MeDIP-seq and nCpG analyses illuminate sexually dimorphic methylation of gonadal development genes with high historic methylation in turtle hatchlings with temperature-dependent sex determination

Background

DNA methylation alters gene expression but not DNA sequence and mediates some cases of phenotypic plasticity. Temperature-dependent sex determination (TSD) epitomizes phenotypic plasticity where environmental temperature drives embryonic sexual fate, as occurs commonly in turtles. Importantly, the temperature-specific transcription of two genes underlying gonadal differentiation is known to be induced by differential methylation in TSD fish, turtle and alligator. Yet, how extensive is the link between DNA methylation and TSD remains unclear. Here we test for broad differences in genome-wide DNA methylation between male and female hatchling gonads of the TSD painted turtle Chrysemys picta using methyl DNA immunoprecipitation sequencing, to identify differentially methylated candidates for future study. We also examine the genome-wide nCpG distribution (which affects DNA methylation) in painted turtles and test for historic methylation in genes regulating vertebrate gonadogenesis.

Results

Turtle global methylation was consistent with other vertebrates (57% of the genome, 78% of all CpG dinucleotides). Numerous genes predicted to regulate turtle gonadogenesis exhibited sex-specific methylation and were proximal to methylated repeats. nCpG distribution predicted actual turtle DNA methylation and was bimodal in gene promoters (as other vertebrates) and introns (unlike other vertebrates). Differentially methylated genes, including regulators of sexual development, had lower nCpG content indicative of higher historic methylation.

Conclusions

Ours is the first evidence suggesting that sexually dimorphic DNA methylation is pervasive in turtle gonads (perhaps mediated by repeat methylation) and that it targets numerous regulators of gonadal development, consistent with the hypothesis that it may regulate thermosensitive transcription in TSD vertebrates. However, further research during embryogenesis will help test this hypothesis and the alternative that instead, most differential methylation observed in hatchlings is the by-product of sexual differentiation and not its cause.

Electronic supplementary material

The online version of this article (doi:10.1186/s13072-017-0136-2) contains supplementary material, which is available to authorized users.

Transcriptomic responses to environmental temperature by turtles with temperature-dependent and genotypic sex determination assessed by RNAseq inform the genetic architecture of embryonic gonadal development

Vertebrate sexual fate is decided primarily by the individual's genotype (GSD), by the environmental temperature during development (TSD), or both. Turtles exhibit TSD and GSD, making them ideal to study the evolution of sex determination. Here we analyze temperature-specific gonadal transcriptomes (RNA-sequencing validated by qPCR) of painted turtles (Chrysemys picta TSD) before and during the thermosensitive period, and at equivalent stages in soft-shell turtles (Apalone spinifera-GSD), to test whether TSD's and GSD's transcriptional circuitry is identical but deployed differently between mechanisms. Our data show that most elements of the mammalian urogenital network are active during turtle gonadogenesis, but their transcription is generally more thermoresponsive in TSD than GSD, and concordant with their sex-specific function in mammals [e.g., upregulation of Amh, Ar, Esr1, Fog2, Gata4, Igf1r, Insr, and Lhx9 at male-producing temperature, and of β-catenin, Foxl2, Aromatase (Cyp19a1), Fst, Nf-kb, Crabp2 at female-producing temperature in Chrysemys]. Notably, antagonistic elements in gonadogenesis (e.g., β-catenin and Insr) were thermosensitive only in TSD early-embryos. Cirbp showed warm-temperature upregulation in both turtles disputing its purported key TSD role. Genes that may convert thermal inputs into sex-specific development (e.g., signaling and hormonal pathways, RNA-binding and heat-shock) were differentially regulated. Jak-Stat, Nf-κB, retinoic-acid, Wnt, and Mapk-signaling (not Akt and Ras-signaling) potentially mediate TSD thermosensitivity. Numerous species-specific ncRNAs (including Xist) were differentially-expressed, mostly upregulated at colder temperatures, as were unannotated loci that constitute novel TSD candidates. Cirbp showed warm-temperature upregulation in both turtles. Consistent transcription between turtles and alligator revealed putatively-critical reptilian TSD elements for male (Sf1, Amh, Amhr2) and female (Crabp2 and Hspb1) gonadogenesis. In conclusion, while preliminary, our data helps illuminate the regulation and evolution of vertebrate sex determination, and contribute genomic resources to guide further research into this fundamental biological process.

