Chromosome-level genome assembly of milk thistle (Silybum marianum (L.) Gaertn.)

Silybum marianum (L.) Gaertn., commonly known as milk thistle, is a medicinal plant belonging to the Asteraceae family. This plant has been recognized for its medicinal properties for over 2,000 years. However, the genome of this plant remains largely undiscovered, having no reference genome at a chromosomal level. Here, we assembled the chromosome-level genome of S. marianum, allowing for the annotation of 53,552 genes and the identification of transposable elements comprising 58% of the genome. The genome assembly from this study showed 99.1% completeness as determined by BUSCO assessment, while the previous assembly (ASM154182v1) showed 36.7%. Functional annotation of the predicted genes showed 50,329 genes (94% of total genes) with known protein functions in public databases. Comparative genome analysis among Asteraceae plants revealed a striking conservation of collinearity between S. marianum and C. cardunculus. The genomic information generated from this study will be a valuable resource for milk thistle breeding and for use by the larger research community.

Vertically Stackable Ovonic Threshold Switch Oscillator Using Atomic Layer Deposited Ge0.6Se0.4 Film for High-Density Artificial Neural Networks

Nanodevice oscillators (nano-oscillators) have received considerable attention to implement in neuromorphic computing as hardware because they can significantly improve the device integration density and energy efficiency compared to complementary metal oxide semiconductor circuit-based oscillators. This work demonstrates vertically stackable nano-oscillators using an ovonic threshold switch (OTS) for high-density neuromorphic hardware. A vertically stackable Ge0.6Se0.4 OTS-oscillator (VOTS-OSC) is fabricated with a vertical crossbar array structure by growing Ge0.6Se0.4 film conformally on a contact hole structure using atomic layer deposition. The VOTS-OSC can be vertically integrated onto peripheral circuits without causing thermal damage because the fabrication temperature is <400 °C. The fabricated device exhibits oscillation characteristics, which can serve as leaky integrate-and-fire neurons in spiking neural networks (SNNs) and coupled oscillators in oscillatory neural networks (ONNs). For practical applications, pattern recognition and vertex coloring are demonstrated with SNNs and ONNs, respectively, using semiempirical simulations. This structure increases the oscillator integration density significantly, enabling complex tasks with a large number of oscillators. Moreover, it can enhance the computational speed of neural networks due to its rapid switching speed.

Impact of operation voltage and NH3 annealing on the fatigue characteristics of ferroelectric AlScN thin films grown by sputtering

This work investigates the impact of the magnitude of cycling voltage on the fatigue characteristics of 40 nm-thick AlScN ferroelectric thin film. The fatigue rate and the rejuvenation of remanent polarization vary with the cycling voltage. The primary fatigue mechanism is identified to be the interfacial layer formation and domain wall pinning at high and low cycling voltages, respectively. Additionally, annealing the film under the NH3 atmosphere decreases the fatigue rate and improves endurance by eliminating impurities in the film. The amount of trapped charges at the interface also decreases after NH3 annealing, leading to a reduction in leakage current. Furthermore, the ferroelectric performance of the AlScN film is not degraded after the thermal annealing at 900 °C under the NH3 environment, suggesting its robustness against the severe thermal budget. It is concluded that NH3 annealing is a promising method to address the reliability issue of the AlScN film.

A Cold-Shock Protein from the South Pole-Dwelling Soil Bacterium Arthrobacter sp. Confers Cold Tolerance to Rice

Low temperature is a critical environmental factor restricting the physiology of organisms across kingdoms. In prokaryotes, cold shock induces the expression of various genes and proteins involved in cellular processes. Here, a cold-shock protein (ArCspA) from the South Pole-dwelling soil bacterium Arthrobacter sp. A2-5 was introduced into rice, a monocot model plant species. Four-week-old 35S:ArCspA transgenic rice plants grown in a cold chamber at 4 °C survived for 6 days. Cold stress significantly decreased the chlorophyll content in WT plants after 4 days compared with that in 35S:ArCspA transgenic plants. RNA-seq analysis was performed on WT and 35S:ArCspA transgenic rice with/without cold stress. GO terms such as “response to stress (GO:0006950)”, “response to cold (GO:0009409)”, and “response to heat (GO:0009408)” were significantly enriched among the upregulated genes in the 35S:ArCspA transgenic rice under normal conditions, even without cold-stress treatment. The expression of five cold stress-related genes, Rab16B (Os11g0454200), Rab21 (Os11g0454300), LEA22 (Os01g0702500), ABI5 (Os01 g0859300), and MAPK5 (Os03g0285800), was significantly upregulated in the transgenic rice compared with the WT rice. These results indicate that the ArCspA gene might be involved in the induction of cold-responsive genes and provide cold tolerance.

Rice protein-binding microarrays: a tool to detect cis-acting elements near promoter regions in rice

The present study showed that a rice (Oryza sativa)-specific protein-binding microarray (RPBM) can be applied to analyze DNA-binding motifs with a TF where binding is evaluated in extended natural promoter regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements. Transcription factors (TFs) regulate gene expression at the transcriptional level by binding a specific DNA sequence. Thus, predicting the DNA-binding motifs of TFs is one of the most important areas in the functional analysis of TFs in the postgenomic era. Although many methods have been developed to address this challenge, many TFs still have unknown DNA-binding motifs. In this study, we designed RPBM with 40-bp probes and 20-bp of overlap, yielding 49 probes spanning the 1-kb upstream region before the translation start site of each gene in the entire genome. To confirm the efficiency of RPBM technology, we selected two previously studied TFs, OsWOX13 and OsSMF1, and an uncharacterized TF, OsWRKY34. We identified the ATTGATTG and CCACGTCA DNA-binding sequences of OsWOX13 and OsSMF1, respectively. In total, 635 and 932 putative feature genes were identified for OsWOX13 and OsSMF1, respectively. We discovered the CGTTGACTTT DNA-binding sequence and 195 putative feature genes of OsWRKY34. RPBM could be applicable in the analysis of DNA-binding motifs for TFs where binding is evaluated in the promoter and 5' upstream CDS regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements.

