Ultra-Rare Genetic Variation in the Epilepsies : A Whole-Exome Sequencing Study of 17,606 Individuals

Sequencing-based studies have identified novel risk genes associated with severe epilepsies and revealed an excess of rare deleterious variation in less-severe forms of epilepsy. To identify the shared and distinct ultra-rare genetic risk factors for different types of epilepsies, we performed a whole-exome sequencing (WES) analysis of 9,170 epilepsy-affected individuals and 8,436 controls of European ancestry. We focused on three phenotypic groups: severe developmental and epileptic encephalopathies (DEEs), genetic generalized epilepsy (GGE), and non-acquired focal epilepsy (NAFE). We observed that compared to controls, individuals with any type of epilepsy carried an excess of ultra-rare, deleterious variants in constrained genes and in genes previously associated with epilepsy; we saw the strongest enrichment in individuals with DEEs and the least strong in individuals with NAFE. Moreover, we found that inhibitory GABA(A) receptor genes were enriched for missense variants across all three classes of epilepsy, whereas no enrichment was seen in excitatory receptor genes. The larger gene groups for the GABAergic pathway or cation channels also showed a significant mutational burden in DEEs and GGE. Although no single gene surpassed exome-wide significance among individuals with GGE or NAFE, highly constrained genes and genes encoding ion channels were among the lead associations; such genes included CACNAIG, EEF1A2, and GABRG2 for GGE and LGI1, TRIM3, and GABRG2 for NAFE. Our study, the largest epilepsy WES study to date, confirms a convergence in the genetics of severe and less-severe epilepsies associated with ultra-rare coding variation, and it highlights a ubiquitous role for GABAergic inhibition in epilepsy etiology.Peer reviewe

Anaerobiosis revisited: growth of Saccharomyces cerevisiae under extremely low oxygen availability

The budding yeast Saccharomyces cerevisiae plays an important role in biotechnological applications, ranging from fuel ethanol to recombinant protein production. It is also a model organism for studies on cell physiology and genetic regulation. Its ability to grow under anaerobic conditions is of interest in many industrial applications. Unlike industrial bioreactors with their low surface area relative to volume, ensuring a complete anaerobic atmosphere during microbial cultivations in the laboratory is rather difficult. Tiny amounts of O2 that enter the system can vastly influence product yields and microbial physiology. A common procedure in the laboratory is to sparge the culture vessel with ultrapure N2 gas; together with the use of butyl rubber stoppers and norprene tubing, O2 diffusion into the system can be strongly minimized. With insights from some studies conducted in our laboratory, we explore the question ‘how anaerobic is anaerobiosis?’. We briefly discuss the role of O2 in non-respiratory pathways in S. cerevisiae and provide a systematic survey of the attempts made thus far to cultivate yeast under anaerobic conditions. We conclude that very few data exist on the physiology of S. cerevisiae under anaerobiosis in the absence of the anaerobic growth factors ergosterol and unsaturated fatty acids. Anaerobicity should be treated as a relative condition since complete anaerobiosis is hardly achievable in the laboratory. Ideally, researchers should provide all the details of their anaerobic set-up, to ensure reproducibility of results among different laboratories. A correction to this article is available online at http://eprints.whiterose.ac.uk/131930/ https://doi.org/10.1007/s00253-018-9036-

Intrapartum transperineal ultrasound assessment of fetal head progression in active second stage of labor and mode of delivery

OBJECTIVE: To compare longitudinal changes in angle of progression (AoP) and midline angle (MLA) during the active second stage of labor according to the mode of delivery. METHODS: A three-dimensional transperineal ultrasound volume was acquired in a series of nulliparous women at the beginning of the active second stage (T1) and every 20 min thereafter (T2, T3, T4, T5 and T6). Following delivery, all ultrasound volumes were analyzed and AoP and MLA were measured. RESULTS: Among 71 women included in the study, 58 underwent spontaneous vaginal delivery (group A) and 13 underwent operative delivery (group B) (eight by vacuum extraction and five by Cesarean section). When compared with Group B, Group A had a wider AoP only at T1 (140.0 +/- 20.2 degrees vs. 122.9 +/- 16.7 degrees ; P = 0.010) and T2 (149.7 +/- 20.7 degrees vs. 126.9 +/- 17.5 degrees ; P = 0.006). MLA was narrower in group A only at T3 (21.2 +/- 11.7 degrees vs. 40.8 +/- 27.9 degrees ; P = 0.043), T4 (18.2 +/- 15.0 degrees vs. 47.4 +/- 29.6 degrees ; P = 0.020) and T5 (18.3 +/- 6.0 degrees vs. 34.7 +/- 4.2 degrees ; P = 0.034). On stepwise forward multiple logistic regression analysis, both AoP and MLA were independently associated with operative delivery (OR = 0.955 and OR = 1.018, respectively). CONCLUSION: Ultrasonographic assessment of fetal head descent in the second stage of labor may play a role in the prediction of the mode of delivery

A first insight into peach [Prunus persica (L.) Batsch] SNP variability

Three factors may have reduced the diversity at both individual gene and whole genome levels in cultivated peach: its self-compatible mating system, the narrow genetic basis of most commercial cultivars, and the recent strong selection towards agronomically interesting traits. Previous diversity analyses with markers such as simple sequence repeats (SSRs) have revealed low levels of genetic variability. Here, we sequenced 23 genome-wide distributed DNA fragments in 47 occidental peach varieties, also observing reduced variability levels. On average, there was one single nucleotide polymorphism (SNP) every 598 bp and one indel every 4,189 bp. As expected, variability was higher in non-coding than in coding regions (one SNP every 390 non-coding bp versus one in 1,850 bp in coding DNA). In general, SNPs were observed at relatively high frequency, mean minor allele frequency = 0.225, meaning that a large proportion of the SNPs discovered by sequencing similar germplasm will be useful for other purposes, such as association mapping. The average heterozygosity of the varieties was 0.28, with a low correlation between SSR and SNP heterozygosity. The whole sequence of two candidate genes, a pectate lyase 1 candidate for fruit firmness (CGPAA2668) and a sucrose synthase 1 candidate for sugar content (CGPPB6189), in the 47 varieties revealed that they both may have suffered a process of balancing selection.This research was funded in part by Projects AGL2009-07305/AGR and by the Consolider-Ingenio 2010 Program (CSD2007-00036), both from the Spanish Ministry of Science and Innovation, and by the ISAFRUIT Integrated Project. The ISAFRUIT Project was funded by the European Commission under Thematic Priority 5—Food Quality and Safety of the 6th Framework Programme of RTD (Contract No. FP6-FOOD-CT-2006-016279).Peer reviewe