the basement membrane ECM. Decreasing stiffness of the follicle ECM reduced cortical tension of follicle cells, and of nurse cells indirectly, accelerating border cell migration. Increasing follicle cell cortical tension slowed border cell migration. These results may inform how ECM stiffness affects cell migration within other complex tubular tissues, such as blood vessels.

This preprint has been assigned the following badges: New Hypothesis, New Materials, Cross-Validation

Read the preprint on bioRxiv ( Molina López et al., 2022 ): https://doi.org/10.1101/2022.12.19.520983 .

Historical view of medical Spanish instruction in a medical school at the US-Mexico border region

With a growing speaking Spanish population in the USA, it is necessary to help meet their healthcare needs. The Paul L. Foster School of Medicine is located in El Paso at the US-Mexico border. The medical Spanish curriculum is required for all medical students and begins on their first day of medical school, with conversational Spanish and medical Spanish through the preclerkship years. One of the key elements to the success of this course is the use of instructors with expertise in language instruction with an emphasis on task-based instruction. In addition to language instruction, this course also emphasizes instruction and experience in the culture of the US-Mexico border region. While taught medical Spanish, students are also prompted to understand when their skills are not adequate for the situation, in which case they need to enlist a skilled translator. Students report that, on a daily basis, they productively use what they learned in this preclerkship curriculum.

Crown Reconstruction of Erosive Wear Using High-viscosity Glass Ionomer Cement: A Case Report

The aim of this clinical report is to present a possible alternative treatment, with 24-month follow-up, for restoring tooth loss due to extensive erosive tooth wear. A 21-year-old male patient, complaining of intense sensitivity in the maxillary posterior teeth, and presenting severe wear on maxillary premolar and molar teeth due to gastroesophageal reflux, sought care in the university clinics. The planned treatment was to refer for medical treatment and perform restorations with the high-viscosity glass ionomer cement Equia Forte (GC Corporation, Tokyo, Japan), aiming to restore the dental anatomy and to consequently decrease the pain symptomatology. A silicone guide, obtained from a diagnostic waxing, was used during the restorative approach considering the patient's occlusion. After all the clinical steps of the restorative technique, an occlusal adjustment of restorations was performed. During monthly recalls up to 24 months, the treatment was stable and in service. In addition, the patient reported no pain and improved chewing, leading to a better quality of life.

Online quality and readability assessment of Early childhood caries information available on websites from distinct countries: A cross-sectional study

AIM

To assess the quality and readability of ECC-related Web information available in English, Spanish, and Brazilian Portuguese language.

METHODS

This study assessed the quality and readability of information related to ECC in three different languages found on the most popular Internet search engines worldwide. Websites were retrieved from different search engines using specific strategies. DISCERN questionnaire, JAMA benchmark criteria, and language-based readability formulas were used by two independent investigators to evaluate the quality and readability of websites. Also, contents were categorised according to aetiology, prevention, and treatment of ECC. The statistical analysis was performed using Spearman's rank correlation coefficient, hierarchical clustering analysis by Ward's minimum variance method, and Mann-Whitney U test. P values < 0.05 were considered significant.

CONCLUSION

ECC-related digital contents were considered simple, accessible and of poor quality, independently of their language and authorship. These findings indicate the importance of professional counseling to empower parents in selecting and consuming adequate information towards the improvement of children's oral health.

Evaluation of Proanthocyanidin-based dentifrices on dentin-wear after erosion and dental abrasion - In situ study

Background

Proanthocyanidin has been considered as a preventive agent against erosion because of its properties, which involves remineralization, reduction of demineralization and matrix metalloproteinases (MMPs) inhibition. Thus, the aim of this in situ study was to evaluate the effect of proanthocyanidin-based dentifrices on wear resistance of dentin specimens subjected to erosion associated with abrasion.

Material and Methods

This crossover double-blinded study was performed in 5 phases of 5 days each, with 10 healthy volunteers who wore 5 palatal devices (1 for each phase) with 4 dentin specimens. The groups under study were: G1 – placebo dentifrice (negative control group); G2 – 0.012% chlorhexidine dentifrice (1st positive control group); G3 – NaF 1110 ppm fluoride dentifrice (2nd positive control group); G4 – 10% purified proanthocyanidin dentifrice (1st test group); G5 – fluoride + proanthocyanidin dentifrice (2nd test group). Erosion was performed by palatal device immersion in acid beverage (Coca-cola®), 3 times daily for 5 minutes during 5 days. Abrasion was applied after the first and third erosive cycles by using a eletric toothbrush during 15 seconds in each specimen with the application of the studied dentifrices slurry. The response variable was depth of dentin loss (µm) measured by profilometry. Data were analyzed by Repeated Measures Analysis of Variance followed by LSD Fisher’s test (p<0.05).

Results

Data (G1: 1.76 ± 0.55A; G2: 1.19 ± 0.42B; G3: 1.29 ± 0.34B; G4: 0.93 ± 0.38C; G5: 0.82 ± 0.34C) showed that G4 and G5 did not presented significant difference between them, but showed less dentine loss when compared to all other groups. G1 presented the highest dentin wear.

