Biodegradable Polymeric Micro/Nano-Structures with Intrinsic Antifouling/Antimicrobial Properties: Relevance in Damaged Skin and Other Biomedical Applications

Bacterial colonization of implanted biomedical devices is the main cause of healthcare-associated infections, estimated to be 8.8 million per year in Europe. Many infections originate from damaged skin, which lets microorganisms exploit injuries and surgical accesses as passageways to reach the implant site and inner organs. Therefore, an effective treatment of skin damage is highly desirable for the success of many biomaterial-related surgical procedures. Due to gained resistance to antibiotics, new antibacterial treatments are becoming vital to control nosocomial infections arising as surgical and post-surgical complications. Surface coatings can avoid biofouling and bacterial colonization thanks to biomaterial inherent properties (e.g., super hydrophobicity), specifically without using drugs, which may cause bacterial resistance. The focus of this review is to highlight the emerging role of degradable polymeric micro- and nano-structures that show intrinsic antifouling and antimicrobial properties, with a special outlook towards biomedical applications dealing with skin and skin damage. The intrinsic properties owned by the biomaterials encompass three main categories: (1) physical–mechanical, (2) chemical, and (3) electrostatic. Clinical relevance in ear prostheses and breast implants is reported. Collecting and discussing the updated outcomes in this field would help the development of better performing biomaterial-based antimicrobial strategies, which are useful to prevent infections.

Optical Interrogation of Sympathetic Neuronal Effects on Macroscopic Cardiomyocyte Network Dynamics

Cardiac stimulation via sympathetic neurons can potentially trigger arrhythmias. We present approaches to study neuron-cardiomyocyte interactions involving optogenetic selective probing and all-optical electrophysiology to measure activity in an automated fashion. Here we demonstrate the utility of optical interrogation of sympathetic neurons and their effects on macroscopic cardiomyocyte network dynamics to address research targets such as the effects of adrenergic stimulation via the release of neurotransmitters, the effect of neuronal numbers on cardiac behavior, and the applicability of optogenetics in mechanistic in vitro studies. As arrhythmias are emergent behaviors that involve the coordinated activity of millions of cells, we image at macroscopic scales to capture complex dynamics. We show that neurons can both decrease and increase wave stability and re-entrant activity in culture depending on their induced activity-a finding that may help us understand the often conflicting results seen in experimental and clinical studies.

Ranbow: A fast and accurate method for polyploid haplotype reconstruction

Reconstructing haplotypes from sequencing data is one of the major challenges in genetics. Haplotypes play a crucial role in many analyses, including genome-wide association studies and population genetics. Haplotype reconstruction becomes more difficult for higher numbers of homologous chromosomes, as it is often the case for polyploid plants. This complexity is compounded further by higher heterozygosity, which denotes the frequent presence of variants between haplotypes. We have designed Ranbow, a new tool for haplotype reconstruction of polyploid genome from short read sequencing data. Ranbow integrates all types of small variants in bi- and multi-allelic sites to reconstruct haplotypes. To evaluate Ranbow and currently available competing methods on real data, we have created and released a real gold standard dataset from sweet potato sequencing data. Our evaluations on real and simulated data clearly show Ranbow’s superior performance in terms of accuracy, haplotype length, memory usage, and running time. Specifically, Ranbow is one order of magnitude faster than the next best method. The efficiency and accuracy of Ranbow makes whole genome haplotype reconstruction of complex genome with higher ploidy feasible.

We focus on the problem of reconstructing haplotypes for polyploid genomes. Our approach explored using short read sequence data from a highly heterozygous hexaploid genome. We observed that short read data from strongly heterozygous organisms open up a way for haplotype reconstruction by supplying overlap information between reads. We therefore investigated the role of heterozygosity and ploidy number. Though higher heterozygosity provides more useful reads for reconstructing haplotypes, polyploidy increases the challenge in assembling reads into longer sequences. We called this the problem of “Ambiguity of Merging” fragments. We addressed this problem by designing a new algorithm called Ranbow. Ranbow was evaluated on real and simulated data from the genomes of tetraploid Capsella bursa-pastoris (Shepherd’s Purse) and hexaploid Ipomoea batatas (sweet potato). We were able to show that our method achieved high accuracy and long assembled haplotypes in a feasible amount of time, performing at a level consistently superior to other algorithms.

