Potassium transporter OsHAK17 may contribute to saline-alkaline tolerant mechanisms in rice (Oryza sativa).

Rice production is seriously affected by saline-alkaline stress worldwide. To elucidate the saline-alkaline tolerance mechanisms in a novel tolerant rice variety, Shwe Nang Gyi (SNG), we investigated ion accumulation in SNG and Koshihikari (KSH), which is a saline-alkaline sensitive rice variety, and the candidates for saline-alkaline inducible genes in SNG using RNA-seq. SNG had superior ion accumulation capacity, such as K and Zn, compared to KSH. In contrast, SNG accumulated the same level of Na content in its leaf blades as KSH despite the higher dry weight of the SNG leaf blades. We further found that the expression of numerous genes, including several K+ transporter/high-affinity K+ transporter/K+ uptake protein/K+ transporter (HAK/KUP/KT) family members, were upregulated in SNG, and that OsHAK17 and OsHAK21 expression levels in the roots were significantly higher in SNG than in KSH. Moreover, yeast complementation analysis revealed that OsHAK17 was involved in K+ uptake under high-Na conditions. These results suggested that SNG has an effective K+ acquisition system supported by OsHAK17 functioning in saline-alkaline environments.

Metabolomic Profiling of Mice with Tacrolimus-Induced Nephrotoxicity: Carnitine Deficiency in Renal Tissue.

Tacrolimus (TAC)-induced chronic nephrotoxicity (TAC nephrotoxicity) has a detrimental effect on long-term kidney graft survival. However, the pathogenesis of TAC nephrotoxicity remains largely unknown. We explored it by focusing on metabolic changes in renal tissues. In this study, mice were separated into TAC and control groups (n = 5/group). TAC was administered to the TAC group (1 mg/kg/d for 28 days) subcutaneously. The control group was similarly treated with normal saline. Renal tissue metabolomes were evaluated. Renal fibrosis was observed only in the TAC group. Metabolomic analysis showed that carnitine and related metabolites were substantially lower in the TAC group than in the control group, presumably due to impaired biosynthesis and reabsorption. Low carnitine levels impair antioxidation in renal tissues and ß-oxidation in mitochondria, which may lead to renal tissue damage. This metabolomic analysis revealed that carnitine deficiency in renal tissue appears to explain TAC nephrotoxicity.

Orthotopic kidney transplantation from a living renal donor after interventional therapy for bilateral arteriosclerosis obliterans of the iliac arteries: A case report and literature review.

Introduction: Orthotopic kidney transplantation is an option when heterotopic kidney transplantation into the iliac fossa is inappropriate. We report a case of orthotopic kidney transplantation following stenting of both external iliac arteries to treat arteriosclerosis obliterans. Case presentation: A 56-year-old woman on hemodialysis for end-stage kidney disease underwent living-donor kidney transplantation. Desensitization therapy was administered because of her history of sensitization by pregnancy. Stents had been placed previously in both external iliac arteries. The left kidney was removed via an oblique lumbar incision. The two graft arteries were conjoined and anastomosed to the native renal artery end-to-end. The urinary tract was reconstructed by uretero-ureterostomy with ureteral stent placement. Renal function improved promptly after surgery. Conclusion: Preoperative imaging of vascular anatomy is important for successful orthotopic kidney transplantation in patients who have previously undergone stenting of both external iliac arteries for arteriosclerosis obliterans.

Glucosinolate Catabolism Maintains Glucosinolate Profiles and Transport in Sulfur-Starved Arabidopsis.

