Association of DNA Methylation at CPT1A Locus with Metabolic Syndrome in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) Study

In this study, we conducted an epigenome-wide association study of metabolic syndrome (MetS) among 846 participants of European descent in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN). DNA was isolated from CD4+ T cells and methylation at ~470,000 cytosine-phosphate-guanine dinucleotide (CpG) pairs was assayed using the Illumina Infinium HumanMethylation450 BeadChip. We modeled the percentage methylation at individual CpGs as a function of MetS using linear mixed models. A Bonferroni-corrected P-value of 1.1 x 10⁻⁷ was considered significant. Methylation at two CpG sites in CPT1A on chromosome 11 was significantly associated with MetS (P for cg00574958 = 2.6x10^-14 and P for cg17058475 = 1.2x10^-9). Significant associations were replicated in both European and African ancestry participants of the Bogalusa Heart Study. Our findings suggest that methylation in CPT1A is a promising epigenetic marker for MetS risk which could become useful as a treatment target in the future.     

School start time influences melatonin and cortisol levels in children and adolescents – a community-based study

School start time influences sleep parameters. Differences between circadian sleep parameters on weekends and weekdays have been associated with obesity, sleep, and psychiatric disorders. Moreover, circadian rhythm dysregulation affects the secretion of some hormones, such as melatonin and cortisol. In the current study, we investigate the effect of school start time on cortisol and melatonin levels in a community sample of Brazilian children and adolescents. This was a cross-sectional study of 454 students (mean age, 12.81 ± 2.56 years; 58.6% female). From this sample, 80 participants were randomly selected for saliva collection to measure melatonin and cortisol levels. Circadian sleep parameters were assessed by self-reported sleep and wake up schedules and the Morningness–Eveningness Questionnaire. The outcomes, salivary melatonin and cortisol levels, were measured in morning, afternoon and night saliva samples, and behavior problems were assessed using the Child Behavior Checklist (CBCL). The main results revealed that morning school start time decreased the secretion of melatonin. Morning melatonin levels were significantly positively correlated with the sleep midpoint on weekdays and on weekends. Afternoon melatonin levels were positively correlated with the sleep midpoint on weekends in the morning school students. Conversely, in the afternoon school students, night melatonin levels were negatively correlated with the sleep midpoint on weekdays. Cortisol secretion did not correlate with circadian sleep parameters in any of the school time groups. In conclusion, school start time influences melatonin secretion, which correlated with circadian sleep parameters. This correlation depends on the presence of psychiatric symptoms. Our findings emphasize the importance of drawing attention to the influence of school start time on the circadian rhythm of children and adolescents.     

Polyploidy does not control all: Lineage‐specific average chromosome length constrains genome size evolution in ferns

Recent studies investigating the evolution of genome size diversity in ferns have shown that they have a distinctive genome profile compared with other land plants. Ferns are typically characterized by possessing medium‐sized genomes, although a few lineages have evolved very large genomes. Ferns are different from other vascular plant lineages as they are the only group to show evidence for a correlation between genome size and chromosome number. In this study, we aim to explore whether the evolution of fern genome sizes is not only shaped by chromosome number changes arising from polyploidy but also by constraints on the average amount of DNA per chromosome. We selected the genus Asplenium L. as a model genus to study the question because of the unique combination of a highly conserved base chromosome number and a high frequency of polyploidy. New genome size data for Asplenium taxa were combined with existing data and analyzed within a phylogenetic framework. Genome size varied substantially between diploid species, resulting in overlapping genome sizes among diploid and tetraploid spleenworts. The observed additive pattern indicates the absence of genome downsizing following polyploidy. The genome size of diploids varied non‐randomly and we found evidence for clade‐specific trends towards larger or smaller genomes. The 578‐fold range of fern genome sizes have arisen not only from repeated cycles of polyploidy but also through clade‐specific constraints governing accumulation and/or elimination of DNA.     

Pyrosequencing protocol using a universal biotinylated primer for mutation detection and SNP genotyping

DNA sequencing has markedly changed the nature of biomedical research, identifying millions of polymorphisms along the human genome that now require further analysis to study the genetic basis of human diseases. Among the DNA-sequencing platforms available, Pyrosequencing has become a useful tool for medium-throughput single nucleotide polymorphism (SNP) genotyping, mutation detection, copy-number studies and DNA methylation analysis. Its 96-well genotyping format allows reliable results to be obtained at reasonable costs in a few minutes. However, a specific biotinylated primer is usually required for each SNP under study to allow the capture of single-stranded DNA template for the Pyrosequencing assay. Here, we present an alternative to the standard labeling of PCR products for analysis by Pyrosequencing that circumvents the requirement of specific biotinylated primers for each SNP of interest. This protocol uses a single biotinylated primer that is simultaneously incorporated into all M13-tagged PCR products during the amplification reaction. The protocol covers all steps from the PCR amplification and capture of single-stranded template, its preparation, and the Pyrosequencing assay itself. Once the correct primer stoichiometry has been determined, the assay takes around 2 h for PCR amplification, followed by 15-20 min (per plate) to obtain the genotypes.     