Application of Genomic Big Data in Plant Breeding:Past, Present, and Future

Plant breeding has a long history of developing new varieties that have ensured the food security of the human population. During this long journey together with humanity, plant breeders have successfully integrated the latest innovations in science and technologies to accelerate the increase in crop production and quality. For the past two decades, since the completion of human genome sequencing, genomic tools and sequencing technologies have advanced remarkably, and adopting these innovations has enabled us to cost down and/or speed up the plant breeding process. Currently, with the growing mass of genomic data and digitalized biological data, interdisciplinary approaches using new technologies could lead to a new paradigm of plant breeding. In this review, we summarize the overall history and advances of plant breeding, which have been aided by plant genomic research. We highlight the key advances in the field of plant genomics that have impacted plant breeding over the past decades and introduce the current status of innovative approaches such as genomic selection, which could overcome limitations of conventional breeding and enhance the rate of genetic gain.

Genome-wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea

Hybrids are extensively used in agriculture to deliver an increase in yield, yet the molecular basis of heterosis is not well understood. Global DNA methylation analysis, transcriptome analysis and small RNA profiling were aimed to understand the epigenetic effect of the changes in gene expression level in the two hybrids and their parental lines. Increased DNA methylation was observed in both the hybrids as compared to their parents. This increased DNA methylation in hybrids showed that majority of the 24-nt siRNA clusters had higher expression in hybrids than the parents. Transcriptome analysis revealed that various phytohormones (auxin and salicylic acid) responsive hybrid-MPV DEGs were significantly altered in both the hybrids in comparison to MPV. DEGs associated with plant immunity and growth were overexpressed whereas DEGs associated with basal defence level were repressed. This antagonistic patterns of gene expression might contribute to the greater growth of the hybrids. It was also noticed that some common as well as unique changes in the regulatory pathways were associated with heterotic growth in both the hybrids. Approximately 70% and 67% of down-regulated hybrid-MPV DEGs were found to be differentially methylated in ICPH 2671 and ICPH 2740 hybrid, respectively. This reflected the association of epigenetic regulation in altered gene expressions. Our findings also revealed that miRNAs might play important roles in hybrid vigour in both the hybrids by regulating their target genes, especially in controlling plant growth and development, defence and stress response pathways. The above finding provides an insight into the molecular mechanism of pigeonpea heterosis.

Robot-Assisted Partial Nephrectomy for Treatment of Juxtaglomerular Cell Tumor of the Kidney: A Case Report

Background: A juxtaglomerular cell tumor (JGCT), or a reninoma, is a rare renal tumor that can cause secondary hypertension. This is the first reported JGCT that was resected through robotic surgery. Case: We present a case of a 27-year-old female patient with 1.35-cm-sized JGCT in the lower pole of the right kidney. We effectively removed a JGCT through robot-assisted partial nephrectomy without any complications. Conclusion: The robot-assisted partial nephrectomy procedure could be a suitable choice for JGCT resection.

Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean

Somatic embryogenesis is an important tissue culture technique that sometimes leads to phenotypic variation via genetic and/or epigenetic changes. To understand the genomic and epigenomic impacts of somatic embryogenesis, we characterized soybean (Glycine max) epigenomes sampled from embryos at 10 different stages ranging from 6 weeks to 13 years of continuous culture. We identified genome-wide increases in DNA methylation from cultured samples, especially at CHH sites. The hypermethylation almost exclusively occurred in regions previously possessing non-CG methylation and was accompanied by increases in the expression of genes encoding the RNA-directed DNA methylation (RdDM) machinery. The epigenomic changes were similar between somatic and zygotic embryogenesis. Following the initial global wave of hypermethylation, rare decay events of maintenance methylation were observed, and the extent of the decay increased with time in culture. These losses in DNA methylation were accompanied by downregulation of genes encoding the RdDM machinery and transcriptome reprogramming reminiscent of transcriptomes during late-stage seed development. These results reveal a process for reinforcing already silenced regions to maintain genome integrity during somatic embryogenesis over the short term, which eventually decays at certain loci over longer time scales.

QTL Analysis of Resistance to High-Intensity UV-B Irradiation in Soybean (Glycine max [L.] Merr.)

High-intensity ultraviolet-B (UV-B) irradiation is a complex abiotic stressor resulting in excessive light exposure, heat, and dehydration, thereby affecting crop yields. In the present study, we identified quantitative trait loci (QTLs) for resistance to high-intensity UV-B irradiation in soybean (Glycine max [L.]). We used a genotyping-by-sequencing approach using an F6 recombinant inbred line (RIL) population derived from a cross between Cheongja 3 (UV-B sensitive) and Buseok (UV-B resistant). We evaluated the degree of leaf damage by high-intensity UV-B radiation in the RIL population and identified four QTLs, UVBR12-1, 6-1, 10-1, and 14-1, for UV-B stress resistance, together explaining 20% of the observed phenotypic variation. The genomic regions containing UVBR12-1 and UVBR6-1 and their syntenic blocks included other known biotic and abiotic stress-related QTLs. The QTL with the highest logarithm of odds (LOD) score of 3.76 was UVBR12-1 on Chromosome 12, containing two genes encoding spectrin beta chain, brain (SPTBN, Glyma.12g088600) and bZIP transcription factor21/TGACG motif-binding 9 (bZIP TF21/TGA9, Glyma.12g088700). Their amino acid sequences did not differ between the mapping parents, but both genes were significantly upregulated by UV-B stress in Buseok but not in Cheongja 3. Among five genes in UVBR6-1 on Chromosome 6, Glyma.06g319700 (encoding a leucine-rich repeat family protein) had two nonsynonymous single nucleotide polymorphisms differentiating the parental lines. Our findings offer powerful genetic resources for efficient and precise breeding programs aimed at developing resistant soybean cultivars to multiple stresses. Furthermore, functional validation of the candidate genes will improve our understanding of UV-B stress defense mechanisms.