Glucosinolates (GSLs) are sulfur (S)-rich specialized metabolites present in Brassicales order plants. Our previous study found that GSL can function as a S source in Arabidopsis seedlings via its catabolism catalyzed by two ß-glucosidases (BGLUs), BGLU28 and BGLU30. However, as GSL profiles in plants vary among growth stages and organs, the potential contribution of BGLU28/30-dependent GSL catabolism at the reproductive growth stage needs verification. Thus, in this study, we assessed growth, metabolic and transcriptional phenotypes of mature bglu28/30 double mutants grown under different S conditions. Our results showed that compared to wild-type plants grown under -S, mature bglu28/30 mutants displayed impaired growth and accumulated increased levels of GSL in their reproductive organs and rosette leaves of before-bolting plants. In contrast, the levels of primary S-containing metabolites, glutathione and cysteine decreased in their mature seeds. Furthermore, the transport of GSL from rosette leaves to the reproductive organs was stimulated in the bglu28/30 mutants under -S. Transcriptome analysis revealed that genes related to other biological processes, such as ethylene response, defense response and plant response to heat, responded differentially to -S in the bglu28/30 mutants. Altogether, these findings broadened our understanding of the roles of BGLU28/30-dependent GSL catabolism in plant adaptation to nutrient stress.

Role of Potassium-Dependent Alternative Splicing of MYB59 in the Maintenance of Potassium Concentration in Shoots of Arabidopsis thaliana.

Potassium (K) is a major plant nutrient. K+ is taken up by channel and transporter proteins in roots and translocated from roots to shoots via the xylem. In Arabidopsis thaliana, the K+ transporter NPF7.3 mediates K+ loading into the xylem and the transcription factor MYB59 is responsible for NPF7.3 expression. Here, we demonstrate that MYB59 is regulated by alternative splicing in response to K availability. Three splicing isoforms of MYB59 are detected in roots: an isoform with the first intron spliced out encodes a protein with the full DNA-binding motif (MYB59α), and two isoforms with the first intron retained partially or completely encode a protein missing part of the DNA-binding motif (MYB59ß). Functional analysis showed that only MYB59α is capable of inducing the expression of NPF7.3. The abundance of the MYB59α isoform increased under low K, but the total abundance of MYB59 transcripts did not change, indicating that MYB59α is increased by modification of the splicing pattern in response to low K. Although MYB59α is increased by low K, NPF7.3 expression remained constant independent of K. In addition, there was no significant difference in NPF7.3 expression between an MYB59 knockout mutant and the wild type under normal K. These results suggest that an unknown mechanism is involved in NPF7.3 expression under normal K and switches roles with MYB59 under low K. We propose that the regulation of MYB59 by alternative splicing is required for the maintenance of shoot K concentration in adaptation to low K.

Retroperitoneoscopic Donor Nephrectomy on the Right Side Provides Equivalent Outcomes and Donor Safety to That on the Left Side.

BACKGROUND: The left kidney is typically selected for laparoscopic donor nephrectomy. In contrast, right kidney donation raises concerns for donor safety, and venous anastomosis may be difficult to achieve due to the short renal vein. We investigated the safety and operative outcomes of right donor nephrectomy compared with those of the left. METHODS: We retrospectively analyzed the clinical records of living donor-kidney transplant donors and evaluated operative outcomes such as operative time, ischemic time, blood loss, and surgical complications in the donor. RESULTS: We identified 79 donors (left:right = 62:17 cases) between May 2020 and March 2023. There were no significant differences between the 2 groups regarding age, sex, body mass index, and number of renal arteries. Although the operative time (left and right: 190 and 225 minutes, excluding waiting time; P = .009) and warm ischemic time (left and right: 143 and 193 seconds, P = .021) were significantly longer on the right side, the total ischemic time (82 and 86 minutes, P = .463) and blood loss (left and right: 35 and 25 mL, P = .159) were comparable between the groups. There were no significant differences between the groups regarding the surgical complications. CONCLUSIONS: Operative outcomes were similar in both donor sides in the retroperitoneoscopic donor nephrectomies. The right side should be considered for donation in this operative procedure.

Three-dimensional vessel wall MRI to characterize thrombus prior to endovascular thrombectomy for large vessel occlusion stroke.

