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Pangenomes are collections of annotated genome sequences of multiple individuals of a species 1 . The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants 2 . Here we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes. An expanded catalogue of sequence variation in the crop includes structurally complex loci that are rich in gene copy number variation. To demonstrate the utility of the pangenome, we focus on four loci involved in disease resistance, plant architecture, nutrient release and trichome development. Novel allelic variation at a powdery mildew resistance locus and population-specific copy number gains in a regulator of vegetative branching were found. Expansion of a family of starch-cleaving enzymes in elite malting barleys was linked to shifts in enzymatic activity in micro-malting trials. Deletion of an enhancer motif is likely to change the developmental trajectory of the hairy appendages on barley grains. Our findings indicate that allelic diversity at structurally complex loci may have helped crop plants to adapt to new selective regimes in agricultural ecosystems., Competing Interests: Competing interests: K.B., C.D., M.E.J., S.M.K., Q.L., E.M., P.R.P., B.S., H.C.T., M.T.S.N., C.V. and M.W.R. are current or previous Carlsberg A/S employees. P.A.P. and D.V. are SECOBRA Recherches employees. The other authors declare no competing interests., (© 2024. The Author(s).)

Excessive salt intake causes hypertension and heart diseases. B-type natriuretic peptide (BNP) is a surrogate marker of heart disease, and a slightly elevated BNP level is associated with a poor prognosis. Our previous cross-sectional study demonstrated that plasma BNP has a significant positive association with daily salt intake in the general population. However, the relationship between changes in salt intake and changes in plasma BNP remains unknown. We recruited 3051 participants without hypertension or electrocardiogram abnormalities who underwent annual health check-ups for two consecutive years. Clinical parameters, including plasma BNP, were obtained, and daily salt intake was evaluated using urinary samples. Annual changes in these parameters were calculated. The median plasma BNP level was 12.9 pg/mL, and the daily salt intake was 8.73 ± 1.89 g. The annual changes in plasma BNP and daily salt intake were 4.79 ± 36.38% and 2.01 ± 21.80%, respectively. Participants in the highest quartile of annual changes in daily salt intake showed the largest annual changes in plasma BNP. Annual changes in plasma BNP indicated a significant positive association with daily salt intake. Moreover, multiple linear regression analyses revealed that annual changes in plasma BNP showed a significant positive association with daily salt intake after adjustments. Our study showed a significant positive relationship between annual changes in plasma BNP and annual changes in daily salt intake. The suppression of plasma BNP is therefore induced by salt intake restriction. The monitoring of plasma BNP while reducing salt intake may therefore prevent heart diseases and lead to improved prognoses in the general population without heart diseases., (© 2022. The Author(s), under exclusive licence to The Japanese Society of Hypertension.)

Carrot is a major source of provitamin A in a human diet. Two of the most important traits for carrot breeding are carotenoid contents and root color. To examine genomic regions related to these traits and develop DNA markers for carrot breeding, we performed an association analysis based on a general liner model using genome-wide single nucleotide polymorphism (SNPs) in two F 2 populations, both derived from crosses of orange root carrots bred in Japan. The analysis revealed 21 significant quantitative trait loci (QTLs). To validate the detection of the QTLs, we also performed a QTL analysis based on a composite interval mapping of these populations and detected 32 QTLs. Eleven of the QTLs were detected by both the association and QTL analyses. The physical position of some QTLs suggested two possible candidate genes, an Orange (Or) gene for visual color evaluation, and the α- and β-carotene contents and a chromoplast-specific lycopene β-cyclase (CYC-B) gene for the β/α carotene ratio. A KASP marker developed on the Or distinguished a quantitative color difference in a different, related breeding line. The detected QTLs and the DNA marker will contribute to carrot breeding and the understanding of carotenoid biosynthesis and accumulation in orange carrots., (© 2022. The Author(s).)

