Prebiotic effect of galacto-N-biose on the intestinal lactic acid bacteria as enhancer of acetate production and hypothetical colonization

Galacto-N-biose (GNB) is an important core structure of glycan of mucin glycoproteins in the gastrointestinal (GI) mucosa. Because certain beneficial bacteria inhabiting the GI tract, such as bifidobacteria and lactic acid bacteria, harbor highly specialized GNB metabolic capabilities, GNB is considered a promising prebiotic for nourishing and manipulating beneficial bacteria in the GI tract. However, the precise interactions between GNB and beneficial bacteria and their accompanying health-promoting effects remain elusive. First, we evaluated the proliferative tendency of beneficial bacteria and their production of beneficial metabolites using gut bacterial strains. By comparing the use of GNB, glucose, and inulin as carbon sources, we found that GNB enhanced acetate production in Lacticaseibacillus casei, Lacticaseibacillus rhamnosus, Lactobacillus gasseri, and Lactobacillus johnsonii. The ability of GNB to promote acetate production was also confirmed by RNA-seq analysis, which indicated the upregulation of gene clusters that catalyze the deacetylation of N-acetylgalactosamine-6P and biosynthesize acetyl-CoA from pyruvate, both of which result in acetate production. To explore the in vivo effect of GNB in promoting acetate production, antibiotic-treated BALB/cA mice were administered with GNB with L. rhamnosus, resulting in a fecal acetate content that was 2.7-fold higher than that in mice administered with only L. rhamnosus. Moreover, 2 days after the last administration, a 3.7-fold higher amount of L. rhamnosus was detected in feces administered with GNB with L. rhamnosus than in feces administered with only L. rhamnosus. These findings strongly suggest the prebiotic potential of GNB in enhancing L. rhamnosus colonization and converting L. rhamnosus into higher acetate producers in the GI tract.

IMPORTANCE

Specific members of lactic acid bacteria, which are commonly used as probiotics, possess therapeutic properties that are vital for human health enhancement by producing immunomodulatory metabolites such as exopolysaccharides, short-chain fatty acids, and bacteriocins. The long residence time of probiotic lactic acid bacteria in the GI tract prolongs their beneficial health effects. Moreover, the colonization property is also desirable for the application of probiotics in mucosal vaccination to provoke a local immune response. In this study, we found that GNB could enhance the beneficial properties of intestinal lactic acid bacteria that inhabit the human GI tract, stimulating acetate production and promoting intestinal colonization. Our findings provide a rationale for the addition of GNB to lactic acid bacteria-based functional foods. This has also led to the development of therapeutics supported by more rational prebiotic and probiotic selection, leading to an improved healthy lifestyle for humans.

Investigation of removal and inactivation efficiencies of human sapovirus in drinking water treatment processes by applying an in vitro cell-culture system

Here, we examined the efficiencies of drinking water treatment processes for the removal and inactivation of human sapovirus (HuSaV). We applied a recently developed in vitro cell-culture system to produce purified solutions of HuSaV containing virus concentrations high enough to conduct virus-spiking experiments, to develop an integrated cell culture-polymerase chain reaction (ICC-PCR) assay to quantify the infectivity of HuSaV, and to conduct virus-spiking experiments. In virus-spiking coagulation-sedimentation-rapid sand filtration (CS-RSF) and coagulation-microfiltration (C-MF) experiments, HuSaV removals of 1.6-3.7-log₁₀ and 1.2->4.3-log₁₀, respectively, were observed. The removal ratios observed with CS-RSF were comparable and correlated with those of murine norovirus (MNV, a widely used surrogate for human noroviruses) and pepper mild mottle virus (PMMoV, a potential surrogate for human enteric viruses in physical and physicochemical drinking water treatment processes), and those observed with C-MF were higher than but still correlated with those of MNV and PMMoV, indicating that MNV and PMMoV are both potential surrogates for HuSaV in CS-RSF and C-MF. For astrovirus (AstV, a representative human enteric virus), removal ratios of 1.8-3.3-log₁₀ and 1.1->4.0-log₁₀ were observed with CS-RSF and C-MF, respectively. The removal ratios of AstV observed with CS-RSF were comparable and correlated with those of PMMoV, and those observed with C-MF were higher than but still correlated with those of PMMoV, indicating that PMMoV is a potential surrogate for AstV in CS-RSF and C-MF. When the efficacy of chlorine treatment was examined by using the developed ICC-PCR assay, 3.8-4.0-log₁₀ inactivation of HuSaV was observed at a CT value (free-chlorine concentration [C] multiplied by contact time [T]) of 0.02 mg-Cl₂·min/L. The infectivity reduction ratios of HuSaV were comparable with those of MNV. For AstV, 1.3-1.7-log₁₀ and >3.4-log₁₀ inactivation, as evaluated by ICC-PCR, was observed at CT values of 0.02 and 0.09 mg-Cl₂·min/L, respectively. These results indicate that HuSaV and AstV are both highly sensitive to chlorine treatment and more sensitive than a chlorine-resistant virus, coxsackievirus B5 (1.3-log₁₀ inactivation at a CT value of 0.4 mg-Cl₂·min/L, as evaluated by the ICC-PCR assay).

Non-vernalization requirement for flowering in Brassica rapa conferred by a dominant allele of FLOWERING LOCUS T

KEY MESSAGE

We identified and characterized a dominant FT allele for flowering without vernalization in Brassica rapa, while demonstrating its potential for deployment in breeding to accelerate flowering in various Brassicaceae crops. Controlling the timing of flowering is key to improving yield and quality of several agricultural crops including the Brassicas. Many Brassicaceae crops possess a conserved flowering mechanism in which FLOWERING LOCUS C (FLC) represses the transcription of flowering activators such as FLOWERING LOCUS T (FT) during vernalization. Here, we employed genetic analysis based on next-generation sequencing to identify a dominant FT allele, BraA.FT.2-C, for flowering in the absence of vernalization in the Brassica rapa cultivar 'CHOY SUM EX CHINA 3'. BraA.FT.2-C harbors two large insertions upstream of its coding region and is expressed without vernalization, despite FLC expression. We show that BraA.FT.2-C offers an opportunity to introduce flowering without vernalization requirement into winter-type brassica crops, including B. napus, which have many functional FLC paralogs. Furthermore, we demonstrated the feasibility of using B. rapa harboring BraA.FT.2-C as rootstock for grafting to induce flowering in radish (Raphanus sativus), which requires vernalization for flowering. We believe that the ability of BraA.FT.2-C to overcome repression by FLC can have significant applications in brassica crops breeding to increase yields by accelerating or delaying flowering.

