Isolation and sequencing of a single copy of an introgressed chromosome from a complex genome for gene and SNP identification.

KEY MESSAGE: This manuscript describes the identification, isolation and sequencing of a single chromosome containing high value resistance genes from a complex polyploid where sequencing the whole genome is too costly. The large complex genomes of many crops constrain the use of new technologies for genome-assisted selection and genetic improvement. One method to simplify a genome is to break it into individual chromosomes by flow cytometry; however, in many crop species most chromosomes cannot be isolated individually. Flow sorting of a single copy of a chromosome has been developed in wheat, and here we demonstrate its use to identify markers of interest in an Erianthus/Sacchurum hybrid. Erianthus/Saccharum hybrids are of interest because Erianthus is known to be highly resistant to soil borne diseases which cause extensive sugarcane yield losses in Australia. Sugarcane (Saccharum) cultivars are autopolyploids with a highly complex genome and over 100 chromosomes. Flow cytometry for sugarcane, as in most crops, does not resolve individual chromosomes to a karyotype peak for sorting. To isolate a single chromosome, we used genomic in situ hybridization (GISH) to identify the flow karyotype region containing the Erianthus chromosomes, flow sorted single chromosomes from this region, PCR screened for the Erianthus chromosomes and sequenced them. One Erianthus chromosome amplified and sequenced well, and from this data we could identify 57 resistant type genes and SNPs in nearly half of these genes. We developed KASP SNP assays and demonstrated that the identified SNP markers segregated as expected in a small introgression population. The pipeline we developed here to flow sort and sequence single chromosomes could be used in any crop with a large complex genome to rapidly discover and develop markers to important loci.

A linkage disequilibrium-based approach to position unmapped SNPs in crop species.

BACKGROUND: High-density SNP arrays are now available for a wide range of crop species. Despite the development of many tools for generating genetic maps, the genome position of many SNPs from these arrays is unknown. Here we propose a linkage disequilibrium (LD)-based algorithm to allocate unassigned SNPs to chromosome regions from sparse genetic maps. This algorithm was tested on sugarcane, wheat, and barley data sets. We calculated the algorithm's efficiency by masking SNPs with known locations, then assigning their position to the map with the algorithm, and finally comparing the assigned and true positions. RESULTS: In the 20-fold cross-validation, the mean proportion of masked mapped SNPs that were placed by the algorithm to a chromosome was 89.53, 94.25, and 97.23% for sugarcane, wheat, and barley, respectively. Of the markers that were placed in the genome, 98.73, 96.45 and 98.53% of the SNPs were positioned on the correct chromosome. The mean correlations between known and new estimated SNP positions were 0.97, 0.98, and 0.97 for sugarcane, wheat, and barley. The LD-based algorithm was used to assign 5920 out of 21,251 unpositioned markers to the current Q208 sugarcane genetic map, representing the highest density genetic map for this species to date. CONCLUSIONS: Our LD-based approach can be used to accurately assign unpositioned SNPs to existing genetic maps, improving genome-wide association studies and genomic prediction in crop species with fragmented and incomplete genome assemblies. This approach will facilitate genomic-assisted breeding for many orphan crops that lack genetic and genomic resources.

Strategies and considerations for implementing genomic selection to improve traits with additive and non-additive genetic architectures in sugarcane breeding.

KEY MESSAGE: Simulations highlight the potential of genomic selection to substantially increase genetic gain for complex traits in sugarcane. The success rate depends on the trait genetic architecture and the implementation strategy. Genomic selection (GS) has the potential to increase the rate of genetic gain in sugarcane beyond the levels achieved by conventional phenotypic selection (PS). To assess different implementation strategies, we simulated two different GS-based breeding strategies and compared genetic gain and genetic variance over five breeding cycles to standard PS. GS scheme 1 followed similar routines like conventional PS but included three rapid recurrent genomic selection (RRGS) steps. GS scheme 2 also included three RRGS steps but did not include a progeny assessment stage and therefore differed more fundamentally from PS. Under an additive trait model, both simulated GS schemes achieved annual genetic gains of 2.6-2.7% which were 1.9 times higher compared to standard phenotypic selection (1.4%). For a complex non-additive trait model, the expected annual rates of genetic gain were lower for all breeding schemes; however, the rates for the GS schemes (1.5-1.6%) were still greater than PS (1.1%). Investigating cost-benefit ratios with regard to numbers of genotyped clones showed that substantial benefits could be achieved when only 1500 clones were genotyped per 10-year breeding cycle for the additive genetic model. Our results show that under a complex non-additive genetic model, the success rate of GS depends on the implementation strategy, the number of genotyped clones and the stage of the breeding program, likely reflecting how changes in QTL allele frequencies change additive genetic variance and therefore the efficiency of selection. These results are encouraging and motivate further work to facilitate the adoption of GS in sugarcane breeding.