BACKGROUND AND PURPOSE: Endovascular thrombectomy (EVT) for acute ischemic stroke (AIS) caused by large vessel occlusion requires rapid and reliable imaging of the vessel course including the clot to reduce complications and ensure success. However, no method to acquire this information has been established. METHODS: Six consecutive patients with AIS caused by large vessel occlusion underwent EVT in our institute. High-resolution vessel wall MRI was performed using three-dimensional (3D) variable refocusing flip angle pulse and turbo spin-echo sequences (VRFA-TSE) with the volume isotropic turbo spin-echo acquisition (VISTA) technique. This study evaluated the effectiveness of 3D proton density-weighted (PDW) VRFA-TSE (called PDW-VISTA) compared with T2-weighted (T2W) VRFA-TSE (called T2W-VISTA) to demonstrate the cerebral vessels including the occluded invisible lesion. RESULTS: PDW-VISTA and T2W-VISTA were successfully performed in all cases. PDW-VISTA was more useful to visualize the anterior circulation than T2W-VISTA by clearly revealing invisible vessels, whereas PDW-VISTA and T2W-VISTA had similar findings in the posterior circulation. The vessel courses shown by 3D PDW-VISTA imaging before treatment and digital subtraction angiography after treatment showed good agreement in all cases. Furthermore, 3D PDW-VISTA imaging demonstrated the length and size of the clot. CONCLUSIONS: PDW-VISTA imaging was found to more clearly depict the cerebral vessels including occluded lesion than T2W-VISTA imaging. Findings of thrombus size and length were important for correctly placing the stent retriever and securing safety during the procedure.

Creatinine reduction ratio on postoperative day 2 predicts long-term outcomes after living donor kidney transplantation.

OBJECTIVES: To evaluate the relationship between the creatinine reduction ratio between postoperative days 1 and 2 and post-transplantation clinical outcomes after living donor kidney transplantation. METHODS: Clinical data of patients who underwent living donor kidney transplantation at Jichi Medical University Hospital, Tochigi, Japan, between 2006 and 2019 were retrieved. The creatinine reduction ratio between postoperative days 1 and 2 was calculated based on the formula: (Cre1 - Cre2) × 100/Cre1; patients were then classified into either the slow graft function (creatinine reduction ratio between postoperative days 1 and 2 ≤30%) or immediate graft function (creatinine reduction ratio between postoperative days 1 and 2 >30%) group. We carried out the log-rank test and multivariate Cox proportional hazards regression analyses to assess graft survival and rejection-free survival, and the unpaired t-test and multivariate linear regression to assess post-transplantation estimated glomerular filtration rates. Multivariate analyses used age, sex, dialysis duration, ABO compatibility, donor-specific antibody positivity and medically complex living donors as explanatory variables. RESULTS: Of the 272 patients, 30 and 242 were in the slow graft function and immediate graft function groups, respectively. Multivariate Cox proportional hazards regression analyses showed a significantly higher incidence of overall and death-censored graft loss in the slow graft function group than the immediate graft function group. The frequency of rejection after 1 week post-transplantation did not differ within the groups. Post-transplantation estimated glomerular filtration rates tended to decline earlier in the slow graft function group than in the immediate graft function group; however, the difference was not statistically significant. CONCLUSIONS: The creatinine reduction ratio between postoperative days 1 and 2 could potentially predict long-term outcomes after living donor kidney transplantation. Using the creatinine reduction ratio between postoperative days 1 and 2 and other conventional indicators might allow accurate risk classification and appropriate therapeutic interventions.

Development of strangulation ileus associated with the ureter of the transplanted kidney 18 years after kidney transplantation.