Conclusions

Proanthocyanidin and the combination of proanthocyanidin and fluoride dentifrices revealed the best results, showing that these formulations could be a promising alternative for patients who suffer with dentin erosion.

Key words:Dentin, erosion, cross-liking agent, metalloproteinases, toothpastes.

AB0019 TREATMENT OF AUTOIMMUNE AND INFLAMMATORY SKIN DISEASES USING SKIN-TARGETING BIFUNCTIONAL ANTIBODIES: A LOCALIZED IMMUNOMODULATION APPROACH

Background:

Current treatment approaches for autoimmune conditions comprise primarily of systemic immunosuppressants or cytokine blockade. The concentration of therapeutic molecules to the tissues that are the sites of autoimmune and inflammatory diseases is a promising approach with the potential to induce therapeutic benefit and avert risks associated with systemic immunotherapies. Pandion Therapeutics is developing a bifunctional antibody platform that can drive localized immune modulation by combining a “tether antibody” that targets a tissue of choice and “an effector end” that activates specific regulatory immune pathways to restore immune-homeostasis.

Objectives:

Here we report the engineering of a skin-tethered PD-1 agonist and a skin-tethered CD39 that inhibit T cell activation and function and deplete local ATP, respectively, modulating different arms of the immune system in a tissue specific manner.

Methods:

Biophysical assays were performed to characterize Skin-tethered immune effectors for drug-like properties and in vitro and in vivo assays for target binding, cellular activity and tissue specific-localization. Moreover, these bifunctionals were tested in pathway-relevant preclinical models such as Vitiligo and Contact Hypersensitivity.

Results:

Biophysical characterization of the bifunctional molecules showed desired drug like properties including specificity, stability, and manufacturability. The skin tethered bifunctionals showed effector activity in in vitro assays and selectively localized to the skin. Skin localization strikingly correlated with a tether-dependent efficacy compared to a non-tether control.

Conclusion:

We believe that this therapeutic approach has the potential to drive the resolution of cutaneous inflammation, providing an opportunity for developing new targeted therapies for autoimmune and inflammatory skin diseases.

Disclosure of Interests:

Susmita Borthakur Shareholder of: Pandion Therapeutics Inc., Employee of: Pandion therapeutics Inc., Purvi Mande: None declared, Daniel Rios: None declared, Patrick Halvey: None declared, Angela Boisvert: None declared, MIchael Rowe: None declared, Anisha Agrawal: None declared, Minasri Borah: None declared, Mike Cianci: None declared, Joanne L. Viney Shareholder of: Pandion therapeutics Inc., Consultant of: Harpoon, Finch, Quench, HotSpot, Employee of: Pandion Therapeutics Inc., Katalin Kis-Toth: None declared, Kevin L. Otipoby Shareholder of: Pandion Therapeutics Inc., Employee of: Pandion Therapeutics Inc., Ivan Mascanfroni: None declared, Nathan Higginson-Scott Shareholder of: Pandion Therapeutics Inc., Consultant of: Mediar Tx, Employee of: Pandion Therapeutics Inc.

Treatment of Autoimmune and Inflammatory Skin Diseases Using Skin-Targeting Bifunctional Antibodies: A Localized Immunomodulation Approach

Current treatment approaches for autoimmune conditions comprise primarily of systemic immunosuppressants or cytokine blockade. Concentration of therapeutic molecules to the tissues that are the sites of autoimmune and inflammatory diseases is a promising approach with the potential to induce therapeutic benefit and avert risks associated with systemic immunotherapies.

Pandion Therapeutics is developing a bifunctional antibody platform that can drive localized immune modulation. The platform combines a “tether antibody” that targets a tissue of choice and “an effector end” that activates specific regulatory immune pathways to restore immune-homeostasis.

Here we report the engineering of a skin-tethered PD-1 agonist and a skin-tethered CD39 that inhibit T cell activation and function and deplete local ATP, respectively, modulating different arms of the immune system in a tissue specific manner. These skin-tethered immune effectors were assessed for drug-like properties in biophysical assays and in vitro and in vivo assays for target binding, cellular activity and tissue specific-localization. Moreover, these bifunctionals were tested in pathway-relevant preclinical models such as Vitiligo and Contact Hypersensitivity. Strikingly, a selective accumulation of the tethered bifunctionals to the skin was observed and correlated with a tether-dependent efficacy compared to a non-tether control.

We believe that this therapeutic approach has the potential to drive the resolution of cutaneous inflammation, providing an opportunity for developing new targeted therapies for autoimmune and inflammatory skin diseases.

Cryolipolysis with Plate for Treatment of Localized Adiposity

BACKGROUND

Cryolipolysis is a non-invasive method capable of reducing the thickness of the fat layer.

OBJECTIVE

To evaluate the effects of cryolipolysis with the use of plate applicators in the treatment of abdominal fat in women.