Mutations in RZF1, a zinc-finger protein, reduce magnesium uptake in roots and translocation to shoots in rice

Magnesium (Mg) homeostasis is critical for maintaining many biological processes, but little information is available to comprehend the molecular mechanisms regulating Mg concentration in rice (Oryza sativa). To make up for the lack of information, we aimed to identify mutants defective in Mg homeostasis through a forward genetic approach. As a result of the screening of 2,825 M2 seedlings mutated by ion-beam irradiation, we found a rice mutant that showed reduced Mg content in leaves and slightly increased Mg content in roots. Radiotracer 28Mg experiments showed that this mutant, named low-magnesium content 1 (LMGC1), has decreased Mg2+ influx in the root and Mg2+ translocation from root to shoot. Consequently, LMGC1 is sensitive to the low Mg condition and prone to develop chlorosis in the young mature leaf. The MutMap method identified a 7.4-kbp deletion in the LMGC1 genome leading to a loss of two genes. Genome editing using CRISPR-Cas9 further revealed that one of the two lost genes, a gene belonging to the RanBP2-type zinc-finger family that we named RanBP2-TYPE ZINC FINGER1 (OsRZF1), was the causal gene of the low Mg phenotype. OsRZF1 is a nuclear protein and may have a fundamental role in maintaining Mg homeostasis in rice plants.

Fate of charge order in overdoped La-based cuprates

In high-temperature cuprate superconductors, stripe order refers broadly to a coupled spin and charge modulation with a commensuration of eight and four lattice units, respectively. How this stripe order evolves across optimal doping remains a controversial question. Here we present a systematic resonant inelastic x-ray scattering study of weak charge correlations in La2-xSrxCuO4 and La1.8-xEu0.2SrxCuO4. Ultra high energy resolution experiments demonstrate the importance of the separation of inelastic and elastic scattering processes. Long-range temperature-dependent stripe order is only found below optimal doping. At higher doping, short-range temperature-independent correlations are present up to the highest doping measured. This transformation is distinct from and preempts the pseudogap critical doping. We argue that the doping and temperature-independent short-range correlations originate from unresolved electron-phonon coupling that broadly peaks at the stripe ordering vector. In La2-xSrxCuO4, long-range static stripe order vanishes around optimal doping and we discuss both quantum critical and crossover scenarios.

Anatomic and functional discordance among patients with non-obstructive coronary disease

Background

Non-obstructive coronary artery disease (CAD) is associated with increased adverse cardiovascular (CV) events. However, it is unclear if functional stenosis, as assessed by FFRCT <0.80, further stratifies risk among patients with non-obstructive CAD and which factors contribute to this anatomic-functional discordance (stenosis <50% and FFRCT <0.80).

Purpose

We hypothesized that patients with anatomically non-obstructive CAD by CTA and an abnormal FFRCT value of ≤0.80 have a phenomenon termed anatomic-functional discordance, and this discordance would be associated with increased adverse outcomes.

Methods

Patients in the ADVANCE (Assessing Diagnostic Value of Non-invasive FFRCT in Coronary Care) Registry who had exclusively non-obstructive CAD (anatomic stenosis <50%) were stratified by FFRCT >0.80 in all coronary vessels (concordant) vs. FFRCT <0.80 in at least one vessel (discordant). Baseline patient demographics, coronary computed tomography angiography findings, downstream testing and clinical outcomes were compared between groups. The primary composite endpoint included revascularization, CV hospitalization, heart failure, arrhythmia, non-fatal myocardial infarction, unplanned hospitalization for an acute coronary syndrome leading to urgent revascularization, and all-cause death.

Results

Among 1,261 patients with non-obstructive CAD, 543 (43.1%) had functional stenosis with FFRCT <0.80. Patients in the discordant group were older, more likely to have hypertension, hyperlipidemia, and had significantly higher indexed left ventricular (LV) mass and significantly lower coronary volume-to-mass ratios when compared with patients in the concordant group. Downstream non-invasive testing was more common among patients with discordance (35.9% vs 20.2%, p<0.0001) and more frequently resulted in a positive downstream test (10.3% vs. 3.3%, p<0.0001). Invasive angiography was also more common among patients with discordance (25.2% vs. 11.6%, p<0.0001). Anatomic-functional discordance was associated with higher rates of CV hospitalization and percutaneous coronary intervention (both p<0.0001), but no significant difference in all-cause death. After adjustment, anatomic-functional discordance was associated with a significantly higher risk of the composite endpoint (adjusted HR 2.79, 95% CI 1.67–4.65), Figure 1. As shown in Figure 2, the more vessels with anatomic-functional discordance, the higher the rate of adverse cardiac events.

Conclusion

Anatomic-functional discordance was present in nearly half of patients with exclusively non-obstructive CAD. The lower coronary volume: LV mass ratio may reflect abnormal coronary physiology at lower thresholds of anatomical stenosis among those with discordance. Compared to patients with concordance, patients with discordance had worse clinical outcomes suggesting that anatomic-functional discordance may stratify risk for adverse CV events among patients with non-obstructive CAD.

Funding Acknowledgement

Type of funding sources: Other. Main funding source(s): The analysis was an investigator-initiated analysis sponsored by Heart Flow.

Epigenetic regulation of ecotype-specific expression of the heat-activated transposon ONSEN

Transposable elements are present in a wide variety of organisms; however, our understanding of the diversity of mechanisms involved in their activation is incomplete. In this study, we analyzed the transcriptional activation of the ONSEN retrotransposon, which is activated by high-temperature stress in Arabidopsis thaliana. We found that its transcription is significantly higher in the Japanese ecotype Kyoto. Considering that transposons are epigenetically regulated, DNA methylation levels were analyzed, revealing that CHH methylation was reduced in Kyoto compared to the standard ecotype, Col-0. A mutation was also detected in the Kyoto CMT2 gene, encoding a CHH methyltransferase, suggesting that it may be responsible for increased expression of ONSEN. CHH methylation is controlled by histone modifications through a self-reinforcing loop between DNA methyltransferase and histone methyltransferase. Analysis of these modifications revealed that the level of H3K9me2, a repressive histone marker for gene expression, was lower in Kyoto than in Col-0. The level of another repressive histone marker, H3K27me1, was decreased in Kyoto; however, it was not impacted in a Col-0 cmt2 mutant. Therefore, in addition to the CMT2 mutation, other factors may reduce repressive histone modifications in Kyoto.