Electric field induced alignment of graphene oxide nanoplatelets in polyethersulfone matrix

In recent years, in order to obtain improved mechanical, thermal, electrical and barrier/transport properties, aligned carbonaceous nanomaterials/polymer nanocomposite films have been receiving growing attention. Correspondingly, the edge oxidized graphene oxide (EOGO) nanoplatelets alignment influence on the structure of the polyethersulfone (PES) membrane films for potential applications in water treatment field has been investigated. Aligned GO/PES nanocomposite membrane films were prepared by non-solvent phase inversion technique after the starting sol phase was preliminarily exposed to high electric fields (50 kV m^-1). Either AC (100, 1000 Hz) or DC mode electric fields were alternatively employed, and the results from both vertical and horizontal field configurations were investigated for structural and morphological comparison. Both XRD, FTIR-ATR, EIS, SEM, TEM and tensile strength analyses were applied in order to characterize the films. The microscopic analyses results have demonstrated successful GO/PES nanocomposite formation and alignment of GO nanoplatelets with the field direction in the matrix at low to moderate (0.02-0.1% wt) GO loadings where the flakes were dispersed and exfoliated sufficiently. However, at higher loading levels (1 and 2% wt) the nanoplateles were mostly agglomerated and the big flakes consisting of irregular plates could not orient their axis parallel to the electric field at the employed field strengths. The results suggest a more effective role of higher frequencies (1000 Hz versus 100 Hz) electric field for alignment of GO nanoplatelets. Simple tensile tests have also similarly confirmed GO alignment under the electric fields at both low (0.1% wt) and moderately high (0.5% wt) GO contents. The tensile strength improvement of the horizontal field processed PES/GO nanocomposite up to 24% compared to its vertical field processed counterpart could be accounted as a proof of the successful alignment of the nanoplatelets. However, EIS results unveiled that non-solvent phase inversion casting method, in its general form, may not be a suitable method for producing materials with tailored properties, due to its random and uncontrollable pore forming mechanism.

Contribution of retrotransposition to developmental disorders

Mobile genetic Elements (MEs) are segments of DNA which can copy themselves and other transcribed sequences through the process of retrotransposition (RT). In humans several disorders have been attributed to RT, but the role of RT in severe developmental disorders (DD) has not yet been explored. Here we identify RT-derived events in 9738 exome sequenced trios with DD-affected probands. We ascertain 9 de novo MEs, 4 of which are likely causative of the patient's symptoms (0.04%), as well as 2 de novo gene retroduplications. Beyond identifying likely diagnostic RT events, we estimate genome-wide germline ME mutation rate and selective constraint and demonstrate that coding RT events have signatures of purifying selection equivalent to those of truncating mutations. Overall, our analysis represents a comprehensive interrogation of the impact of retrotransposition on protein coding genes and a framework for future evolutionary and disease studies.

P2794Real-world reasons and outcomes for 1-month versus longer dual antiplatelet therapy strategies with a polymer-free biolimus A9-coated stent: insights from the all-comers FREEDOM registry

Background

The LEADERS FREE trial established the favourable clinical profile of a new polymer-free biolimus A9-eluting stent (PF-BES) in patients at high bleeding risk when used with a 1-month dual anti-platelet therapy (DAPT) strategy.

Purpose

This is the first study evaluating real-world reasons and outcomes for a 1-month versus longer DAPT strategies following PF-BES percutaneous coronary intervention (PCI).

Methods

FREEDOM is an all-comers registry including all patients who underwent PCI with at least one PF-BES at 10 sites, between January 2016 and July 2018. Patients were stratified according to DAPT strategy at discharge (1-month vs >1-month). Baseline features, reasons for PF-BES as reported by the treating physician, and outcomes were compared between groups. Primary outcomes were the 390-day estimates of a patient-oriented composite endpoint (POCE: death, myocardial infarction (MI) or target vessel revascularization) and of a device-oriented composite endpoint (DOCE: cardiac death, target vessel-MI or ischemia-driven target lesion revascularization). Incidence rates were adjusted for clinically relevant factors and outcome predictors. To avoid survival bias, landmark analyses starting from 1-month post-PCI were further carried.

