The Enterprise,a massive transposon carrying Spok meiotic drive genes

The genomes of eukaryotes are full of parasitic sequences known as transposable elements (TEs). Here, we report the discovery of a putative giant tyrosine-recombinase-mobilized DNA transposon, Enterprise, from the model fungus Podospora anserina. Previously, we described a large genomic feature called the Spok block which is notable due to the presence of meiotic drive genes of the Spok gene family. The Spok block ranges from 110 kb to 247 kb and can be present in at least four different genomic locations within P. anserina, despite what is an otherwise highly conserved genome structure. We propose that the reason for its varying positions is that the Spok block is not only capable of meiotic drive but is also capable of transposition. More precisely, the Spok block represents a unique case where the Enterprise has captured the Spoks, thereby parasitizing a resident genomic parasite to become a genomic hyperparasite. Furthermore, we demonstrate that Enterprise (without the Spoks) is found in other fungal lineages, where it can be as large as 70 kb. Lastly, we provide experimental evidence that the Spok block is deleterious, with detrimental effects on spore production in strains which carry it. This union of meiotic drivers and a transposon has created a selfish element of impressive size in Podospora, challenging our perception of how TEs influence genome evolution and broadening the horizons in terms of what the upper limit of transposition may be.

Transposable elements (TEs) are major agents of change in eukaryotic genomes. Their ability to selfishly parasitize their host replication machinery has large impacts on both genome size and on gene regulation (Chénais et al. 2012). In extreme cases, TEs can contribute up to 85% of genomic content (Schnable et al. 2009), and expansion and reduction of TEs can result in rapid changes in both genome size and architecture (Haas et al. 2009; Möller and Stukenbrock 2017; Talla et al. 2017). Generally, TEs have small sizes (∼50–12,000 bp) and accomplish these large-scale changes through their sheer number. For example, there are ∼1.1 million Alu elements in the human genome, which have had a large impact on genome evolution (Jurka 2004; Bennett et al. 2008). The largest known cases among Class I retrotransposons are long terminal repeat (LTR) elements that can be as large as 30 kb, but among Class II DNA transposons, Mavericks/Polintons are known to grow as large as 40 kb through the capture of additional open reading frames (ORFs) (Arkhipova and Yushenova 2019). Recently, a behemoth TE named Teratorn was described in teleost fish; it can be up to 182 kb in length, dwarfing all other known TEs. Teratorn has achieved this impressive size by fusing a piggyBac DNA transposon with a herpesvirus, thereby blurring the line between TEs and viruses (Inoue et al. 2017, 2018). Truly massive transposons may be lurking in the depths of many eukaryotic genomes, but the limitations of short-read genome sequencing technologies and the lack of population-level high-quality assemblies may make them difficult to identify.The Spok block is a large genomic feature that was first identified thanks to the presence of the spore killing (Spok) genes in species from the genus Podospora (Grognet et al. 2014; Vogan et al. 2019). The Spoks are selfish genetic elements that bias their transmission to the next generation in a process known as meiotic drive. Here, drive occurs by inducing the death of spores that do not inherit them, through a single protein that operates as both a toxin and an antidote (Grognet et al. 2014; Vogan et al. 2019). The first Spok gene described, Spok1, was discovered in Podospora comata (Grognet et al. 2014). In P. anserina, the homologous gene Spok2 is found at high population frequencies, whereas two other genes of the Spok family, Spok3 and Spok4, are at low to intermediate frequencies (Vogan et al. 2019). Unlike Spok1 and Spok2, however, Spok3 and Spok4 are always associated with a large genomic region (the Spok block). The Spok block can be located at different chromosomal locations in different individuals but is never found more than once in natural strains. The number of Spok genes and the location of the Spok block (which carries Spok3, Spok4, or both) define the overall meiotic driver behavior of a given genome, which can be classified into the so-called Podospora spore killers or Psks (van der Gaag et al. 2000; Vogan et al. 2019). The Spok block stands out not only because of its size, typically around 150 kb, but also because there is otherwise high genome collinearity among strains of P. anserina and with the related species P. comata and P. pauciseta (Vogan et al. 2019).The fact that the Spok block is found at unique genomic positions between otherwise highly similar strains is of prime interest as each novel Spok block position creates a unique meiotic drive type (Psk) due to the intricacies of meiosis in Podospora (Vogan et al. 2019). We therefore set out to determine the mechanism through which the Spok block relocates throughout the genome. Additionally, we annotated the gene content of the various Spok blocks to describe their composition and understand what represents the minimal component of the Spok block. Lastly, we conducted fitness assays to investigate whether the presence of the Spok block imparts any detrimental effects upon the host.     