Evaluation of standard treatments for managing adult Japanese patients with inadequately controlled moderate-to-severe atopic dermatitis: Two-year data from the ADDRESS-J disease registry

Atopic dermatitis (AD), a chronic relapsing inflammatory skin disease with a high disease burden, is one of the most common dermatological conditions in Japan. Herein, we report the disease profiles and current AD treatment during 2‐year management of Japanese adults with moderate‐to‐severe AD. ADDRESS‐J was a prospective, longitudinal, observational study that evaluated real‐world effectiveness and safety of current AD treatments of adult patients with moderate‐to‐severe AD (Investigator's Global Assessment score 3 or 4) in Japan. The maximum follow‐up period was 2 years. Among 300 patients enrolled, 288 had ≥1 post‐baseline evaluation and were analyzed (mean age, 35.5 years; 60.1% male). Almost all patients (99.7%) received topical therapy; the most commonly used therapy was topical corticosteroids of the second‐highest potency (86.5%) (e.g., 0.1% mometasone furoate) followed by medium‐potency topical corticosteroids (50.3%) (e.g., 0.05% clobetasol butyrate). At month 12 of the study, 10.4% of patients had Investigator's Global Assessment 0/1, similarly at month 24 (10.8%). A total of 132 patients (45.8%) had ≥1 AD flare‐up during the observation period, with the majority of first flares occurring within the first year of the study. Various physician‐ and patient‐reported outcomes improved considerably during the first 3 months of the study, with only minor changes after this time. In this cohort, 16.7% of patients had skin infections requiring treatment; 7.3% had adverse events (AE) potentially related to treatment; 1.7% had serious AE; and 1.0% had treatment discontinuations due to AE. Limitations include missing data at later timepoints and the inclusion criteria limiting generalizability. In summary, this analysis of the ADDRESS‐J study showed that some patients with moderate or severe AD respond to conventional therapies, while others do not. For those with inadequately controlled moderate‐to‐severe AD, the newly emerged systemic agents, such as biologics, may provide a potential strategy for long‐term disease management.

Lactose-Appended Hydroxypropyl-β-Cyclodextrin Lowers Cholesterol Accumulation and Alleviates Motor Dysfunction in Niemann-Pick Type C Disease Model Mice

Niemann-Pick disease type C (NPC) is characterized by the accumulation of glycolipids such as free cholesterol, sphingomyelin, and gangliosides in late endosomes/lysosomes (endolysosomes) due to abnormalities in the membrane proteins NPC1 or NPC2. The main symptoms of NPC caused by free cholesterol accumulation in various tissues vary depending on the time of onset, but hepatosplenomegaly and neurological symptoms accompanied by decreased motor, cognitive, and mental functions are observed in all age groups. However, the efficacy of NPC treatment remains limited. Herein, we have fabricated lactose-appended hydroxypropyl-β-cyclodextrin (Lac-HPβCD) and evaluated its lowering effects on cholesterol accumulation in NPC model mice. We reveal that Lac-HPβCD lowers cholesterol accumulation in the liver and spleen by reducing the amount of free cholesterol. Moreover, Lac-HPβCD reduces the amount of free cholesterol in the cerebrum and slightly alleviates motor dysfunction. These results suggest that Lac-HPβCD has potential for the treatment of NPC.

<i>In Vivo</i> Digestibility of Carbohydrate Rich in Isomaltomegalosaccharide Produced from Starch by Dextrin Dextranase

Slowly digestible carbohydrates are needed for nutritional support in diabetic patients with malnutrition. They are a good source of energy and have the advantage that their consumption produces a low postprandial peak in blood glucose levels because they are slowly and completely digested in the small intestine. A high-amount isomaltomegalosaccharide containing carbohydrate (H-IMS), made from starch by dextrin dextranase, is a mixture of glucose polymers which has a continuous linear structure of α-1,6-glucosidic bonds and a small number of α-1,4-glucosidic bonds at the reducing ends. It has a broad degree of polymerization (DP) distribution with glucans of DP 10－30 as the major component. In our previous study, H-IMS has been shown to exhibit slow digestibility in vitro and not to raise postprandial blood glucose to such levels as that raised by dextrin in vivo. This marks it out as a potentially useful slowly digestible carbohydrate, and this study aimed to evaluate its in vivo digestibility. The amount of breath hydrogen emitted following oral administration of H-IMS was measured to determine whether any indigestible fraction passed through to and was fermented in the large intestine. Total carbohydrate in the feces was also measured. H-IMS, like glucose and dextrin, did not result in breath hydrogen excretion. Carbohydrate excretion with dietary H-IMS was no different from that of glucose or water. These results show that the H-IMS is completely digested and absorbed in the small intestine, indicating its potential as a slowly digestible carbohydrate in the diet of diabetic patients.

High-performance pipeline for MutMap and QTL-seq

Summary

Bulked segregant analysis implemented in MutMap and QTL-seq is a powerful and efficient method to identify loci contributing to important phenotypic traits. However, the previous pipelines were not user-friendly to install and run. Here, we describe new pipelines for MutMap and QTL-seq. These updated pipelines are approximately 5-8 times faster than the previous pipeline, are easier for novice users to use, and can be easily installed through bioconda with all dependencies.

Availability

The new pipelines of MutMap and QTL-seq are written in Python and can be installed via bioconda. The source code and manuals are available online (MutMap: https://github.com/YuSugihara/MutMap, QTL-seq: https://github.com/YuSugihara/QTL-seq).

Red-Beet Betalain Pigments Inhibit Amyloid-β Aggregation and Toxicity in Amyloid-β Expressing Caenorhabditis elegans

Betalain pigments are mainly produced by plants belonging to the order of Caryophyllales. Betalains exhibit strong antioxidant activity and responds to environmental stimuli and stress in plants. Recent reports of antioxidant, anti-inflammatory and anti-cancer properties of betalain pigments have piqued interest in understanding their biological functions. We investigated the effects of betalain pigments (betanin and isobetanin) derived from red-beet on amyloid-β (Aβ) aggregation, which causes Alzheimer's disease. Non-specific inhibition of Aβ aggregation against Aβ40 and Aβ42 by red-beet betalain pigments, in vitro was demonstrated using the thioflavin t fluorescence assay, circular dichroism spectroscopy analysis, transmission electron microscopy and nuclear magnetic resonance (NMR) analysis. Furthermore, we examined the ability of red-beet betalain pigments to interfere with Aβ toxicity by using the transgenic Caenorhabditis elegans model, which expresses the human Aβ42 protein intracellularly within the body wall muscle. It responds to Aβ-toxicity with paralysis and treatment with 50 μM red-beet betalain pigments significantly delayed the paralysis of C. elegans. These results suggest that betalain pigments reduce Aβ-induced toxicity.