Membranous nephropathy (MN) is the leading cause of nephrotic syndrome in adults. We previously reported that the prevalence of phospholipase A2 receptor (PLA2R)- and thrombospondin type 1 domain containing 7A (THSD7A)-associated MN patients in Japan is 52.7% and 9.1%, respectively. In addition to PLA2R and THSD7A, we assessed the presence of newly discovered target antigens, neural epidermal growth factor-like 1 (NELL-1), semaphorin 3B (SEMA3B), and exostosin 1/exostosin 2 (Ext1/Ext2), in renal specimens from patients with primary and secondary MN by immunohistochemistry. We found enhanced glomerular staining of PLA2R, THSD7A, NELL-1, and Ext1/Ext2 in 53.6%, 8.7%, 1.5%, and 13.0% of the renal samples, respectively, in patients with primary MN. None of the patient specimens showed enhanced staining of SEMA3B. Enhanced glomerular staining of PLA2R, NELL-1, and Ext1/Ext2 was detected in 5.7%, 8.6%, and 22.9% of the patients with secondary MN, respectively. Based on our findings, we recommend the assessment of PLA2R, THSD7A and NELL-1 in addition to clinical information and IgG4 staining to differentiate between primary and secondary MN. This would aid in distinguishing secondary MN patients from primary MN patients who coincidentally have some secondary characteristics., (© 2022. The Author(s).)

Circadian fluctuation disorder of the intrarenal renin-angiotensin system (RAS) causes that of blood pressure (BP) and renal damage. In renal damage with an impaired glomerular filtration barrier, liver-derived angiotensinogen (AGT) filtered through damaged glomeruli regulates intrarenal RAS activity. Furthermore, glomerular permeability is more strongly affected by glomerular hypertension than by systemic hypertension. Thus, we aimed to clarify whether the circadian rhythm of intrarenal RAS activity is influenced by AGT filtered through damaged glomeruli due to glomerular capillary pressure. Rats with adriamycin nephropathy and an impaired glomerular filtration barrier were compared with control rats. In adriamycin nephropathy rats, olmesartan medoxomil (an angiotensin II type 1 receptor blocker) or hydralazine (a vasodilator) was administered, and the levels of intrarenal RAS components in the active and rest phases were evaluated. Moreover, the diameter ratio of afferent to efferent arterioles (A/E ratio), an indicator of glomerular capillary pressure, and the glomerular sieving coefficient (GSC) based on multiphoton microscopy in vivo imaging, which reflects glomerular permeability, were determined. Mild renal dysfunction was induced, and the systemic BP increased, resulting in increased A/E ratios in the adriamycin nephropathy rats compared with the control rats. Fluctuations in intrarenal RAS activity occurred in parallel with circadian fluctuations in glomerular capillary pressure, which disappeared with olmesartan treatment and were maintained with hydralazine treatment. Furthermore, the GSCs for AGT also showed similar changes. In conclusion, intrarenal RAS activity is influenced by the filtration of liver-derived AGT from damaged glomeruli due to circadian fluctuation disorder of the glomerular capillary pressure.

The use of DNA markers has revolutionized selection in crop breeding by linkage mapping and QTL analysis, but major problems still remain for polyploid species where marker-assisted selection lags behind the situation in diploids because of its high genome complexity. To overcome the complex genetic mode in the polyploids, we investigated the development of a strategy of genome-wide association study (GWAS) using single-dose SNPs, which simplify the segregation patterns associated polyploids, with respect to the development of DNA markers. In addition, we employed biparental populations for the GWAS, wherein the SNP allele frequency could be predicted. The research investigated whether the method could be used to effectively develop DNA markers for petal color in autohexaploid chrysanthemum (Chrysanthemum morifolium; 2n = 6x = 54). The causal gene for this trait is already-known CmCCD4a encoding a dioxygenase which cleaves carotenoids in petals. We selected 9,219 single-dose SNPs, out of total 52,489 SNPs identified by dd-RAD-Seq, showing simplex (1 × 0) and double-simplex (1 × 1) inheritance pattern according to alternative allele frequency with respect to the SNP loci in the F 1 population. GWAS, using these single-dose SNPs, discovered highly reproducible SNP markers tightly linked to the causal genes. This is the first report of a straightforward GWAS-based marker developing system for use in autohexaploid species.