MATERIALS AND METHODS

The sample was composed of 15 participants, who were evaluated before and at the end of the intervention. Three applications of cryolipolysis were performed in the infraumbilical portion of the abdominal region. The volunteers were divided into three groups G-1 (temperature of -2°C), G-2 (temperature of -3°C) and G3 (temperature of -4°C).

RESULTS

There was a reduction in plicometry measurements in groups G2 and G3, in the comparison between the initial and final moments (p <0.05), and a reduction in perimetry and ultrasound (p < 0.05) in all groups. It was found that the G3 group was subject to higher risk of first degree burns and redness when compared to the other groups.

CONCLUSION

It is suggested that plate cryolipolysis is a possibly effective resource for reducing adiposity, as shown in the evaluation of perimetry, plicometry, and ultrasound results, and in the photographic analysis.

Effect of in situ aspartame mouthwash to prevent intrinsic and extrinsic erosive tooth wear

Background

The aim was to evaluate whether aspartame regular mouthwash prior to erosive challenges with citric or hydrochloric acids would be able to prevent erosive enamel wear.

Material and Methods

This randomized, single blind in situ study was conducted with 3 crossover phases of 5 days. Polished bovine enamel blocks (n=252) were randomly divided among 6 groups/ 3 phases/ 21 volunteers. The groups under study were: aspartame solution (0.024% of aspartame in deionized water - experimental group), deionized water (negative-control) and stannous-containing solution (Elmex® Erosion Protection Dental Rinse; positive-control); subjected to erosion on citric acid or hydrochloric acid. Four times per day the volunteers rinsed the intraoral appliance with the respective solutions (in situ) prior to immersion of half of the appliance in 0.05M citric acid and the other half in 0.01M hydrochloric acid for 120 seconds (extraoral). The response variable was enamel loss by profilometry. Data were analyzed by ANOVA and Tukey’s test (p<0.05).

Results

No difference on enamel loss was found between aspartame solution and deionized water. Stannous-solution resulted in less enamel loss compared to deionized water. Hydrochloric acid resulted in higher enamel loss than citric acid.

Conclusions

In this model, aspartame was not able to prevent erosive tooth wear against citric or hydrochloric acids.

Key words:Dental erosion, aspartame, stannous fluoride, citric acid, hydrochloric acid.

Resin-Based Materials Protect Against Erosion/Abrasion-a Prolonged In Situ Study

While patient compliance is key to preventive measures related to dental erosion, the application of resin-based materials could serve as an additional treatment to inhibit erosion progression. This in situ study evaluated the effect of applying resin-based materials, including resin infiltrant, on previously eroded enamel subjected to prolonged erosive and abrasive challenges. The factors under study were types of treatment (infiltrant [Icon], sealant [Helioseal Clear], adhesive [Adper Scotchbond Multi-Purpose Plus], and control [no treatment]); wear conditions (erosion [ERO] and erosion + abrasion [ERO + ABR]) and challenge time (5 and 20 days) in a single-phase study. The blocks were prepared from bovine enamel, eroded (0.01 M HCl, pH 2.3 for 30 seconds) and randomized among treatments, wear conditions, and volunteers. The application of resin-based materials followed the manufacturers' recommendations. Twenty-one volunteers wore the palatal intraoral device, in which one row corresponded to ERO and the other to ERO + ABR. In each row, all treatments were represented (2 blocks per treatment). For 20 days, the erosive challenge was performed 4 times/day (immersion in 0.01 M HCl, pH 2.3, for 2 minutes) for the ERO condition. For the ERO + ABR condition, two of the erosive challenges were followed by abrasion for 15 seconds with fluoride dentifrice slurry. Enamel and/or material loss was measured using profilometry (initial, after treatment, and after the end of the fifth and 20th days of in situ erosive challenge) and analyzed by ANOVA models and Tukey's test (α=0.05). The results showed that the application of resin-based materials did not cause superficial enamel loss. The infiltrant group showed a thicker layer of material above the enamel compared with the other materials (p=0.001). After the erosive challenge, there was no difference between the conditions ERO and ERO + ABR (p=0.869). All materials protected the enamel against erosion progression compared with the control group (p=0.001). Based on these results, we conclude that the application of resin-based materials results in protection of previously eroded enamel subjected to in situ erosive and abrasive challenge for 20 days.

Prevention of erosive tooth wear: targeting nutritional and patient-related risks factors

This article provides an overview of the nutritional and patient-related risk factors involved in the aetiology of erosive tooth wear (ETW) and the preventive strategies to counteract them. The first step is to diagnose clinical signs of ETW and to recognise causal factors. Low pH and high buffer capacity of foods/drinks are the major risk factors, while the calcium concentration is the main protective factor. Reduction of frequency of consumption and contact time of erosive foods/drinks with the teeth, use of straws appropriately positioned and consumption of dairy products are advisable. Oral hygiene has a role in the development of ETW, however, postponing toothbrushing is not clinically advisable. In cases of drug abuse, chronic alcoholism, GERD or bulimia, the patient must be referred to a doctor. Immediately after vomiting, patients might be advised to rinse the mouth. Saliva has an important protective role and patients with reduced salivary flow can benefit from the use of chewing gum. Recent studies have focused on improving the protective capacity of the acquired pellicle as well as on the role of protease inhibitors on dentine erosion. However, the degree of evidence for these preventive measures is low. Clinical trials are necessary before these measures can be recommended.

