Altered DNA methylation at age-associated CpG sites in children with growth disorders: impact on age estimation?

Age estimation based on DNA methylation (DNAm) can be applied to children, adolescents and adults, but many CG dinucleotides (CpGs) exhibit different kinetics of age-associated DNAm across these age ranges. Furthermore, it is still unclear how growth disorders impact epigenetic age predictions, and this may be particularly relevant for a forensic application. In this study, we analyzed buccal mucosa samples from 95 healthy children and 104 children with different growth disorders. DNAm was analysed by pyrosequencing for 22 CpGs in the genes PDE4C, ELOVL2, RPA2, EDARADD and DDO. The relationship between DNAm and age in healthy children was tested by Spearman’s rank correlation. Differences in DNAm between the groups “healthy children” and the (sub-)groups of children with growth disorders were tested by ANCOVA. Models for age estimation were trained (1) based on the data from 11 CpGs with a close correlation between DNAm and age (R ≥ 0.75) and (2) on five CpGs that also did not present significant differences in DNAm between healthy and diseased children. Statistical analysis revealed significant differences between the healthy group and the group with growth disorders (11 CpGs), the subgroup with a short stature (12 CpGs) and the non-short stature subgroup (three CpGs). The results are in line with the assumption of an epigenetic regulation of height-influencing genes. Age predictors trained on 11 CpGs with high correlations between DNAm and age revealed higher mean absolute errors (MAEs) in the group of growth disorders (mean MAE 2.21 years versus MAE 1.79 in the healthy group) as well as in the short stature (sub-)groups; furthermore, there was a clear tendency for overestimation of ages in all growth disorder groups (mean age deviations: total growth disorder group 1.85 years, short stature group 1.99 years). Age estimates on samples from children with growth disorders were more precise when using a model containing only the five CpGs that did not present significant differences in DNAm between healthy and diseased children (mean age deviations: total growth disorder group 1.45 years, short stature group 1.66 years). The results suggest that CpGs in genes involved in processes relevant for growth and development should be avoided in age prediction models for children since they may be sensitive for alterations in the DNAm pattern in cases of growth disorders.

Molecular and morphological findings in a sample of oral surgery patients: What can we learn for multivariate concepts for age estimation?

It has already been proposed that a combined use of different molecular and morphological markers of aging in multivariate models may result in a greater accuracy of age estimation. However, such an approach can be complex and expensive, and not every combination may be useful. The significance and usefulness of combined analyses of D-aspartic acid in dentine, pentosidine in dentine, DNA methylation in buccal swabs at five genomic regions (PDE4C, RPA2, ELOVL2, DDO, and EDARADD), and third molar mineralization were tested by investigating a sample of 90 oral surgery patients. Machine learning models for age estimation were trained and evaluated, and the contribution of each parameter to multivariate models was tested by assessment of the predictor importance. For models based on D-aspartic acid, pentosidine, and the combination of both, mean absolute errors (MAEs) of 2.93, 3.41, and 2.68 years were calculated, respectively. The additional inclusion of the five DNAm markers did not improve the results. The sole DNAm-based model revealed a MAE of 4.14 years. In individuals under 28 years of age, the combination of the DNAm markers with the third molar mineralization stages reduced the MAE from 3.85 to 2.81 years. Our findings confirm that the combination of parameters in multivariate models may be very useful for age estimation. However, the inclusion of many parameters does not necessarily lead to better results. It is a task for future research to identify the best selection of parameters for the different requirements in forensic practice.

Device-device communication stability of leadless anti-tachycardia pacemaker and subcutaneous implantable cardioverter defibrillator over 18 months

Background

A novel modular cardiac rhythm management (mCRM) therapy approach is evaluated in this study: the performance of an anti-tachycardia pacing enabled leadless pacemaker (LP) commanded by a subcutaneous-ICD (S-ICD) via wireless, intra-body, device-device communication (DDC).

Objectives

To investigate long-term DDC performance of linked S-ICD to LP (mCRM System) and factors that impact DDC performance.