Melatonin is a hormone produced by the pineal gland, predominantly at night, and plays a pivotal role in regulating the circadian rhythm as well as a variety of biological functions, including anti-inflammation, anti-oxidation, inhibition of sympathetic nerve activity, and preservation of endothelial cell function. The intrarenal renin-angiotensin system (RAS) is one of the most important contributors in the pathophysiology of chronic kidney disease (CKD) and hypertension, independent of the circulating RAS, due to sodium reabsorption and inflammation and fibrosis in the kidney. However, the relationship between melatonin secretion and intrarenal RAS activation has remained unknown. It has been recently shown that impaired nighttime melatonin secretion is associated with nighttime urinary angiotensinogen excretion, a surrogate marker of intrarenal RAS activation and renal damage in patients with CKD. Moreover, it has also been indicated that melatonin administered exogenously exercises antioxidant effects that ameliorate intrarenal RAS activation and renal injury in chronic progressive CKD animal models. As a result, the new roles of melatonin in suppressing RAS in the kidney via amelioration of reactive oxygen species have been clarified. Therefore, we review the relationship between melatonin and intrarenal RAS activation and indicate the possibility of a new strategy to suppress CKD, which is a risk factor for cardiovascular and end-stage renal diseases.

Intrarenal renin-angiotensin system (RAS) activation plays an important role in the development of hypertension and renal damage. However, the association between daytime and night-time intrarenal RAS activation and renal structural damage in normotensive IgA nephropathy patients is unclear. We investigated the relationships between urinary angiotensinogen (U-AGT) excretion, which reflects intrarenal RAS activity, and renal structural damage (i.e., endocapillary and mesangial cell hypercellularity, arteriolar hyalinosis and arteriosclerosis levels, and global glomerulosclerosis and tubulointerstitial fibrosis percentages) in 27 normotensive IgA nephropathy patients (age 39.2 ± 13.6 years, 10 men and 17 women, estimated glomerular filtration rate (eGFR) 74.0 ± 17.3 ml/min/1.73 m 2 , urinary protein excretion 0.58 ± 0.50 g/day, and U-AGT excretion 64.9 ± 100.6 μg/day). The arteriosclerosis level had a significant positive association with the daytime and night-time U-AGT excretion levels. By contrast, the endocapillary and mesangial cell hypercellularity and arteriolar hyalinosis levels and global glomerulosclerosis and tubulointerstitial fibrosis percentages did not correlate with the daytime and night-time U-AGT excretion levels. The daytime and night-time U-AGT excretion levels were higher in patients with arteriosclerotic changes than in patients without these changes. Multiple linear regression analysis revealed that the arteriosclerosis levels had a significant positive association with the U-AGT excretion levels at night after adjusting for age, sex, body mass index, and the eGFR. However, when diastolic BP was added as an independent variable, the relationship between U-AGT excretion and arteriosclerosis at night disappeared. In normotensive IgA nephropathy patients, intrarenal RAS activation at night due to nocturnal hypertension may be associated with arteriosclerosis.

Abnormal blood pressure (BP) variability (BPV), occurring as beat-to-beat, 24 h, and day-to-day fluctuations, is related to target organ damage. However, the associations between abnormal BPV and renal structural changes have not been clearly investigated. We evaluated the day time and night time BP s.d. and average real variability (ARV), which reflected short-term BPV, the night time to day time (N/D) ratio of systolic BP (SBP), and the 7-day BPV, in 29 normotensive IgA nephropathy (IgAN) patients. We further compared the results with renal structural changes. The degree of arteriosclerosis was positively correlated with age, s.d. of night time SBP and the N/D ratio of SBP, and was negatively correlated with the estimated glomerular filtration rate (eGFR). The degree of arteriolar hyalinosis was positively correlated with age, night time SBP, s.d. of day time and night time SBP, day time and night time ARV, the N/D ratio of SBP and 7-day SBP, and was negatively correlated with the eGFR. A multiple linear regression analysis revealed that the level of arteriolar hyalinosis, but not arteriosclerosis, was associated with the s.d. of night time SBP (β=0.63, P<0.01) or night time ARV (β=0.61, P<0.01) after adjustment for age, sex, body mass index, the eGFR and night time SBP. Multiple linear regression analyses indicated no significant correlation between the degree of arteriolar hyalinosis and the N/D ratio of SBP or 7-day SBP s.d. or between the degree of arteriosclerosis and any of the BPV parameters. In conclusion, short-term night time BPV was found to be associated with arteriolar hyalinosis in normotensive IgAN patients.