The genome sequence of segmental allotetraploid peanut Arachis hypogaea

Like many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report the genome sequence of peanut and show that after its polyploid origin, the genome has evolved through mobile-element activity, deletions and by the flow of genetic information between corresponding ancestral chromosomes (that is, homeologous recombination). Uniformity of patterns of homeologous recombination at the ends of chromosomes favors a single origin for cultivated peanut and its wild counterpart A. monticola. However, through much of the genome, homeologous recombination has created diversity. Using new polyploid hybrids made from the ancestral species, we show how this can generate phenotypic changes such as spontaneous changes in the color of the flowers. We suggest that diversity generated by these genetic mechanisms helped to favor the domestication of the polyploid A. hypogaea over other diploid Arachis species cultivated by humans.

Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean

BACKGROUND

Plant domestication provides a unique model to study genome evolution. Many studies have been conducted to examine genes, genetic diversity, genome structure, and epigenome changes associated with domestication. Interestingly, domesticated accessions have significantly higher [A] and [T] values across genome-wide polymorphic sites than accessions sampled from the corresponding progenitor species. However, the relative contributions of different genomic regions to this genome divergence pattern and underlying mechanisms have not been well characterized.

RESULTS

Here, we investigate the genome-wide base-composition patterns by analyzing millions of SNPs segregating among 100 accessions from a teosinte-maize comparison set and among 302 accessions from a wild-domesticated soybean comparison set. We show that non-genic part of the genome has a greater contribution than genic SNPs to the [AT]-increase observed between wild and domesticated accessions in maize and soybean. The separation between wild and domesticated accessions in [AT] values is significantly enlarged in non-genic and pericentromeric regions. Motif frequency and sequence context analyses show the motifs (PyCG) related to solar-UV signature are enriched in these regions, particularly when they are methylated. Additional analysis using population-private SNPs also implicates the role of these motifs in relatively recent mutations. With base-composition across polymorphic sites as a genome phenotype, genome scans identify a set of putative candidate genes involved in UV damage repair pathways.

CONCLUSIONS

The [AT]-increase is more pronounced in genomic regions that are non-genic, pericentromeric, transposable elements; methylated; and with low recombination. Our findings establish important links among UV radiation, mutation, DNA repair, methylation, and genome evolution.

Urinary Incontinences Are Related with Fall and Fragility Fractures in Elderly Population: Nationwide Cohort Study

Background

This prospective cohort study used nationwide claims data to investigate the incidence of fall and fragility fractures in association with urinary incontinence (UI) in the elderly, and to compare mortality after fragility fractures in elderly patients with or without incontinence.

Methods

A total of 39,854 Korean adults (age, 66-80 years) who participated in health examinations between 2007 and 2012 and were followed up until 2015 were analyzed. Patient and comparison groups were classified according to the presence or absence of UI. The cumulative incidence of osteoporotic fragility fractures and falls in the 2 groups was assessed and compared. Hazard ratios for fragility fractures were calculated for the risk of UI in association with falls using a Cox proportional hazards model.

Results

Of 39,854 elderly participants, 5,703 were classified in the UI group, while 34,151 were placed in the comparison group. Fall rates were significantly higher (20.8%) in the incontinence group than in the comparison group (4.7%) (P<0.001). Women in the incontinence group (13.9%) showed a significantly higher incidence of all types of fragility fractures than those in the comparison group (11.8%) (P=0.005). After adjustment for confounders, UI was not a significant risk factor for fragility fractures in men (P=0.878) or women (P=0.324).

Conclusions

This study demonstrated that elderly women with UI have a significantly higher incidence of osteoporotic fragility fractures. In addition, elderly women are at higher risk for falls.

Genetic and epigenetic divergence of duplicate genes in two legume species

Soybean (Glycine max) and common bean (Phaseolus vulgaris) share a polyploidy event ~59 MYA, followed by a Glycine-specific whole genome duplication (WGD) ~8-13 MYA. Duplicated genes were classified into five categories: singletons, dispersed, proximal, tandem, or WGD/segmental and found strong correlations between gene category and functional annotation. Photosynthesis and transcriptional regulation-related Gene Ontology terms were significantly over-represented in singletons and WGD genes, respectively, aligning with the gene balance hypothesis. We found that the divergence of gene expression and DNA methylation between WGD-derived paralogs increased with age and that WGD genes, initially retained via dosage constraints, subsequently underwent expression divergence, associated with other factors such as DNA methylation. Genes derived from different modes of duplication differed in breadth, level, and specificity of expression in both species. Orthologous genes and ungrouped genes (genes not in an ortholog group) differed in expression patterns. The protein divergence rates of WGD paralog pairs containing an ungrouped gene were higher than those for which both copies had orthologs. We propose that many ungrouped genes are derived from divergent and redundant gene copies, concordant with the neofunctionalization hypothesis. Tandemly duplicated genes were distinct from WGD-derived genes, indicating that mode of duplication contributes to the evolutionary fate of duplicated genes.

Low-Dose Unenhanced Computed Tomography with Iterative Reconstruction for Diagnosis of Ureter Stones

PURPOSE

To study the clinical application of low-dose unenhanced computed tomography with iterative reconstruction technique (LDCT-IR) on renal colic in the emergency department.

MATERIALS AND METHODS

We conducted a prospective, single-blinded, randomized, and non-inferiority study. From March 2014 to August 2015, 112 patients with renal colic were included, and were randomized to either LDCT-IR (n=46) or standard-dose unenhanced CT (SDCT) (n=66) groups. The accuracy of urolithiasis diagnosis was the primary endpoint of this study. Radiation dose, size and location of the stone, hydronephrosis, other diseases except urolithiasis, and results of treatment were analyzed between the two groups.

RESULTS

The average effective dose radiation of SDCT was approximately four times higher than that of LDCT-IR (6.52 mSv vs. 1.63 mSv, p<0.001). There was no significant difference in the accuracy of ureteral stone diagnosis between the two groups (LDCT-IR group: 96.97% vs. SDCT group: 98.96%, p=0.392). No significant difference was observed regarding the size and location of a stone, hydronephrosis, and diagnosis of other diseases, except urolithiasis. False negative results were found in two LDCT-IR patients and in one SDCT patient. In these patients, stones were misread as vascular calcification, and were difficult to diagnose because evidence of hydronephrosis and ureteral dilatation was not found.