Pharmacokinetic and pharmacodynamic similarity between SAR341402 insulin aspart and Japan-approved NovoRapid in healthy Japanese subjects

This study compared the pharmacokinetic and glucodynamic profiles of biosimilar SAR341402 insulin aspart to Japan-approved insulin aspart (NovoRapid) in healthy Japanese males. In this single-center, randomized, double-blind, single-dose, two-period, crossover study, subjects received 0.3 U/kg of SAR341402 or NovoRapid before undergoing a 10 h euglycemic clamp procedure. Plasma insulin aspart concentrations and blood glucose levels were measured, and glucose infusion rates (GIRs) were assessed. Primary endpoints were maximum plasma insulin aspart concentration (INS-C_max), area under the plasma insulin concentration–time curve to the last quantifiable concentration (INS-AUC_last), area under the GIR–time curve during the clamp (GIR-AUC_0–10 h), and maximum GIR (GIR_max). Forty subjects were randomized with 39 completing both treatment periods. Pharmacokinetic exposure showed a mean ratio between products of 1.00 (90% confidence interval [CI] 0.94–1.05) for INS-C_max and 1.02 (90% CI 1.00–1.04) for INS-AUC_last. Glucodynamic activity showed a mean ratio between products of 1.00 (95% CI 0.93–1.06) for GIR-AUC_0–10 h and 1.01 (95% CI 0.95–1.08) for GIR_max. The 90% CIs for pairwise treatment ratios were within the predefined equivalence range of 0.80–1.25. Both treatments were well tolerated. We concluded that similar pharmacokinetic exposure and glucodynamic potency were shown for SAR341402 and NovoRapid in healthy Japanese males.

Nonmagnetic J=0 State and Spin-Orbit Excitations in K_{2}RuCl_{6}

Spin-orbit Mott insulators composed of t_{2g}^{4} transition metal ions may host excitonic magnetism due to the condensation of spin-orbital J=1 triplons. Prior experiments suggest that the 4d antiferromagnet Ca_{2}RuO_{4} embodies this notion, but a J=0 nonmagnetic state as a basis of the excitonic picture remains to be confirmed. We use Ru L_{3}-edge resonant inelastic x-ray scattering to reveal archetypal J multiplets with a J=0 ground state in the cubic compound K_{2}RuCl_{6}, which are well described within the LS-coupling scheme. This result highlights the critical role of unquenched orbital moments in 4d-electron compounds and calls for investigations of quantum criticality and excitonic magnetism on various crystal lattices.

Preparation and Analysis of α-1,6 Glucan as a Slowly Digestible Carbohydrate

Carbohydrate materials that produce lower postprandial blood glucose increase are required for diabetic patients. To develop slowly digestible carbohydrates, the effect of degree of polymerization (DP) of α-1,6 glucan on its digestibility was investigated in vitro and in vivo. We prepared four fractions of α-1,6 glucan composed primarily of DP 3–9, DP 10–30, DP 31–150, and DP 151+ by fractionating a dextran hydrolysate. An in vitro experiment using digestive enzymes showed that the glucose productions of DP 3–9, DP 10–30, DP 31–150, and DP 151+ were 70.3, 53.4, 28.2, and 19.2 % in 2 h, and 92.1, 83.9, 39.6, and 33.3 % in 24 h relative to dextrin, respectively. An in vivo glycemic response showed that the incremental area under the curve (iAUC) of blood glucose levels of α-1,6 glucan with DP 3–9, DP 10–30, DP 31–150, and DP 151+ were 99.5, 84.3, 65.4, and 40.1 % relative to dextrin, respectively. These results indicated that α-1,6 glucan with higher DP had stronger resistance to digestion and produced a smaller blood glucose response. DP 10–30 showed significantly lower maximum blood glucose levels than dextrin; however, no significant difference was observed in iAUC, indicating that DP 10–30 was slowly digestible. In addition, α-1,6 glucan was also produced using an enzymatic reaction with dextrin dextranase (DDase). This produced similar results to DP 10–30. The DDase product can be synthesized from dextrin at low cost. This glucan is expected to be useful as a slowly digestible carbohydrate source.

Trans-stenotic pressure gradient as derived from CT improves patient management: ADVANCE registry

Background

The change in fractional flow reserve derived from CT (FFRCT) value across a coronary stenosis (ΔFFRCT) improves the physiological characterization of coronary artery disease (CAD). The role of ΔFFRCT in guiding risk-stratification and downstream testing in patients with stable CAD is unknown.

Purpose

To investigate the incremental value of ΔFFRCT at predicting early revascularization and improving efficacy of resource utilization.

Methods

Patients with CAD on CT coronary angiography (CTCA) were enrolled in an international multicenter registry. Patients with non-evaluable FFRCT analysis were excluded. The CTCA was assessed for: stenosis severity as per CAD-Reporting and Data System (CAD-RADS), lesion length and lesion-specific FFRCT measured 2 cm distal to stenosis. Risk factors and actual treatment (revascularization vs medical therapy) at 90-day follow-up were recorded. Multivariable logistic regression analysis for early revascularization was conducted. The incremental discrimination for revascularization prediction was compared among 3 models (model 1: risk factors + lesion length and location + CAD-RADS; model 2: model 1 + lesion-specific FFRCT; model 3: model 2 + ΔFFRCT). Simulating ICA referral for patients with CAD-RADS ≥3 and lesion-specific FFRCT ≤0.8, the potential impact of ΔFFRCT at reducing ICA referral and improving the ratio of subsequent revascularization was assessed.

Results

Of 4730 patients (66±10 years; 34% female), 2092 (42.7%) underwent ICA and 1168 (24.7%) underwent early revascularization. With increasing ΔFFRCT, a higher incidence of revascularization (Figure 1A) and an increase in the revascularization to ICA ratio was observed (Figure 1B). ΔFFRCT &gt;0.13 was the optimal cut-off for predicting revascularization as determined by the Youden index. ΔFFRCT remained an independent predictor for early revascularization (odds ratio per 0.05 increase with 95% CI, 1.31 [1.26–1.35]; p&lt;0.0001) after adjusting for risk factors, CAD-RADS, lesion length and location, and FFRCT. Among the 3 models, model 3, which included ΔFFRCT showed the highest AUC and improved discrimination power compared to model 2 (0.87 [0.86–0.88] vs 0.85 [0.84–0.86]; p&lt;0.0001] (Figure 2), with the greatest incremental value for ΔFFRCT observed in patients with lesion-specific FFRCT between 0.71–0.80. In patients with CAD-RADS ≥3 and lesion-specific FFRCT ≤0.8, a diagnostic strategy incorporating ΔFFRCT &gt;0.13 would potentially reduce ICA referral by 32.2% (1638 to 1110) and improve the revascularization to ICA ratio from 65.2% [1068/1638] to 73.1% [811/1110].

Conclusions

The characterization of CAD with ΔFFRCT improves the identification of patients requiring early revascularization as compared to a standard diagnostic strategy of CTCA with FFRCT, particularly for those with lesion-specific FFRCT of 0.71–0.80. ΔFFRCT has the potential to aid decision making for ICA referral and improve the efficiency of resource utilization.