Improved genomic prediction of clonal performance in sugarcane by exploiting non-additive genetic effects.

KEY MESSAGE: Non-additive genetic effects seem to play a substantial role in the expression of complex traits in sugarcane. Including non-additive effects in genomic prediction models significantly improves the prediction accuracy of clonal performance. In the recent decade, genetic progress has been slow in sugarcane. One reason might be that non-additive genetic effects contribute substantially to complex traits. Dense marker information provides the opportunity to exploit non-additive effects in genomic prediction. In this study, a series of genomic best linear unbiased prediction (GBLUP) models that account for additive and non-additive effects were assessed to improve the accuracy of clonal prediction. The reproducible kernel Hilbert space model, which captures non-additive genetic effects, was also tested. The models were compared using 3,006 genotyped elite clones measured for cane per hectare (TCH), commercial cane sugar (CCS), and Fibre content. Three forward prediction scenarios were considered to investigate the robustness of genomic prediction. By using a pseudo-diploid parameterization, we found significant non-additive effects that accounted for almost two-thirds of the total genetic variance for TCH. Average heterozygosity also had a major impact on TCH, indicating that directional dominance may be an important source of phenotypic variation for this trait. The extended-GBLUP model improved the prediction accuracies by at least 17% for TCH, but no improvement was observed for CCS and Fibre. Our results imply that non-additive genetic variance is important for complex traits in sugarcane, although further work is required to better understand the variance component partitioning in a highly polyploid context. Genomics-based breeding will likely benefit from exploiting non-additive genetic effects, especially in designing crossing schemes. These findings can help to improve clonal prediction, enabling a more accurate identification of variety candidates for the sugarcane industry.

Accuracy of genomic prediction of complex traits in sugarcane.

KEY MESSAGE: Complex traits in sugarcane can be accurately predicted using genome-wide DNA markers. Genomic single-step prediction is an attractive method for genomic selection in commercial breeding programs. Sugarcane breeding programs have achieved up to 1% genetic gain in key traits such as tonnes of cane per hectare (TCH), commercial cane sugar (CCS) and Fibre content over the past decades. Here, we assess the potential of genomic selection to increase the rate of genetic gain for these traits by deriving genomic estimated breeding values (GEBVs) from a reference population of 3984 clones genotyped for 26 K SNP. We evaluated the three different genomic prediction approaches GBLUP, genomic single step (GenomicSS), and BayesR. GenomicSS combining pedigree and SNP information from historic and recent breeding programs achieved the most accurate predictions for most traits (0.3-0.44). This method is attractive for routine genetic evaluation because it requires relatively little modification to the existing evaluation and results in breeding value estimates for all individuals, not only those genotyped. Adding information from early-stage trials added up to 5% accuracy for CCS and Fibre, but 0% for TCH, reflecting the importance of competition effects for TCH. These GEBV accuracies are sufficiently high that, combined with the right breeding strategy, a doubling of the rate of genetic gain could be achieved. We also assessed the flowering traits days to flowering, gender and pollen viability and found high heritabilities of 0.57, 0.78 and 0.72, respectively. The GEBV accuracies indicated that genomic selection could be used to improve these traits. This could open new avenues for breeders to manage their breeding programs, for example, by synchronising flowering time and selecting males with high pollen viability.

Persistent myopathy despite release of partial obstruction: in vivo reversal of dysfunction and transcriptional responses using rapamycin.

