Search

Recent years have witnessed rapid progress in the field of epitranscriptomics. Functional interpretation of the epitranscriptome relies on sequencing technologies that determine the location and stoichiometry of various RNA modifications. However, contradictory results have been reported among studies, bringing the biological impacts of certain RNA modifications into doubt. Here, we develop a synthetic RNA library resembling the endogenous transcriptome but without any RNA modification. By incorporating this modification-free RNA library into established mapping techniques as a negative control, we reveal abundant false positives resulting from sequence bias or RNA structure. After calibration, precise and quantitative mapping expands the understanding of two representative modification types, N6-methyladenosine (m6A) and 5-methylcytosine (m5C). We propose that this approach provides a systematic solution for the calibration of various RNA-modification mappings and holds great promise in epitranscriptomic studies. This work describes the generation of a modification-free RNA library that resembles endogenous transcriptome sequence and expression level, which can be used as a negative control in epitranscriptomic sequencing methods to obtain high-confidence and quantitative maps of various RNA modifications.

Modification on nucleic acid plays a pivotal role in controlling gene expression. Various kinds of modifications greatly increase the information-encoding capacity of DNA and RNA by introducing extra chemical group to existing bases instead of altering the genetic sequences. As a marker on DNA or RNA, nucleic acid modification can be recognized by specific proteins, leading to versatile regulation of gene expression. However, modified and regular bases are often indistinguishable by most conventional molecular methods, impeding detailed functional studies that require the information of genomic location. Recently, new technologies are emerging to resolve the positions of varied modifications on both DNA and RNA. Intriguingly, by integrating regional targeting tools and effector proteins, researchers begin to actively control the modification status of desired gene in vivo. In this review, we summarize the characteristics of DNA and RNA modifications, the available mapping and editing tools, and the potential application as well as deficiency of these technologies in basic and translational researches.

N

It is highly necessary to understand the molecular mechanism underlying the salt stress response in green algae, which may contribute to finding the evolutionary cues of abiotic stress response in plants. Here, we reported a comprehensive temporal investigation of transcriptomes using data at eight different time points, from an early stage (2 h) to a late stage (up to 96 h) in

The past few years have witnessed rapid progress in the field of RNA modifications. As the most prevailing modification on eukaryotic mRNA, m

A new transcriptome-wide method produces reliable m6A maps at single-base resolution and reveals site conservation in mammals., N6-methyladenosine (m6A) is one of the most abundant messenger RNA modifications in eukaryotes involved in various pivotal processes of RNA metabolism. The most popular high-throughput m6A identification method depends on the anti-m6A antibody but suffers from poor reproducibility and limited resolution. Exact location information is of great value for understanding the dynamics, machinery, and functions of m6A. Here, we developed a precise and high-throughput antibody-independent m6A identification method based on the m6A-sensitive RNA endoribonuclease recognizing ACA motif (m6A-sensitive RNA-Endoribonuclease–Facilitated sequencing or m6A-REF-seq). Whole-transcriptomic, single-base m6A maps generated by m6A-REF-seq quantitatively displayed an explicit distribution pattern with enrichment near stop codons. We used independent methods to validate methylation status and abundance of individual m6A sites, confirming the high reliability and accuracy of m6A-REF-seq. We applied this method on five tissues from human, mouse, and rat, showing that m6A sites are conserved with single-nucleotide specificity and tend to cluster among species.

Here we report the function of a general regulatory factor, GENERAL REGULATORY FACTOR11 (GRF11), in terms of the iron (Fe) deficiency response. Physiological and molecular responses of the loss-of-function Arabidopsis thaliana grf11 mutant to Fe supply were investigated. Genes involved in posttranscriptional regulation of FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT) were also analyzed. In addition, the molecular link between the signaling molecule nitric oxide (NO) and Fe deficiency responses was further dissected. Our results suggest that GRF11 is necessary for induction of Fe-deficiency-tolerance mechanisms. The FIT protein can bind to the promoter of GRF11, which contains an E-box motif. GRF11 also positively affects FIT transcription but has no influence on the genes involved in posttranscriptional regulation of FIT. Furthermore, NO positively regulates GRF11 induction upon the onset of Fe deficiency. We propose that, upon the onset of Fe deficiency, induction of FIT expression is dependent on GRF11, which acts downstream of NO to mediate Fe deficiency responses.