CONCLUSION

LDCT-IR, as a first-line imaging test, was non-inferior to SDCT with respect to diagnosis of ureter stones, and was clinically available for the evaluation of renal colic.

Genomic and epigenomic immunity in common bean: the unusual features of NB-LRR gene family

In plants, a key class of genes comprising most of disease resistance (R) genes encodes Nucleotide-binding leucine-rich repeat (NL) proteins. Access to common bean (Phaseolus vulgaris) genome sequence provides unparalleled insight into the organization and evolution of this large gene family (∼400 NL) in this important crop. As observed in other plant species, most common bean NL are organized in cluster of genes. However, a particularity of common bean is that these clusters are often located in subtelomeric regions close to terminal knobs containing the satellite DNA khipu. Phylogenetically related NL are spread between different chromosome ends, suggesting frequent exchanges between non-homologous chromosomes. NL peculiar location, in proximity to heterochromatic regions, led us to study their DNA methylation status using a whole-genome cytosine methylation map. In common bean, NL genes displayed an unusual body methylation pattern since half of them are methylated in the three contexts, reminiscent of the DNA methylation pattern of repeated sequences. Moreover, 90 NL were also abundantly targeted by 24 nt siRNA, with 90% corresponding to methylated NL genes. This suggests the existence of a transcriptional gene silencing mechanism of NL through the RdDM (RNA-directed DNA methylation) pathway in common bean that has not been described in other plant species.

Can recording only the day-time voided volumes predict bladder capacity?

Purpose

This study aimed to demonstrate a method to easily assess bladder capacity using knowledge of day-time voided volumes, which can be obtained even from patients with nocturnal enuresis where the first morning void cannot accurately predict the bladder capacity due to bladder emptying overnight.

Materials and Methods

We evaluated 177 healthy children from 7 Korean medical centres entered the study between January 2008 and January 2009. Voided volumes measured for more than 48 hours were recorded in the frequency volume chart (FVC).

Results

Most voided volumes during day-time were showed between 30% and 80% of the maximal voided volume (MVV). The maximal voided volume during day-time (MVVDT) was significantly less than the MVV (179.5±71.1 mL vs. 227.0±79.2 mL, p<0.001). The correlation coefficients with the MVV were 0.801 for the estimated MVV using the MVVDT (MVVDT×1.25), which suggested a fairly strong relationship between the MVVDT×1.25 and the MVV.

Conclusions

The MVV derived from the FVC excluding the FMV was less than if the FMV had been included. When an accurate first morning voided volume cannot be obtained, as in patients with nocturnal enuresis, calculating MVVDT×1.25 allows estimation of the bladder capacity in place of the MVV.

Genic C-Methylation in Soybean Is Associated with Gene Paralogs Relocated to Transposable Element-Rich Pericentromeres

Most plants are polyploid due to whole-genome duplications (WGD) and can thus have duplicated genes. Following a WGD, paralogs are often fractionated (lost) and few duplicate pairs remain. Little attention has been paid to the role of DNA methylation in the functional divergence of paralogous genes. Using high-resolution methylation maps of accessions of domesticated and wild soybean, we show that in soybean, a recent paleopolyploid with many paralogs, DNA methylation likely contributed to the elimination of genetic redundancy of polyploidy-derived gene paralogs. Transcriptionally silenced paralogs exhibit particular genomic features as they are often associated with proximal transposable elements (TEs) and are preferentially located in pericentromeres, likely due to gene movement during evolution. Additionally, we provide evidence that gene methylation associated with proximal TEs is implicated in the divergence of expression profiles between orthologous genes of wild and domesticated soybean, and within populations.

Global transcriptome analysis identifies weight regain-induced activation of adaptive immune responses in white adipose tissue of mice

Objective:

Studies have indicated that weight regain following weight loss predisposes obese individuals to metabolic disorders; however, the molecular mechanism of this potential adverse effect of weight regain is not fully understood. Here we investigated global transcriptome changes and the immune response in mouse white adipose tissue caused by weight regain.

Design:

We established a diet switch protocol to compare the effects of weight regain with those of weight gain without precedent weight loss, weight loss maintenance and chow diet. We conducted a time course analysis of global transcriptome changes in gonadal white adipose tissue (gWAT) during the weight fluctuation. Co-expression network analysis was used to identify functional modules associated with the weigh regain phenotype. Immune cell populations in gWAT were characterized by flow-cytometric immunophenotyping. Metabolic phenotypes were monitored by histological analysis of adipose tissue and liver, and blood-chemistry and body weight/composition analyses.

Results:

In total, 952 genes were differentially expressed in the gWAT in the weight regain vs the weight gain group. Upregulated genes were associated with immune response and leukocyte activation. Co-expression network analysis showed that genes involved in major histocompatibility complex I and II-mediated antigen presentation and T-cell activation function were upregulated. Consistent with the transcriptome analysis results, flow cytometry demonstrated significant increases in subsets of T cells and proinflammatory M1 macrophages in the gWAT in the weight regain as compared to the weight gain group. In addition, upregulation of adaptive immune responses was associated with high incidence of adipocyte death and upregulation of high mobility group box 1, a well-known component of damage-associated molecular patterns.

Conclusions:

Our global transcriptome analysis identified weight regain-induced activation of adaptive immune responses in mouse white adipose tissue. Results suggest that activation of adipocyte death-associated adaptive immunity in adipose tissue may contribute to unfavorable metabolic effects of weight regain following weight loss.

Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs

Chromatin modifications, such as cytosine methylation of DNA, play a significant role in mediating gene expression in plants, which affects growth, development, and cell differentiation. As root hairs are single-cell extensions of the root epidermis and the primary organs for water uptake and nutrients, we sought to use root hairs as a single-cell model system to measure the impact of environmental stress. We measured changes in cytosine DNA methylation in single-cell root hairs as compared with multicellular stripped roots, as well as in response to heat stress. Differentially methylated regions (DMRs) in each methylation context showed very distinct methylation patterns between cell types and in response to heat stress. Intriguingly, at normal temperature, root hairs were more hypermethylated than were stripped roots. However, in response to heat stress, both root hairs and stripped roots showed hypomethylation in each context, especially in the CHH context. Moreover, expression analysis of mRNA from similar tissues and treatments identified some associations between DMRs, genes and transposons. Taken together, the data indicate that changes in DNA methylation are directly or indirectly associated with expression of genes and transposons within the context of either specific tissues/cells or stress (heat).

Transcriptomic Profiling of Soybean in Response to High-Intensity UV-B Irradiation Reveals Stress Defense Signaling

The depletion of the ozone layer in the stratosphere has led to a dramatic spike in ultraviolet B (UV-B) intensity and increased UV-B light levels. The direct absorption of high-intensity UV-B induces complex abiotic stresses in plants, including excessive light exposure, heat, and dehydration. However, UV-B stress signaling mechanisms in plants including soybean (Glycine max [L.]) remain poorly understood. Here, we surveyed the overall transcriptional responses of two soybean genotypes, UV-B-sensitive Cheongja 3 and UV-B-resistant Buseok, to continuous UV-B irradiation for 0 (control), 0.5, and 6 h using RNA-seq analysis. Homology analysis using UV-B-related genes from Arabidopsis thaliana revealed differentially expressed genes (DEGs) likely involved in UV-B stress responses. Functional classification of the DEGs showed that the categories of immune response, stress defense signaling, and reactive oxygen species (ROS) metabolism were over-represented. UV-B-resistant Buseok utilized phosphatidic acid-dependent signaling pathways (based on subsequent reactions of phospholipase C and diacylglycerol kinase) rather than phospholipase D in response to UV-B exposure at high fluence rates, and genes involved in its downstream pathways, such as ABA signaling, mitogen-activated protein kinase cascades, and ROS overproduction, were upregulated in this genotype. In addition, the DEGs for TIR-NBS-LRR and heat shock proteins are positively activated. These results suggest that defense mechanisms against UV-B stress at high fluence rates are separate from the photomorphogenic responses utilized by plants to adapt to low-level UV light. Our study provides valuable information for deep understanding of UV-B stress defense mechanisms and for the development of resistant soybean genotypes that survive under high-intensity UV-B stress.

Widespread natural variation of DNA methylation within angiosperms

BACKGROUND

DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant species is still unclear. To understand the variation in genomic patterning of DNA methylation across flowering plant species, we compared single base resolution DNA methylomes of 34 diverse angiosperm species.

RESULTS

By analyzing whole-genome bisulfite sequencing data in a phylogenetic context, it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Furthermore, low levels of CHH methylation are observed in a number of species, especially in clonally propagated species.

CONCLUSIONS

These results reveal the extent of variation in DNA methylation in angiosperms and show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.

Widespread natural variation of DNA methylation within angiosperms

BACKGROUND

DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant species is still unclear. To understand the variation in genomic patterning of DNA methylation across flowering plant species, we compared single base resolution DNA methylomes of 34 diverse angiosperm species.

RESULTS

By analyzing whole-genome bisulfite sequencing data in a phylogenetic context, it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Furthermore, low levels of CHH methylation are observed in a number of species, especially in clonally propagated species.

CONCLUSIONS

These results reveal the extent of variation in DNA methylation in angiosperms and show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.

Numerical Simulation of PU Foaming Flow in a Refrigerator Cabinet

We have developed a numerical method for unsteady three-dimensional (3D) simulation of rigid polyurethane (PU) foaming flow in a refrigerator cabinet in this study. The governing equation for the compressible foaming flow is approximated with the Navier-Stokes equation, which means the foaming flow is assumed to be Newtonian. Numerical methods of simulation for unsteady compressible PU foaming flow with a free surface have been designed using a finite volume method (FVM) and the semi-implicit method for pressure-linked equations (SIMPLE) scheme as a pressure correction method. The formulation of numerical methods is developed on the basis of hexahedral meshes. Air in a refrigerator cabinet is neglected in the numerical method, and the free surface is traced with the volume of fluid (VOF) method. Viscosity and density of foam are assumed to be uniform in space and time-dependent, which are obtained with experimental methods. Results of numerical simulation for filling pattern and a finally filled position have been compared with the experimental results in a plate mold and a simple refrigerator cabinet. Simulation results of foaming fronts and finally filled position show good agreement with the experimental results. Numerical simulation of PU foaming flow is a useful tool to design a new refrigerator model and predict foam quality related to distance of foaming flow, air trapping, and location of finally filled position.

Nocturia: The circadian voiding disorder

Nocturia is a prevalent condition of waking to void during the night. The concept of nocturia has evolved from being a symptomatic aspect of disease associated with the prostate or bladder to a form of lower urinary tract disorder. However, recent advances in circadian biology and sleep science suggest that it might be important to consider nocturia as a form of circadian dysfunction. In the current review, nocturia is reexamined with an introduction to sleep disorders and recent findings in circadian biology in an attempt to highlight the importance of rediscovering nocturia as a problem of chronobiology.

Human Neural Stem Cells Overexpressing a Carboxylesterase Inhibit Bladder Tumor Growth

Bladder cancer is a significant clinical and economic problem. Despite intravesical chemotherapy and immunotherapy, up to 80% of patients with non-muscle-invasive bladder cancer develop recurrent tumors, of which 20% to 30% evolve into more aggressive, potentially lethal tumors. Recently, bladder cancer cells are considered to be mediators of resistance to current therapies and therefore represent strong candidates as biologic targets. No effective chemotherapy has yet been developed for advanced bladder cancer. It is desirable that a drug can be delivered directly and specifically to bladder cancer cells. Stem cells have selective migration ability toward cancer cells, and therapeutic genes can be easily transduced into stem cells. In suicide gene therapy for cancer, stem cells carry a gene encoding a carboxylesterase (CE) enzyme that transforms an inert CPT-11 prodrug into a toxic SN-38 product, a topoisomerase 1 inhibitor. In immunodeficient mice, systemically transplanted HB1.F3.CE stem cells migrated toward the tumor implanted by the TCCSUP bladder cancer cell line, and, in combination with CPT-11, the volume of tumors was significantly reduced. These findings may contribute to the development of a new selective chemotherapeutic strategy against bladder cancer. Mol Cancer Ther; 15(6); 1201-7. ©2016 AACR.

Landscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes

Background

Terminal repeat retrotransposons in miniature (TRIMs) are a unique group of small long terminal repeat retrotransposons that are difficult to identify. Thus far, only a few TRIMs have been characterized in the euphyllophytes, and their evolutionary and biological significance as well as their transposition mechanisms are poorly understood.

Results

Using a combination of de novo and homology-based methods, we annotate TRIMs in 48 plant genome sequences, spanning land plants to algae. The TRIMs are grouped into 156 families including 145 that were previously undefined. Notably, we identify the first TRIMs in a lycophyte and non-vascular plants. The majority of the TRIM families are highly conserved and shared within and between plant families. Unlike other long terminal repeat retrotransposons, TRIMs are enriched in or near genes; they are also targeted by sRNAs between 21 and 24 nucleotides in length, and are frequently found in CG body-methylated genes. Importantly, we also identify putative autonomous retrotransposons and very recent transpositions of a TRIM element in Oryza sativa.

Conclusions

We perform the most comprehensive analysis of TRIM transposons thus far and report that TRIMs are ubiquitous across plant genomes. Our results show that TRIMs are more frequently associated with large and CG body-methylated genes that have undergone strong purifying selection. Our findings also indicate that TRIMs are likely derived from internal deletions of large long terminal repeat retrotransposons. Finally, our data and methodology are important resources for the characterization and evolutionary and genomic studies of long terminal repeat retrotransposons in other genomes.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0867-y) contains supplementary material, which is available to authorized users.

A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean

Soybean (Glycine max) and common bean (Phaseolus vulgaris) share a paleopolyploidy (whole-genome duplication [WGD]) event, approximately 56.5 million years ago, followed by a genus Glycine-specific polyploidy, approximately 10 million years ago. Cytosine methylation is an epigenetic mark that plays an important role in the regulation of genes and transposable elements (TEs); however, the role of DNA methylation in the fate/evolution of genes following polyploidy and speciation has not been fully explored. Whole-genome bisulfite sequencing was used to produce nucleotide resolution methylomes for soybean and common bean. We found that, in soybean, CG body-methylated genes were abundant in WGD genes, which were, on average, more highly expressed than single-copy genes and had slower evolutionary rates than unmethylated genes, suggesting that WGD genes evolve more slowly than single-copy genes. CG body-methylated genes were also enriched in shared single-copy genes (single copy in both species) that may be responsible for the broad and high expression patterns of this class of genes. In addition, diverged methylation patterns in non-CG contexts between paralogs were due mostly to TEs in or near genes, suggesting a role for TEs and non-CG methylation in regulating gene expression post polyploidy. Reference methylomes for both soybean and common bean were constructed, providing resources for investigating epigenetic variation in legume crops. Also, the analysis of methylation patterns of duplicated and single-copy genes has provided insights into the functional consequences of polyploidy and epigenetic regulation in plant genomes.

A new approach for annotation of transposable elements using small RNA mapping

Transposable elements (TEs) are mobile genomic DNA sequences found in most organisms. They so densely populate the genomes of many eukaryotic species that they are often the major constituents. With the rapid generation of many plant genome sequencing projects over the past few decades, there is an urgent need for improved TE annotation as a prerequisite for genome-wide studies. Analogous to the use of RNA-seq for gene annotation, we propose a new method for de novo TE annotation that uses as a guide 24 nt-siRNAs that are a part of TE silencing pathways. We use this new approach, called TASR (for Transposon Annotation using Small RNAs), for de novo annotation of TEs in Arabidopsis, rice and soybean and demonstrate that this strategy can be successfully applied for de novo TE annotation in plants.Executable PERL is available for download from: http://tasr-pipeline.sourceforge.net/.

Transcriptomic changes due to water deficit define a general soybean response and accession-specific pathways for drought avoidance

BACKGROUND

Among abiotic stresses, drought is the most common reducer of crop yields. The slow-wilting soybean genotype PI 416937 is somewhat robust to water deficit and has been used previously to map the trait in a bi-parental population. Since drought stress response is a complex biological process, whole genome transcriptome analysis was performed to obtain a deeper understanding of the drought response in soybean.

RESULTS

Contrasting data from PI 416937 and the cultivar 'Benning', we developed a classification system to identify genes that were either responding to water-deficit in both genotypes or that had a genotype x environment (GxE) response. In spite of very different wilting phenotypes, 90% of classifiable genes had either constant expression in both genotypes (33%) or very similar response profiles (E genes, 57%). By further classifying E genes based on expression profiles, we were able to discern the functional specificity of transcriptional responses at particular stages of water-deficit, noting both the well-known reduction in photosynthesis genes as well as the less understood up-regulation of the protein transport pathway. Two percent of classifiable genes had a well-defined GxE response, many of which are located within slow-wilting QTLs. We consider these strong candidates for possible causal genes underlying PI 416937's unique drought avoidance strategy.

CONCLUSIONS

There is a general and functionally significant transcriptional response to water deficit that involves not only known pathways, such as down-regulation of photosynthesis, but also up-regulation of protein transport and chromatin remodeling. Genes that show a genotypic difference are more likely to show an environmental response than genes that are constant between genotypes. In this study, at least five genes that clearly exhibited a genotype x environment response fell within known QTL and are very good candidates for further research into slow-wilting.

Predicting recurrence and progression of non-muscle-invasive bladder cancer in Korean patients: a comparison of the EORTC and CUETO models

PURPOSE

This study aimed to confirm the utility of the European Organization for Research and Treatment of Cancer (EORTC) and the Spanish Urological Club for Oncological Treatment (CUETO) scoring systems and to determine which model is preferred as a prognostic model in Korean patients with non-muscle-invasive bladder cancer.