Methods

The mCRM System was implanted in 37 canine subjects: 33 with an S-ICD and an LP; 4 with an S-ICD and 2 LPs. The S-ICD was implanted using a Parsonnet pouch in the first 8 subjects. Communication thresholds were measured in three postures up to 18 months. Percent tissue encapsulation of the LP was measured at necropsy and ranged from 6% to 100% (mean: 62%). S-ICD system migration was evaluated radiographically at implant vs. at necropsy in two planes (anterior-posterior and left lateral) and evaluated 0–3 scale: none, minimal, moderate, significant. Communication thresholds were evaluated at 0 vs. 3 days using a t-test and 3 days through 18 months using a linear regression analysis. A repeated measures generalized linear model (GLM) was used to evaluate if test posture, percent tissue encapsulation of the LP, Parsonnet pouch use, or S-ICD system migration (no/ minimal migration vs. moderate/significant migration) were significant predictors of DDC performance at the subject's termination time point.

Results

DDC was successful for each tested posture and time point for all subjects (n=37), with 355 tests in Left Lateral (LL), 371 tests in Dorsal (D), and 355 tests in Right Lateral (RL). Follow up data are available up to 18 months for 19 subjects at the time of this abstract; additional follow-up data will be added to the analysis for presentation. Communication thresholds decreased between 0 days and 3 days (LL P<0.01, D P<0.01, RL P<0.05) and did not change significantly from 3 days through 18 months (LL P=0.90, D P=0.83, RL P=0.83). The GLM showed that there is no significant difference in communication thresholds for test posture (P=0.24 LL vs. D, P=0.24 RL vs. D), percent tissue encapsulation of the LP (P=0.63), Parsonnet pouch use (P=0.65), or S-ICD system migration (P=0.95).

Conclusion

Longitudinal studies demonstrate low and stable communication thresholds of a novel mCRM system over time for all three tested postures, regardless of factors such as LP encapsulation, Parsonnet pouch use, or S-ICD system migration.

Device Communication Threshold Stability

Funding Acknowledgement

Type of funding source: Private company. Main funding source(s): Boston Scientific

Magnetic diagnostic suite of the C-2W field-reversed configuration experiment

A fundamental component of any magnetically confined fusion experiment is a firm understanding of the magnetic field. The increased complexity of the C-2W machine warrants an equally enhanced diagnostic capability. C-2W is outfitted with over 700 magnetic field probes of various types. They are both internal and external to the vacuum vessel. Inside, a linear array of innovative in-vacuum annular flux loop/B-dot combination probes provide information about plasma shape, size, pressure, energy, temperature, and trapped flux when coupled with established theoretical interpretations. A linear array of B-dot probes complement the azimuthally averaged measurements. A Mirnov array of 64 3D probes, with both low and high frequency resolution, detail plasma motion and MHD modal content via singular value decomposition analysis. Internal Rogowski probes measure axial currents flowing in the plasma jet. Outside, every feed-through for an internal probe has an external axial field probe. There are many external loops that measure the plasma formation dynamics and the total external magnetic flux. The external measurements are primarily used to characterize eddy currents in the vessel during a plasma shot. Details of these probes and the data derived from their signals are described.

Particle and heat flux diagnostics on the C-2W divertor electrodes

A suite of diagnostics was developed to measure particle and heat fluxes arriving at the divertor electrodes of the C-2W experiment at TAE Technologies. The divertor electrodes consist of 4 concentric rings, each equipped with a bolometer, electrostatic energy analyzer, and thermocouple mounted at two opposing azimuthal locations. These probes provide measurements of the power flux to the divertor electrodes as well as measurements of the ion current density, ion energy distribution, and total energy deposition. The thermocouples also provide calibration points for inferring the heat deposition profile via thermographic imaging of the electrodes with a fast infrared camera. The combined measurements enable the calculation of the energy lost per escaping electron/ion pair, which is an important metric for understanding electron heat transport in the open field lines that surround the field-reversed configuration plasma in C-2W.