Aluminum (Al) toxicity is one of the most widespread problems for crop production on acid soils, and nitric oxide (NO) is a key signaling molecule involved in the mediation of various biotic and abiotic stresses in plants. Here we found that exogenous application of the NO donor sodium nitroprusside (SNP) exacerbated the inhibition of Al-induced root growth in rice bean [Vigna umbellata (Thunb.) Ohwi & Ohashi 'Jiangnan', Fabaceae]. This was accompanied by an increased accumulation of Al in the root apex. However, Al treatments had no effect on endogenous NO concentrations in root apices. These results indicate that a change in NO concentration is not the cause of Al-induced root growth inhibition and the adverse effect of SNP on Al-induced root growth inhibition should result from increased Al accumulation. Al could significantly induce citrate efflux but SNP had no effects on citrate efflux either in the absence or presence of Al. On the other hand, SNP pretreatment significantly increased Al-induced malondialdehyde accumulation and Evans Blue staining, indicating an intensification of the disruption of plasma membrane integrity. Furthermore, SNP pretreatment also caused greater induction of pectin methylesterase activity by Al, which could be the cause of the increased Al accumulation. Taken together, it is concluded that NO exacerbates Al-induced root growth inhibition by affecting cell wall and plasma membrane properties.

Because of the increasing need for anesthesia in the CCL, anesthesiologists are often involved in diagnostic and interventional procedures in this setting. Safe delivery of anesthesia requires adequate preparation and familiarity with the procedure and its surroundings. Radiation safety is of paramount importance for the patient and the practitioner, and ready access to the services of anesthesia support personnel, the pharmacy, and the stat laboratory is a key factor for success. In the CCL, and the traditional operating room environment, anesthesiologists shall continue to advance and improve patient care while reducing morbidity and mortality.

†Background and Aims Formation of cluster roots is one of the most specific root adaptations to nutrient deficiency. In white lupin (Lupinus albus), cluster roots can be induced by phosphorus (P) or iron (Fe) deficiency. The aim of the present work was to investigate the potential shared signalling pathway in P- and Fe-deficiencyinduced cluster root formation. †Methods Measurements were made of the internal concentration of nutrients, levels of nitric oxide (NO), citrate exudation and expression of some specific genes under four P × Fe combinations, namely (1) 50 mM P and 10 mM Fe (+P + Fe); (2) 0 P and 10 mM Fe (‐P + Fe); (3) 50 mM P and 0 Fe (+P‐Fe); and (4) 0 P and 0 Fe (‐P‐Fe), and these were examined in relation to the formation of cluster roots. †Key Results The deficiency of P, Fe or both increased the cluster root number and cluster zones. It also enhanced NO accumulation in pericycle cells and rootlet primordia at various stages of cluster root development. The formation of cluster roots and rootlet primordia, together with the expression of LaSCR1 and LaSCR2 which is crucial in cluster root formation, were induced by the exogenous NO donor S-nitrosoglutathione (GSNO) under the +P + Fe condition, but were inhibited by the NO-specific endogenous scavenger 2-(4-carboxyphenyl)-4, 4, 5, 5-tetramethylimidazoline-1-oxyl- 3-oxide (cPTIO) under ‐P + Fe, +P‐Fe and ‐P‐Fe conditions. However, cluster roots induced by an exogenous supply of the NO donor did not secrete citrate, unlike those formed under ‐P or ‐Fe conditions. †Conclusions NO plays an important role in the shared signalling pathway of the P- and Fe-deficiency-induced formation of cluster roots in white lupin.