Epidemiologic characteristics of death by poisoning in 1991-2001 in Korea

The purpose of this study was to investigate the epidemiologic characteristics of the death by poisoning in Korea. We recoded the Death Certificates Database by injury based on the short version of the International Classification of External Causes of Injuries (ICECI). We evaluated the mortality rate by total injury and poisoning, and analyzed the mortality rate by age, gender, year and month, toxic agent, and intent. Adjusted odds ratios were calculated to evaluate the effects of socioeconomic factors on suicidal poisoning death. The total number of death cases by injury was 346,656. The proportion of death cases by injury decreased from 13.53% of all death cases in 1991 to 11.89% in 2001. However, the mortality rate by poisoning increased rapidly from 1998, and then remained stable. The number of suicidal poisoning deaths has gradually increased, and its mortality rate was 6.41 (per 100,000) in 2001. Major toxic agents were pesticides and herbicides (50.90%) in 2001. Adjusted odds ratios of suicidal poisoning versus other poisonings showed significant differences in education attainment, region, and marital status. In conclusion, the mortality rate by poisoning has increased, and the proportion of suicidal poisoning also has increased compared to that of accidental poisoning.     

Effect of resin hydrophilicity and water storage on resin strength

This study evaluated the change in the ultimate tensile strength (UTS) of five polymerised resin blends of increasing hydrophilicity, after ageing in distilled water or silicon oil. Resin blocks were prepared from each resin blend by dispensing the uncured resin into a flexible, embedding mould, containing multiple cavities. The resins were polymerised in the moulds under nitrogen at 551.6 kPa and light-activated at 125 degrees C for 10 min. After dry ageing for 24 h at 37 degrees C, the middle third of each resin specimen was trimmed into an 'I' shape. Fifteen control specimens were randomly selected from each resin blend for baseline UTS evaluation. The UTS of the experimental specimens were determined after 1, 3, 6 and 12 months of ageing in water or oil. The UTS of each group of resins at different storage periods in water or oil were analysed using the Friedman multiple ANOVA on ranks and Dunn's multiple comparison tests at 95% confidence level. Significant reduction (p < 0.01) in UTS was observed in Groups II-V resins after 12-month storage in water, while the most hydrophobic Group I resin showed no significant change (p > 0.05) in the same period. The percentage reduction in UTS increased with the hydrophilicity of the resin blends. Long-term water storage of hydrophilic resin blends such as those employed in dentine adhesives, resulted in a marked reduction in their mechanical strength that may compromise the durability of resin-dentine bonds.     

