Comparative analysis reveals within-population genome size variation in a rotifer is driven by large genomic elements with highly abundant satellite DNA repeat elements.

BACKGROUND: Eukaryotic genomes are known to display an enormous variation in size, but the evolutionary causes of this phenomenon are still poorly understood. To obtain mechanistic insights into such variation, previous studies have often employed comparative genomics approaches involving closely related species or geographically isolated populations within a species. Genome comparisons among individuals of the same population remained so far understudied-despite their great potential in providing a microevolutionary perspective to genome size evolution. The rotifer Brachionus asplanchnoidis represents one of the most extreme cases of within-population genome size variation among eukaryotes, displaying almost twofold variation within a geographic population. RESULTS: Here, we used a whole-genome sequencing approach to identify the underlying DNA sequence differences by assembling a high-quality reference genome draft for one individual of the population and aligning short reads of 15 individuals from the same geographic population including the reference individual. We identified several large, contiguous copy number variable regions (CNVs), up to megabases in size, which exhibited striking coverage differences among individuals, and whose coverage overall scaled with genome size. CNVs were of remarkably low complexity, being mainly composed of tandemly repeated satellite DNA with only a few interspersed genes or other sequences, and were characterized by a significantly elevated GC-content. CNV patterns in offspring of two parents with divergent genome size and CNV patterns in several individuals from an inbred line differing in genome size demonstrated inheritance and accumulation of CNVs across generations. CONCLUSIONS: By identifying the exact genomic elements that cause within-population genome size variation, our study paves the way for studying genome size evolution in contemporary populations rather than inferring patterns and processes a posteriori from species comparisons.

Small, but surprisingly repetitive genomes: transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex.

BACKGROUND: The causes and consequences of genome size variation across Eukaryotes, which spans five orders of magnitude, have been hotly debated since before the advent of genome sequencing. Previous studies have mostly examined variation among larger taxonomic units (e.g., orders, or genera), while comparisons among closely related species are rare. Rotifers of the Brachionus plicatilis species complex exhibit a seven-fold variation in genome size and thus represent a unique opportunity to study such changes on a relatively short evolutionary timescale. Here, we sequenced and analysed the genomes of four species of this complex with nuclear DNA contents spanning 110-422 Mbp. To establish the likely mechanisms of genome size change, we analysed both sequencing read libraries and assemblies for signatures of polyploidy and repetitive element content. We also compared these genomes to that of B. calyciflorus, the closest relative with a sequenced genome (293 Mbp nuclear DNA content). RESULTS: Despite the very large differences in genome size, we saw no evidence of ploidy level changes across the B. plicatilis complex. However, repetitive element content explained a large portion of genome size variation (at least 54%). The species with the largest genome, B. asplanchnoidis, has a strikingly high 44% repetitive element content, while the smaller B. plicatilis genomes contain between 14 and 25% repetitive elements. According to our analyses, the B. calyciflorus genome contains 39% repetitive elements, which is substantially higher than previously reported (21%), and suggests that high repetitive element load could be widespread in monogonont rotifers. CONCLUSIONS: Even though the genome sizes of these species are at the low end of the metazoan spectrum, their genomes contain substantial amounts of repetitive elements. Polyploidy does not appear to play a role in genome size variations in these species, and these variations can be mostly explained by changes in repetitive element content. This contradicts the naïve expectation that small genomes are streamlined, or less complex, and that large variations in nuclear DNA content between closely related species are due to polyploidy.

Rates of nucleotide substitution in sexual and anciently asexual rotifers.

The class Bdelloidea of the phylum Rotifera is the largest well studied eukaryotic taxon in which males and meiosis are unknown, and the only one for which these indications of ancient asexuality are supported by cytological and molecular genetic evidence. We estimated the rates of synonymous and nonsynonymous substitutions in the hsp82 heat shock gene in bdelloids and in facultatively sexual rotifers of the class Monogononta, employing distance based and maximum likelihood methods. Relative-rate tests, using acanthocephalan rotifers as an outgroup, showed slightly higher rates of nonsynonymous substitution and slightly lower rates of synonymous substitution in bdelloids as compared with monogononts. The opposite trend, however, was seen in intraclass pairwise comparisons. If, as it seems, bdelloids have evolved asexually, an equality of bdelloid and monogonont substitution rates would suggest that the maintenance of sexual reproduction in monogononts is not attributable to an effect of sexual reproduction in limiting the load of deleterious nucleotide substitutions.

A randomized study of 5-fluorouracil and filtration surgery.