To investigate the expression of melatonin MT1 receptor in rats with acute necrotizing pancreatitis (ANP) and the protective effects of melatonin (MT) pre-intervention for the pancreas.Fifty-four male Sprague-Dawley (SD) rats were randomly divided into three groups: sham-operation group, ANP group and MT-pretreated group. The models of ANP were induced by retrograde injection sodium taurocholate into the bili-pancreatic duct. MT group undergoing intraperitoneal injection 50 mg/kg 30 minutes before the establishment of ANP models. Four, 8 and 12 hours after the onset of operation, the levels of serum amylase and pathological changes of the pancreas were observed. The contents of malondialdehyde (MDA), superoxide dismutase (SOD) and tumor necrosis factor-alpha (TNFα) in the pancreas were measured. The expression of MT1 protein and MT1 mRNA in pancreas were separately analyzed by immunohistochemistry and real-time PCR.(1) Pancreatic pathological damage in ANP groups was progressive exacerbated. It was obviously ameliorated in MT group as compared with ANP group (P0.05); (2) Compared with SO group, the levels of serum amylase, MDA and TNFα in the pancreas were significantly increased in ANP group (P0.05 or P0.01). They were markedly decreased in MT group as compared with ANP group [12 h, (2348.00 ± 278.90) U/L vs (3194.83 ± 538.10) U/L, (2.255 ± 0.472) µmol/L vs (2.960 ± 0.722) µmol/L, (102.929 ± 29.399) ng/L vs (378.544 ± 183.454) ng/L, P0.05]. The level of SOD was decreased in ANP group compared with SO group (P0.05) and increased in MT group [12 h, (11.448 ± 1.594) U/L vs (8.427 ± 1.950) U/L, P0.05]; (3) Compared with SO group, the expression of MT1 protein and MT1 mRNA in ANP group were down-regulated as the severity of the disease increased (P0.05). They were significantly higher in MT group than ANP group.Melatonin pre-intervention is able to increase SOD level and decrease MDA, TNFα levels, thereby reducing pancreatic injury. The MT1 might play an important role in the pathogenesis of ANP. MT might exert protective effects for the pancreas in ANP rats through increase the expression of MT1.

In a previous study, we noted that mesenteric venous pH falls during the reductions in intestinal blood flow caused by sympathetic stimulation and that alpha 2-receptor antagonists enhanced autoregulatory escape (the partial recovery that blood flow undergoes despite sustained sympathetic stimulation). In addition, other studies indicated that increased [H+] selectively inhibits the responsiveness of postjunctional alpha 2-receptors to norepinephrine (NE). Therefore, we investigated the role of H+ in escape by 1) measuring the rate of unbuffered H+ release during sympathetic stimulation in isolated loops of canine small bowel, 2) infusing acidic buffer intra-arterially and determining the effects of acidosis on sympathetic vasoconstriction and escape, 3) ascertaining the effects of acidosis on the release rate of endogenous NE during sympathetic stimulation, and 4) determining whether acidosis exerts effects in vivo on post-junctional responses to the selective alpha 1- and alpha 2-agonists, phenylephrine and clonidine, respectively. Our findings were that 1) the rate at which the gut released H+ into blood increased during sympathetic stimulation, 2) infusing acidic buffer to lower venous pH from 7.3 to 7.1 attenuated the initial vasoconstrictor response after 30 s of stimulation, 3) acidosis caused blood flow to return further toward control despite continued stimulation and thus enhanced escape, 4) acidosis did not impair NE release at either 30 s or 6 min of stimulation, and 5) acidosis inhibited the intestinal vasoconstrictor effects of selective alpha 2- but not alpha 1-agonists. The results support the hypothesis that escape from sympathetic vasoconstriction occurs, in part, because increased [H+] inhibits alpha 2-mediated postjunctional responses to neuronally released NE.

The partial recovery that intestinal blood flow undergoes during continued sympathetic nerve stimulation is termed autoregulatory escape. This study tested two hypotheses that might explain escape: 1) diminishing norepinephrine (NE) release during sustained stimulation and 2) an alpha 2-receptor-mediated competition between local and neural control mechanisms. The rates of NE release before and during stimulation of the perivascular sympathetic nerves were determined by measuring blood flow in isolated loops of canine small intestine and assaying the concentrations of NE in arterial and venous blood. The presence of functional alpha 2-receptors was demonstrated by clonidine injections, and the effects of alpha 2-receptor blockade were studied during yohimbine infusions. The time course of NE release was inconsistent with a cause-effect relationship; NE release was greatest during the phase when resistance had already escaped. Deliberately altering NE release by changing the stimulus duration did not affect escape. The study demonstrated 1) that diminished NE release during continued sympathetic stimulation does not occur and cannot account for escape, 2) that resistance vessels in the canine intestinal circulation possess functional alpha 2-receptors which are responsible for part of the vasoconstriction caused by sympathetic stimulation, 3) that blockade of presynaptic alpha 2-receptors significantly enhanced NE release during the initial 30-s period but not during the escape phase, and 4) that alpha 2-receptor blockade enhances autoregulatory escape. Altogether these findings indicate that the postsynaptic alpha 2-receptors on intestinal resistance vessels deserve further investigation as the possible site at which local and neural mechanisms compete to influence vascular resistance.