Results

Following PF-BES PCI, 328 (40.3%) patients were discharged with 1-month DAPT and 485 (59.6%) patients with longer DAPT (median 12 months, IQR 6–12 months). Patients with hypertension or on oral anticoagulation (OAT) were more likely and patients with a previous or an index MI were less likely to be discharged on 1-month DAPT. Patients prescribed with 1-month DAPT were more likely to have had a PF-BES for a LEADERS FREE high bleeding risk criterium than those with longer DAPT (90.2% vs 69.9%, p=0.001). The same association was observed when the reason for PF-BES was a planned major surgery (13.1% vs 6.2%; p=0.001) or OAC to be continued after PCI (38.7% vs 16.5%, p<0.001). Conversely, patients with planned longer DAPT were more likely to have had a PF-BES following the operator preference (2.4% vs 15.5%, p<0.001) or for a reason other than a LEADERS FREE criterium or operator preference (5.2% vs 11.3%, p<0.001). No between-groups differences in the occurrence of the primary outcomes (1-month vs >1-month DAPT: POCE 11.9% vs 13.2%, p=0.747; adj-HR 1.29 [95% CI 0.78–2.10]; DOCE: 4.8% vs 8.1%, p=0.500; adj-HR 1.01 [95% CI 0.50–2.07]) and of bleedings (any: 11.3% vs 9.4%, p=0.472; adj-HR 0.87 [95% CI 0.51–1-50]; BARC 3–5: 4.2% vs 2.2%; p=0.108; adj-HR 1.50 [95% CI 0.58–3.87]) were observed. Landmark analyses showed similar results.

Conclusions

In a large contemporary all-comers registry, factors reflecting the operator-perceived patient high bleeding risk were the main drivers of a very-short DAPT strategy following PF-BES PCI. We found no interaction of DAPT duration with outcomes following PF-BES PCI, an observation warranting investigation in adequately powered randomised studies.

P2820Contemporary indications, dual antiplatelet therapy strategies and clinical outcomes for a polymer-free biolimus A9-coated stent: the all-comers FREEDOM registry

Background

The absence of a polymer-coat along with fast drug absorption represent the benchmark counterpart of the favourable clinical profile of a new polymer-free biolimus A9-eluting stent (PF-BES), also when used with a very short dual antiplatelet therapy (DAPT) strategy. Its current use in the real-world setting has not been thoroughly assessed.

Purpose

We evaluated contemporary patterns of indications, DAPT strategies and outcomes for the PF-BES.

Methods

FREEDOM is a multicenter registry including all patients who underwent percutaneous coronary intervention (PCI) with at least one PF-BES at 10 italian sites. Reasons for PF-BES PCI and planned antithrombotic regimen at discharge were collected. Primary outcomes were the 390-day Kaplan Meier estimates of a patient-oriented composite endpoint (POCE: death, any myocardial infarction [MI] or any target vessel revascularization [TVR]) and of a device-oriented composite endpoint (DOCE: cardiac death, target vessel-MI or ischemia-driven target lesion revascularization [ID-TLR]). The independent outcomes predictors were assessed through multivariate Cox proportional hazards analysis.

Results

Between January 2016 and July 2018, 858 patients (age: 74±10 years, 64.6% males, 58.7% acute coronary syndrome presentation) underwent PF-BES PCI. Main reasons for PF-BES physician's choice were advanced age (26.0%), oral anticoagulation (OAT) to be continued after PCI (25.3%), operator preference for PF-BES (9.9%), planned major surgery (8.6%), cancer (8.6%), anemia (7.9%) and recent bleeding (7.0%). Overall, the operator choice to implant a PF-BES reflected a perceived high bleeding risk in 77.7% of patients. At discharge, 99.2% of patients were on DAPT, 19.5% on triple therapy, and 0.8% on single antiplatelet therapy plus OAT. Planned DAPT duration was 1-month in 40.3% of patients, with 33.8% of these being on triple therapy. At 390-day follow-up (median 340 days, interquartile range: 187–390 days) the incident estimate of POCE was 13.1% (any MI 3.7%, any TVR 3.4%) and of DOCE was 7.1% (TV-MI 3.6%, ID-TLR 1.4%); while 390-day estimate of any bleeding event was 11.1% (BARC 3–5 bleeding 3.0%). Independent predictors of 390-day POCE were eGFR≤60 ml/min (HR 1.81; 95% CI 1.09–3.04, p=0.028), a history of cancer (HR 2.62; 95% CI 1.43–4.81, p=0.002) and severely calcified lesion/s (HR 2.05; 95% CI 1.09–3.85, p=0.025). Independent predictors of DOCE were a previous MI (HR 2.06; 95% CI 1.03–4.15, p=0.041), a history of cancer (HR 2.69; 95% CI 1.18–6.13, p=0.019) and bifurcation lesion/s (HR 2.66; 95% CI 1.38–5.13, p=0.004).