The application of visible absorption spectroscopy to the analysis of uranium in aqueous solutions

Through assay analysis into an excess of 1M H₂SO₄ at fixed temperature a technique has been developed for uranium concentration analysis by visible absorption spectroscopy over an assay concentration range of 1.8-13.4mgU/g. Once implemented for a particular spectrophotometer and set of spectroscopic cells this technique promises to provide more rapid results than a classical method such as Davies-Gray (DG) titration analysis. While not as accurate and precise as the DG method, a comparative analysis study reveals that the spectroscopic method can analyze for uranium in well characterized uranyl(VI) solution samples to within 0.3% of the DG results. For unknown uranium solutions in which sample purity is less well defined agreement between the developed spectroscopic method and DG analysis is within 0.5%. The technique can also be used to detect the presence of impurities that impact the colorimetric analysis, as confirmed through the analysis of ruthenium contamination. Finally, extending the technique to other assay solution, 1M HNO₃, HCl and Na₂CO₃, has also been shown to be viable. Of the four aqueous media the carbonate solution yields the largest molar absorptivity value at the most intensely absorbing band, with the least impact of temperature.

Increased Abundance of M Cells in the Gut Epithelium Dramatically Enhances Oral Prion Disease Susceptibility

Many natural prion diseases of humans and animals are considered to be acquired through oral consumption of contaminated food or pasture. Determining the route by which prions establish host infection will identify the important factors that influence oral prion disease susceptibility and to which intervention strategies can be developed. After exposure, the early accumulation and replication of prions within small intestinal Peyer's patches is essential for the efficient spread of disease to the brain. To replicate within Peyer's patches, the prions must first cross the gut epithelium. M cells are specialised epithelial cells within the epithelia covering Peyer's patches that transcytose particulate antigens and microorganisms. M cell-development is dependent upon RANKL-RANK-signalling, and mice in which RANK is deleted only in the gut epithelium completely lack M cells. In the specific absence of M cells in these mice, the accumulation of prions within Peyer's patches and the spread of disease to the brain was blocked, demonstrating a critical role for M cells in the initial transfer of prions across the gut epithelium in order to establish host infection. Since pathogens, inflammatory stimuli and aging can modify M cell-density in the gut, these factors may also influence oral prion disease susceptibility. Mice were therefore treated with RANKL to enhance M cell density in the gut. We show that prion uptake from the gut lumen was enhanced in RANKL-treated mice, resulting in shortened survival times and increased disease susceptibility, equivalent to a 10-fold higher infectious titre of prions. Together these data demonstrate that M cells are the critical gatekeepers of oral prion infection, whose density in the gut epithelium directly limits or enhances disease susceptibility. Our data suggest that factors which alter M cell-density in the gut epithelium may be important risk factors which influence host susceptibility to orally acquired prion diseases.

TNF-α augments RANKL-dependent intestinal M cell differentiation in enteroid cultures

Microfold (M) cells are phagocytic intestinal epithelial cells in the follicle-associated epithelium of Peyer's patches that transport particulate antigens from the gut lumen into the subepithelial dome. Differentiation of M cells from epithelial stem cells in intestinal crypts requires the cytokine receptor activator of NF-κB ligand (RANKL) and the transcription factor Spi-B. We used three-dimensional enteroid cultures established with small intestinal crypts from mice as a model system to investigate signaling pathways involved in M cell differentiation and the influence of other cytokines on RANKL-induced M cell differentiation. Addition of RANKL to enteroids induced expression of multiple M cell-associated genes, including Spib, Ccl9 [chemokine (C-C motif) ligand 9], Tnfaip2 (TNF-α-induced protein 2), Anxa5 (annexin A5), and Marcksl1 (myristoylated alanine-rich protein kinase C substrate) in 1 day. The mature M cell marker glycoprotein 2 (Gp2) was strongly induced by 3 days and expressed by 11% of cells in enteroids. The noncanonical NF-κB pathway was required for RANKL-induced M cell differentiation in enteroids, as addition of RANKL to enteroids from mice with a null mutation in the mitogen-activated protein kinase kinase kinase 14 (Map3k14) gene encoding NF-κB-inducing kinase failed to induce M cell-associated genes. While the cytokine TNF-α alone had little, if any, effect on expression of M cell-associated genes, addition of TNF-α to RANKL consistently resulted in three- to sixfold higher levels of multiple M cell-associated genes than RANKL alone. One contributing mechanism is the rapid induction by TNF-α of Relb and Nfkb2 (NF-κB subunit 2), genes encoding the two subunits of the noncanonical NF-κB heterodimer. We conclude that endogenous activators of canonical NF-κB signaling present in the gut-associated lymphoid tissue microenvironment, including TNF-α, can play a supportive role in the RANKL-dependent differentiation of M cells in the follicle-associated epithelium.

