RNA-Seq analysis of rice roots reveals the involvement of post-transcriptional regulation in response to cadmium stress

Widely-spread cadmium (Cd) pollution in the soil threatens both crop production and human health. How plants deal with the excess Cd are largely unknown. To evaluate the molecular mechanism by which plants respond to Cd stress, rice seedlings were treated with two concentrations of Cd and subjected to deep RNA sequencing. Comprehensive RNA-Seq analysis of rice roots under two gradients of Cd treatment revealed 1,169 Cd toxicity-responsive genes. These genes were involved in the reactive oxygen species scavenging system, stress response, cell wall formation, ion transport, and signal transduction. Nine out of 93 predicted long non coding RNAs (lncRNAs) were detected as Cd-responsive lncRNAs due to their high correlation with the Cd stress response. In addition, we analyzed alternative splicing (AS) events under different Cd concentrations. 476 differential alternatively spliced genes with 542 aberrant splicing events were identified. GO analysis indicated that these genes were highly enriched in oxidation reduction and cellular response to chemical stimulus. Real-time qRT-PCR validation analysis strengthened the reliability of our RNA-Seq results. The results suggest that post-transcriptional AS regulation may also be involved in plant responses to high Cd stress

Spatial variations of prokaryotic communities in surface water from India Ocean to Chinese marginal seas and their underlining environmental determinants

To illustrate the biogeographic patterns of prokaryotic communities in surface sea water, 24 samples were systematically collected across a large distance from Indian Ocean to Chinese marginal seas, with an average distance of 453 km between two adjacent stations. A total of 841,364 quality reads was produced by the high throughput DNA sequencing of the 16S rRNA genes. Phylogenetic analysis showed that Proteobacteria were predominant in all samples, with Alphaproteobacteria and Gammaproteobacteria being the two most abundant components. Cyanobacteria represented the second largest fraction of the total quality reads, and mainly included Prochlorococcus and Synechococcus. The semi-closed marginal seas, including South China Sea (SCS) and nearby regions, exhibited a transition in community composition between oceanic and coastal seas, based on the distribution patterns of Prochlorococcus and Synechococcus as well as a non-metric multidimensional scaling (NMDS) analysis. Distinct clusters of prokaryotes from coastal and open seas, and from different water masses in Indian Ocean were obtained by Bray-Curtis dissimilarity analysis at the OTU level, revealing a clear spatial heterogeneity. The major environmental factors correlated with the community variation in this broad scale were identified as salinity, temperature and geographic distance. Community comparison among regions shows that anthropogenic contamination is another dominant factor in shaping the biogeographic patterns of the microorganisms. These results suggest that environmental factors involved in complex interactions between land and sea act synergistically in driving spatial variations in coastal areas

Actor-recipient role affects neural responses to self in emotional situations

People often take either the role of an actor or that of recipient in positive and negative interpersonal events when they interact with others. The present study investigated how the actor-recipient role affected the neural responses to self in emotional situations. Twenty-five participants were scanned while they were presented with positive and negative interpersonal events and were asked to rate the degree to which the actor/the recipient was that kind of person who caused the interpersonal event. Half of the trials were self-relevant events and the other half were other-relevant events. Results showed that people were more likely to isolate self from negative events when they played the role of actor relative to recipient. Pregenual anterior cingulate cortex (pgACC) and posterior dorsal anterior cingulate cortex (pdACC) were more active for self than other only in negative events. More importantly, also in negative interpersonal events, dorsal medial prefrontal cortex (dmPFC) showed greater self-related activations (self - other) when participants played the role of recipient relative to actor, while activities in orbitofrontal cortex (OFC) were greater for self than other only when the evaluation target played the role of recipient. These results showed that the actor-recipient role affected neural responses to self in emotional situations, especially when a recipient role was played in negative situations