Conclusions

In a large, contemporary all-comers registry, the main reasons for PF-BES use reflected in most cases the operator-perceived high bleeding risk of the patient. Following PF-BES PCI, a very-short DAPT strategy was frequently implemented. The outcomes observed in this registry suggest a favorable safety and efficacy profile for the PF-BES in a real-world clinical setting.

Exome-wide assessment of the functional impact and pathogenicity of multinucleotide mutations

Approximately 2% of de novo single-nucleotide variants (SNVs) appear as part of clustered mutations that create multinucleotide variants (MNVs). MNVs are an important source of genomic variability as they are more likely to alter an encoded protein than a SNV, which has important implications in disease as well as evolution. Previous studies of MNVs have focused on their mutational origins and have not systematically evaluated their functional impact and contribution to disease. We identified 69,940 MNVs and 91 de novo MNVs in 6688 exome-sequenced parent–offspring trios from the Deciphering Developmental Disorders Study comprising families with severe developmental disorders. We replicated the previously described MNV mutational signatures associated with DNA polymerase zeta, an error-prone translesion polymerase, and the APOBEC family of DNA deaminases. We estimate the simultaneous MNV germline mutation rate to be 1.78 × 10⁻¹⁰ mutations per base pair per generation. We found that most MNVs within a single codon create a missense change that could not have been created by a SNV. MNV-induced missense changes were, on average, more physicochemically divergent, were more depleted in highly constrained genes (pLI ≥ 0.9), and were under stronger purifying selection compared with SNV-induced missense changes. We found that de novo MNVs were significantly enriched in genes previously associated with developmental disorders in affected children. This shows that MNVs can be more damaging than SNVs even when both induce missense changes, and are an important variant type to consider in relation to human disease.

Pathogenicity and selective constraint on variation near splice sites

Mutations that perturb normal pre-mRNA splicing are significant contributors to human disease. We used exome sequencing data from 7833 probands with developmental disorders (DDs) and their unaffected parents, as well as more than 60,000 aggregated exomes from the Exome Aggregation Consortium, to investigate selection around the splice sites and quantify the contribution of splicing mutations to DDs. Patterns of purifying selection, a deficit of variants in highly constrained genes in healthy subjects, and excess de novo mutations in patients highlighted particular positions within and around the consensus splice site of greater functional relevance. By using mutational burden analyses in this large cohort of proband–parent trios, we could estimate in an unbiased manner the relative contributions of mutations at canonical dinucleotides (73%) and flanking noncanonical positions (27%), and calculate the positive predictive value of pathogenicity for different classes of mutations. We identified 18 patients with likely diagnostic de novo mutations in dominant DD-associated genes at noncanonical positions in splice sites. We estimate 35%–40% of pathogenic variants in noncanonical splice site positions are missing from public databases.

Quantifying the contribution of recessive coding variation to developmental disorders

We estimated the genome-wide contribution of recessive coding variation in 6040 families from the Deciphering Developmental Disorders study. The proportion of cases attributable to recessive coding variants was 3.6% in patients of European ancestry, compared with 50% explained by de novo coding mutations. It was higher (31%) in patients with Pakistani ancestry, owing to elevated autozygosity. Half of this recessive burden is attributable to known genes. We identified two genes not previously associated with recessive developmental disorders, KDM5B and EIF3F, and functionally validated them with mouse and cellular models. Our results suggest that recessive coding variants account for a small fraction of currently undiagnosed nonconsanguineous individuals, and that the role of noncoding variants, incomplete penetrance, and polygenic mechanisms need further exploration.