MATERIALS AND METHODS

Between 1985 and 2011, 531 patients who were treated by transurethral resection of bladder cancer were retrospectively analyzed by use of the EORTC and CUETO models. Statistically, we performed Kaplan-Meier survival analysis; calculated Harrell's concordance index, receiver operating characteristic (ROC) curve, and cutoff values; and performed univariate and multivariate Cox proportional hazards regression analyses.

RESULTS

For risk of recurrence, with the use of the EORTC model, all groups had statistically significant differences except between the group with a score of 0 and the group with a score of 1-4. With the use of the CUETO model, all groups differed significantly. For risk of progression, with the use of the EORTC model, significant differences were observed between all groups except between the group with a score of 2-6 and the group with a score of 7-13. With the use of the CUETO model, a significant difference was observed between the group with a score of 0 and the other groups. The concordance index of the EORTC and CUETO models was 0.759 and 0.836 for recurrence and 0.704 and 0.745 for progression, respectively. The area under the ROC curve for the EORTC and CUETO models was 0.832 and 0.894 for recurrence and 0.722 and 0.724 for progression, respectively.

CONCLUSIONS

Both scoring systems, especially the CUETO model, showed value in predicting recurrence and progression in Korean patients, which will help in individualizing treatment and follow-up schedules.

Febrile urinary tract infection after prostate biopsy and quinolone resistance

Purpose

Complications after prostate biopsy have increased and various causes have been reported. Growing evidence of increasing quinolone resistance is of particular concern. In the current retrospective study, we evaluated the incidence of infectious complications after prostate biopsy and identified the risk factors.

Materials and Methods

The study population included 1,195 patients who underwent a prostate biopsy between January 2007 and December 2012 at Chung-Ang University Hospital. Cases of febrile UTI that occurred within 7 days were investigated. Clinical information included age, prostate-specific antigen, prostate volume, hypertension, diabetes, body mass index, and biopsy done in the quinolone-resistance era. Patients received quinolone (250 mg intravenously) before and after the procedure, and quinolone (250 mg) was orally administered twice daily for 3 days. We used univariate and multivariate analysis to investigate the predictive factors for febrile UTI.

Results

Febrile UTI developed in 39 cases (3.1%). Core numbers increased from 2007 (8 cores) to 2012 (12 cores) and quinolone-resistant bacteria began to appear in 2010 (quinolone-resistance era). In the univariate analysis, core number≥12 (p=0.024), body mass index (BMI)>25 kg/m² (p=0.004), and biopsy done in the quinolone-resistance era (p=0.014) were significant factors. However, in the multivariate analysis adjusted for core number, the results were not significant, with the exception of BMI>25 kg/m² (p=0.011) and biopsy during the quinolone-resistance era (p=0.035), which were significantly associated with febrile UTI.

Conclusions

Quinolone resistance is the main cause of postbiopsy infections in our center. We suggest that further evaluation is required to validate similar trends. Novel strategies to find alternative prophylactic agents are also necessary.

Pilot study of low-dose nonenhanced computed tomography with iterative reconstruction for diagnosis of urinary stones

Purpose

To evaluate the efficacy of low-dose computed tomography (LDCT) for detecting urinary stones with the use of an iterative reconstruction technique for reducing radiation dose and image noise.

Materials and Methods

A total of 101 stones from 69 patients who underwent both conventional nonenhanced computed tomography (CCT) and LDCT were analyzed. Interpretations were made of the two scans according to stone characteristics (size, volume, location, Hounsfield unit [HU], and skin-to-stone distance [SSD]) and radiation dose by dose-length product (DLP), effective dose (ED), and image noise. Diagnostic performance for detecting urinary stones was assessed by statistical evaluation.

Results

No statistical differences were found in stone characteristics between the two scans. The average DLP and ED were 384.60±132.15 mGy and 5.77±1.98 mSv in CCT and 90.08±31.80 mGy and 1.34±0.48 mSv in LDCT, respectively. The dose reduction rate of LDCT was nearly 77% for both DLP and ED (p<0.01). The mean objective noise (standard deviation) from three different areas was 23.0±2.5 in CCT and 29.2±3.1 in LDCT with a significant difference (p<0.05); the slight increase was 21.2%. For stones located throughout the kidney and ureter, the sensitivity and specificity of LDCT remained 96.0% and 100%, with positive and negative predictive values of 100% and 96.2%, respectively.

Conclusions

LDCT showed significant radiation reduction while maintaining high image quality. It is an attractive option in the diagnosis of urinary stones.

Accessing epigenetic variation in the plant methylome

Cytosine DNA methylation is the addition of a methyl group to the 5' position of a cytosine, which plays a crucial role in plant development and gene silencing. Genome-wide profiling of DNA methylation is now possible using various techniques and strategies. Using these technologies, we are beginning to elucidate the extent and impact of variation in DNA methylation between individuals and/or tissues. Here, we review the different techniques used to analyze the methylomes at the whole-genome level and their applications to better understand epigenetic variations in plants.

Safety and efficacy of 8-mg once-daily vs 4-mg twice-daily silodosin in patients with lower urinary tract symptoms suggestive of benign prostatic hyperplasia (SILVER Study): a 12-week, double-blind, randomized, parallel, multicenter study

OBJECTIVE

To show the noninferiority of silodosin 8-mg once-daily (QD) to 4-mg twice-daily (BID) in efficacy and safety in patients with lower urinary tract symptoms or benign prostatic hyperplasia in the Korean population.

METHODS

A prospective, multicenter, double-blind, randomized, comparative study was conducted. A total of 532 male patients aged ≥50 years with lower urinary tract symptoms or benign prostatic hyperplasia were included. All patients received silodosin QD or BID for 12 weeks. The primary end point was the change from baseline in total International Prostate Symptom Score (IPSS) at 12 weeks. Adverse drug reactions, vital signs, and laboratory tests were recorded.