Ethylene modulates sphingolipid synthesis in Arabidopsis

Sphingolipids have essential structural and bioactive functions in membranes and in signaling. However, how plants regulate sphingolipid biosynthesis in the response to stress remains unclear. Here, we reveal that the plant hormone ethylene can modulate sphingolipid synthesis. The fungal toxin Fumonisin B1 (FB1) inhibits the activity of ceramide synthases, perturbing sphingolipid homeostasis and thus inducing cell death. We used FB1 to test the role of ethylene signaling in sphingolipid synthesis in Arabidopsis thaliana. The etr1-1 and ein2 mutants, which have disrupted ethylene signaling, exhibited hypersensitivity to FB1; by contrast, the eto1-1 and ctr1-1 mutants, which have enhanced ethylene signaling, exhibited increased tolerance to FB1. Gene expression analysis showed that during FB1 treatment, transcripts of genes involved in de novo sphingolipid biosynthesis were down-regulated in ctr1-1 mutants but up-regulated in ein2 mutants. Strikingly, under normal conditions, ctr1-1 mutants contained less ceramides and hydroxyceramides, compared with wild type. After FB1 treatment, ctr1-1 and ein2 mutants showed a significant improvement in sphingolipid contents, except the ctr1-1 mutants showed little change in hydroxyceramide levels. Treatment of wild-type seedlings with the ethylene precursor 1-aminocyclopropane carboxylic acid (ACC) down-regulated genes involved in the sphingolipid de novo biosynthesis pathway, thus reducing sphingolipid contents and partially rescuing FB1-induced cell death. Taking these results together, we propose that ethylene modulates sphingolipids by regulating the expression of genes related to the de novo biosynthesis of sphingolipids

New Frontiers in The Intrarenal Renin-Angiotensin System: A Critical Review of Classical and New Paradigms

The renin-angiotensin system (RAS) is well recognized as one of the oldest and most important regulators of arterial blood pressure, cardiovascular and renal function. New frontiers have recently emerged in the RAS research well beyond its classic paradigm as a potent vasoconstrictor, an aldosterone release stimulator, or a sodium-retaining hormone. First, two new members of the RAS have been uncovered, which include the renin/(Pro)renin receptor (PRR) and angiotensin-converting enzyme 2 (ACE2). Recent studies suggest that prorenin may act on the PRR independent of the classical ACE/ANG II/AT1 receptor axis, whereas ACE2 may degrade ANG II to generate ANG (1-7), which activates the Mas receptor. Second, there is increasing evidence that ANG II may function as an intracellular peptide to activate intracellular and/or nuclear receptors. Third, currently there is a debate on the relative contribution of systemic versus intrarenal RAS to the physiological regulation of blood pressure and the development of hypertension. The objectives of this article are to review and discuss the new insights and perspectives derived from recent studies using novel transgenic mice that either overexpress or are deficient of one key enzyme, ANG peptide, or receptor of the RAS. This information may help us better understand how ANG II acts, both independently or through interactions with other members of the system, to regulate the kidney function and blood pressure in health and disease

Power to punish norm violations affects the neural processes of fairness-related decision making

Punishing norm violations is considered an important motive during rejection of unfair offers in the Ultimatum Game (UG). The present study investigates the impact of the power to punish norm violations on people’s responses to unfairness and associated neural correlates. In the UG condition participants had the power to punish norm violations, while an alternate condition, the Impunity Game (IG), was presented where participants had no power to punish norm violations since rejection only reduced the responder’s income to zero. Results showed that unfair offers were rejected more often in UG compared to IG. At the neural level, anterior insula and dorsal anterior cingulate cortex were more active when participants received and rejected unfair offers in both UG and IG. Moreover, greater dorsolateral prefrontal cortex activity was observed when participants rejected than accepted unfair offers in UG but not in IG. Ventromedial prefrontal cortex activation was higher in UG than IG when unfair offers were accepted as well as when rejecting unfair offers in IG as opposed to UG. Taken together, our results demonstrate that the power to punish norm violations affects not only people’s behavioral responses to unfairness but also the neural correlates of the fairness-related social decision-making process

The TCA pathway is an important player in the regulatory network governing Vibrio alginolyticus adhesion under adversity