Sleep and daytime sleepiness in retinitis pigmentosa patients

OBJECTIVE: We examined sleep, daytime sleepiness and the ability to stay awake during the day in patients affected with retinitis pigmentosa (RP), to further delineate the role of photoreceptors in the circadian cycle. METHODS: Twelve individuals diagnosed with RP (40 +/- 8 years) And 12 normally sighted healthy individuals (39 +/- 7 years) matched for age, body mass index (BMI) and sex were selected for the study. Participants had their sleep recorded on two consecutive nights and were monitored on the two following days. On the first day, their ability to stay awake and on the second, their sleep propensity were assessed using the Maintenance of Wakefulness Test (MWT) and the Multiple Sleep Latency Test (MSLT), respectively. Self-report measures were obtained using the Pittsburgh Sleep Quality Index (PSQI), the Epworth Sleepiness Scale (ESS), and the Toronto Hospital Alertness Test (THAT). RESULTS: Subjective daytime sleepiness (ESS: 9 +/- 5 vs. 6 +/- 4, P=0.053) and objectively measured sleep propensity (MSLT: 10 +/- 5 vs. 17 +/- 3 min, P < 0.000) were significantly higher in RP patients than controls, whilst their alertness (THAT: 29 +/- 9 vs. 38 +/- 7, P=0.016) and ability to stay awake (MWT: 21 +/- 9 vs. 29 +/- 2 min, P=0.006) were significantly reduced. Retinitis pigmentosa participants had more disturbed nighttime sleep, with significantly more awakenings (arousal index: 14 +/- 8 vs. 8 +/- 6 h, P=0.039), and tended to have less rapid eye movement (REM) sleep (19 +/- 5 vs. 22 +/- 3%, P=0.094). CONCLUSION: Patients with RP have increased daytime sleepiness, reduced alertness and more disturbed nighttime sleep of poorer quality than their normally sighted counterparts, suggesting an influence of photoreceptor degeneration on the circadian cycle.     

p53 codon 72 polymorphism and risk of cervical carcinoma in Korean women

A common polymorphism of the wild type p53 is known at codon 72 of exon 4, with 2 alleles encoding either arginine (CGC, p53Arg) or proline (CCC, p53Pro). A recent study suggested that this polymorphism affects the susceptibility of p53 protein to human papillomavirus E6 oncoprotein mediated degradation and that individuals homozygous for p53Arg are seven times more susceptible to HPV-associated carcinogenesis of the cervix than heterozygotes. To examine whether the p53Arg genotype could be a risk factor for HPV-associated cervical carcinomas in the Korean population, we analyzed the p53 codon 72 polymorphism status of HPV-positive invasive cervical carcinomas from 52 Korean women and 103 healthy control samples. The proportion of individuals homozygous for p53Arg, homozygous for p53Pro, and heterozygous for the two alleles were 40%, 19%, and 41% in normal healthy controls; 42%, 17%, and 40% in women with HPV-positive invasive cervical carcinoma. There were no significant differences in the distribution of p53 genotypes between controls and cervical carcinomas. This finding indicates that the p53Arg genotype is not associated with an increased susceptibility to cervical carcinoma in Korean women.     

Aperture maneuver with compelled breath (AMC) for moving tumors: a feasibility study with a moving phantom

Respiration causes target motion, which is known to be one of the technical bottlenecks in radiotherapy, especially for stereotactic radio-surgery and intensity modulated radiotherapy (IMRT). To overcome this problem, aperture maneuver with compelled breath (AMC) has been developed. In order to simulate compelled respiratory motion, a moving phantom using a ventilator was designed. As the air flow was forced to the bellows, which simulates the lungs, by a ventilator, a film connected to the ventilator moved like the respiratory target motion. A software was developed to transfer multileaf collimator motion from breathless to actual periodic breathing conditions. Static fields as well as step-and-shoot IMRT fields were modified in accordance with moving shapes to follow the target position, using the software with the controlled breathing information. Film dosimetry for a small field and for IMRT fields with a moving phantom was performed. To evaluate clinical implementation, five healthy volunteers were tested to breathe through a ventilator, and all of them could adapt the compelled breath without any difficulties. Additive margins for a moving target with AMC were not larger than 3 mm for respiratory organ motions up to 18 mm, while those with the static beam were 9 mm. For IMRT fields, large discrepancies were present between a static target and a moving target with the static beam, while they coincided well with AMC. Clinical acceptable differences between the dose distributions from a static target with the static beam and from a moving target with AMC revealed that this technique could be applied clinically.     