Funding Acknowledgement

Type of funding sources: Private company. Main funding source(s): HeartFlow, Inc., Redwood City, CA, USA ΔFFRCT and actual treatmentROC curve for early revascularization

Comparison of valve durability among different transcatheter and surgical aortic valve prostheses: a network meta-analysis

Background

Durability of different transcatheter heart valve (THV) is critical as the indication of transcatheter aortic valve replacement (TAVR) expands to patients with longer life-expectancy.

Purpose

We aimed to compare the durability of THV systems (balloon-expandable [BE] and self-expandable [SE]) and surgical aortic valve replacement (SAVR) prosthesis.

Methods

PUBMED and EMBASE were searched through February 2021 for randomized trials investigating parameters of valve durability after TAVR and/or SAVR in severe aortic stenosis. A network meta-analysis using random-effect model was performed. Synthesis was performed with 5-year follow-up data for echocardiographic outcomes and longest available follow-up data for clinical outcomes.

Results

Ten trials with a total of 9,388 patients (BE-THV: 2,562; SE-THV 2,863; SAVR:3,963) were included. Follow-up ranged from 1–6 years. SE-THV demonstrated significantly larger effective orifice area, lower mean aortic valve gradient (AVG), and less increase in mean AVG at 5-years compared to BE-THV and SAVR (Figure 1). Structural valve deterioration (SVD) was less frequent in SE-THV compared to BE-THV and SAVR (HR 0.14, 95% CI 0.07–0.27; HR 0.34, 95% CI 0.24–0.47, respectively) (Figure 1). Total moderate-severe aortic regurgitation and re-intervention was more frequent in BE-THV (HR 4.21, 95% CI 2.40–7.39; HR 2.22, 95% CI 1.16–4.26, respectively) and SE-THV (HR 7.51, 95% CI 3.89–14.5; HR 2.86, 95% CI 1.59–5.13, respectively) compared to SAVR.

Conclusion

TAVR with SE-THV demonstrated favorable forward-flow hemodynamics and lowest risk of SVD compared to BE-THV and SAVR at mid-term. However, both THV systems suffer an increased risk of aortic regurgitation and re-intervention, and long-term data from newer generation valve is warranted.

Funding Acknowledgement

Type of funding sources: None.

P2Y12 inhibitors in patients with non-ST-segment elevation acute coronary syndrome: systematic review and network meta-analysis of randomized trials

Background

Based on a recent randomized control trial (RCT), prasugrel is recommended in preference to ticagrelor for patients with non-ST-segment elevation ACS (NSTE-ACS), however, limited data exists.

Objectives

We aimed to investigate the effect of P2Y12 inhibitors on ischemic and bleeding events in NSTE-ACS patients.

Methods

Clinical trials enrolling NSTE-ACS patients were identified and relevant data was extracted. We performed a network meta-analysis on efficacy and safety outcomes.

Results

Our study including a total of 37, 268 patients with NSTE-ACS from 11 RCTs. Prasugrel decreased major adverse cardiovascular events (MACE) when compared to clopidogrel (Hazard ratio (HR): 0.84; 95% confidence interval (CI) [0.71–0.99]). For MACE, prasugrel showed the highest likelihood of event reduction (P-score=0.97) in comparison to ticagrelor (P-score=0.29) and clopidogrel (P-score=0.24). Prasugrel decreased myocardial infarction (HR: 0.82; 95% CI [0.68–0.99]) but increased major bleeding without statistical significance (HR: 1.30; 95% CI [0.97–1.74]) when compared to clopidogrel. Ticagrelor reduced cardiovascular death (HR: 0.79; 95% CI [0.66–0.94]) but increased major bleeding (HR: 1.33; 95% CI [1.00–1.77], p=0.049) in comparison to clopidogrel. There was no significant difference between prasugrel and ticagrelor for each endpoint, but prasugrel had higher likelihood of event reduction than ticagrelor for all endpoints except cardiovascular death.

Conclusions

Prasugrel and ticagrelor had comparable risk for each endpoint, but prasugrel had the highest probability being the best treatment in reducing the primary endpoint. This study highlights the need for further large-scale RCTs to investigate the optimal P2Y12 inhibitor selection in NSTE-ACS patients.

Funding Acknowledgement

Type of funding sources: None.

Polyploid QTL-seq towards rapid development of tightly linked DNA markers for potato and sweetpotato breeding through whole-genome resequencing

Potato (Solanum tuberosum L.) and sweetpotato (Ipomoea batatas L.), which are nutritionally and commercially important tuberous crops, possess a perplexing heredity because of their autopolyploid genomes. To reduce cross-breeding efforts for selecting superior cultivars from progenies with innumerable combinations of traits, DNA markers tightly linked to agronomical traits are required. To develop DNA markers, we developed a method for quantitative trait loci (QTL) mapping using whole-genome next-generation sequencing (NGS) in autopolyploid crops. To apply the NGS-based bulked segregant method, QTL-seq was modified. (1) Single parent-specific simplex (unique for one homologous chromosome) single-nucleotide polymorphisms (SNPs), which present a simple segregation ratio in the progenies, were exploited by filtering SNPs by SNP index (allele frequency). (2) Clusters of SNPs, which were inherited unevenly between bulked progenies with opposite phenotypes, especially those with an SNP index of 0 for the bulk that did not display the phenotypes of interest, were explored. These modifications allowed for separate tracking of alleles located on each of the multiple homologous chromosomes. By applying this method, clusters of SNPs linked to the potato cyst nematode resistance H1 gene and storage root anthocyanin (AN) content were identified in tetraploid potato and hexaploid sweetpotato, respectively, and completely linked DNA markers were developed at the site of the presented SNPs. Thus, polyploid QTL-seq is a versatile method that is free from specialized manipulation for sequencing and construction of elaborate linkage maps and facilitates rapid development of tightly linked DNA markers in autopolyploid crops, such as potato and sweetpotato.

Sat-BSA: an NGS-based method using local de novo assembly of long reads for rapid identification of genomic structural variations associated with agronomic traits

Advances in next generation sequencing (NGS)-based methodologies have accelerated the identifications of simple genetic variants such as point mutations and small insertions/deletions (InDels). Structural variants (SVs) including large InDels and rearrangements provide vital sources of genetic diversity for plant breeding. However, their analysis remains a challenge due to their complex nature. Consequently, novel NGS-based approaches are needed to rapidly and accurately identify SVs. Here, we present an NGS-based bulked-segregant analysis (BSA) technique called Sat-BSA (SVs associated with traits) for identifying SVs controlling traits of interest in crops. Sat-BSA targets allele frequencies at all SNP positions to first identify candidate genomic regions associated with a trait, which is then reconstructed by long reads-based local de novo assembly. Finally, the association between SVs, RNA-seq-based gene expression patterns and trait is evaluated for multiple cultivars to narrow down the candidate genes. We applied Sat-BSA to segregating F₂ progeny obtained from crosses between turnip cultivars with different tuber colors and successfully isolated two genes harboring SVs that are responsible for tuber phenotypes. The current study demonstrates the utility of Sat-BSA for the identification of SVs associated with traits of interest in species with large and heterozygous genomes.