In situ Effect of Chewing Gum with and without CPP-ACP on Enamel Surface Hardness Subsequent to ex vivo Acid Challenge

The erosion-protective effect of casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) is controversial. This study aimed to investigate the ability of CPP-ACP chewing gum to prevent a single event of erosive demineralization in situ. Bovine enamel blocks (n = 120) were randomly assigned to 3 phases according to the baseline surface hardness: phase I (PI) - chewing gum with CPP-ACP, phase II (PII) - chewing gum without CPP-ACP, and control phase (PIII) - salivary effect without stimulation (no gum). Nineteen volunteers participated in this study during 3 crossover phases of 2 h. In PI and PII, the volunteers wore intraoral palatal appliances for 120 min and chewed a unit of the corresponding chewing gum for the final 30 min. In the control phase the volunteers wore the appliance for 2 h, without chewing gum. Immediately after intraoral use, the appliances were extraorally immersed in a cola drink for 5 min to promote erosive demineralization. The percentage of surface hardness loss was calculated. The data were analyzed by ANOVA models and Tukey's test. Lower enamel hardness loss was found after the use of chewing gum with CPP-ACP (PI: 32.7%) and without CPP-ACP (PII: 33.5%) compared to the salivary effect without stimulation (PIII: 39.8%) (p < 0.05). There was no difference between PI and PII (p > 0.05). The results suggest that the use of chewing gum immediately before an erosive demineralization can diminish enamel hardness loss. However, the presence of CPP-ACP in the chewing gum cannot enhance this protective effect.

Characterization of the Probiotic Yeast Saccharomyces boulardii in the Healthy Mucosal Immune System

The probiotic yeast Saccharomyces boulardii has been shown to ameliorate disease severity in the context of many infectious and inflammatory conditions. However, use of S. boulardii as a prophylactic agent or therapeutic delivery vector would require delivery of S. boulardii to a healthy, uninflamed intestine. In contrast to inflamed mucosal tissue, the diverse microbiota, intact epithelial barrier, and fewer inflammatory immune cells within the healthy intestine may all limit the degree to which S. boulardii contacts and influences the host mucosal immune system. Understanding the nature of these interactions is crucial for application of S. boulardii as a prophylactic agent or therapeutic delivery vehicle. In this study, we explore both intrinsic and immunomodulatory properties of S. boulardii in the healthy mucosal immune system. Genomic sequencing and morphological analysis of S. boulardii reveals changes in cell wall components compared to non-probiotic S. cerevisiae that may partially account for probiotic functions of S. boulardii. Flow cytometry and immunohistochemistry demonstrate limited S. boulardii association with murine Peyer’s patches. We also show that although S. boulardii induces a systemic humoral immune response, this response is small in magnitude and not directed against S. boulardii itself. RNA-seq of the draining mesenteric lymph nodes indicates that even repeated administration of S. boulardii induces few transcriptional changes in the healthy intestine. Together these data strongly suggest that interaction between S. boulardii and the mucosal immune system in the healthy intestine is limited, with important implications for future work examining S. boulardii as a prophylactic agent and therapeutic delivery vehicle.

Pulp tissue response to Portland cement associated with different radio pacifying agents on pulpotomy of human primary molars

The objective of this research was to evaluate the response of Portland cement associated with different radio pacifying agents on pulp treatment of human primary teeth by clinical and radiographic exams and microscopic analysis. Thirty mandibular primary molars were randomly divided into the following groups: Group I - Portland cement; Group II - Portland cement with iodoform (Portland cement + CHI3 ); Group III - Portland cement with zirconium oxide (Portland cement + ZrO2 ); and treated by pulpotomy technique (removal of a portion of the pulp aiming to maintain the vitally of the remaining radicular pulp tissue using a therapeutic dressing). Clinical and radiographic evaluations were recorded at 6, 12 and 24 months follow-up. The teeth at the regular exfoliation period were extracted and processed for histological analysis. Data were tested using statistical analysis with a significance level of 5%. The microscopic findings were descriptively analysed. All treated teeth were clinically and radiographically successful at follow-up appointments. The microscopic analysis revealed positive response to pulp repair with hard tissue barrier formation and pulp calcification in the remaining roots of all available teeth. The findings of this study suggest that primary teeth pulp tissue exhibited satisfactory biological response to Portland cement associated with radio pacifying agents. However, further studies with long-term follow-up are needed to determine the safe clinical indication of this alternative material for pulp therapy of primary teeth.

An endogenous nanomineral chaperones luminal antigen and peptidoglycan to intestinal immune cells

In humans and other mammals it is known that calcium and phosphate ions are secreted from the distal small intestine into the lumen. However, why this secretion occurs is unclear. Here, we show that the process leads to the formation of amorphous magnesium-substituted calcium phosphate nanoparticles that trap soluble macromolecules, such as bacterial peptidoglycan and orally fed protein antigens, in the lumen and transport them to immune cells of the intestinal tissue. The macromolecule-containing nanoparticles utilize epithelial M cells to enter Peyer's patches, small areas of the intestine concentrated with particle-scavenging immune cells. In wild-type mice, intestinal immune cells containing these naturally formed nanoparticles expressed the immune tolerance-associated molecule 'programmed death-ligand 1', whereas in NOD1/2 double knockout mice, which cannot recognize peptidoglycan, programmed death-ligand 1 was undetected. Our results explain a role for constitutively formed calcium phosphate nanoparticles in the gut lumen and show how this helps to shape intestinal immune homeostasis.