Methods for derivation of human embryonic stem cells

The expanded blastocysts, developed from 2PN-stage embryos, are generally divided into three categories: a good blastocyst containing a large and distinguishable inner cell mass (ICM), a blastocyst with a small and distinct ICM, and a blastocyst with a poorly defined ICM. In this study, we introduce methods for the derivation of human embryonic stem cells (hESCs) depending on the quality of the blastocysts. An immunosurgical method was used for the good expanded blastocysts. This method, however, raises the probability of ICM loss in cases of hESC derivation from blastocysts with smaller or indistinct ICMs. Furthermore, this method is also associated with a risk of the contamination of the hESCs with animal pathogens. To overcome these shortcomings, the partial- or whole-embryo culture method was used. For blastocysts with no visible ICM, the whole-embryo culture method was used to establish hESCs via the seeding of the entire blastocyst without its zona pellucida directly on a STO feeder layer. However, trophectodermal overgrowth tends to hinder the expansion of the ICM during the initial steps of hESC derivation. Therefore, the partial-embryo culture method was developed to establish hESCs from blastocysts with smaller ICMs. The surgical isolation of the region containing the ICM with an ultra-fine glass pipette alleviates trophectoderm overgrowth. This method is also applicable to blastocysts with large and distinct ICMs, and the efficiency of this method is comparable to that of the immunosurgical method.     

Hydrogen peroxide-induced phospholipase D2 activation in lymphocytic leukemic L1210 cells

Extracellular hydrogen peroxide (H2O2) has been implicated in the activation of phospholipase D (PLD). However, it was still unclear how this activation occurs and what the molecular identity of the H2O2-stimulated PLD isozyme is. This study shows that H2O2 potently increases the PLD activity in mouse lymphocytic leukemic L1210 cells, which contain exclusively PLD2. In addition, H2O2 increased PLD activity only in PLD2-transfected COS-7 cells and not in PLD1-transfected cells. This suggests that PLD2 is selectively activated by H2O2. Depletion of extracellular Ca2+ with EGTA completely blocked the H2O2-induced PLD activation, indicating that Ca2+ influx is required. Moreover, pretreatment of the cells with the protein kinase C (PKC) inhibitors GF-109203X and RO-31-8220 and down-regulation of PKCalpha by prolonged treatment with 4beta-phorbol 12-myristate 13-acetate inhibited the H2O2-stimulated PLD2 activity, which points to the involvement of PKCalpha. Based on these new findings we suggest that PLD2 activity is specifically up-regulated by H2O2 and that the H2O2-induced PLD2 activation is mediated by Ca2+ influx and PKCalpha activation.     

Evaluation of surface and build-up region dose for intensity-modulated radiation therapy in head and neck cancer

Despite much development, there remains dosimetric uncertainty in the surface and build-up regions in intensity-modulated radiation therapy treatment plans for head and neck cancers. Experiments were performed to determine the dosimetric discrepancies in the surface and build-up region between the treatment planning system (TPS) prediction and experimental measurement using radiochromic film. A head and neck compression film phantom was constructed from two semicylindrical solid water slabs. Treatment plans were generated using two commercial TPSs (PINNACLE3 and CORVUS) for two cases, one with a shallow (approximately 0.5 cm depth) target and another with a deep (approximately 6 cm depth) target. The plans were evaluated for a 54 Gy prescribed dose. For each case, two pieces of radiochromic film were used for dose measurement. A small piece of film strip was placed on the surface and another was inserted within the phantom. Overall, both TPSs showed good agreement with the measurement. For the shallow target case, the dose differences were within +/- 300 cGy (5.6% with respect to the prescribed dose) for PINNACLE3 and +/- 240 cGy (4.4%) for CORVUS in 90% of the region of interest. For the deep target case, the dose differences were +/- 350 (6.5%) for PINNACLE3 and +/- 260 cGy (4.8%) for CORVUS in 90% of the region of interest. However, it was found that there were significant discrepancies from the surface to about 0.2 cm in depth for both the shallow and deep target cases. It was concluded that both TPSs overestimated the surface dose for both shallow and deep target cases. The amount of overestimation ranges from 400 to 1000 cGy (approximately 7.4% to 18.5% with respect to the prescribed dose, 5400 cGy).