Deficiency in alcohol dehydrogenase 2 reduces arsenic in rice grains by suppressing silicate transporters

Paddy fields are anaerobic and facilitate arsenite (As(III)) elution from the soil. Paddy-field rice accumulates arsenic (As) in its grains because silicate transporters actively assimilate As(III) during the reproductive stage. Reducing the As level in rice grains is an important challenge for agriculture. Using a forward genetic approach, we isolated a rice (Oryza sativa) mutant, low arsenic line 3 (las3), whose As levels were decreased in aerial tissues, including grains. The low-As phenotype was not observed in young plants before heading (emergence of the panicle). Genetic analyses revealed that a deficiency in alcohol dehydrogenase (ADH) 2 by mutation is responsible for the phenotype. Among the three rice ADH paralogues, ADH2 was the most efficiently produced in root tissue under anaerobic conditions. In wild-type (WT), silicon and As concentrations in aerial tissues increased with growth. However, the increase was suppressed in las3 during the reproductive stage. Accordingly, the gene expression of two silicate transporters, Lsi1 and Lsi2, was increased in WT around the time of heading, whereas the increase was suppressed in las3. These results indicate that the low-As phenotype in las3 is due to silicate transporter suppression. Measurement of intracellular pH by 31P-nuclear magnetic resonance revealed intracellular acidification of las3 roots under hypoxia, suggesting that silicate transporter suppression in las3 might arise from an intracellular pH decrease, which is known to be facilitated by a deficiency in ADH activity under anaerobic conditions. This study provides valuable insight into reducing As levels in rice grains.

Lactose-appended β-cyclodextrin as an effective nanocarrier for brain delivery

The blood-brain barrier (BBB) prevents the permeability of drugs into the brain, and as such limits the management of various brain diseases. To overcome this barrier, drug-encapsulating nanoparticles or vesicles, drug conjugates, and other types of drug delivery systems (DDSs) have been developed. However, the brain-targeting ability of nanoparticles or vesicles is still insufficient. Recently, among the various brain-targeting ligands previously studied for facilitating transcellular BBB transport, several sugar-appended nanocarriers for brain delivery were identified. Meanwhile, cyclodextrins (CyDs) have been used as nanocarriers for drug delivery since they can encapsulate hydrophobic compounds with high biocompatibility. Therefore, in this study, we created various sugar-appended β-cyclodextrins (β-CyDs) to discover novel brain-targeting ligands. As a result, of the six sugar-appended CyDs, lactose-appended β-CyD (Lac-β-CyD) showed greater cellular uptake in hCMEC/D3 cells, human brain microvascular endothelial cells, than other sugar-appended β-CyDs did. In addition, the permeability of Lac-β-CyD within the in vitro human BBB model was greater than that of other sugar-appended β-CyDs. Moreover, Lac-β-CyD significantly accumulated in the mouse brain after intravenous administration. Thus, Lac-β-CyD efficiently facilitated the accumulation of the model drug into the mouse brain. These findings suggest that Lac-β-CyD has the potential to be a novel carrier for drugs across the BBB.

Lumi-Map, a Real-Time Luciferase Bioluminescence Screen of Mutants Combined with MutMap, Reveals Arabidopsis Genes Involved in PAMP-Triggered Immunity

Plants recognize pathogen-associated molecular patterns (PAMPs) to activate PAMP-triggered immunity (PTI). However, our knowledge of PTI signaling remains limited. In this report, we introduce Lumi-Map, a high-throughput platform for identifying causative single-nucleotide polymorphisms (SNPs) for studying PTI signaling components. In Lumi-Map, a transgenic reporter plant line is produced that contains a firefly luciferase (LUC) gene driven by a defense gene promoter, which generates luminescence upon PAMP treatment. The line is mutagenized and the mutants with altered luminescence patterns are screened by a high-throughput real-time bioluminescence monitoring system. Selected mutants are subjected to MutMap analysis, a whole-genome sequencing-based method of rapid mutation identification, to identify the causative SNP responsible for the luminescence pattern change. We generated nine transgenic Arabidopsis reporter lines expressing the LUC gene fused to multiple promoter sequences of defense-related genes. These lines generate luminescence upon activation of FLAGELLIN-SENSING 2 (FLS2) by flg22, a PAMP derived from bacterial flagellin. We selected the WRKY29-promoter reporter line to identify mutants in the signaling pathway downstream of FLS2. After screening 24,000 ethylmethanesulfonate-induced mutants of the reporter line, we isolated 22 mutants with altered WRKY29 expression upon flg22 treatment (abbreviated as awf mutants). Although five flg22-insensitive awf mutants harbored mutations in FLS2 itself, Lumi-Map revealed three genes not previously associated with PTI. Lumi-Map has the potential to identify novel PAMPs and their receptors as well as signaling components downstream of the receptors.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

A novel WD40-repeat protein involved in formation of epidermal bladder cells in the halophyte quinoa

Halophytes are plants that grow in high-salt environments and form characteristic epidermal bladder cells (EBCs) that are important for saline tolerance. To date, however, little has been revealed about the formation of these structures. To determine the genetic basis for their formation, we applied ethylmethanesulfonate mutagenesis and obtained two mutants with reduced levels of EBCs (rebc) and abnormal chloroplasts. In silico subtraction experiments revealed that the rebc phenotype was caused by mutation of REBC, which encodes a WD40 protein that localizes to the nucleus and chloroplasts. Phylogenetic and transformant analyses revealed that the REBC protein differs from TTG1, a WD40 protein involved in trichome formation. Furthermore, rebc mutants displayed damage to their shoot apices under abiotic stress, suggesting that EBCs may protect the shoot apex from such stress. These findings will help clarify the mechanisms underlying EBC formation and function.

Developmental Modulation of Root Cell Wall Architecture Confers Resistance to an Oomycete Pathogen

The cell wall is the primary interface between plant cells and their immediate environment and must balance multiple functionalities, including the regulation of growth, the entry of beneficial microbes, and protection against pathogens. Here, we demonstrate how API, a SCAR2 protein component of the SCAR/WAVE complex, controls the root cell wall architecture important for pathogenic oomycete and symbiotic bacterial interactions in legumes. A mutation in API results in root resistance to the pathogen Phytophthora palmivora and colonization defects by symbiotic rhizobia. Although api mutant plants do not exhibit significant overall growth and development defects, their root cells display delayed actin and endomembrane trafficking dynamics and selectively secrete less of the cell wall polysaccharide xyloglucan. Changes associated with a loss of API establish a cell wall architecture with altered biochemical properties that hinder P. palmivora infection progress. Thus, developmental stage-dependent modifications of the cell wall, driven by SCAR/WAVE, are important in balancing cell wall developmental functions and microbial invasion.