Common genetic variants contribute to risk of rare severe neurodevelopmental disorders

There are thousands of rare human disorders that are caused by single deleterious, protein-coding genetic variants¹. However, patients with the same genetic defect can have different clinical presentations^2-4, and some individuals who carry known disease-causing variants can appear unaffected⁵. Here, to understand what explains these differences, we study a cohort of 6,987 children assessed by clinical geneticists to have severe neurodevelopmental disorders such as global developmental delay and autism, often in combination with abnormalities of other organ systems. Although the genetic causes of these neurodevelopmental disorders are expected to be almost entirely monogenic, we show that 7.7% of variance in risk is attributable to inherited common genetic variation. We replicated this genome-wide common variant burden by showing, in an independent sample of 728 trios (comprising a child plus both parents) from the same cohort, that this burden is over-transmitted from parents to children with neurodevelopmental disorders. Our common-variant signal is significantly positively correlated with genetic predisposition to lower educational attainment, decreased intelligence and risk of schizophrenia. We found that common-variant risk was not significantly different between individuals with and without a known protein-coding diagnostic variant, which suggests that common-variant risk affects patients both with and without a monogenic diagnosis. In addition, previously published common-variant scores for autism, height, birth weight and intracranial volume were all correlated with these traits within our cohort, which suggests that phenotypic expression in individuals with monogenic disorders is affected by the same variants as in the general population. Our results demonstrate that common genetic variation affects both overall risk and clinical presentation in neurodevelopmental disorders that are typically considered to be monogenic.

De novo mutations in regulatory elements in neurodevelopmental disorders

We previously estimated that 42% of patients with severe developmental disorders carry pathogenic de novo mutations in coding sequences. The role of de novo mutations in regulatory elements affecting genes associated with developmental disorders, or other genes, has been essentially unexplored. We identified de novo mutations in three classes of putative regulatory elements in almost 8,000 patients with developmental disorders. Here we show that de novo mutations in highly evolutionarily conserved fetal brain-active elements are significantly and specifically enriched in neurodevelopmental disorders. We identified a significant twofold enrichment of recurrently mutated elements. We estimate that, genome-wide, 1-3% of patients without a diagnostic coding variant carry pathogenic de novo mutations in fetal brain-active regulatory elements and that only 0.15% of all possible mutations within highly conserved fetal brain-active elements cause neurodevelopmental disorders with a dominant mechanism. Our findings represent a robust estimate of the contribution of de novo mutations in regulatory elements to this genetically heterogeneous set of disorders, and emphasize the importance of combining functional and evolutionary evidence to identify regulatory causes of genetic disorders.

Identification of genetic variants affecting vitamin D receptor binding and associations with autoimmune disease

Large numbers of statistically significant associations between sentinel SNPs and case-control status have been replicated by genome-wide association studies. Nevertheless, few underlying molecular mechanisms of complex disease are currently known. We investigated whether variation in binding of a transcription factor, the vitamin D receptor (VDR), whose activating ligand vitamin D has been proposed as a modifiable factor in multiple disorders, could explain any of these associations. VDR modifies gene expression by binding DNA as a heterodimer with the Retinoid X receptor (RXR). We identified 43,332 genetic variants significantly associated with altered VDR binding affinity (VDR-BVs) using a high-resolution (ChIP-exo) genome-wide analysis of 27 HapMap lymphoblastoid cell lines. VDR-BVs are enriched in consensus RXR::VDR binding motifs, yet most fell outside of these motifs, implying that genetic variation often affects the binding affinity only indirectly. Finally, we compared 341 VDR-BVs replicating by position in multiple individuals against background sets of variants lying within VDR-binding regions that had been matched in allele frequency and were independent with respect to linkage disequilibrium. In this stringent test, these replicated VDR-BVs were significantly (q < 0.1) and substantially (>2-fold) enriched in genomic intervals associated with autoimmune and other diseases, including inflammatory bowel disease, Crohn's disease and rheumatoid arthritis. The approach's validity is underscored by RXR::VDR motif sequence being predictive of binding strength and being evolutionarily constrained. Our findings are consistent with altered RXR::VDR binding contributing to immunity-related diseases. Replicated VDR-BVs associated with these disorders could represent causal disease risk alleles whose effect may be modifiable by vitamin D levels.