Two distinct mechanisms segregate Prospero in the longitudinal glia underlying the timing of interactions with axons

Prospero is required in dividing longitudinal glia (LG) during axon guidance; initially to enable glial division in response to neuronal contact, and subsequently to maintain glial precursors in a quiescent state with mitotic potential. Only Prospero-positive LG respond to neuronal ablation by over-proliferating, mimicking a glial-repair response. Prospero is distributed unequally through the progeny cells of the longitudinal glioblast lineage. Just before axon contact the concentration of Prospero is higher in two of the four progeny cells, and after axon guidance Prospero is present only in six out of ten progeny LG. Here we ask how Prospero is distributed unequally in these two distinct phases. We show that before neuronal contact, longitudinal glioblasts undergo invaginating divisions, perpendicular to the ectodermal layer. Miranda is required to segregate Prospero asymmetrically up to the four glial-progeny stage. After neuronal contact, Prospero is present in only the LG that activate Notch signalling in response to Serrate provided by commissural axons, and Numb is restricted to the glia that do not contain Prospero. As a result of this dual regulation of Prospero deployment, glia are coupled to the formation and maintenance of axonal trajectories.     

Purification of native myosin filaments from muscle

Analysis of the structure and function of native thick (myosin-containing) filaments of muscle has been hampered in the past by the difficulty of obtaining a pure preparation. We have developed a simple method for purifying native myosin filaments from muscle filament suspensions. The method involves severing thin (actin-containing) filaments into short segments using a Ca(2+)-insensitive fragment of gelsolin, followed by differential centrifugation to purify the thick filaments. By gel electrophoresis, the purified thick filaments show myosin heavy and light chains together with nonmyosin thick filament components. Contamination with actin is below 3.5%. Electron microscopy demonstrates intact thick filaments, with helical cross-bridge order preserved, and essentially complete removal of thin filaments. The method has been developed for striated muscles but can also be used in a modified form to remove contaminating thin filaments from native smooth muscle myofibrils. Such preparations should be useful for thick filament structural and biochemical studies.     

Evaluation of bone height in osseous free flap mandible reconstruction: an indirect measure of bone mass

Osseous free flaps have become the preferred method of mandibular reconstruction after oncologic surgical ablation. To elucidate the long-term effects of free flap mandibular reconstruction on bone mass, maintenance or reduction in bone height over time was used as an indirect measure of preservation or loss in bone mass. Factors potentially influencing bone mass preservation were evaluated; these included site of reconstruction (central, body, ramus), patient age, length of follow-up, adjuvant radiotherapy, and the delayed placement of osseointegrated dental implants. A retrospective analysis of patients undergoing osseous free flap mandible reconstruction for oncologic surgical defects between 1987 and 1995 was performed. Postoperative Panorex examinations were used to evaluate bone height and bony union after osteotomy. Fixation hardware was used as a reference to eliminate magnification as a possible source of error in measurement. There were 48 patients who qualified for this study by having at least 24 months of follow-up. There were 27 male and 21 female patients, with a mean age of 45 years (range, 5 to 75 years). Mandibular defects were anterior (24) and lateral (24). Osseous donor sites included the fibula (35), radius (6), scapula (4), and ilium (3). There were between zero and four segmental osteotomies per patient (excluding the ends of the graft). Nineteen percent of all patients had delayed placement of osseointegrated dental implants. Initial Panorex examinations were taken between 1 and 9 months postoperatively (mean, 2 months). Follow-up Panorex examinations were taken 24 to 104 months postoperatively (mean, 47 months). The bony union rate after osteotomy was 97 percent. Bone height measurements were compared by site and type of reconstruction. The mean loss in fibula height by site of reconstruction was 2 percent in central segments, 7 percent in body segments, and 5 percent in ramus segments. The mean loss in bone height after radial free flap mandible reconstruction was 33 percent in central segments and 37 percent in body segments; ramus segments did not lose height. The central and body segments reconstructed with scapular free flaps did not lose height, but one ramus segment lost 20 percent of height. There was no loss in bone height in mandibular body reconstruction with the ilium free flap. Fibula free flaps did not significantly lose bone height when evaluated with respect to age, follow-up, radiation therapy, or dental implant placement. The retention in bone height demonstrated in this study suggests that bone mass is preserved after osseous free flap mandible reconstruction. The greatest amount of bone loss was seen after multiply osteotomized radial free flaps were used for central mandibular reconstruction. The ability of the fibula free flap to maintain mass over time, coupled with its known advantages, further supports its use as the "work horse" donor site for mandible reconstruction.