We conducted a randomized study of 26 patients with a poor prognosis undergoing filtration surgery with and without a low dose of 5-fluorouracil. Mean preoperative intraocular pressure (+/- S.E.M.) in the 5-fluorouracil group (n = 14) was 38.4 +/- 3.08 mm Hg; in the control group (n = 12) it was 41.2 +/- 5.0 mm Hg. Mean postoperative intraocular pressure (+/- S.E.M.) at six to 18 months was 14.4 +/- 1.4 mm Hg in the 5-fluorouracil group and 30.7 +/- 3.9 mm Hg in the control group (P less than .01). Of 14 patients in the 5-fluorouracil group, 12 had a successful outcome at 12 months. Of 12 patients in the control group, three had a successful outcome during this same interval.

A prospective, randomized study of 5-fluorouracil and filtration surgery.

Our study shows that use of a small dose of subconjunctival 5-FU provides significantly lower postoperative intraocular pressure than does no antimetabolite treatment. Morphology of the postoperative blebs suggests that increased filtration results in lower intraocular pressure in the 5-FU group. Corneal epithelial defects were as common with a low dose as with higher doses previously described.

Application of a self-tonometer to home tonometry.

Although home tonometry has been advocated in the management and diagnosis of glaucoma, the lack of proper instrumentation has precluded its routine performance. We have developed a self-tonometer that can be used by the patient at home and at work and have evaluated the performance of the instrument under these conditions. The results show that reproducibility of self-tonometer measurements is +/- 1.4 mm Hg and is independent of the user. When the readings of the self-tonometer in a given individual were compared with those of the Goldmann tonometer, they varied by +/- 2.4 mm Hg. Patients who could be trained in the clinic performed well and safely on their own. An average of fewer than five attempts was necessary to obtain four readings at each time of day. Our preliminary findings obtained during home tonometry demonstrated some of the benefits of repeated diurnal curves.

Lens injury following iridotomy with a Q-switched neodymium-YAG laser.

By scanning electron microscopy, we studied eight lenses from eyes that had received a neodymium-YAG laser iridotomy one day prior to elective intracapsular cataract extraction. In some of these cases, pitting lesions were found on the anterior-equatorial lens surface, thereby showing that lenticular damage may occur following this procedure if the iridotomy is applied too centrally. It is recommended that care be taken to ensure that the iridotomy be placed at a site peripheral to the outer circumference of the lens.

Gynaecological laparoscopy: clinical experiences of two anaesthetic techniques.

Two anaesthetic techniques were assessed in 120 fit young women having non-emergency gynaecologial laparoscopy as in-patients. One group breathed halothane spontaneously via a face mask, and the second group were given neuromuscular blocking drugs and ventilation was controlled. There was no significant difference in intraoperative anaesthetic or surgical complications between the two groups although morbidity was greater in the intubated group when assessed 4 h after surgery. After 24 h there was no difference in postoperative morbidity. In an appendix to the study, 40 day-stay patients having the same operation under similar conditions were reviewed. After 24 h abdominal pain, lethargy and weakness were still present; 30% of the patients stated that they would prefer to be admitted overnight for a similar procedure in the future.

Postoperative analgesia for Caesarean section using epidural methadone.

A prospective randomised double blind study was carried out to compare the use of epidural methadone, morphine and bupivacaine for pain relief after Caesarean section. The results indicate that methadone is the most effective agent with few side effects. Subsequently this method was used routinely for postoperative analgesia in all patients undergoing Caesarean section. A retrospective study of 178 patients having this method of analgesia was carried out and indicated that epidural methadone is an effective and safe method of postoperative pain relief.

Acute epiglottitis and severe croup. Experience in two English regions.

The case histories of 50 children who required tracheal intubation for epiglottitis or croup in two English regions have been reviewed. The incidence of severe croup was different in the two regions. The presentation of epiglottitis was variable, and the correct diagnosis was frequently made only at laryngoscopy. Unexpected and rapid deterioration occurred in both diseases, and cyanosis was commonly present on hospital admission and at laryngoscopy. Two children required planned tracheostomy and there were two deaths. The principles of safe management are discussed.

Postoperative analgesia using epidural methadone. Administration by the lumbar route for thoracic pain relief.

The effectiveness of methadone given postoperatively by the lumbar epidural route to patients following upper abdominal or thoracic surgery was assessed. Intermittent injections of methadone diluted in large volumes of normal saline were given during the first 48 hours after surgery. Pain relief was assessed by both the patient and an observer using a visual linear analogue scoring system. Methadone 4-5 mg in 18-20 ml normal provided good postoperative pain relief for 6-8 hours.