Nimodipine confers clinical improvement in two models of experimental autoimmune encephalomyelitis

Multiple sclerosis is characterised by inflammatory neurodegeneration, with axonal injury and neuronal cell death occurring in parallel to demyelination. Regarding the molecular mechanisms responsible for demyelination and axonopathy, energy failure, aberrant expression of ion channels and excitotoxicity have been suggested to lead to Ca2+ overload and subsequent activation of calcium-dependent damage pathways. Thus, the inhibition of Ca2+ influx by pharmacological modulation of Ca2+ channels may represent a novel neuroprotective strategy in the treatment of secondary axonopathy. We therefore investigated the effects of the L-type voltage-gated calcium channel blocker nimodipine in two different models of mouse experimental autoimmune encephalomyelitis (EAE), an established experimental paradigm for multiple sclerosis. We show that preventive application of nimodipine (10 mg/kg per day) starting on the day of induction had ameliorating effects on EAE in SJL/J mice immunised with encephalitic myelin peptide PLP139-151 , specifically in late-stage disease. Furthermore, supporting these data, administration of nimodipine to MOG35-55 -immunised C57BL/6 mice starting at the peak of pre-established disease, also led to a significant decrease in disease score, indicating a protective effect on secondary CNS damage. Histological analysis confirmed that nimodipine attenuated demyelination, axonal loss and pathological axonal β-amyloid precursor protein accumulation in the cerebellum and spinal cord in the chronic phase of disease. Of note, we observed no effects of nimodipine on the peripheral immune response in EAE mice with regard to distribution, antigen-specific proliferation or activation patterns of lymphocytes. Taken together, our data suggest a CNS-specific effect of L-type voltage-gated calcium channel blockade to inflammation-induced neurodegeneration.

Activation of Wnt signaling promotes hippocampal neurogenesis in experimental autoimmune encephalomyelitis

Background

Disease progression in multiple sclerosis (MS) and experimental autoimmune encephalomyelitis (EAE), as one of its animal models, is characterized by demyelination and neuronal damage in white and gray matter structures, including the hippocampus. It is thought that dysfunction of the hippocampus, a primary locus of learning and memory consolidation, may contribute to cognitive impairment in MS patients. Previously, we reported an increased generation of hippocampal neuronal progenitors in the acute stage of EAE, whereas the microenvironmental signals triggering this process remained uninvestigated.

Results

In the present study, we used the Wnt signaling reporter mouse Axin2^LacZ, to elucidate the molecular mechanisms underlying the activation of the hippocampal neurogenic niche upon autoimmune neuroinflammation. Histological and enzymatic examinations of β-gal during the disease course of EAE, allowed us to survey hippocampal Wnt/β-catenin activity, one of the key signaling pathways of adult neurogenesis. We found that Wnt signaling is transiently upregulated in the acute stage of disease, consistent with a timely induction of canonical Wnt ligands. The enhancement of signaling coincided with hippocampal neuronal damage and local expression of immune cytokines such as TNFα and IFNγ, implicating the role of the inflammatory milieu in activation of the Wnt/β-catenin pathway. Supporting this finding, we show that transient exposure to pro-inflammatory cytokine TNFα triggers Wnt signaling in hippocampal organotypic slice cultures. Importantly, inflammation-mediated activation of the Wnt/β-catenin pathway was associated with enhanced neurogenesis in vitro and in vivo, indicating its potential role in hippocampal tissue regeneration and repair.

Conclusions

This study raises the possibility that enhancement of Wnt signaling may support neurogenic processes to cope with neuronal deficits upon immune-mediated neuroinflammation.

Electronic supplementary material

The online version of this article (doi:10.1186/s13024-016-0117-0) contains supplementary material, which is available to authorized users.