In Vitro Effects of Resin Infiltration on Enamel Erosion Inhibition

Resin-based materials that show promising effects for preventing the progression of erosion have been studied. This in vitro study evaluated the effects of applying resin-based materials, including resin infiltration, on previously eroded enamel subjected to erosive challenges. The influence of enamel surface etching prior to application of the material was also studied. Bovine enamel blocks were immersed in hydrochloric acid (HCl), 0.01 M (pH 2.3), for 30 seconds in order to form a softened erosion lesion. The blocks were then randomly divided into nine groups (n=12) and treated as follows: C = control without treatment; Hel = pit & fissure resin sealant (Helioseal Clear); Adh = two-step self-etching adhesive system (AdheSe); Tet = two-step conventional adhesive system (Tetric N-bond); and Inf = infiltrant (Icon). The Helno, Adhno, Tetno, and Infno groups received the same materials without (or with no) surface conditioning. The depth of the material's penetration into softened erosion lesions was qualitatively analyzed using reflection and fluorescence confocal microscopy. After application of the materials, the blocks were immersed in HCl for two minutes; this step was followed by immersion in artificial saliva for 120 minutes four times a day for five days (erosive cycling). Both the enamel alteration and material thickness were analyzed using profilometry, and the results were submitted to Kruskal-Wallis and Dunn tests (p>0.05). Images from the confocal microscopy showed minimal penetration of Adh/Adhno and deep penetration of Inf/Infno into the erosive lesions. The groups Hel, Adh, Inf, Tetno, and Infno resulted in the formation of a layer of material over the enamel, which was effective in inhibiting the progression of erosion. In conclusion, the infiltrant, with or without etching, was able to penetrate and protect the enamel against dental erosion. The other resin-based materials, except for the two-step conventional adhesive, were able to penetrate and inhibit the progression of erosive lesions only when they were applied after enamel etching.

Normal curvature of glenoid surface can be restored when performing an inlay osteochondral allograft: an anatomic computed tomographic comparison

PURPOSE

The purpose of this study was to quantitatively measure the morphology of the glenoid and to assess feasibility of using the medial tibial plateau surface as a donor for osteoarticular allograft reconstruction of the glenoid.

METHODS

Using computed tomography (CT), 10 tibias and 10 scapular models from our database (5 males and 5 females in each group) were randomly selected. Commercial software (Mimics, Materialize, Inc., Plymouth, MI) was used to extract the bone contours from the CT images and to reconstruct the 3-dimensional (3D) geometry of the scapula and tibia. By utilizing the software Creo Elements/Pro 5.0 (Parametric Technology Corp., Needham, MA), mean length and width of both the glenoid and medial tibial plateau were calculated. Radius of curvature was then measured in each 3D CT model at three intermediate segment points that were established within the length line at 25, 50, and 75 percent from superior to inferior in the glenoid and from posterior to anterior in the medial tibial plateau. Statistical analysis was performed and determined to be significant for P < 0.05.

RESULTS

The mean (± SD) radius of curvature values at the established 25, 50, and 75 percent segments of the glenoid were 47.4 ± 17.5 mm, 51.2 ± 12.4 mm, and 45.9 ± 17.0 mm, respectively. For the medial tibial plateau, the radius of curvature at 25, 50, and 75 percent were 43.5 ± 9.7 mm, 37.4 ± 14.3 mm and 52.3 ± 21.5 mm, respectively. Values of the glenoid length were 34.0 ± 2.9 mm, and width values were 24.4 ± 2.3 mm. For the medial tibial plateau, the length was 42.6 ± 2.7 mm, and the width was 23.3 ± 4.3 mm. There was no statistical difference in the radius of curvature and dimensional surface area between the glenoid and medial tibial plateau surfaces.

CONCLUSION

The 3D CT-based anatomic study found that there is a statistically similar relationship in the radius of curvature of the glenoid and the medial tibial plateau surface. This concept may allow the medial tibial plateau to be used as a donor for osteoarticular allograft reconstruction of the glenoid, especially in young patients where previous studies have demonstrated that the success rate in shoulder replacements is not as good as in older patients.

The usefulness of cone beam computed tomography for treatment of complex odontoma

BACKGROUND

Odontomas are odontogenic tumours, resulting from epithelial growth and differentiated mesenchymal cells, clinically asymptomatic, and often associated with changes to the eruption of the permanent dentition. In recent years, cone beam computed tomography (CBCT) has been used in the diagnosis and treatment planning of this condition.