Current and potential medical therapy for obstruction-induced myopathic bladder dysfunction (from benign prostatic hyperplasia or posterior urethral valves) focuses on symptoms. The persistent tissue pathology and dysfunction after release of obstruction is often deemed irreversible without any systematic therapeutic approaches. As rapamycin can attenuate bladder smooth muscle hypertrophy and dysfunction during the genesis of partial obstruction in vivo, we tested whether rapamycin could improve persistent function after release of obstruction (de-obstruction or REL). Female Sprague-Dawley rat bladders were partially obstructed (PBO) by suturing around both the urethra and a para-urethral steel rod, then removing the rod. One day prior to release of obstruction (preREL), voiding parameters and residual urine volume of preREL+future rapa, preREL+future veh groups were recorded. Release of obstruction (REL) was performed by suture removal following 6 weeks of PBO. For 4 more weeks after the de-obstruction, REL animals were randomized to rapamycin (REL+rapa) or vehicle (REL+veh). PBO for 6 weeks were used as positive controls. In shams, the urethra was exposed, but no suture tied. Voiding parameters and residual urine volume were measured prior to sacrifice of sham and REL+veh or REL+rapa, and PBO. Rapamycin efficacy was tested by pair-wise comparison of changes in individual voiding data from preREL+future veh or preREL+future rapa versus REL+veh or REL+rapa, respectively, as well as by comparisons of REL+veh to REL+rapa groups. Bladders were weighed and processed for a high-throughput QPCR array, and histopathology. Bladder/body mass ratios with PBO increased significantly and remained higher in the release phase in REL+veh animals. REL+rapa versus REL+veh improved residual volumes and micturition fractions toward sham levels. Three genes encoding extracellular proteins, BMP2, SOD3, and IGFBP7, correlated with functional improvement by Pearson's correlations. The promoters of these genes showed enrichment for several motifs including circadian E-boxes. While obstruction and REL augmented CLOCK and NPAS2 expression above sham levels, rapamycin treatment during release significantly blocked their expression. This experimental design of pharmaco-intervention during the de-obstruction phase revealed a novel pathway dysregulated during the clinically relevant treatment phase of obstructive bladder myopathy.

Sugarcane Smut, Caused by Sporisorium scitamineum, a Major Disease of Sugarcane: A Contemporary Review.

Sugarcane smut caused by the fungus Sporisorium scitamineum is one of the major diseases of sugarcane worldwide, causing significant losses in productivity and profitability of this perennial crop. Teliospores of this fungus are airborne, can travel long distances, and remain viable in hot and dry conditions for >6 months. The disease is easily recognized by its long whiplike sorus produced on the apex or side shoots of sugarcane stalks. Each sorus can release ≤100 million teliospores in a day; the spores are small (≤7.5 µ) and light and can survive in harsh environmental conditions. The airborne teliospores are the primary mode of smut spread around the world and across cane-growing regions. The most effective method of managing this disease is via resistant varieties. Because of the complex genomic makeup of sugarcane, selection for resistant traits is difficult in sugarcane breeding programs. In recent times, the application of molecular markers as a rapid tool of discarding susceptible genotypes early in the selection program has been investigated. Large effect resistance loci have been identified and have the potential to be used for marker-assisted selection to increase the frequency of resistant breeding lines in breeding programs. Recent developments in omics technologies (genomics, transcriptomics, proteomics, and metabolomics) have contributed to our understanding and provided insights into the mechanism of resistance and susceptibility. This knowledge will further our understanding of smut and its interactions with sugarcane genotypes and aid in the development of durable resistant varieties.

DNA Methylation Reduces the Yes-Associated Protein 1/WW Domain Containing Transcription Regulator 1 Pathway and Prevents Pathologic Remodeling during Bladder Obstruction by Limiting Expression of BDNF.

Chronic bladder obstruction and bladder smooth muscle cell (SMC) stretch provide fibrotic and mechanical environments that can lead to epigenetic change. Therefore, we examined the role of DNA methylation in bladder pathology and transcriptional control. Sprague-Dawley female rats underwent partial bladder obstruction by ligation of a silk suture around the proximal urethra next to a 0.9-mm steel rod. Sham operation comprised passing the suture around the urethra. After 2 weeks, rats were randomized to normal saline or DNA methyltransferase inhibitor, 5-aza-2-deoxycytidine (DAC) at 1 mg/kg, three times/week intraperitoneally. After 6 weeks, bladders were weighed and divided for histology and RNA analysis by high-throughput real-time quantitative PCR arrays. DAC treatment during obstruction in vivo profoundly augmented brain-derived neurotrophic factor (BDNF) expression compared with the obstruction with vehicle group, which was statistically correlated with pathophysiologic parameters. BDNF, cysteine rich angiogenic inducer 61 (CYR61), and connective tissue growth factor (CTGF) expression clustered tightly together using Pearson's correlation analysis. Their promoters were associated with the TEA domain family member 1 (TEAD1) and Yes-associated protein 1/WW domain containing transcription regulator 1 pathways. Interestingly, DAC treatment increased BDNF expression in bladder SMCs (P < 0.0002). Stretch-induced BDNF was inhibited by the YAP/WWTR1 inhibitor verteporfin. Verteporfin improved the SMC phenotype (proliferative markers and SMC marker expression), in part by reducing BDNF. Expression of BDNF is limited by DNA methylation and associated with pathophysiologic changes during partial bladder outlet obstruction and SMC phenotypic change in vitro.