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The SCAR protein API controls actin and endomembrane trafficking dynamics

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SCAR proteins of several plant species can support symbiosis and pathogen infection

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A mutation in API affects specific biochemical properties of plant cell walls

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An altered wall architecture results in root resistance to Phytophthora palmivora

Arabidopsis SMN2/HEN2, Encoding DEAD-Box RNA Helicase, Governs Proper Expression of the Resistance Gene SMN1/RPS6 and Is Involved in Dwarf, Autoimmune Phenotypes of mekk1 and mpk4 Mutants

In Arabidopsis thaliana, a mitogen-activated protein kinase pathway, MEKK1-MKK1/MKK2-MPK4, is important for basal resistance and disruption of this pathway results in dwarf, autoimmune phenotypes. To elucidate the complex mechanisms activated by the disruption of this pathway, we have previously developed a mutant screening system based on a dwarf autoimmune line that overexpressed the N-terminal regulatory domain of MEKK1. Here, we report that the second group of mutants, smn2, had defects in the SMN2 gene, encoding a DEAD-box RNA helicase. SMN2 is identical to HEN2, whose function is vital for the nuclear RNA exosome because it provides non-ribosomal RNA specificity for RNA turnover, RNA quality control and RNA processing. Aberrant SMN1/RPS6 transcripts were detected in smn2 and hen2 mutants. Disease resistance against Pseudomonas syringae pv. tomato DC3000 (hopA1), which is conferred by SMN1/RPS6, was decreased in smn2 mutants, suggesting a functional connection between SMN1/RPS6 and SMN2/HEN2. We produced double mutants mekk1smn2 and mpk4smn2 to determine whether the smn2 mutations suppress the dwarf, autoimmune phenotypes of the mekk1 and mpk4 mutants, as the smn1 mutations do. As expected, the mekk1 and mpk4 phenotypes were suppressed by the smn2 mutations. These results suggested that SMN2 is involved in the proper function of SMN1/RPS6. The Gene Ontology enrichment analysis using RNA-seq data showed that defense genes were downregulated in smn2, suggesting a positive contribution of SMN2 to the genome-wide expression of defense genes. In conclusion, this study provides novel insight into plant immunity via SMN2/HEN2, an essential component of the nuclear RNA exosome.

High-Temperature Charge-Stripe Correlations in La_{1.675}Eu_{0.2}Sr_{0.125}CuO_{4}

We use resonant inelastic x-ray scattering to investigate charge-stripe correlations in La_{1.675}Eu_{0.2}Sr_{0.125}CuO_{4}. By differentiating elastic from inelastic scattering, it is demonstrated that charge-stripe correlations precede both the structural low-temperature tetragonal phase and the transport-defined pseudogap onset. The scattering peak amplitude from charge stripes decays approximately as T^{-2} towards our detection limit. The in-plane integrated intensity, however, remains roughly temperature independent. Therefore, although the incommensurability shows a remarkably large increase at high temperature, our results are interpreted via a single scattering constituent. In fact, direct comparison to other stripe-ordered compounds (La_{1.875}Ba_{0.125}CuO_{4}, La_{1.475}Nd_{0.4}Sr_{0.125}CuO_{4}, and La_{1.875}Sr_{0.125}CuO_{4}) suggests a roughly constant integrated scattering intensity across all these compounds. Our results therefore provide a unifying picture for the charge-stripe ordering in La-based cuprates. As charge correlations in La_{1.675}Eu_{0.2}Sr_{0.125}CuO_{4} extend beyond the low-temperature tetragonal and pseudogap phase, their emergence heralds a spontaneous symmetry breaking in this compound.

Mortality after transcatheter versus surgical aortic valve replacement: an updated meta-analysis of randomised trials

Background

To determine whether transcatheter aortic valve implantation (TAVI) improves early (30-day) and midterm (1-year) mortality compared with surgical aortic valve replacement (SAVR), we performed an updated meta-analysis of all the currently available randomised controlled trials (RCTs).

Methods

To identify all RCTs providing both 30-day and 1‑year mortality after TAVI versus SAVR, PubMed and ClinicalTrials.gov were searched up to and including July 2019. A risk difference (RD) and its 95% confidence interval were generated using data of prespecified outcomes in both the TAVI and SAVR groups. Study-specific estimates were pooled using inverse variance-weighted averages of RDs in the random-effects model.

Results

We identified seven eligible high-quality RCTs including a total of 7631 as-treated patients. Pooled analyses demonstrated significantly lower 30-day (RD −0.60%; p = 0.046) and 1‑year all-cause mortality (RD −1.12%; p = 0.03) after TAVI than after SAVR. No funnel plot asymmetry was detected for 30-day and 1‑year mortality. Meta-regression analyses indicated that RDs of 30-day and 1‑year mortality between TAVI and SAVR were not modulated by mean Society of Thoracic Surgeons Predicted Risk of Mortality score. Bleeding complications at 30 days and 1 year and stage 2/3 acute kidney injury at 30 days were significantly less frequent after TAVI than after SAVR, whereas major vascular complications and new permanent pacemaker implantation at 30 days and 1 year were significantly more frequent after TAVI than after SAVR.

Conclusion

The best evidence from the present meta-analysis of all the currently available RCTs suggests that TAVI may reduce 30-day and 1‑year all-cause mortality compared with SAVR.

Electronic supplementary material

The online version of this article (10.1007/s12471-020-01378-1) contains supplementary material, which is available to authorized users.

Robust weak antilocalization due to spin-orbital entanglement in Dirac material Sr3SnO

The presence of both inversion (P) and time-reversal (T) symmetries in solids leads to a double degeneracy of the electronic bands (Kramers degeneracy). By lifting the degeneracy, spin textures manifest themselves in momentum space, as in topological insulators or in strong Rashba materials. The existence of spin textures with Kramers degeneracy, however, is difficult to observe directly. Here, we use quantum interference measurements to provide evidence for the existence of hidden entanglement between spin and momentum in the antiperovskite-type Dirac material Sr3SnO. We find robust weak antilocalization (WAL) independent of the position of EF. The observed WAL is fitted using a single interference channel at low doping, which implies that the different Dirac valleys are mixed by disorder. Notably, this mixing does not suppress WAL, suggesting contrasting interference physics compared to graphene. We identify scattering among axially spin-momentum locked states as a key process that leads to a spin-orbital entanglement.