Most brain disease-associated and eQTL haplotypes are not located within transcription factor DNase-seq footprints in brain

Dense genotyping approaches have revealed much about the genetic architecture both of gene expression and disease susceptibility. However, assigning causality to genetic variants associated with a transcriptomic or phenotypic trait presents a far greater challenge. The development of epigenomic resources by ENCODE, the Epigenomic Roadmap and others has led to strategies that seek to infer the likely functional variants underlying these genome-wide association signals. It is known, for example, that such variants tend to be located within areas of open chromatin, as detected by techniques such as DNase-seq and FAIRE-seq. We aimed to assess what proportion of variants associated with phenotypic or transcriptomic traits in the human brain are located within transcription factor binding sites. The bioinformatic tools, Wellington and HINT, were used to infer transcription factor footprints from existing DNase-seq data derived from central nervous system tissues with high spatial resolution. This dataset was then employed to assess the likely contribution of altered transcription factor binding to both expression quantitative trait loci (eQTL) and genome-wide association study (GWAS) signals. Surprisingly, we show that most haplotypes associated with GWAS or eQTL phenotypes are located outside of DNase-seq footprints. This could imply that DNase-seq footprinting is too insensitive an approach to identify a large proportion of true transcription factor binding sites. Importantly, this suggests that prioritising variants for genome engineering studies to establish causality will continue to be frustrated by an inability of footprinting to identify the causative variant within a haplotype.

Foxn1 regulates key target genes essential for T cell development in postnatal thymic epithelial cells

Thymic epithelial cell differentiation, growth and function depend on the expression of the transcription factor Foxn1, however its target genes have never been physically identified. Using novel static and inducible genetic model systems and chromatin studies, we provide now a genome wide map of direct Foxn1 target genes for postnatal thymic epithelia and define the Foxn1 binding motif. We detail the function of Foxn1 in these cells and demonstrate that in addition to the transcriptional control of genes involved in the attraction and lineage commitment of T cell precursors, Foxn1 regulates the expression of genes involved in antigen processing and thymocyte selection. Thus, critical events in thymic lympho-stromal cross-talk and T cell selection are indispensably choreographed by Foxn1.

Cardiac Rhythm Monitoring After Acute Decompensation for Heart Failure: Results from the CARRYING ON for HF Pilot Study

BACKGROUND

There's scarce evidence about cardiovascular events (CV) in patients with hospitalization for acute heart failure (HF) and no indication for immediate device implant.

OBJECTIVE

The CARdiac RhYthm monitorING after acute decompensatiON for Heart Failure study was designed to assess the incidence of prespecified clinical and arrhythmic events in this patient population.

METHODS

In this pilot study, 18 patients (12 (67%) male; age 72±10; 16 (89%) NYHA II-III), who were hospitalized for HF with low left ventricular ejection fraction (LVEF) (<40%) and no immediate indication for device implant received an implantable loop recorder (ILR) before hospital discharge. Follow-up visits were scheduled at 3 and 6 months, and at every 6 months until study closure; device data were remotely reviewed monthly. CV mortality, unplanned CV hospitalization, and major arrhythmic events during follow-up were analyzed.

RESULTS

During a median follow-up of 593 days, major CV occurred in 13 patients (72%); of those, 7 patients had at least 1 cardiac arrhythmic event, 2 had at least a clinical event (CV hospitalization or CV death), and 4 had both an arrhythmic and a CV event. Six (33%) patients experienced 10 major clinical events, 5 of them (50%) were HF related. During follow-up, 2 (11%) patients died due to a CV cause and 3 (16%) patients received a permanent cardiac device.

CONCLUSIONS

After an acute HF hospitalization, patients with LVEF<40% and who are not readily eligible for permanent cardiac device implant have a known high incidence of major CV event. In these patients, ILR allows early detection of major cardiac arrhythmias and the ability to react appropriately in a timely manner.

TRIAL REGISTRATION

ClinicalTrials.gov NCT01216670; https://clinicaltrials.gov/ct2/show/NCT01216670.