Acetazolamide potentiates the anti-tumor potential of HDACi, MS-275, in neuroblastoma.

BACKGROUND: Neuroblastoma (NB), a tumor of the primitive neural crest, despite aggressive treatment portends a poor long-term survival for patients with advanced high stage NB. New treatment strategies are required. METHODS: We investigated coordinated targeting of essential homeostatic regulatory factors involved in cancer progression, histone deacetylases (HDACs) and carbonic anhydrases (CAs). RESULTS: We evaluated the antitumor potential of the HDAC inhibitor (HDACi), pyridylmethyl-N-{4-[(2-aminophenyl)-carbamoyl]-benzyl}-carbamate (MS-275) in combination with a pan CA inhibitor, acetazolamide (AZ) on NB SH-SY5Y, SK-N-SH and SK-N-BE(2) cells. The key observation was that the combination AZ + MS-275 significantly inhibited growth, induced cell cycle arrest and apoptosis, and reduced migration capacity of NB cell line SH-SY5Y. In addition, this combination significantly inhibited tumor growth in vivo, in a pre-clinical xenograft model. Evidence was obtained for a marked reduction in tumorigenicity and in the expression of mitotic, proliferative, HIF-1α and CAIX. NB xenografts of SH-SY5Y showed a significant increase in apoptosis. CONCLUSION: MS-275 alone at nanomolar concentrations significantly reduced the putative cancer stem cell (CSC) fraction of NB cell lines, SH-SY5Y and SK-N-BE(2), in reference to NT2/D1, a teratocarcinoma cell line, exhibiting a strong stem cell like phenotype in vitro. Whereas stemness genes (OCT4, SOX2 and Nanog) were found to be significantly downregulated after MS-275 treatment, this was further enhanced by AZ co-treatment. The significant reduction in initial tumorigenicity and subsequent abrogation upon serial xenografting suggests potential elimination of the NB CSC fraction. The significant potentiation of MS-275 by AZ is a promising therapeutic approach and one amenable for administration to patients given their current clinical utility.

Do youth with type 1 diabetes exercise safely? A focus on patient practices and glycemic outcomes.

OBJECTIVE: Insulin adjustments have been shown to reduce glycemic excursions during and after exercise, but little is known about their use in youth with type 1 diabetes (T1D). We aimed to assess practices in youth with T1D around exercise, assess factors that influence practices, and examine associations between key behaviors and glycemic outcomes. RESEARCH DESIGN AND METHODS: We developed the 'Type 1 Diabetes Report of Exercise Practices Survey (T1D-REPS)' and piloted this tool in 100 youth with T1D on an insulin pump. Participants completed a 3-day physical activity recall and 30 days of pump/glucose data were collected. Chart review was conducted for key clinical measures. RESULTS: Eighty-four percent of participants modified their insulin regimen around exercise; only 40% reported adjusting prandial insulin immediately before exercise while 68% reported some modification (suspension or decrease) of basal insulin during exercise. Following exercise, only 10% reported reducing overnight basal insulin. Those who performed ≥ 5 glucose checks/day adjusted basal insulin during exercise more frequently than those with fewer daily glucose checks (33% vs. 13%, p = 0.05, chi-squared = 3.7), and were more likely to report decreasing insulin dose for the bedtime snack following exercise (50% vs. 17%, p = 0.004, chi-squared = 8.2). CONCLUSIONS: Despite several studies showing the frequency of hypoglycemia during and after exercise, many youth are not adjusting insulin for exercise. A tool designed to capture patient practices and provide clinicians with a framework for patient education may lead to improved safety around exercise in youth with T1D.