The Role of Skin Hardness, Thickness, and Sensory Loss on Standing Foot Power in the Development of Plantar Ulcers in Patients with Diabetes Mellitus—A Preliminary Study

This article presents the results of a study on patients with diabetic neuropathy to find the relationships between the foot pressures characterized by power ratio (PR), foot sole hardness (Shore values), and foot sole soft tissue thickness. The results showed that the increase in PR values for diabetic patients in the upper sensation loss levels (S = 7.5 to 10 g) compared to the corresponding increase in lower sensation loss (S=3 to 4.5 g)were of the order of 5 times in the lateralheel and big toe, respectively, and 4 times in the first metatarsal head regions. The increase in PR values for diabetic patients in the upper Shore value regions (30 to 40) compared to the corresponding increase in lower Shore value regions (20 to 30) were of the order of 3.4 times in lateral heel and 2.4, 2.0, and 2.3 times in the first, second, and lateral metatarsal head regions, respectively. At sites contiguous to frank ulcers for foot sole hardness (Shore values of 50) at sensation level > 10 g PR was as high as 59, and foot sole thickness values were also greater than the corresponding normal values. The study shows all measured parameters may play a part in the development of plantar ulcers.

Electrochemical Sensor Based on Fe Doped Hydroxyapatite-Carbon Nanotubes Composite for L-Dopa Detection in the Presence of Uric Acid

A novel amperometric sensor based on iron doped hydroxyapatite (Fe-HA) and multiwalled carbon nanotubes (CNT) composite immobilized on a glassy carbon electrode (GCE) has been fabricated. The hybrid composite made of Fe-HA nanoparticles and CNT promotes electron transfer kinetics between the analyte levodopa (L-dopa) and the modified GC electrode. Under optimum conditions, the fabricated sensor gave a linear response range of 1.0 x 10(-7)-1.1 x 10(-6) M with the detection limit as low as 62 nM. The Fe-HA/CNT modified electrode showed good selectivity towards the determination of L-dopa in the presence of ascorbic acid (AA), uric acid (UA) and other common interferents. The sensor displays a high sensitivity, good reproducibility and long-term stability and it was successfully applied for the detection of L-dopa in pharmaceutical and medicinal plant samples.

Long-term results of percutaneous balloon valvuloplasty of congenital aortic stenosis in adolescents and young adults

Balloon aortic valvuloplasty (BAV) is a well accepted modality of treatment in congenital aortic stenosis in all age groups. Although in infants and children it is the modality of choice, in adolescents and young adults, it is of debatable efficacy.

AIM

To evaluate long-term results of aortic valvuloplasty particularly in adolescent and adults (>12 years) and compare the outcome in other age groups that are <1 year and between 1 are 11 years.

SETTING

Tertiary referral center.

PATIENTS

165 consecutive patients treated at the median age of 9 years (1 day to 64 years). The follow-up was up to 14 years (median 3 years). The whole cohort was divided into 3 age-based subgroups: Group A (<1 year) n=45, Group B (1 year-11 years) n=52, and Group C (>12 years) n=68. The characteristics of each subgroup were mutually compared.

INTERVENTION

Percutaneous balloon valvuloplasty with mean (SD) balloon to annulus ratio of 0.93. Main outcome measures were repeat BAV, significant aortic regurgitation (AR), and aortic valve replacement/repair.