INTRODUCTION: After kidney transplantation, patients should be treated with caution and monitored for surgical complications. Among the possible surgical complications, strangulation ileus after kidney transplantation is rare. CASE PRESENTATION: A 59-year-old woman who had undergone kidney transplantation at 41 years of age presented to our hospital with lower abdominal pain. She was diagnosed with strangulation ileus and underwent emergency surgery. In the lower right abdomen, the small intestine was compressed by cord-like tissue running from the intraperitoneal space to the retroperitoneal space. We confirmed that the cord-like tissue was the ureter of the transplanted kidney. The necrotic small intestine was resected, and ureter-ureteral anastomosis of the ureter of the transplanted kidney was performed. CONCLUSION: All surgical procedures, including ureteroneocystostomy, require careful attention. The occurrence of some postoperative surgical complications can be prevented by carefully performing the kidney transplantation procedure.

Local Application of Magnesium Sulfate Solution Suppressed Cortical Spreading Ischemia and Reduced Brain Damage in a Rat Subarachnoid Hemorrhage-Mimicking Model.

OBJECTIVE: Cortical spreading depolarization (CSD), cortical spreading ischemia (CSI), and early brain injury are involved in the occurrence of delayed brain ischemia after subarachnoid hemorrhage (SAH). We tested whether local application of magnesium (Mg) sulfate solution suppressed CSD and CSI, and decreased brain damage in a rat SAH-mimicking model. METHODS: Nitric oxide synthase inhibitor L-NG-nitroarginine methyl ester (L-NAME) and high concentration potassium solution were topically applied to simulate the environment after SAH. We irrigated the parietal cortex with artificial cerebrospinal fluid (ACSF), containing L-NAME (1 mM), K+ (35 mM), and Mg2+ (5 mM). Forty-five rats were divided into 3 groups: sham surgery (sham group), L-NAME + [K+]ACSF (control group), and L-NAME + [K+]ACSF + [Mg2+] (Mg group). CSD was induced by topical application with 1 M KCl solution in 3 groups. The effects of Mg administration on CSD and cerebral blood flow were evaluated. Histological brain tissue damage, body weight, and neurological score were assessed at 2 days after insult. RESULTS: Mg solution significantly shortened the total depolarization time, and reduced CSI, histological brain damage, and brain edema compared with those of the control group (P < 0.05). Body weight loss was significantly suppressed in the Mg group (P < 0.05), but neurological score did not improve. CONCLUSIONS: Local application of Mg suppressed CSI and reduced brain damage in a rat SAH-mimicking model. Mg irrigation therapy may be beneficial to suppress brain damage due to CSI after SAH.

Differences in mineral accumulation and gene expression profiles between two metal hyperaccumulators, Noccaea japonica and Noccaea caerulescens ecotype Ganges, under excess nickel condition.

Here we compare mineral accumulation and global gene expression patterns between two metal hyperaccumulator plants - Noccaea japonica, originating from Ni-rich serpentine soils, and Noccaea caerulescens (ecotype Ganges), originating from Zn/Pb-mine soils - under excess Ni conditions. Significant differences in the accumulation of K, P, Mg, B, and Mo were explained by the expression levels of specific transporters for each mineral. We previously showed that total Ni accumulation in the whole plant is higher in N. caerulescens than in N. japonica. Here we found a similar tendency for Fe under excess Ni; however, the expression of iron-regulated transporter 1 (IRT1), which encodes the primary Fe uptake transporter and causes excess Ni uptake in Arabidopsis thaliana, was higher in N. japonica. NjIRT1 has a point mutation at Asp100, which is essential for Fe transport, and so might lack its Fe and possibly Ni transport function. Noccaea japonica might have lost its IRT1 function, which would prevent excess Ni uptake via IRT1 in Ni-rich soils, and come to rely on other transporters.

Hypophysitis induced by ipilimumab and nivolumab combination therapy for advanced renal cell carcinoma: A case report.

Ipilimumab and nivolumab combination therapy is effective against unresectable or metastatic renal cell carcinoma. However, it is associated with many immune-related adverse events, including hypophysitis that is difficult to diagnose early because of non-specific initial symptoms. Herein, we report the case of a 54-year-old man with metastatic renal cell carcinoma who developed hypophysitis after receiving ipilimumab and nivolumab combination therapy. The initial symptom was headache. However, endocrine tests showed decreased levels of cortisol, free thyroxine and thyroid-stimulating hormone. Moreover, magnetic resonance imaging revealed pituitary enlargement. Accordingly, we diagnosed hypophysitis and immediately started hydrocortisone replacement therapy, which improved the symptoms.