Using quantitative PCR with retrotransposon-based insertion polymorphisms as markers in sugarcane.

Sugarcane is the main source of the world's sugar and is becoming increasingly important as a source of biofuel. The highly polyploid and heterozygous nature of the sugarcane genome has meant that characterization of the genome has lagged behind that of other important crops. Here we developed a method using a combination of quantitative PCR with a transposable marker system to score the relative number of alleles with a transposable element (TE) present at a particular locus. We screened two genera closely related to Saccharum (Miscanthus and Erianthus), wild Saccharum, traditional cultivars, and 127 modern cultivars from Brazilian and Australian breeding programmes. We showed how this method could be used in various ways. First, we showed that the method could be extended to be used as part of a genotyping system. Secondly, the history of insertion and timing of the three TEs examined supports our current understanding of the evolution of the Saccharum complex. Thirdly, all three TEs were found in only one of the two main lineages leading to the modern sugarcane cultivars and are therefore the first TEs identified that could potentially be used as markers for Saccharum spontaneum.

Local receptors as novel regulators for peripheral clock expression.

Mammalian circadian control is determined by a central clock in the brain suprachiasmatic nucleus (SCN) and synchronized peripheral clocks in other tissues. Increasing evidence suggests that SCN-independent regulation of peripheral clocks also occurs. We examined how activation of excitatory receptors influences the clock protein PERIOD 2 (PER2) in a contractile organ, the urinary bladder. PERIOD2::LUCIFERASE-knock-in mice were used to report real-time PER2 circadian dynamics in the bladder tissue. Rhythmic PER2 activities occurred in the bladder wall with a cycle of ∼ 24 h and peak at ∼ 12 h. Activation of the muscarinic and purinergic receptors by agonists shifted the peak to an earlier time (7.2 ± 2.0 and 7.2 ± 0.9 h, respectively). PER2 expression was also sensitive to mechanical stimulation. Aging significantly dampened PER2 expression and its response to the agonists. Finally, muscarinic agonist-induced smooth muscle contraction also exhibited circadian rhythm. These data identified novel regulators, endogenous receptors, in determining local clock activity, in addition to mediating the central control. Furthermore, the local clock appears to reciprocally align receptor activity to circadian rhythm for muscle contraction. The interaction between receptors and peripheral clock represents an important mechanism for maintaining physiological functions and its dysregulation may contribute to age-related organ disorders.

Insertion/deletion polymorphisms in the ΔNp63 promoter are a risk factor for bladder exstrophy epispadias complex.

Bladder exstrophy epispadias complex (BEEC) is a severe congenital anomaly; however, the genetic and molecular mechanisms underlying the formation of BEEC remain unclear. TP63, a member of TP53 tumor suppressor gene family, is expressed in bladder urothelium and skin over the external genitalia during mammalian development. It plays a role in bladder development. We have previously shown that p63(-/-) mouse embryos developed a bladder exstrophy phenotype identical to human BEEC. We hypothesised that TP63 is involved in human BEEC pathogenesis. RNA was extracted from BEEC foreskin specimens and, as in mice, ΔNp63 was the predominant p63 isoform. ΔNp63 expression in the foreskin and bladder epithelium of BEEC patients was reduced. DNA was sequenced from 163 BEEC patients and 285 ethnicity-matched controls. No exon mutations were detected. Sequencing of the ΔNp63 promoter showed 7 single nucleotide polymorphisms and 4 insertion/deletion (indel) polymorphisms. Indel polymorphisms were associated with an increased risk of BEEC. Significantly the sites of indel polymorphisms differed between Caucasian and non-Caucasian populations. A 12-base-pair deletion was associated with an increased risk with only Caucasian patients (p = 0.0052 Odds Ratio (OR) = 18.33), whereas a 4-base-pair insertion was only associated with non-Caucasian patients (p = 0.0259 OR = 4.583). We found a consistent and statistically significant reduction in transcriptional efficiencies of the promoter sequences containing indel polymorphisms in luciferase assays. These findings suggest that indel polymorphisms of the ΔNp63 promoter lead to a reduction in p63 expression, which could lead to BEEC.

A comprehensive genetic map of sugarcane that provides enhanced map coverage and integrates high-throughput Diversity Array Technology (DArT) markers.