BAX inhibitor-1 is a Ca(2+) channel critically important for immune cell function and survival

The endoplasmic reticulum (ER) serves as the major intracellular Ca(2+) store and has a role in the synthesis and folding of proteins. BAX (BCL2-associated X protein) inhibitor-1 (BI-1) is a Ca(2+) leak channel also implicated in the response against protein misfolding, thereby connecting the Ca(2+) store and protein-folding functions of the ER. We found that BI-1-deficient mice suffer from leukopenia and erythrocytosis, have an increased number of splenic marginal zone B cells and higher abundance and nuclear translocation of NF-κB (nuclear factor-κ light-chain enhancer of activated B cells) proteins, correlating with increased cytosolic and ER Ca(2+) levels. When put into culture, purified knockout T cells and even more so B cells die spontaneously. This is preceded by increased activity of the mitochondrial initiator caspase-9 and correlated with a significant surge in mitochondrial Ca(2+) levels, suggesting an exhausted mitochondrial Ca(2+) buffer capacity as the underlying cause for cell death in vitro. In vivo, T-cell-dependent experimental autoimmune encephalomyelitis and B-cell-dependent antibody production are attenuated, corroborating the ex vivo results. These results suggest that BI-1 has a major role in the functioning of the adaptive immune system by regulating intracellular Ca(2+) homeostasis in lymphocytes.

Sequence analysis of a rainbow trout cDNA library and creation of a gene index

Expressed sequence tag (EST) projects have produced extremely valuable resources for identifying genes affecting phenotypes of interest. A large-scale EST sequencing project for rainbow trout was initiated to identify and functionally annotate as many unique transcripts as possible. Over 45,000 5' ESTs were obtained by sequencing clones from a single normalized library constructed using mRNA from six tissues. The production of this sequence data and creation of a rainbow trout Gene Index eliminating redundancy and providing annotation for these sequences will facilitate research in this species.

Mutations in NYX, encoding the leucine-rich proteoglycan nyctalopin, cause X-linked complete congenital stationary night blindness

During development, visual photoreceptors, bipolar cells and other neurons establish connections within the retina enabling the eye to process visual images over approximately 7 log units of illumination. Within the retina, cells that respond to light increment and light decrement are separated into ON- and OFF-pathways. Hereditary diseases are known to disturb these retinal pathways, causing either progressive degeneration or stationary deficits. Congenital stationary night blindness (CSNB) is a group of stable retinal disorders that are characterized by abnormal night vision. Genetic subtypes of CSNB have been defined and different disease actions have been postulated. The molecular bases have been elucidated in several subtypes, providing a better understanding of the disease mechanisms and developmental retinal neurobiology. Here we have studied 22 families with 'complete' X-linked CSNB (CSNB1; MIM 310500; ref. 4) in which affected males have night blindness, some photopic vision loss and a defect of the ON-pathway. We have found 14 different mutations, including 1 founder mutation in 7 families from the United States, in a novel candidate gene, NYX. NYX, which encodes a glycosylphosphatidyl (GPI)-anchored protein called nyctalopin, is a new and unique member of the small leucine-rich proteoglycan (SLRP) family. The role of other SLRP proteins suggests that mutant nyctalopin disrupts developing retinal interconnections involving the ON-bipolar cells, leading to the visual losses seen in patients with complete CSNB.

Mutations in ABC1 in Tangier disease and familial high-density lipoprotein deficiency

Genes have a major role in the control of high-density lipoprotein (HDL) cholesterol (HDL-C) levels. Here we have identified two Tangier disease (TD) families, confirmed 9q31 linkage and refined the disease locus to a limited genomic region containing the gene encoding the ATP-binding cassette transporter (ABC1). Familial HDL deficiency (FHA) is a more frequent cause of low HDL levels. On the basis of independent linkage and meiotic recombinants, we localized the FHA locus to the same genomic region as the TD locus. Mutations in ABC1 were detected in both TD and FHA, indicating that TD and FHA are allelic. This indicates that the protein encoded by ABC1 is a key gatekeeper influencing intracellular cholesterol transport, hence we have named it cholesterol efflux regulatory protein (CERP).