Long-term impact of baseline serum uric acid levels on living kidney donors: a retrospective study.

BACKGROUND: Preoperative characteristics of living kidney donors are commonly considered during donor selection and postoperative follow-up. However, the impact of preoperative uric acid (UA) levels is poorly documented. The aim of this study was to evaluate the association between preoperative serum UA levels and post-donation long-term events and renal function. METHODS: This was a single-center retrospective analysis of 183 living kidney donors. The donors were divided into high (≥5.5 mg/dl) and low (< 5.5 mg/dl) UA groups. We analyzed the relationship between preoperative UA levels and postoperative estimated glomerular filtration rate (eGFR), as well as adverse events (cardiovascular events and additional prescriptions for hypertension, gout, dyslipidemia, and diabetes mellitus), over 5 years after donation. RESULTS: In total, 44 donors experienced 52 adverse events over 5 years. The incidence of adverse events within 5 years was significantly higher in the high UA group than in the low UA group (50% vs. 24%, p = 0.003); this was true even after the exclusion of hyperuricemia-related events (p = 0.047). UA emerged as an independent risk factor for adverse events (p = 0.012). Donors with higher UA levels had lower eGFRs after donation, whereas body mass index, hemoglobin A1c, blood pressure, and low-density lipoprotein cholesterol did not have any impact on the eGFR. CONCLUSIONS: The findings suggest that preoperative UA levels should be considered during donor selection and postoperative follow-up.

Roles of Non-Coding RNAs in Response to Nitrogen Availability in Plants.

Nitrogen (N) is an essential nutrient for plant growth and development; therefore, N deficiency is a major limiting factor in crop production. Plants have evolved mechanisms to cope with N deficiency, and the role of protein-coding genes in these mechanisms has been well studied. In the last decades, regulatory non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), small interfering RNAs (siRNAs), and long ncRNAs (lncRNAs), have emerged as important regulators of gene expression in diverse biological processes. Recent advances in technologies for transcriptome analysis have enabled identification of N-responsive ncRNAs on a genome-wide scale. Characterization of these ncRNAs is expected to improve our understanding of the gene regulatory mechanisms of N response. In this review, we highlight recent progress in identification and characterization of N-responsive ncRNAs in Arabidopsis thaliana and several other plant species including maize, rice, and Populus.

HbA1c and Aortic Calcification Index as Noninvasive Predictors of Pre-Existing Histopathological Damages in Living Donor Kidney Transplantation.

We previously reported that allografts from living donors may have pre-existing histopathological damages, defined as the combination of interstitial fibrosis (ci), tubular atrophy (ct), and arteriolar hyalinosis (ah) scores of ≧1, according to the Banff classification. We examined preoperative characteristics to identify whether the degree of these damages was related to metabolic syndrome-related factors of donors. We conducted a single-center cross-sectional analysis including 183 living kidney donors. Donors were divided into two groups: chronic change (ci + ct ≧ 1 ∩ ah ≧ 1, n = 27) and control (n = 156). Preoperative characteristics, including age, sex, blood pressure, hemoglobin A1c (HbA1c), aortic calcification index (ACI), and psoas muscle index (PMI), were analyzed. Comparing the groups, the baseline estimated glomerular filtration rate was not significantly different; however, we observed a significant difference for ACI (p = 0.009). HbA1c (p = 0.016) and ACI (p = 0.006) were independent risk factors to predict pre-existing histopathological damages, whereas PMI was not. HbA1c correlated with ct scores (p = 0.035), and ACI correlated with ci (p = 0.005), ct (p = 0.021), and ah (p = 0.017). HbA1c and ACI may serve as preoperative markers for identifying pre-existing damages on the kidneys of living donors.