Mutations in ZMYND10, a gene essential for proper axonemal assembly of inner and outer dynein arms in humans and flies, cause primary ciliary dyskinesia

Primary ciliary dyskinesia (PCD) is a ciliopathy characterized by airway disease, infertility, and laterality defects, often caused by dual loss of the inner dynein arms (IDAs) and outer dynein arms (ODAs), which power cilia and flagella beating. Using whole-exome and candidate-gene Sanger resequencing in PCD-affected families afflicted with combined IDA and ODA defects, we found that 6/38 (16%) carried biallelic mutations in the conserved zinc-finger gene BLU (ZMYND10). ZMYND10 mutations conferred dynein-arm loss seen at the ultrastructural and immunofluorescence level and complete cilia immotility, except in hypomorphic p.Val16Gly (c.47T>G) homozygote individuals, whose cilia retained a stiff and slowed beat. In mice, Zmynd10 mRNA is restricted to regions containing motile cilia. In a Drosophila model of PCD, Zmynd10 is exclusively expressed in cells with motile cilia: chordotonal sensory neurons and sperm. In these cells, P-element-mediated gene silencing caused IDA and ODA defects, proprioception deficits, and sterility due to immotile sperm. Drosophila Zmynd10 with an equivalent c.47T>G (p.Val16Gly) missense change rescued mutant male sterility less than the wild-type did. Tagged Drosophila ZMYND10 is localized primarily to the cytoplasm, and human ZMYND10 interacts with LRRC6, another cytoplasmically localized protein altered in PCD. Using a fly model of PCD, we conclude that ZMYND10 is a cytoplasmic protein required for IDA and ODA assembly and that its variants cause ciliary dysmotility and PCD with laterality defects.

Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease

BACKGROUND

Vitamin D insufficiency has been implicated in autoimmunity. ChIP-seq experiments using immune cell lines have shown that vitamin D receptor (VDR) binding sites are enriched near regions of the genome associated with autoimmune diseases. We aimed to investigate VDR binding in primary CD4+ cells from healthy volunteers.

METHODS

We extracted CD4+ cells from nine healthy volunteers. Each sample underwent VDR ChIP-seq. Our results were analyzed in relation to published ChIP-seq and RNA-seq data in the Genomic HyperBrowser. We used MEMEChIP for de novo motif discovery. 25-Hydroxyvitamin D levels were measured using liquid chromatography-tandem mass spectrometry and samples were divided into vitamin D sufficient (25(OH)D ≥75 nmol/L) and insufficient/deficient (25(OH)D <75 nmol/L) groups.

RESULTS

We found that the amount of VDR binding is correlated with the serum level of 25-hydroxyvitamin D (r = 0.92, P= 0.0005). In vivo VDR binding sites are enriched for autoimmune disease associated loci, especially when 25-hydroxyvitamin D levels (25(OH)D) were sufficient (25(OH)D ≥75: 3.13-fold, P<0.0001; 25(OH)D <75: 2.76-fold, P<0.0001; 25(OH)D ≥75 enrichment versus 25(OH)D <75 enrichment: P= 0.0002). VDR binding was also enriched near genes associated specifically with T-regulatory and T-helper cells in the 25(OH)D ≥75 group. MEME ChIP did not identify any VDR-like motifs underlying our VDR ChIP-seq peaks.

CONCLUSION

Our results show a direct correlation between in vivo 25-hydroxyvitamin D levels and the number of VDR binding sites, although our sample size is relatively small. Our study further implicates VDR binding as important in gene-environment interactions underlying the development of autoimmunity and provides a biological rationale for 25-hydroxyvitamin D sufficiency being based at 75 nmol/L. Our results also suggest that VDR binding in response to physiological levels of vitamin D occurs predominantly in a VDR motif-independent manner.

CRACK GROWTH BEHAVIOR OF STYRENE-BUTADIENE RUBBER, NATURAL RUBBER, AND POLYBUTADIENE RUBBER COMPOUNDS: COMPARISON OF PURE-SHEAR VERSUS STRIP TENSILE TEST

Fatigue crack growth experiments on different carbon black–filled rubber compounds have been carried out to evaluate the influence of pure-shear and strip tensile testing mode by using sine and pulse as waveforms. In a previous set of experimental investigations regarding the influence of both waveform and tested material, it was found that the mode I of crack opening sometimes propagates too quickly to be properly monitored in tests involving strip-tensile specimens. An alternative test methodology based on pure-shear test mode has been investigated, optimizing both the shape of the specimen and the test equipment. Data obtained from the different compound formulations were consistent with the theoretical background and resulted in similar ranking of compound crack growth resistance for the two testing modes; in addition, pure-shear mode showed a higher sensitivity to formula variations.