Mutations of the forkhead/winged-helix gene, FKHL7, in patients with Axenfeld-Rieger anomaly

Genetic linkage, genome mismatch scanning, and analysis of patients with alterations of chromosome 6 have indicated that a major locus for development of the anterior segment of the eye, IRID1, is located at 6p25. Abnormalities of this locus lead to glaucoma. FKHL7 (also called "FREAC3"), a member of the forkhead/winged-helix transcription-factor family, has also been mapped to 6p25. DNA sequencing of FKHL7 in five IRID1 families and 16 sporadic patients with anterior-segment defects revealed three mutations: a 10-bp deletion predicted to cause a frameshift and premature protein truncation prior to the FKHL7 forkhead DNA-binding domain, as well as two missense mutations of conserved amino acids within the FKHL7 forkhead domain. Mf1, the murine homologue of FKHL7, is expressed in the developing brain, skeletal system, and eye, consistent with FKHL7 having a role in ocular development. However, mutational screening and genetic-linkage analyses excluded FKHL7 from underlying the anterior-segment disorders in two IRID1 families with linkage to 6p25. Our findings demonstrate that, although mutations of FKHL7 result in anterior-segment defects and glaucoma in some patients, it is probable that at least one more locus involved in the regulation of eye development is also located at 6p25.

Loss-of-function mutations in a calcium-channel alpha1-subunit gene in Xp11.23 cause incomplete X-linked congenital stationary night blindness

X-linked congenital stationary night blindness (CSNB) is a recessive non-progressive retinal disorder characterized by night blindness, decreased visual acuity, myopia, nystagmus and strabismus. Two distinct clinical entities of X-linked CSNB have been proposed. Patients with complete CSNB show moderate to severe myopia, undetectable rod function and a normal cone response, whereas patients with incomplete CSNB show moderate myopia to hyperopia and subnormal but measurable rod and cone function. The electrophysiological and psychophysical features of these clinical entities suggest a defect in retinal neurotransmission. The apparent clinical heterogeneity in X-linked CSNB reflects the recently described genetic heterogeneity in which the locus for complete CSNB (CSNB1) was mapped to Xp11.4, and the locus for incomplete CSNB (CSNB2) was refined within Xp11.23 (ref. 5). A novel retina-specific gene mapping to the CSNB2 minimal region was characterized and found to have similarity to voltage-gated L-type calcium channel alpha1-subunit genes. Mutation analysis of this new alpha1-subunit gene, CACNA1F, in 20 families with incomplete CSNB revealed six different mutations that are all predicted to cause premature protein truncation. These findings establish that loss-of-function mutations in CACNA1F cause incomplete CSNB, making this disorder an example of a human channelopathy of the retina.

Approaches to detection of distantly related proteins by database searches

The searching of protein databases as a method of identifying newly sequenced genes is commonplace in molecular biology laboratories. However, it is a procedure that is not usually formally taught to students, and method cookbooks discuss it only briefly. This article uses a single family of highly diverged uracil-DNA glycosylases, which fall into two distinct groups, to highlight some of the difficulties associated with identification of such proteins by database searching.

Identification of Sonic hedgehog as a candidate gene responsible for holoprosencephaly

Holoprosencephaly (HPE) is a genetically and phenotypically heterogenous disorder involving the development of forebrain and midface, with an incidence of 1:16,000 live born and 1:250 induced abortions. This disorder is associated with several distinct facies and phenotypic variability: in the most extreme cases, anophthalmia or cyclopia is evident along with a congenital absence of the mature nose. The less severe form features facial dysmorphia characterized by ocular hypertelorism, defects of the upper lip and/or nose, and absence of the olfactory nerves or corpus callosum. Several intermediate phenotypes involving both the brain and face have been described. One of the gene loci, HPE3, maps to the terminal band of chromosome 7. We have performed extensive physical mapping studies and established a critical interval for HPE3, and subsequently identified the sonic hedgehog (SHH) gene as the prime candidate for the disorder. SHH lies within 15-250 kilobases (kb) of chromosomal rearrangements associated with HPE, suggesting that a 'position effect' has an important role in the aetiology of HPE. As detailed in the accompanying report, this role for SHH is confirmed by the detection of point mutations in hereditary HPE patients.