BACKGROUND: Sugarcane genetic mapping has lagged behind other crops due to its complex autopolyploid genome structure. Modern sugarcane cultivars have from 110-120 chromosomes and are in general interspecific hybrids between two species with different basic chromosome numbers: Saccharum officinarum (2n = 80) with a basic chromosome number of 10 and S. spontaneum (2n = 40-128) with a basic chromosome number of 8. The first maps that were constructed utilised the single dose (SD) markers generated using RFLP, more recent maps generated using AFLP and SSRs provided at most 60% genome coverage. Diversity Array Technology (DArT) markers are high throughput allowing greater numbers of markers to be generated. RESULTS: Progeny from a cross between a sugarcane variety Q165 and a S. officinarum accession IJ76-514 were used to generate 2467 SD markers. A genetic map of Q165 was generated containing 2267 markers, These markers formed 160 linkage groups (LGs) of which 147 could be placed using allelic information into the eight basic homology groups (HGs) of sugarcane. The HGs contained from 13 to 23 LGs and from 204 to 475 markers with a total map length of 9774.4 cM and an average density of one marker every 4.3 cM. Each homology group contained on average 280 markers of which 43% were DArT markers 31% AFLP, 16% SSRs and 6% SNP markers. The multi-allelic SSR and SNP markers were used to place the LGs into HGs. CONCLUSIONS: The DArT array has allowed us to generate and map a larger number of markers than ever before and consequently to map a larger portion of the sugarcane genome. This larger number of markers has enabled 92% of the LGs to be placed into the 8 HGs that represent the basic chromosome number of the ancestral species, S. spontaneum. There were two HGs (HG2 and 8) that contained larger numbers of LGs verifying the alignment of two sets of S. officinarum chromosomes with one set of S. spontaneum chromosomes and explaining the difference in basic chromosome number between the two ancestral species. There was also evidence of more complex structural differences between the two ancestral species.

Comparative mapping in the Poaceae family reveals translocations in the complex polyploid genome of sugarcane.

BACKGROUND: The understanding of sugarcane genetics has lagged behind that of other members of the Poaceae family such as wheat, rice, barley and sorghum mainly due to the complexity, size and polyploidization of the genome. We have used the genetic map of a sugarcane cultivar to generate a consensus genetic map to increase genome coverage for comparison to the sorghum genome. We have utilized the recently developed sugarcane DArT array to increase the marker density within the genetic map. The sequence of these DArT markers plus SNP and EST-SSR markers was then used to form a bridge to the sorghum genomic sequence by BLAST alignment to start to unravel the complex genomic architecture of sugarcane. RESULTS: Comparative mapping revealed that certain sugarcane chromosomes show greater levels of synteny to sorghum than others. On a macrosyntenic level a good collinearity was observed between sugarcane and sorghum for 4 of the 8 homology groups (HGs). These 4 HGs were syntenic to four sorghum chromosomes with from 98% to 100% of these chromosomes covered by these linked markers. Four major chromosome rearrangements were identified between the other four sugarcane HGs and sorghum, two of which were condensations of chromosomes reducing the basic chromosome number of sugarcane from x = 10 to x = 8. This macro level of synteny was transferred to other members within the Poaceae family such as maize to uncover the important evolutionary relationships that exist between sugarcane and these species. CONCLUSIONS: Comparative mapping of sugarcane to the sorghum genome has revealed new information on the genome structure of sugarcane which will help guide identification of important genes for use in sugarcane breeding. Furthermore of the four major chromosome rearrangements identified in this study, three were common to maize providing some evidence that chromosome reduction from a common paleo-ancestor of both maize and sugarcane was driven by the same translocation events seen in both species.

Reduced flow after tubularized incised plate urethroplasty--increased fibrogenesis, elastin fiber loss or neither?