Elevated Expression of Vacuolar Nickel Transporter Gene IREG2 Is Associated With Reduced Root-to-Shoot Nickel Translocation in Noccaea japonica.

A number of metal hyperaccumulator plants, including nickel (Ni) hyperaccumulators, have been identified in the genus Noccaea. The ability to accumulate Ni in shoots varies widely among species and ecotypes in this genus; however, little is known about the molecular mechanisms underlying this intra- and inter-specific variation. Here, in hydroponic culture, we compared Ni accumulation patterns between Noccaea japonica, which originated in Ni-enriched serpentine soils in Mt. Yubari (Hokkaido, Japan), and Noccaea caerulescens ecotype Ganges, which originated in zinc/lead-mine soils in Southern France. Both Noccaea species showed extremely high Ni tolerance compared with that of the non-accumulator Arabidopsis thaliana. But, following treatment with 200 µM Ni, N. caerulescens showed leaf chlorosis, whereas N. japonica did not show any stress symptoms. Shoot Ni concentration was higher in N. caerulescens than in N. japonica; this difference was due to higher efficiency of root-to-shoot Ni translocation in N. caerulescens than N. japonica. It is known that the vacuole Ni transporter IREG2 suppresses Ni translocation from roots to shoots by sequestering Ni in the root vacuoles. The expression level of the IREG2 gene in the roots of N. japonica was 10-fold that in the roots of N. caerulescens. Moreover, the copy number of IREG2 per genome was higher in N. japonica than in N. caerulescens, suggesting that IREG2 expression is elevated by gene multiplication in N. japonica. The heterologous expression of IREG2 of N. japonica and N. caerulescens in yeast and A. thaliana confirmed that both IREG2 genes encode functional vacuole Ni transporters. Taking these results together, we hypothesize that the elevation of IREG2 expression by gene multiplication causes the lower root-to-shoot Ni translocation in N. japonica.

A case report of nivolumab-induced myasthenia gravis and myositis in a metastatic renal cell carcinoma patient.

We present a 78-year-old male with renal cell carcinoma who developed myasthenia gravis complicated by myositis after nivolumab administration, which was verified by the presence of antibodies against the acetylcholine receptor. The initial symptom was posterior neck pain, and biochemical examination of blood showed elevated levels of hepatic enzymes and creatine phosphokinase. The level of antibody against the acetylcholine receptor increased 4.1-fold. His condition progressed rapidly resulting in respiratory failure 15 days after conservative therapy.

Factors related to suboptimal recovery of renal function after living donor nephrectomy: a retrospective study.

BACKGROUND: The renal function of the remaining kidney in living donors recovers up to 60~70% of pre-donation estimated-glomerular filtration rate (eGFR) by compensatory hypertrophy. However, the degree of this hypertrophy varies from donor to donor and the factors related to it are scarcely known. METHODS: We analyzed 103 living renal transplantations in our institution and divided them into two groups: compensatory hypertrophy group [optimal group, 1-year eGFR ≥60% of pre-donation, n = 63] and suboptimal compensatory hypertrophy group (suboptimal group, 1-year eGFR < 60% of pre-donation, n = 40). We retrospectively analyzed the factors related to suboptimal compensatory hypertrophy. RESULTS: Baseline eGFRs were the same in the two groups (optimal versus suboptimal: 82.0 ± 13.1 ml/min/1.73m2 versus 83.5 ± 14.8 ml/min/1.73m2, p = 0.588). Donor age (optimal versus suboptimal: 56.0 ± 10.4 years old versus 60.7 ± 8.7 years old, p = 0.018) and uric acid (optimal versus suboptimal: 4.8 ± 1.2 mg/dl versus 5.5 ± 1.3 mg/dl, p = 0.007) were significantly higher in the suboptimal group. The rate of pathological chronicity finding on 1-h biopsy (ah≧1 ∩ ct + ci≧1) was much higher in the suboptimal group (optimal versus suboptimal: 6.4% versus 25.0%, p = 0.007). After the multivariate analysis, the pathological chronicity finding [odds ratio (OR): 4.8, 95% confidence interval (CI): 1.3-17.8, p = 0.021] and uric acid (per 1.0 mg/dl, OR: 1.5, 95% CI: 1.1-2.2, p = 0.022) were found to be independent risk factors for suboptimal compensatory hypertrophy. CONCLUSION: Chronicity findings on baseline biopsy and higher uric acid were associated with insufficient recovery of the post-donated renal function.