Activation of the intrarenal renin-angiotensin system (RAS) has a critical role in the pathophysiology of the circadian rhythm of blood pressure (BP) and renal injury, independent of circulating RAS. Although it is clear that the circulating RAS has a circadian rhythm, reports of a circadian rhythm in tissue-specific RAS are limited. Clinical studies evaluating intrarenal RAS activity by urinary angiotensinogen (AGT) levels have indicated that urinary AGT levels were equally low during both the daytime and nighttime in individuals without chronic kidney disease (CKD) and that urinary AGT levels were higher during the daytime than at nighttime in patients with CKD. Moreover, urinary AGT levels of the night-to-day (N/D) ratio of urinary AGT were positively correlated with the levels of N/D of urinary protein, albumin excretion and BP. In addition, animal studies have demonstrated that the expression of intrarenal RAS components, such as AGT, angiotensin II (AngII) and AngII type 1 receptor proteins, increased and peaked at the same time as BP and urinary protein excretion during the resting phase, and the amplitude of the oscillations of these proteins was augmented in a chronic progressive nephritis animal compared with a control. Thus, the circadian rhythm of intrarenal RAS activation may lead to renal damage and hypertension, which both are associated with diurnal variations in BP. It is possible that augmented glomerular permeability increases AGT excretion levels into the tubular lumen and that circadian fluctuation of glomerular permeability influences the circadian rhythm of the intrarenal RAS.

Circulating renin-angiotensin system (RAS) activation is maintained after renal function has deteriorated. The activation of the intrarenal RAS plays a critical role in the pathophysiology of chronic kidney disease (CKD), independently of the circulating RAS. However, the activation of intrarenal RAS and the chymase-dependent pathway after initiation of dialysis has not been clarified. We recruited 19 CKD patients (10 without dialysis and 9 with dialysis) who underwent a heminephrectomy. Circulating RAS was investigated before nephrectomy. The levels of intrarenal RAS components and chymase-positive cells were investigated using radioimmunoassay or immunoblot analysis on samples collected from the removed kidney. Renal damage was evaluated by the extent of tubulointerstitial fibrosis. No significant differences in circulating RAS between nondialysis and dialysis patients were found. However, intrarenal angiotensin II (AngII) and the extent of tubulointerstitial fibrosis in dialysis patients were significantly increased when compared with nondialysis patients. Prorenin and angiotensin-converting enzyme (ACE) levels were dramatically decreased in accordance with renal dysfunction. On the other hand, chymase-positive cells and AngII type 1 receptor (AT1R) expression was significantly increased in dialysis patients when compared with nondialysis patients. In multiple linear regression analyses, there were significant positive and negative relationships between the extent of interstitial fibrosis and angiotensinogen (β=0.45, P=0.042) and prorenin levels (β=-0.85, P<0.01), respectively. In summary, a decrease in prorenin and ACE expression and an increase in chymase, angiotensinogen and AT1R expression in the kidney may augment the intrarenal RAS activation and be associated with renal damage, even after initiation of dialysis.

