Universal DNA methylation age across mammalian tissues.

Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.

Targeted next generation sequencing of RB1 gene for the molecular diagnosis of Retinoblastoma.

BACKGROUND: The spectrum of RB1gene mutations in Retinoblastoma (RB) patients and the necessity of multiple traditional methods for complete variant analysis make the molecular diagnosis a cumbersome, labor-intensive and time-consuming process. Here, we have used targeted next generation sequencing (NGS) approach with in-house analysis pipeline to explore its potential for the molecular diagnosis of RB. METHODS: Thirty-three patients with RB and their family members were selected randomly. DNA from patient blood and/or tumor was used for RB1 gene targeted sequencing. The raw reads were obtained from Illumina Miseq. An in-house bioinformatics pipeline was developed to detect both single nucleotide variants (SNVs) and small insertions/deletions (InDels) and to distinguish between somatic and germline mutations. In addition, ExomeCNV and Cn. MOPS were used to detect copy number variations (CNVs). The pathogenic variants were identified with stringent criteria, and were further confirmed by conventional methods and cosegregation in families. RESULTS: Using our approach, an array of pathogenic variants including SNVs, InDels and CNVs were detected in 85% of patients. Among the variants detected, 63% were germline and 37% were somatic. Interestingly, nine novel pathogenic variants (33%) were also detected in our study. CONCLUSIONS: We demonstrated for the first time that targeted NGS is an efficient approach for the identification of wide spectrum of pathogenic variants in RB patients. This study is helpful for the molecular diagnosis of RB in a comprehensive and time-efficient manner.

Cu(2)ZnSnS(4) nanocrystal dispersions in polar liquids.

Cu(2)ZnSnS(4) (CZTS) nanocrystals sterically stabilized with oleic acid and oleylamine ligands and dispersed in nonpolar organic liquids have been extracted into, and electrostatically stabilized in, polar liquids by covering their surfaces with S(2-).

Imaging "invisible" dopant atoms in semiconductor nanocrystals.

Nanometer-scale semiconductors that contain a few intentionally added impurity atoms can provide new opportunities for controlling electronic properties. However, since the physics of these materials depends strongly on the exact arrangement of the impurities, or dopants, inside the structure, and many impurities of interest cannot be observed with currently available imaging techniques, new methods are needed to determine their location. We combine electron energy loss spectroscopy with annular dark-field scanning transmission electron microscopy (ADF-STEM) to image individual Mn impurities inside ZnSe nanocrystals. While Mn is invisible to conventional ADF-STEM in this host, our experiments and detailed simulations show consistent detection of Mn. Thus, a general path is demonstrated for atomic-scale imaging and identification of individual dopants in a variety of semiconductor nanostructures.

Natural history of Ullrich congenital muscular dystrophy.

OBJECTIVE: To describe the course, complications, and prognosis of Ullrich congenital muscular dystrophy (UCMD), with special reference to life-changing events, including loss of ambulation, respiratory insufficiency, and death. METHODS: Review of the case notes of 13 patients with UCMD, aged 15 years or older at last visit, followed up at a tertiary neuromuscular centre, London, UK, from 1977 to 2007. Data collected were age at onset of symptoms, presenting symptoms, mobility, contractures, scoliosis, skin abnormalities, respiratory function, and feeding difficulties. RESULTS: The mean age at onset of symptoms was 12 months (SD 14 months). Eight patients (61.5%) acquired independent ambulation at a mean age of 1.7 years (SD 0.8 years). Nine patients (69.2%) became constant wheelchair users at a mean age of 11.1 years (SD 4.8 years). Three patients continued to ambulate indoors with assistance. Forced vital capacity (FVC) values were abnormal in all patients from age 6 years. The mean FVC (% predicted) declined at a mean rate of 2.6% (SD 4.1%) yearly. Nine patients (69.2%) started noninvasive ventilation at a mean age of 14.3 years (SD 5.0 years). Two patients died of respiratory insufficiency. CONCLUSION: In Ullrich congenital muscular dystrophy (UCMD), the decline in motor and respiratory functions is more rapid in the first decade of life. The deterioration is invariable, but not always correlated with age or severity at presentation. This information should be of help to better anticipate the difficulties encountered by patients with UCMD and in planning future therapeutic trials in this condition.

Congenital myasthenic syndromes in childhood: diagnostic and management challenges.