CASE REPORT

A 9-year-old male patient, with an unerupted permanent maxillary right central incisor (tooth 11) presented to our clinic. The panoramic radiograph showed impaction of tooth 11 with incomplete root development and the suspicion of an odontome and supernumerary tooth. CBCT was performed and enabled the visualisation of a radiopaque image compatible with an odontome, confirming the presence of an impacted supernumerary tooth on the palatal surface of tooth 11.

TREATMENT

Surgical excision of the odontome and the supernumerary tooth was performed.

FOLLOW-UP

Clinical and radiographic evaluations 2 months after the removal of the lesion showed lack of space for the eruption of tooth 11. The patient was referred for orthodontic treatment and a Hyrax appliance was fitted. The patient has been followed for 12 months.

CONCLUSION

CBCT is an important auxiliary tool, aiding in both correct diagnosis and accurate treatment planning. It is currently a technology accessible to most paediatric dentists and should be beneficial considering the diagnostic information provided as well as the cost-benefit ratio for the patient.

Comprehensive Arthroscopic Management (CAM) procedure: clinical results of a joint-preserving arthroscopic treatment for young, active patients with advanced shoulder osteoarthritis

PURPOSE

The purpose of this study was to examine the surgical outcomes of 29 active patients (30 shoulders) with end-stage, symptomatic glenohumeral arthritis undergoing the comprehensive arthroscopic management (CAM) procedure.

METHODS

In this institutional review board-approved study, patients with advanced glenohumeral osteoarthritis (OA) underwent the CAM procedure, a joint-preserving arthroscopic treatment. All subjects were candidates for shoulder arthroplasty. The CAM procedure involves the combination of glenohumeral chondroplasty; removal of loose bodies if present; humeral osteoplasty and osteophyte resection (goat's beard deformity); anterior, posterior, and inferior capsular release; subacromial decompression; axillary nerve neurolysis; and biceps tenodesis. Outcome measures included pain, American Shoulder and Elbow Surgeons score, Single Assessment Numeric Evaluation score, QuickDASH (short version of Disabilities of the Arm, Shoulder and Hand questionnaire) score, and satisfaction. For survivorship analysis, failure was defined as progression to shoulder arthroplasty.

RESULTS

The mean age was 52 years (range, 33 to 68 years), and there were 23 men and 6 women. Of the 30 shoulders, 6 progressed to an arthroplasty at a mean of 1.9 years (range, 0.9 to 3.4 years). Patients with less than 2.0 mm of joint space on radiographs were more likely to undergo arthroplasty (P = .037). For shoulders that did not progress to arthroplasty (n = 24), the mean follow-up was 2.6 years (range, 2.1 to 4.7 years). The American Shoulder and Elbow Surgeons scores significantly improved from 58 points (SE, 2.4) to 83 points (SE, 3.3) (P < .001), and pain levels decreased with activities of daily living, work, recreation, and sleep (P < .05). The median patient satisfaction rating was 9 (range, 3 to 10). Survivorship analysis showed a 92% survival rate at 1 year and 85% at 2 years. Patients with larger osteophytes had greater improvement in postoperative range of motion but were less satisfied (r = 0.479, P = .038).

CONCLUSIONS

The CAM procedure reduced pain, improved function, and provided reasonable short-term durability for our cohort of young, active patients with advanced shoulder OA and may serve as a joint-preserving alternative to arthroplasty. Patients with less than 2 mm of joint space had a significantly higher failure rate. The CAM procedure is a viable surgical option in young, active patients with advanced OA, showing survivorship of 85% at 2 years.

LEVEL OF EVIDENCE

Level IV, therapeutic case series.

Conditional deletion of RANK in intestinal epithelial cells of mice results in loss of Peyer’s patch M cells and impaired acquisition of orally delivered antigen (49.2)

Microfold (M) cells are antigen-sampling intestinal epithelial cells found in the follicle-associated epithelium (FAE) of Peyer’s patches (PPs). M cells initiate mucosal immune responses by transcytosis of particulate antigens for delivery to antigen-presenting cells that traffic through the intraepithelial pocket of M cells. We previously showed that RANKL from stromal cells in the subepithelial dome of PPs is necessary and sufficient for inducing M cell differentiation. To determine how selective loss of intestinal M cells affects host immune responses to antigens encountered in the gut lumen, we generated mice with a floxed allele of RANK deleted only in intestinal epithelial cells (IEC) by a villin-cre transgene (RANKΔIEC mice). The FAE of PP in RANKΔIEC mice lacked any cells expressing the M-cell marker GP2, proving that RANKL promotes M cell differentiation from intestinal stem cells via a direct action on RANK-expressing IEC. An OT-II T cell adoptive transfer model was used to analyze ovalbumin (OVA)-specific T cell responses 2 to 3 days after gavage with various forms of OVA. RANKΔIEC mice had compromised T cell responses to both soluble OVA and particulate OVA (OVA encapsulated in acid-stable microparticles prepared by spray drying). The RANKΔIEC mouse provides a first-of-its-kind mouse model for the specific assessment of the contribution of intestinal M cells to uptake of protein antigens and pathogenic microorganisms encountered in the intestinal lumen.