Sweetpotato (Ipomoea batatas) is an autohexaploid species with 90 chromosomes (2n = 6x = 90) and a basic chromosome number of 15, and is therefore regarded as one of the most challenging species for high-density genetic map construction. Here, we used single nucleotide polymorphisms (SNPs) identified by double-digest restriction site-associated DNA sequencing based on next-generation sequencing technology to construct a map for sweetpotato. We then aligned the sequence reads onto the reference genome sequence of I. trifida, a likely diploid ancestor of sweetpotato, to detect SNPs. In addition, to simplify analysis of the complex genetic mode of autohexaploidy, we used an S1 mapping population derived from self-pollination of a single parent. As a result, 28,087 double-simplex SNPs showing a Mendelian segregation ratio in the S1 progeny could be mapped onto 96 linkage groups (LGs), covering a total distance of 33,020.4 cM. Based on the positions of the SNPs on the I. trifida genome, the LGs were classified into 15 groups, each with roughly six LGs and six small extra groups. The molecular genetic techniques used in this study are applicable to high-density mapping of other polyploid plant species, including important crops.

We report that disturbance to the circadian rhythm of urinary angiotensinogen (AGT) excretion may lead to renal damage, hypertension and diurnal blood pressure (BP) variations. We aim to clarify the circadian rhythm of the intrarenal renin-angiotensin system (RAS) and its contribution to renal damage, hypertension and BP variations, and to evaluate whether the administration of RAS blockers influences the circadian rhythms of intrarenal RAS components. Anti-thymocyte serum (ATS) nephritis rats were used as a chronic progressive glomerulonephritis model (group A) and compared with control rats (group C). Other rats with ATS nephritis received olmesartan medoxomil (an angiotensin II (AngII) type 1 receptor (AT1R) blocker; group AO) or hydralazine (a vasodilator; group AH). The levels of intrarenal RAS components were evaluated every 6 h. The expression levels of intrarenal AGT, AngII and AT1R were increased in group A and peaked at the same time as BP and urinary protein excretion during the rest phase. The amplitude of the circadian fluctuation of these proteins was more increased in group A than in group C. The circadian fluctuation of these proteins was reduced in groups AO and AH. However, renal function, proteinuria and augmentation of intrarenal RAS components were reduced only in group AO. Intrarenal RAS components, such as AGT, AngII and AT1R proteins, were increased and the amplitude of the oscillations of these proteins was augmented in ATS nephritis rats. Interestingly, renal damage may be linked to the activation of the intrarenal RAS independent of the amplitude of its oscillations and BP.

Central in material design of metal oxides is the increase of surface area and control of intrinsic electronic and optical properties, because of potential applications for energy storage, photocatalysis and photovoltaics. Here, we disclose a facile method, inspired by geochemical process, which gives rise to mesoporous anion-doped metal oxides. As a model system, we demonstrate that simple calcination of a multinuclear coordination cluster results in synchronic chemical reactions: thermal oxidation of Ti8O10(4-aminobenzoate)12 and generation of gases including amino-group fragments. The gas generation during the thermal oxidation of Ti8O10(4-aminobenzoate)12 creates mesoporosity in TiO2. Concurrently, nitrogen atoms contained in the gases are doped into TiO2, thus leading to the formation of mesoporous N-doped TiO2. The mesoporous N-doped TiO2 can be easily synthesized by calcination of the multinuclear coordination cluster, but shows better photocatalytic activity than the one prepared by a conventional sol-gel method. Owing to an intrinsic designability of coordination compounds, this facile synthetic will be applicable to a wide range of metal oxides and anion dopants.

Hydrogenation of iron nanoparticles was performed both computationally and experimentally where previously chemically-bonded iron hydride is considered to be unachievable under ordinary conditions. Density functional theory (DFT) calculations predict that hydrogenated iron nanoparticles are stabilized on a single-layer graphene/Cu substrate. Experimentally, iron nanoparticles were deposited onto a graphene/Cu substrate by vacuum deposition. Hydrogenation was done at 1atm of hydrogen gas and under liquid nitrogen. Mass spectrometry peak confirmed the hydrogen release from hydrogenated iron nanoparticles while a scanning transmission electron microscopy is used in order to link a geometrical shape of iron hydride nanoparticles between experimental and theoretical treatments. The hydrogenated iron nanoparticles were successfully synthesized where hydrogenated iron nanoparticles are stable under ordinary conditions.