Identification of genes from a 500-kb region at 7q11.23 that is commonly deleted in Williams syndrome patients

Williams syndrome (WS) is a multisystem developmental disorder caused by the deletion of contiguous genes at 7q11.23. Hemizygosity of the elastin (ELN) gene can account for the vascular and connective tissue abnormalities observed in WS patients, but the genes that contribute to features such as infantile hypercalcemia, dysmorphic facies, and mental retardation remain to be identified. In addition, the size of the genomic interval commonly deleted in WS patients has not been established. In this study we report the characterization of a 500-kb region that was determined to be deleted in our collection of WS patients. A detailed physical map consisting of cosmid, P1 artificial chromosomes, and yeast artificial chromosomes was constructed and used for gene isolation experiments. Using the techniques of direct cDNA selection and genomic DNA sequencing, three known genes (ELN, LIMK1, and RFC2), a novel gene (WSCR1) with homology to RNA-binding proteins, a gene with homology to restin, and four other putative transcription units were identified. LIMK1 is a protein kinase with two repeats of the LIM/double zinc finger motif, and it is highly expressed in brain. RFC2 is the 40-kDa ATP-binding subunit of replication factor C, which is known to play a role in the elongation of DNA catalyzed by DNA polymerase delta and epsilon. LIMK1 and WSCR1 may be particularly relevant when explaining cognitive defects observed in WS patients.

DNA sequence determination by hybridization: a strategy for efficient large-scale sequencing

The concept of sequencing by hybridization (SBH) makes use of an array of all possible n-nucleotide oligomers (n-mers) to identify n-mers present in an unknown DNA sequence. Computational approaches can then be used to assemble the complete sequence. As a validation of this concept, the sequences of three DNA fragments, 343 base pairs in length, were determined with octamer oligonucleotides. Possible applications of SBH include physical mapping (ordering) of overlapping DNA clones, sequence checking, DNA fingerprinting comparisons of normal and disease-causing genes, and the identification of DNA fragments with particular sequence motifs in complementary DNA and genomic libraries. The SBH techniques may accelerate the mapping and sequencing phases of the human genome project.

Model genomes: The benefits of analysing homologous human and mouse sequences

The human genome initiative has provided the motivating force for launching sequencing projects suitable for testing various DNA-sequencing strategies, as well as motivating the development of mapping and sequencing technologies. In addition to projects targeting selected regions of the human genome, other projects are based on model organisms such as yeast, nematode and mouse. The sequencing of homologous regions of human and mouse genomes is a new approach to genome analysis, and is providing insights into gene evolution, function and regulation which could not be determined so easily from the analysis of just one species.

The primary structure of a mouse-eared bat (Myotis velifer, Chiroptera) hemoglobin

The hemoglobin of the Mouse-Eared Bat Myotis velifer consists of one component. We present the primary structures of the alpha- and beta-globin chains which have been separated by chromatography on carboxymethyl-cellulose CM-52. The sequences have been determined by Edman-degradation with the film technic or the gas phase method, using the native chains and the tryptic peptides, as well as the C-terminal prolyl-peptides obtained by acid hydrolysis of the Asp-Pro-bonds. Compared to the corresponding human chains we found only 13 substitutions in the alpha-chains, but 27 in the beta-chains. The amino-acid residues substituted in the alpha-chains are not involved in any contacts, whereas in the beta-chains, one exchange involves a heme contact, three alpha 1/beta 1- and one alpha 1/beta 2-contacts, the latter [beta 43(CD2)-Glu----Thr] brings for the first time threonine in this position of the beta-chains. Comparison with the Egyptian Fruit Bat (Rousettus aegyptiacus) shows 12 and 25 substitutions in the alpha- and beta-chains, respectively, suggesting a large phylogenetic distance between Micro- and Megachiroptera. We consider this primary structure as a contribution towards solving the problem of the origin of bats and their relation to primates.