The Congenital Myasthenic Syndromes (CMS), a group of heterogeneous genetic disorders of neuromuscular transmission, are often misdiagnosed as congenital muscular dystrophy (CMD) or myopathies and present particular management problems. We present our experience of 46 children with CMS, referred to us between 1992-2007 with provisional diagnoses of congenital myopathy (22/46), CMS or limb-girdle myasthenia (9/46), central hypotonia or neurometabolic disease (5/46), myasthenia gravis (4/46), limb-girdle or congenital muscular dystrophy (4/46) and SMA (2/46). Diagnosis was often considerably delayed (up to 18y4 m), despite the early symptoms in most cases. Diagnostic clues in the neonates were feeding difficulties (29/46), hypotonia with or without limb weakness (21/46), ptosis (19/46), respiratory insufficiency (12/46), contractures (4/46) and stridor (6/46). Twenty-five children had delayed motor milestones. Fatigability developed in 43 and a variable degree of ptosis was eventually present in 40. Over the period of the study, the mainstay of EMG diagnosis evolved from repetitive nerve stimulation to stimulation single fibre EMG. The patients were studied by several different operators. 66 EMGs were performed in 40 children, 29 showed a neuromuscular junction abnormality, 7 were myopathic, 2 had possible neurogenic changes and 28 were normal or inconclusive. A repetitive CMAP was detected in only one of seven children with a COLQ mutation and neither of the two children with Slow Channel Syndrome mutations. Mutations have been identified so far in 32/46 children: 10 RAPSN, 7 COLQ, 6 CHRNE, 7 DOK7, 1 CHRNA1 and 1 CHAT. 24 of 25 muscle biopsies showed myopathic changes with fibre size variation; 14 had type-1 fibre predominance. Three cases showed small type-1 fibres resembling fibre type disproportion, and four showed core-like lesions. No specific myopathic features were associated with any of the genes. Twenty children responded to Pyridostigmine treatment alone, 11 to Pyridostigmine with either 3, 4 DAP or Ephedrine and five to Ephedrine alone. Twenty one children required acute or chronic respiratory support, with tracheostomy in 4 and nocturnal or emergency non-invasive ventilation in 9. Eight children had gastrostomy. Another 11 were underweight for height indicative of failure to thrive and required dietetic input. A high index of clinical suspicion, repeat EMG by an experienced electromyographer and, if necessary, a therapeutic trial of Pyridostigmine facilitates the diagnosis of CMS with subsequent molecular genetic confirmation. This guides rational therapy and multidisciplinary management, which may be crucial for survival, particularly in pedigrees where previous deaths have occurred in infancy.

Swallowing difficulties in Duchenne muscular dystrophy: indications for feeding assessment and outcome of videofluroscopic swallow studies.

Feeding difficulties are known to occur with advancing age in Duchenne muscular dystrophy (DMD). We evaluated the role of videofluoroscopy swallow study (VFSS) in a group of 30 DMD patients with feeding difficulties. Indications for feeding assessment were: respiratory infections potentially attributable to aspiration (n=10) and/or episodes of choking (n=24) subdivided into isolated choking events (n=8) and regular choking during swallowing (n=16). Indications for assessment were analysed in relation to the VFSS results. Median age at assessment was 17.13 years (range 6-31.4). Twenty-four VFSS were performed. Prolonged chewing and effortful bolus transport for solids increased with age. Swallow trigger was normal in the majority of cases. All patients had some post-swallow pharyngeal residue around the laryngeal inlet increasing in volume with age. Although this residue did not result in aspiration, it was worse in patients that were frequently choking. Three patients intermittently had penetration of the supraglottic space that did not reach the vocal folds during the swallow. Our results suggest that reported swallowing problems when assessed are not always associated with difficulties on VFSS. It is the oral phase of swallowing that is most significantly affected in DMD. The pharyngeal phase is well triggered but is weak with incomplete pharyngeal clearance leaving pharyngeal residue. Insufficient or effortful chewing coupled with weak clearance may predispose them to choking episodes either as a one off event or with increasing frequency with age. This study suggests that VFSS may not be of additional benefit to careful feeding history and observation in DMD with feeding difficulties.

Evaluation of paladai cup feeding in breast-fed preterm infants compared with bottle feeding.

This pilot study developed an appropriate procedure to evaluate the paladai cup compared to bottle feeding in preterm infants, using weighed napkins and video analysis to assess amount of spillage, volume consumed, time taken and physiological stability. Paladai results demonstrated increased spillage, increased feed times with more stress cues.