PURPOSE: Low urinary flow rates are common after tubularized incised plate urethroplasty but the etiology remains unclear and may be related to low urethral compliance due to abnormal collagen concentrations and/or fewer elastic fibers in the healed urethral plate. We hypothesized that inserting a preputial mucosal graft over the dorsal raw area after the midline incision may avoid scarring and improve urethral compliance. MATERIALS AND METHODS: Adult rabbits were submitted to tubularized incised plate urethroplasty with or without inlay preputial graft according to a previously described protocol. Tissular concentrations of collagens I, III, IV, VI, VIII and XIII were measured. Histomorphometric analysis was used to quantify elastic fibers in the urethra. Tubularized incised plate urethroplasty with and without inlay preputial graft was compared to normal rabbit urethras (controls). RESULTS: mRNA concentrations for collagens I, II and XIII were similar between controls and operated rabbits. The proportions between collagens I and III were 1.05, 0.87 and 1.21, respectively, in controls and animals undergoing tubularized incised plate urethroplasty with and without inlay preputial graft. mRNA concentrations for collagen IV and collagens VI/VIII tended to be higher and lower, respectively, in the operated urethras, despite showing statistical significance only for collagen VIII in animals undergoing tubularized incised plate urethroplasty with inlay preputial graft vs controls (p=0.02). The operated animals did not demonstrate a reduced number of elastic fibers in the urethral tissues compared to controls. CONCLUSIONS: Elastic fiber number and distribution were similar between tubularized incised plate urethroplasty cases and controls, suggesting that decreased concentrations of elastic fibers do not explain the reduced urethral compliance after tubularized incised plate urethroplasty. The raw area determined by the dorsal urethral incision regenerated after standard tubularized incised plate urethroplasty, while cicatrization with fibrosis occurred in correspondence to the grafted areas after tubularized incised plate urethroplasty with inlay preputial graft.

Rapamycin attenuates bladder hypertrophy during long-term outlet obstruction in vivo: tissue, matrix and mechanistic insights.

PURPOSE: Previous molecular studies showed that the mTOR inhibitor rapamycin prevents bladder smooth muscle hypertrophy in vitro. We investigated the effect of rapamycin treatment in vivo on bladder smooth muscle hypertrophy in a rat model of partial bladder outlet obstruction. MATERIALS AND METHODS: A total of 48 female Sprague-Dawley® rats underwent partial bladder outlet obstruction and received daily subcutaneous injections of rapamycin (1 mg/kg) or vehicle commencing 2 weeks postoperatively. A total of 36 rats underwent sham surgery and received rapamycin or vehicle. Rats were sacrificed 3, 6 and 12 weeks after surgery. Before sacrifice, voiding was observed in a metabolic cage for 24 hours. Bladder-to-body weight in gm bladder weight per kg body weight and post-void residual urine were assessed. We evaluated Col1a1, Col3a1, Eln and Mmp7 mRNA expression and histology. Two-factor ANOVA and the post hoc t test were applied. RESULTS: Bladder outlet obstruction caused a significant increase in bladder weight in all obstructed groups. Three weeks postoperatively (1 week of treatment) there was no difference in the bladder-to-body weight ratio in the obstructed group. However, at 6 and 12 weeks (4 and 10 weeks of treatment, respectively) the bladder-to-body weight ratio of rats with obstruction plus rapamycin was significantly lower than that of rats with obstruction plus vehicle. Post-void residual urine volume after 6 and 12 weeks of obstruction was lower in obstructed rats with rapamycin compared to that in obstructed rats with vehicle. Rapamycin decreased the obstruction induced expression of Col1a1, Col3a1, Eln and Mmp7. CONCLUSIONS: Rapamycin prevents mechanically induced hypertrophy in cardiovascular smooth muscle. In vivo mTOR inhibition may attenuate obstruction induced detrusor hypertrophy and help preserve bladder function.

EZH2 and matrix co-regulate phenotype and KCNB2 expression in bladder smooth muscle cells.