Electron transfer dissociation of dipositive uranyl and plutonyl coordination complexes

Reported here is a comparison of electron transfer dissociation (ETD) and collision-induced dissociation (CID) of solvent-coordinated dipositive uranyl and plutonyl ions generated by electrospray ionization. Fundamental differences between the ETD and CID processes are apparent, as are differences between the intrinsic chemistries of uranyl and plutonyl. Reduction of both charge and oxidation state, which is inherent in ETD activation of [An(VI) O(2) (CH(3) COCH(3) )(4) ](2+) , [An(VI) O(2) (CH(3) CN)(4) ](2) , [U(VI) O(2) (CH(3) COCH(3) )(5) ](2+) and [U(VI) O(2) (CH(3) CN)(5) ](2+) (An = U or Pu), is accompanied by ligand loss. Resulting low-coordinate uranyl(V) complexes add O(2) , whereas plutonyl(V) complexes do not. In contrast, CID of the same complexes generates predominantly doubly-charged products through loss of coordinating ligands. Singly-charged CID products of [U(VI) O(2) (CH(3) COCH(3) )(4,5) ](2+) , [U(VI) O(2) (CH(3) CN)(4,5) ](2+) and [Pu(VI) O(2) (CH(3) CN)(4) ](2+) retain the hexavalent metal oxidation state with the addition of hydroxide or acetone enolate anion ligands. However, CID of [Pu(VI) O(2) (CH(3) COCH(3) )(4) ](2+) generates monopositive plutonyl(V) complexes, reflecting relatively more facile reduction of Pu(VI) to Pu(V).

Gas-phase coordination complexes of U(VI)O2(2+), Np(VI)O2(2+), and Pu(VI)O2(2+) with dimethylformamide

Electrospray ionization of actinyl perchlorate solutions in H(2)O with 5% by volume of dimethylformamide (DMF) produced the isolatable gas-phase complexes, [An(VI)O(2)(DMF)(3)(H(2)O)](2+) and [An(VI)O(2)(DMF)(4)](2+), where An = U, Np, and Pu. Collision-induced dissociation confirmed the composition of the dipositive coordination complexes, and produced doubly- and singly-charged fragment ions. The fragmentation products reveal differences in underlying chemistries of uranyl, neptunyl, and plutonyl, including the lower stability of Np(VI) and Pu(VI) compared with U(VI).

Ensembl 2011

The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish reflecting the popularity and importance of these species in biomedical research. As of Ensembl release 59 (August 2010), 56 species are supported of which 5 have been added in the past year. Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types.

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

SUMMARY

A tool to predict the effect that newly discovered genomic variants have on known transcripts is indispensible in prioritizing and categorizing such variants. In Ensembl, a web-based tool (the SNP Effect Predictor) and API interface can now functionally annotate variants in all Ensembl and Ensembl Genomes supported species.

AVAILABILITY

The Ensembl SNP Effect Predictor can be accessed via the Ensembl website at http://www.ensembl.org/. The Ensembl API (http://www.ensembl.org/info/docs/api/api_installation.html for installation instructions) is open source software.

A database and API for variation, dense genotyping and resequencing data

Background

Advances in sequencing and genotyping technologies are leading to the widespread availability of multi-species variation data, dense genotype data and large-scale resequencing projects. The 1000 Genomes Project and similar efforts in other species are challenging the methods previously used for storage and manipulation of such data necessitating the redesign of existing genome-wide bioinformatics resources.

Results

Ensembl has created a database and software library to support data storage, analysis and access to the existing and emerging variation data from large mammalian and vertebrate genomes. These tools scale to thousands of individual genome sequences and are integrated into the Ensembl infrastructure for genome annotation and visualisation. The database and software system is easily expanded to integrate both public and non-public data sources in the context of an Ensembl software installation and is already being used outside of the Ensembl project in a number of database and application environments.

Conclusions

Ensembl's powerful, flexible and open source infrastructure for the management of variation, genotyping and resequencing data is freely available at http://www.ensembl.org.

Ensembl variation resources

BACKGROUND

The maturing field of genomics is rapidly increasing the number of sequenced genomes and producing more information from those previously sequenced. Much of this additional information is variation data derived from sampling multiple individuals of a given species with the goal of discovering new variants and characterising the population frequencies of the variants that are already known. These data have immense value for many studies, including those designed to understand evolution and connect genotype to phenotype. Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics.

DESCRIPTION

The Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes. This paper provides a detailed description of the sources of data and the methods for creating the Ensembl variation databases. It also explores the utility of the information by explaining the range of query options available, from using interactive web displays, to online data mining tools and connecting directly to the data servers programmatically. It gives a good overview of the variation resources and future plans for expanding the variation data within Ensembl.

CONCLUSIONS

Variation data is an important key to understanding the functional and phenotypic differences between individuals. The development of new sequencing and genotyping technologies is greatly increasing the amount of variation data known for almost all genomes. The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system. All Ensembl data is freely available at http://www.ensembl.org and from the public MySQL database server at ensembldb.ensembl.org.