Application of a CAGE method to an avian development study

© Springer Science+Business Media LLC 2017. Cap analysis of gene expression (CAGE) is a convenient approach for genome-wide identification of promoter regions at single base-pair resolution level and accurate expression estimation of the corresponding transcripts. Depending on the initial biomaterial amount and sequencing technology, different computational pipelines for data processing are available, as well as variations of the CAGE protocol that improve sensitivity and accuracy. Therefore, this chapter elucidates the key steps of sample preparation, sequencing, and data analysis via an example of a promoter expression estimation study in chicken development. We also describe the applicability of this approach for studying other avian and reptilian species

The horizontal root fractures. Diagnosis, clinical management and three-year follow-up

Objective: The aim of this retrospective analysis is to describe and to evaluate the middle third horizontal root fractures, long term clinical management results and to estimate the effect of treatments factors upon healing and survival rate. Methods: Our clinical study included 42 patients presenting a middle third horizontal root fracture in permanent dentition. For each patient at t the parameters recorded were: diastasis, mobility, sensibility, periodontal inflammation, pulpal pathology, associated fracture and dislocation of the coronal fragment. The follow-up was performed after 6 (t1), 12 (t2) and 36 (t3) months after the trauma, both clinically and radiologically. Clinical examination, vitality tests and a radiological evaluation (periapical x-ray) were performed. Results: At t0 it was observed: diastasis (14, 3%), mobility (28, 6%), thermal sensibility (61, 9%), periodontal inflammation (4, 8%), pulpal pathology (38, 1%) and dislocation of the coronal fragment (47, 6%) of the patients. The treatment plan started with the coronal fragment repositioning and the blockage (splint) with the adjacent teeth in 47, 6% of cases. A root canal treatment was performed at t in 52,4% of the fractured teeth. Statistical analysis showed the highest level of significance between pulpal lesions (t) and associated fractures. The mobility, sensibility and pulpar lesions parameters, showed a reduction in relation to the follow up timing, with a main variation remarkably evident between t and t1. The ratio between observation time and the presence of diastasis was statistically significant. Conclusion: The analysis of the clinical results exhibits the high success rate of a conservative approach in the treatment of teeth fractured in the middle third of the root

Reactivity of Cortical Alpha Rhythms to Eye Opening in Mild Cognitive Impairment and Alzheimer's Disease: an EEG Study.

2010 Oct 7. [Epub ahead of print

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

The international Functional Annotation Of the Mammalian Genomes 4 (FANTOM4) research collaboration set out to better understand the transcriptional network that regulates macrophage differentiation and to uncover novel components of the transcriptome employing a series of high-throughput experiments. The primary and unique technique is cap analysis of gene expression (CAGE), sequencing mRNA 5′-ends with a second-generation sequencer to quantify promoter activities even in the absence of gene annotation. Additional genome-wide experiments complement the setup including short RNA sequencing, microarray gene expression profiling on large-scale perturbation experiments and ChIP-chip for epigenetic marks and transcription factors. All the experiments are performed in a differentiation time course of the THP-1 human leukemic cell line. Furthermore, we performed a large-scale mammalian two-hybrid (M2H) assay between transcription factors and monitored their expression profile across human and mouse tissues with qRT-PCR to address combinatorial effects of regulation by transcription factors. These interdependent data have been analyzed individually and in combination with each other and are published in related but distinct papers. We provide all data together with systematic annotation in an integrated view as resource for the scientific community (http://fantom.gsc.riken.jp/4/). Additionally, we assembled a rich set of derived analysis results including published predicted and validated regulatory interactions. Here we introduce the resource and its update after the initial releas

Methylome of human skeletal muscle after acute & chronic resistance exercise training, detraining & retraining

DNA methylation is an important epigenetic modification that can regulate gene expression following environmental encounters without changes to the genetic code. Using Infinium MethylationEPIC BeadChip Arrays (850,000 CpG sites) we analysed for the first time, DNA isolated from untrained human skeletal muscle biopsies (vastus lateralis) at baseline (rest) and immediately following an acute (single) bout of resistance exercise. In the same participants, we also analysed the methylome following a period of muscle growth (hypertrophy) evoked via chronic (repeated bouts-3 sessions/wk) resistance exercise (RE) (training) over 7-weeks, followed by complete exercise cessation for 7-weeks returning muscle back to baseline levels (detraining), and finally followed by a subsequent 7-week period of RE-induced hypertrophy (retraining). These valuable methylome data sets described in the present manuscript and deposited in an open-access repository can now be shared and re-used to enable the identification of epigenetically regulated genes/ networks that are modified after acute anabolic stimuli and hypertrophy, and further investigate the phenomenon of epigenetic memory in skeletal muscle

Football players do not show "neural efficiency" in cortical activity related to visuospatial information processing during football scenes: an EEG mapping study

This study tested the hypothesis of cortical neural efficiency (i.e., reduced brain activation in experts) in the visuospatial information processing related to football (soccer) scenes in football players. Electroencephalographic data were recorded from 56 scalp electrodes in 13 football players and eight matched non-players during the observation of 70 videos with football actions lasting 2.5 s each. During these videos, the central fixation target changed color from red to blue or vice versa. The videos were watched two times. One time, the subjects were asked to estimate the distance between players during each action (FOOTBALL condition, visuospatial). Another time, they had to estimate if the fixation target was colored for a longer time in red or blue color (CONTROL condition, non-visuospatial). The order of the two conditions was pseudo-randomized across the subjects. Cortical activity was estimated as the percent reduction in power of scalp alpha rhythms (about 8-12 Hz) during the videos compared with a pre-video baseline (event-related desynchronization, ERD). In the FOOTBALL condition, a prominent and bilateral parietal alpha ERD (i.e., cortical activation) was greater in the football players than non-players (p < 0.05) in contrast with the neural efficiency hypothesis. In the CONTROL condition, no significant alpha ERD difference was observed. No difference in behavioral response time and accuracy was found between the two groups in any condition. In conclusion, a prominent parietal cortical activity related to visuospatial processes during football scenes was greater in the football players over controls in contrast with the neural efficiency hypothesis

Sleep deprivation and Modafinil affect cortical sources of resting state electroencephalographic rhythms in healthy young adults

Objective: It has been reported that sleep deprivation affects the neurophysiological mechanisms underpinning the vigilance. Here, we tested the following hypotheses in the PharmaCog project (www.pharmacog.org): (i) sleep deprivation may alter posterior cortical delta and alpha sources of resting state eyes-closed electroencephalographic (rsEEG) rhythms in healthy young adults; (ii) after the sleep deprivation, a vigilance enhancer may recover those rsEEG source markers. Methods: rsEEG data were recorded in 36 healthy young adults before (Pre-sleep deprivation) and after (Post-sleep deprivation) one night of sleep deprivation. In the Post-sleep deprivation, these data were collected after a single dose of PLACEBO or MODAFINIL. rsEEG cortical sources were estimated by eLORETA freeware. Results: In the PLACEBO condition, the sleep deprivation induced an increase and a decrease in posterior delta (2–4 Hz) and alpha (8–13 Hz) source activities, respectively. In the MODAFINIL condition, the vigilance enhancer partially recovered those source activities. Conclusions: The present results suggest that posterior delta and alpha source activities may be both related to the regulation of human brain arousal and vigilance in quiet wakefulness. Significance: Future research in healthy young adults may use this methodology to preselect new symptomatic drug candidates designed to normalize brain arousal and vigilance in seniors with dementia