RESULTS

The incidence of significant AR from the whole cohort was 9.9% (8% moderate, 1.9% severe); n=16. Group A=significant AR 9.5% (7.1% moderate, 2.4% severe), Group B=significant AR 11.3% (9.4% moderate, 1.9% severe), and Group C=significant AR 9% (7.5% moderate, 1.5% severe); p value=0.99 (Group C vs Group A) and 0.92 (Group C vs Group B). Repeat BAV rate was 13.3% (n=22 out of 165 patients). Group A - n=5 (11.9%), Group B - n=10 (18.2%), and Group C - n=7 (10.3%). p Value=0.78 (C vs A) and 0.19 (C vs B). Surgery in follow-up was needed in n=4 (2.4%), none in Group A, 2 patients in Group B (3.6%), and 2 patients in group C (2.9%). Patients were followed up for a period of 14 years; Group A=up to 8 years, Group B=up to 13 years, and Group C=up to 14 years. Mean survival probability after the procedure was 8 years (Group A=6.5 years, Group B=8.1 years, and Group C=9.9 years), and p value=0.49 (A vs B), 0.23 (B vs C), and 0.4 (A vs C).

CONCLUSION

There is no statistical difference in the long-term outcome in the adults and adolescents as compared to the children; thus BAV remains an obvious treatment of choice with good long-term outcome.

Use of ADO II device in a large aorto-pulmonary collateral -an interesting case

A 11month old girl was diagnosed to have a large aorto pulmonary collateral during evaluation for respiratory distress and seizures. Echocardiographic evaluation showed a large collateral from the descending aorta to left lung with ventricular dysfunction (left ventricular ejection fraction of 40%). This was confirmed on computed tomography angiogram (CT) scan. The collateral was closed with Amplatzer Ductal Occluder II device under fluoroscopic guidance. To the best of our knowledge, this is the first reported case of large aorto-pulmonary collateral closed successfully with an Amplatzer Ductal Occluder II device.

Physical Mapping and Refinement of the Painted Turtle Genome (Chrysemys picta) Inform Amniote Genome Evolution and Challenge Turtle-Bird Chromosomal Conservation

Comparative genomics continues illuminating amniote genome evolution, but for many lineages our understanding remains incomplete. Here, we refine the assembly (CPI 3.0.3 NCBI AHGY00000000.2) and develop a cytogenetic map of the painted turtle (Chrysemys picta-CPI) genome, the first in turtles and in vertebrates with temperature-dependent sex determination. A comparison of turtle genomes with those of chicken, selected nonavian reptiles, and human revealed shared and novel genomic features, such as numerous chromosomal rearrangements. The largest conserved syntenic blocks between birds and turtles exist in four macrochromosomes, whereas rearrangements were evident in these and other chromosomes, disproving that turtles and birds retain fully conserved macrochromosomes for greater than 300 Myr. C-banding revealed large heterochromatic blocks in the centromeric region of only few chromosomes. The nucleolar-organizing region (NOR) mapped to a single CPI microchromosome, whereas in some turtles and lizards the NOR maps to nonhomologous sex-chromosomes, thus revealing independent translocations of the NOR in various reptilian lineages. There was no evidence for recent chromosomal fusions as interstitial telomeric-DNA was absent. Some repeat elements (CR1-like, Gypsy) were enriched in the centromeres of five chromosomes, whereas others were widespread in the CPI genome. Bacterial artificial chromosome (BAC) clones were hybridized to 18 of the 25 CPI chromosomes and anchored to a G-banded ideogram. Several CPI sex-determining genes mapped to five chromosomes, and homology was detected between yet other CPI autosomes and the globally nonhomologous sex chromosomes of chicken, other turtles, and squamates, underscoring the independent evolution of vertebrate sex-determining mechanisms.

Embedded tooth fragment masquerading as keloid for 11 months

A foreign body retained in the skin can originate from numerous sources and most of the time these foreign bodies are removed without any sequelae. The present article reports a case of persistent swelling in the lower lip misdiagnosed as keloid, which later turned out to be an embedded tooth fragment identified post spontaneous extrusion after 11 months.