BACKGROUND: Partial bladder outlet obstruction (PBO) is a widespread cause of urinary dysfunction and patient discomfort, resulting in immense health care costs. Previously, we found that obstruction is associated with altered regulation of epigenetic machinery and altered function. Here we examined if PBO and chronic bladder obstructive disease (COBD) affect epigenetic marks in a proof of principle gene and explored mechanisms of its epigenetic regulation using in vitro models. METHODS: Archival obstruction tissues from COBD had been created in 200-250 g female Sprague-Dawley rats by surgical ligation of the urethra for 6 weeks, followed by removal of the suture and following animals for 6 more weeks. Obstruction (PBO) is the 6-week ligation only. Sham ligations comprise passing the suture behind the urethra. Histone3 lysine27 trimethylation (H3K27me3) was studied by immunostaining and Chromatin immunoprecipitation (ChIP)/PCR. The interaction of matrix with KCNB2 regulation was studied in human bladder SMC plated on damaged matrix and native collagen and treated with vehicle or UNC1999. Cells were analyzed by immunostaining for cell phenotype, and western blotting for KCNB2, H3K27me3 and EZH2. Effects of conditioned media from these cells were also examined on cell phenotype. siRNA against KCNB2 was examined for effects on cell phenotype and gene expression by RT-qPCR. RESULTS: H3K27me3 increased by immunofluorescence during PBO, and by ChIP/PCR during COBD in the CpG Island (CGI) as well as 350 bp upstream. Obstruction vs. sham also showed an increase in H3K27me3 deposition. In SMC in vitro, EZH2 inhibition restored KCNB2 expression and partially restored SMC phenotype. CONCLUSIONS: Regulation of KCNB2 at the promoter demonstrated dynamic changes in H3K27me3 during COBD and obstruction. In vitro models suggest that matrix plays a role in regulation of EZH2, H3K27me3 and KCNB2, which may play a role in the regulation of smooth muscle phenotype in vivo.

Spontaneous urinary bladder regeneration after subtotal cystectomy increases YAP/WWTR1 signaling and downstream BDNF expression: Implications for smooth muscle injury responses.

Rodents have the capacity for spontaneous bladder regeneration and bladder smooth muscle cell (BSMC) migration following a subtotal cystectomy (STC). YAP/WWTR1 and BDNF (Brain-derived neurotrophic factor) play crucial roles in development and regeneration. During partial bladder outlet obstruction (PBO), excessive YAP/WWTR1 signaling and BDNF expression increases BSMC hypertrophy and dysfunction. YAP/WWTR1 and expression of BDNF and CYR61 were examined in models of regeneration and wound repair. Live cell microscopy was utilized in an ex vivo model of STC to visualize cell movement and division. In Sprague-Dawley female rats, STC was performed by resection of the bladder dome sparing the trigone, followed by closure of the bladder. Smooth muscle migration and downstream effects on signaling and expression were also examined after scratch wound of BSMC with inhibitors of YAP and BDNF signaling. Sham, PBO and incision (cystotomy) were comparators for the STC model. Scratch wound in vitro increased SMC migration and expression of BDNF, CTGF and CYR61 in a YAP/WWTR1-dependent manner. Inhibition of YAP/WWTR1 and BDNF signaling reduced scratch-induced migration. BDNF and CYR61 expression was elevated during STC and PBO. STC induces discrete genes associated with endogenous de novo cell regeneration downstream of YAP/WWTR1 activation.

Optimising clonal performance in sugarcane: leveraging non-additive effects via mate-allocation strategies.

Mate-allocation strategies in breeding programs can improve progeny performance by harnessing non-additive genetic effects. These approaches prioritise predicted progeny merit over parental breeding value, making them particularly appealing for clonally propagated crops such as sugarcane. We conducted a comparative analysis of mate-allocation strategies, exploring utilising non-additive and heterozygosity effects to maximise clonal performance with schemes that solely consider additive effects to optimise breeding value. Using phenotypic and genotypic data from a population of 2,909 clones evaluated in final assessment trials of Australian sugarcane breeding programs, we focused on three important traits: tonnes of cane per hectare (TCH), commercial cane sugar (CCS), and Fibre. By simulating families from all possible crosses (1,225) with 50 progenies each, we predicted the breeding and clonal values of progeny using two models: GBLUP (considering additive effects only) and extended-GBLUP (incorporating additive, non-additive, and heterozygosity effects). Integer linear programming was used to identify the optimal mate-allocation among selected parents. Compared to breeding value-based approaches, mate-allocation strategies based on clonal performance yielded substantial improvements, with predicted progeny values increasing by 57% for TCH, 12% for CCS, and 16% for fibre. Our simulation study highlights the effectiveness of mate-allocation approaches that exploit non-additive and heterozygosity effects, resulting in superior clonal performance. However, there was a notable decline in additive gain, particularly for TCH, likely due to significant epistatic effects. When selecting crosses based on clonal performance for TCH, the inbreeding coefficient of progeny was significantly lower compared to random mating, underscoring the advantages of leveraging non-additive and heterozygosity effects in mitigating inbreeding depression. Thus, mate-allocation strategies are recommended in clonally propagated crops to enhance clonal performance and reduce the negative impacts of inbreeding.