RESULTS

A total of 424 patients were randomized to the silodosin QD or BID groups. These groups were not significantly different in baseline characteristics. The mean total IPSS change in QD group was not inferior to that in BID group (-6.70 and -6.94, respectively; 95% confidence interval, -0.88 to 1.36). The QD and BID groups did not significantly differ in the following: percentages of patients with ≥25% (63.41% and 67.82%, respectively; P = .349) or ≥4-point improvement in total IPSS (65.85% and 69.31%, respectively; P = .457), maximum urinary flow rate improvement ≥30% (47.32% and 40.59%, respectively; P = .172), changes in IPSS voiding subscore (-4.42 ± 4.93 and -4.65 ± 4.77; P = .641), IPSS storage subscore (-2.05 ± 3.07 and -2.52 ± 2.97; P = .117), quality of life (-1.19 ± 1.49 and -1.40 ± 1.42; P = .136), maximum urinary flow rate (3.55 ± 5.93 and 3.74 ± 6.79 mL/s; P = .768), International Continence Society male questionnaire score, Patient Goal Achievement Score, or Treatment Satisfaction Question. The 2 groups had similar frequencies of adverse drug reactions.

CONCLUSION

QD administration of silodosin was not inferior to BID in efficacy. The 2 groups had similar adverse drug reaction profiles.

Current surgical management of vesicoureteral reflux

Vesicoureteral reflux (VUR), a common congenital urinary tract anomaly, refers to retrograde flow of urine from the bladder into the upper urinary tract. The main goal in the treatment of pediatric VUR is to preserve renal function by preventing pyelonephritis. Many surgical management options are available for pediatric VUR. Open ureteral reimplantation has a high success rate but is invasive and is associated with postoperative pain and morbidity. Endoscopic therapy is minimally invasive but has the disadvantages of decreased short-term success and recurrence of reflux over the long term. Laparoscopic or robotic ureteral reimplantation has become increasingly popular owing to its effectiveness and minimal invasiveness, but long-term outcomes have yet to be documented. Urologists should make an effort to select the appropriate surgical strategy by taking into consideration the individual characteristics of the patient such as age, gender, grade of reflux at presentation, status of renal parenchyma, combined bladder and ureteral circumstances, functional status of the bladder and bowel, and preferences of the patients' family.

A nationwide epidemiological study of nocturnal enuresis in Korean adolescents and adults: population based cross sectional study

We performed a nationwide epidemiological study to evaluate the prevalence and characteristics of nocturnal enuresis (NE) in Korean adolescents and adults. A questionnaire was sent via e-mail to 51,073 people aged 16-40 yr by stratified sampling according to age, sex, and region among a 200,000 internet survey panel pool. The questionnaire included following information; presence or absence of NE, frequency of NE, possible risk factors for NE, self-esteem scale score and depression score results, and measures for the treatment of NE. Among the 2,117 responders, 54 (2.6%) had NE (≥1 enuretic episode within 6 months). Of 54 bedwetters, 9.3% wet ≥1 night per week and 20.5% wet ≥1 per month. The prevalence rates remained relatively stable with no apparent trend of reduction with age. The presence of sleep disturbance, family history, urgency, or urge incontinence increased the probability of NE episode significantly. The self-esteem score was lower (P=0.053) and the depression scale score was higher (P=0.003) in bedwetters compared with non-bedwetters. Overall 2.6% of Korean aged 16-40 yr have NE. The higher rate of urgency and urge incontinence in adolescent and adult enuretics suggests that bladder function has an important role in adolescent and adult NE.

Effectiveness of flexible ureteroscopic stone removal for treating ureteral and ipsilateral renal stones: a single-center experience

Purpose

The aim of this study was to evaluate the effectiveness of simultaneous flexible ureteroscopic removal of stones (URS) for ureteral and ipsilateral renal stones and to analyze the predictive factors for renal stone-free status.

Materials and Methods

We retrospectively reviewed the records of patients who underwent simultaneous flexible URS of ureteral and ipsilateral renal stones from January 2010 to May 2012. All operations used a flexible ureteroscope. We identified 74 cases of retrograde intrarenal surgery and 74 ureteral stones (74 patients). Stone-free status was respectively defined as no visible stones and clinically insignificant residual stones <3 mm on a postoperative image study. Predictive factors for stone-free status were evaluated.

Results

The immediate postoperative renal stone-free rate was 70%, which increased to 83% at 1 month after surgery. The immediate postoperative ureteral stone-free rate was 100%. Among all renal stones, 15 (20.3%) were separately located in the renal pelvis, 11 (14.8%) in the upper calyx, 15 (20.3%) in the mid calyx, and 33 (44.6%) in the lower calyx. The mean cumulative stone burden was 92.22±105.75 mm². In a multivariate analysis, cumulative stone burden <100 mm² was a significant predictive factor for postoperative renal stone-free status after 1 month (p<0.01).

Conclusions

Flexible URS can be considered simultaneously for both ureteral and renal stones in selected patients. Flexible URS is a favorable option that promises high stone-free status without significant complications for patients with a stone burden <100 mm².

The effects of α-defensin 1 on electrical field stimulation-induced contraction of rat bladders

This study was designed to investigate the effects of α-defensin 1 on electrical field stimulation (EFS)-induced contractions in isolated rat bladder detrusor muscles. We evaluated the effects of α-defensin 1 (50 pM∼5 nM) on EFS-induced contractions in the detrusor smooth muscles from 35 rats (2-30 Hz). Bladder strips were pretreated with α-defensin 1 and then changes of contractions by adenosine 5'-triphosphate (ATP) were observed. Moreover, after pretreatment with α-defensin 1 for 10 min, changes in concentration-response curves to hydrogen peroxide (H2O2) were investigated. Alpha-defensin 1 has increased EFS-induced contractions, significantly, and the contractile response to ATP (1,2,5,10mM) was also increased significantly when strips were pretreated with α-defensin 1. In addition, alpha-defensin 1 increased H2O2-induced contractions. The present study demonstrates that α-defensin 1 increases EFS-induced contractions of rat detrusor muscles via purinergic contraction coupled with the Rho kinase pathway.