Efficacy and safety of dupilumab in Japanese adults with moderate-to-severe atopic dermatitis: a subanalysis of three clinical trials

Background

Dupilumab, a human monoclonal antibody, blocks the shared receptor unit for interleukin‐4 and interleukin‐13. International phase II and III studies have evaluated the efficacy and safety of dupilumab in adults with moderate‐to‐severe atopic dermatitis (AD), but the effects of dupilumab in Japanese patients have not been reported.

Objectives

To evaluate the efficacy and safety of dupilumab in Japanese patients with moderate‐to‐severe AD.

Methods

We analysed the efficacy and safety of dupilumab in the Japanese cohorts of a 16‐week, phase IIb dose‐finding trial (AD‐1021; NCT01859988); a 16‐week, phase III, placebo‐controlled monotherapy trial (LIBERTY AD SOLO 1; NCT02277743) and a 52‐week, phase III, placebo‐controlled study of dupilumab with topical corticosteroids (LIBERTY AD CHRONOS; NCT02260986).

Results

Twenty‐seven, 106 and 117 Japanese patients were enrolled in AD‐1021, SOLO 1 and CHRONOS, respectively. Baseline disease severity was numerically higher in the Japanese cohort than in the overall study population. Generally, dupilumab significantly improved signs and symptoms of AD, including pruritus and patient quality of life, compared with placebo in the Japanese cohort, consistent with the overall study population. The combined safety profile of dupilumab in the Japanese cohort was similar to that in the total study populations; dupilumab was associated with an increased incidence of injection‐site reactions and conjunctivitis compared with placebo. Dupilumab was associated with rapid reduction in thymus and activation‐regulated chemokine and gradual IgE reductions.

Conclusions

Dupilumab alone or with topical corticosteroids improved signs and symptoms of AD, had an acceptable safety profile, and suppressed biomarkers of type 2 inflammation compared with placebo in Japanese adult patients with moderate‐to‐severe AD.

What's already known about this topic?

Differences in atopic dermatitis (AD) pathology have been reported between Asian and Western populations, in which distinct helper T‐cell activation profiles have been observed.

International clinical studies in adults with moderate‐to‐severe AD have evaluated the efficacy and safety of dupilumab, which blocks interleukin‐4 and interleukin‐13, key molecules in type 2 inflammation.

The effects of dupilumab in Japanese patients specifically have not yet been reported.

What does this study add?

Dupilumab alone or with topical corticosteroids improved signs and symptoms of AD and had an acceptable safety profile compared with placebo in Japanese patients with moderate‐to‐severe AD.

The effects were comparable with those observed in the overall study population.

Reported immunological differences in AD pathology in Asian patients may be secondary to type 2 immune activation.

Plain language summary available online

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Next-generation sequencing-based bulked segregant analysis for QTL mapping in the heterozygous species Brassica rapa

An improved protocol of QTL-seq, an NGS-based method for bulked segregant analysis we previously developed in rice, allowed successful mapping of QTLs of interest in the highly heterozygous genome of B. rapa, demonstrating the power of this elegant method for genetic analyses in heterozygous species of economic importance. Recent advances in next-generation sequencing (NGS) and the various NGS-based methods developed for rapidly identifying candidate genes of interest have accelerated genetic analysis mainly in the model plants rice and Arabidopsis. Brassica rapa includes several economically important crops such as Chinese cabbage, turnip and various leafy vegetables. The application of NGS-based approaches for the analysis of B. rapa has been limited mainly due to its highly heterozygous genome and poor quality of the reference genome sequence currently available for this species. In this study, we have improved QTL-seq, a method for NGS-based bulked segregant analysis we previously developed in rice, extending its applicability for accelerating the genetic analysis and molecular breeding of B. rapa. Addition of new filters to the original QTL-seq pipeline allowed removal of spurious single-nucleotide polymorphisms caused by alignment/sequencing errors and variability between parents, significantly improving accuracy of the analysis. As proof of principle, we successfully applied the new approach to identify candidate genomic regions controlling flowering and trichome formation using segregating F2 progeny obtained from crosses made between cultivars of B. rapa showing contrasting phenotypes for these traits. We strongly believe that the improved QTL-seq method reported here will extend the applicability of NGS-based genetic analysis not only to B. rapa but also to other plant species of economic importance with heterozygous genomes.

Identification of candidate flowering and sex genes in white Guinea yam (D. rotundata Poir.) by SuperSAGE transcriptome profiling

Dioecy (distinct male and female individuals) and scarce to non-flowering are common features of cultivated yam (Dioscorea spp.). However, the molecular mechanisms underlying flowering and sex determination in Dioscorea are largely unknown. We conducted SuperSAGE transcriptome profiling of male, female and monoecious individuals to identify flowering and sex-related genes in white Guinea yam (D. rotundata), generating 20,236 unique tags. Of these, 13,901 were represented by a minimum of 10 tags. A total 88 tags were significantly differentially expressed in male, female and monoecious plants, of which 18 corresponded to genes previously implicated in flower development and sex determination in multiple plant species. We validated the SuperSAGE data with quantitative real-time PCR (qRT-PCR)-based analysis of the expression of three candidate genes.

We further investigated the flowering patterns of 1938 D. rotundata accessions representing diverse geographical origins over two consecutive years. Over 85% of accessions were either male or non-flowering, less than 15% were female, while monoecious plants were rare. Intensity of flowering varied between male and female plants, with the former flowering more abundantly than the latter. Candidate genes identified in this study can be targeted for further validation and to induce regular flowering in poor to non-flowering cultivars. Findings of the study provide important inputs for further studies aiming to overcome the challenge of flowering in yams and to improve efficiency of yam breeding.

Next generation long-culm rice with superior lodging resistance and high grain yield, Monster Rice 1

During late 1960s Green Revolution, researchers utilized semidwarf 1 (sd1) to improve the yield and lodging resistance in rice (Oryza sativa L.). However, sd1 has a negative effect to culm strength and biomass production. To increase yield dramatically in 21^th century, development of next generation long-culm rice for non-lodging and high grain yield independent of sd1 has been needed. The present study developed Monster Rice 1, a long-culm and heavy-panicle type of rice line and compared it with Takanari, a high-yielding semidwarf rice variety about yield and lodging resistance associated traits. Brown rice yield and bending moment at breaking of the basal elongated internode were higher in Monster Rice 1 than those in Takanari due to a large number of spikelets per panicle and thicker culm. Furthermore, to identify QTLs with superior alleles for these traits, QTL and haplotype analyses were performed using F₂ population and recombinant inbred lines derived from a cross between Monster Rice 1 and Takanari. The results from this study suggest that long-culm and heavy-panicle type of rice with a superior lodging resistance by culm strength can perform its high yield potential by using these identified QTLs contributing yield and lodging resistance.