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.

Population Modeling Integrating Pharmacokinetics, Pharmacodynamics, Pharmacogenetics, and Clinical Outcome in Patients With Sunitinib-Treated Cancer.

The tyrosine kinase inhibitor sunitinib is used as first-line therapy in patients with metastasized renal cell carcinoma (mRCC), given in fixed-dose regimens despite its high variability in pharmacokinetics (PKs). Interindividual variability of drug exposure may be responsible for differences in response. Therefore, dosing strategies based on pharmacokinetic/pharmacodynamic (PK/PD) models may be useful to optimize treatment. Plasma concentrations of sunitinib, its active metabolite SU12662, and the soluble vascular endothelial growth factor receptors sVEGFR-2 and sVEGFR-3, were measured in 26 patients with mRCC within the EuroTARGET project and 21 patients with metastasized colorectal cancer (mCRC) from the C-II-005 study. Based on these observations, PK/PD models with potential influence of genetic predictors were developed and linked to time-to-event (TTE) models. Baseline sVEGFR-2 levels were associated with clinical outcome in patients with mRCC, whereas active drug PKs seemed to be more predictive in patients with mCRC. The models provide the basis of PK/PD-guided strategies for the individualization of anti-angiogenic therapies.

[Pharmacokinetics and pharmacodynamics of antibiotics in intensive care]. / Pharmakokinetik und Pharmakodynamik von Antibiotika in der Intensivmedizin.

Optimized dosage regimens of antibiotics have remained obscure since their introduction. During the last two decades pharmacokinetic(PK)-pharmacodynamic(PD) relationships, originally established in animal experiments, have been increasingly used in patients. The action of betalactams is believed to be governed by the time the plasma concentration is above the minimum inhibitory concentration (MIC). Aminoglycosides act as planned when the peak concentration is a multiple of the MIC and vancomycin seems to work best when the area under the plasma vs. time curve (AUC) to MIC has a certain ratio. Clinicians should be aware that these relationships can only be an indication in which direction dosing should go. Larger studies with sufficiently high numbers of patients and particularly severely sick patients are needed to prove the concepts. In times where all antibiotics can be measured with new technologies, the introduction of therapeutic drug monitoring (TDM) is suggested for ICUs (Intensive Care Unit). The idea of a central lab for TDM of antibiotics such as PEAK (Paul Ehrlich Antibiotika Konzentrationsmessung) is supported.

Obligate asex in a rotifer and the role of sexual signals.

Transitions to asexuality have occurred in many animals and plants, yet the biological mechanisms causing such transitions have often remained unclear. Cyclical parthenogens, such as cladocerans, rotifers or aphids often give rise to obligate asexual lineages. In many rotifers, chemical signals that accumulate during population crowding trigger the induction of sexual stages. In this study, I tested two hypotheses on the origin of obligate parthenogenesis in the rotifer Brachionus calyciflorus: (i) that obligate parthenogens have lost the responsiveness to the sexual signal; and (ii) that obligate parthenogens have lost the ability to produce the sexual signal. Pairwise cross-induction assays among three obligate parthenogenetic strains and two cyclically parthenogenetic (sexual) strains were used to test these hypotheses. I found that obligate parthenogens can induce sexual reproduction in sexual strains, but not vice versa. This demonstrates that obligate parthenogens do still produce the sexual signal, but have lost responsiveness to that signal.

A novel mutation in FGFR-3 disrupts a putative N-glycosylation site and results in hypochondroplasia.

Fibroblast growth factor receptor 3 (FGFR3) is a glycoprotein that belongs to the family of tyrosine kinase receptors. Specific mutations in the FGFR3 gene are associated with autosomal dominant human skeletal disorders such as hypochondroplasia, achondroplasia, and thanatophoric dysplasia. Hypochondroplasia (HCH), the mildest form of this group of short-limbed dwarfism disorders, results in approximately 60% of cases from a mutation in the intracellular FGFR3-tyrosine kinase domain. The remaining cases may either be caused by defects in other FGFR gene regions or other yet unidentified genes. We describe a novel HCH mutation, the first found outside the common mutation hot spot of this condition. This point mutation, an N328I exchange in the extracellular Ig domain III of the receptor, seems to be unique as it affects a putative N-glycosylation site that is conserved between different FGFRs and species. The amino acid exchange itself most probably has no impact on the three-dimensional structure of the receptor domain, suggesting that the phenotype is the result of altered receptor glycosylation and its pathophysiological consequences.

Pediatricians' perceptions and practices regarding childhood obesity.

A 42-item Likert format questionnaire examining pediatricians' perceptions and practices concerning childhood obesity was distributed to a national random sample of 500 physicians. The overall response rate was 68%. The majority of pediatricians believed physicians are obligated to counsel parents of obese children regarding the health risks of obesity (83%), that normal weight is important to the health of children (67%), and that physicians should be role models by maintaining their normal weight (59%). However, 70% of these pediatricians believed designing programs and counseling children about weight loss was difficult, 22% felt competent in prescribing weight loss programs for children, and only 11% agreed that counseling children and parents on weight loss is professionally gratifying. At least one-half of the respondents recommended the following weight loss programs/techniques to their patients: (1) decreasing caloric consumption (84%), (2) seeing a dietitian/nutritionist (78%), (3) joining Weight Watchers (66%), (4) aerobic exercise (60%), and (5) behavior modification programs (55%). These pediatricians received most of their weight control information from medical journals (70%) and past experience (68%). We also assessed belief and attitudes concerning the effect of childhood obesity, the role obesity plays in selected diseases, and the etiology of childhood obesity.

Elementary school principals' perceptions of childhood obesity.

This survey assessed school principals' perceptions regarding childhood obesity and the schools' role in dealing with the problem. A randomly selected group of 300 school principals was obtained from the National Association of Elementary School Principals; 227 (76%) administrators returned the questionnaire. Fifty-one percent of the principals believed normal weight was important to child health. Although 35% believed schools were not doing enough to alleviate childhood obesity, responses suggested principals oppose schools becoming obesity treatment centers. They do not believe teachers or parents would support such programs. They perceived the school's role to be educational and referral in nature. However, they supported elimination of "junk food" machines (71%) and provision of low calorie lunches (60%). They believed school nurses play the most important role in treating childhood obesity at school.

School nurses' perceptions of childhood obesity.

A random sample of 250 nurses from the American School Health Association membership were sent a questionnaire concerning childhood obesity; 88% responded. Most (85%) believed normal weight was important to children's health and that school nurses should be role models by maintaining normal weight (77%). Most also believed counseling children and their parents about weight loss was difficult (71%) and that schools need to do more to alleviate childhood obesity (65%). At least 75% believed all schools should offer a comprehensive health curriculum with units on nutrition and weight control. Likewise, all schools should eliminate "junk food" machines and make special low-calorie lunches available. Only 25% felt competent to prescribe weight loss programs for children, and only 30% found counseling about weight loss professionally gratifying. One-fourth believed, that with proper guidance, children could lose significant amounts of weight or maintain that weight loss. The nurses believed in the importance of normal weight, but appeared skeptical of children's abilities to lose weight as well as their own abilities to provide children with guidance to do so. Finally, they perceived a need for schools to be more active and involved in dealing with childhood obesity.