Potential Risks and Limited Indications of the Supraorbital Keyhole Approach for Clipping Internal Carotid Artery Aneurysms.

BACKGROUND: Internal carotid artery (ICA) aneurysm may be a good target for supraorbital keyhole clipping. We discuss the surgical indications and risks of keyhole clipping for ICA aneurysms based on long-term clinical and radiologic results. METHODS: This was a retrospective analysis of 51 patients (aged 35-75 years, mean 62 years) with ICA aneurysms (mean 5.8 ± 1.8 mm) who underwent clipping via the supraorbital keyhole approach between 2005 and 2017. Neurologic and cognitive functions were examined by several methods, including the modified Rankin Scale and Mini-Mental Status Examination. The state of clipping was assessed 1 year and then every few years after the operation. RESULTS: Complete clipping was confirmed in 45 patients (88.2%), dog-ear remnants behind the clip persisted in 4 patients, and wrapping was performed in 2 patients. Mean duration of postoperative hospitalization was 3.4 ± 6.9 days. The mean clinical follow-up period was 6.6 ± 3.2 years. The overall mortality was 0, and overall morbidity (modified Rankin Scale score ≥2 or Mini-Mental Status Examination <24) was 3.9%. Completely clipped aneurysms did not show any recurrence during the mean follow-up period of 6.3 ± 3.1 years, but the 2 (3.9%) aneurysms with neck remnants showed regrowth. CONCLUSIONS: The risk of neck remnant behind the clip blade is a drawback of supraorbital keyhole clipping. The surgical indication requires preoperative simulation and careful checking of the clip blade state is essential.

Genome-Wide Analysis of Long Intergenic Noncoding RNAs Responding to Low-Nutrient Conditions in Arabidopsis thaliana: Possible Involvement of Trans-Acting siRNA3 in Response to Low Nitrogen.

Long intergenic noncoding RNAs (lincRNAs) play critical roles in transcriptional and post-transcriptional regulation of gene expression in a wide variety of organisms. Thousands of lincRNAs have been identified in plant genomes, although their functions remain mostly uncharacterized. Here, we report a genome-wide survey of lincRNAs involved in the response to low-nutrient conditions in Arabidopsis thaliana. We used RNA sequencing data derived from A. thaliana roots exposed to low levels of 12 different nutrients. Using bioinformatics approaches, 60 differentially expressed lincRNAs were identified that were significantly upregulated or downregulated under deficiency of at least one nutrient. To clarify their roles in nutrient response, correlations of expression patterns between lincRNAs and reference genes were examined across the 13 conditions (12 low-nutrient conditions and control). This analysis allowed us to identify lincRNA-RNA pairs with highly positive or negative correlations. In addition, calculating interaction energies of those pairs showed lincRNAs that may act as regulatory interactors; e.g. small interfering RNAs (siRNAs). Among them, trans-acting siRNA3 (TAS3), which is known to promote lateral root development by producing siRNA against Auxin response factor 2, 3, and 4, was revealed as a nitrogen (N)-responsive lincRNA. Furthermore, nitrate transporter 2 was identified as a potential target of TAS3-derived siRNA, suggesting that TAS3 participates in multiple pathways by regulating N transport and root development under low-N conditions. This study provides the first resource for candidate lincRNAs involved in multiple nutrient responses in plants.