Adhesion is a critical step in the initial stage of Vibrio alginolyticus infection; therefore, it is important to understand the underlying mechanisms governing the adhesion of V. alginolyticus and determine if environmental factors have any effect. A greater understanding of this process may assist in developing preventive measures for reducing infection. In our previous research, we presented the first RNA-seq data from V. alginolyticus cultured under stress conditions that resulted in reduced adhesion. Based on the RNA-seq data, we found that the Tricarboxylic acid cycle (TCA pathway) might be closely related to adhesion. Environmental interactions with the TCA pathway might alter adhesion. To validate this, bioinformatics analysis, qPCR, RNAi and in vitro adhesion assays were performed, while V. alginolyticus was treated with various stresses including temperature, pH, salinity and starvation. The expression of genes involved in the TCA pathway was confirmed by qPCR, which reinforced the reliability of the sequencing data. Silencing of these genes was capable of reducing the adhesion ability of V. alginolyticus. Adhesion of V. alginolyticus is influenced substantially by environmental factors and the TCA pathway is sensitive to some environmental stresses, especially changes in pH and starvation. Our results indicated that 1) the TCA pathway plays a key role in V. alginolyticus adhesion: 2) the TCA pathway is sensitive to environmental stresses

The large-scale distribution of ammonia oxidizers in paddy soils is driven by soil pH, geographic distance and climatic factors

Paddy soils distribute widely from temperate to tropical regions, and are characterized by intensive nitrogen fertilization practices in China. Mounting evidence has confirmed the functional importance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in soil nitrification, but little is known about their biogeographic distribution patterns in paddy ecosystems. Here, we used barcoded pyrosequencing to characterize the effects of climatic, geochemical and spatial factors on the distribution of ammonia oxidizers from 11 representative rice-growing regions (75-1945 km apart) of China. Potential nitrification rates varied greatly by more than three orders of magnitude, and were significantly correlated with the abundances of AOA and AOB. The community composition of ammonia oxidizer was affected by multiple factors, but changes in relative abundances of the major lineages could be best predicted by soil pH. The alpha diversity of AOA and AOB displayed contrasting trends over the gradients of latitude and atmospheric temperature, indicating a possible niche separation between AOA and AOB along the latitude. The Bray-Curtis dissimilarities in ammonia-oxidizing community structure significantly increased with increasing geographical distance, indicating that more geographically distant paddy fields tend to harbor more dissimilar ammonia oxidizers. Variation partitioning analysis revealed that spatial, geochemical and climatic factors could jointly explain majority of the data variation, and were important drivers defining the ecological niches of AOA and AOB. Our findings suggest that both AOA and AOB are of functional importance in paddy soil nitrification, and ammonia oxidizers in paddy ecosystems exhibit large-scale biogeographic patterns shaped by soil pH, geographic distance, and climatic factors

Intersubunit concerted cooperative and cis-type mechanisms modulate allosteric gating in two-pore-domain potassium channel TREK-2

In response to diverse stimuli, two-pore-domain potassium channel TREK-2 regulates cellular excitability, and hence plays a key role in mediating neuropathic pain, mood disorders and ischemia through. Although more and more input modalities are found to achieve their modulations via acting on the channel, the potential role of subunit interaction in these modulations remains to be explored. In the current study, the deletion (lack of proximal C-terminus, pCt) or point mutation (G312A) was introduced into TREK-2 subunits to limit K+ conductance and used to report subunit stoichiometry. The constructs were then combined with wild type (WT) subunit to produce concatenated dimers with defined composition, and the gating kinetics of these channels to 2-Aminoethoxydiphenyl borate (2-APB) and extracellular pH (pHo) were characterized. Our results show that combination of WT and pCt/G312A subunits reserves similar gating properties to that of WT dimmers, suggesting that the WT subunit exerts dominant and positive effects on the mutated one, and thus the two subunits controls channel gating via a concerted cooperative manner. Further introduction of pCt into the latter subunit of heterodimeric channel G312A-WT or G312A-G312A attenuated their sensitivity to 2-APB and pHo alkalization, implicating that these signals were transduced by a cis-type mechanism. Together, our findings elucidate the mechanisms for how the two subunits control the pore gating of TREK-2, in which both intersubunit concerted cooperative and cis-type manners modulate the allosteric regulations induced by 2-APB and pHo alkalization

DNA demethylation upregulated Nrf2 expression in Alzheimer's disease cellular model

Nuclear factor erythroid 2-related factor 2 (Nrf2) is an important transcription factor in the defense against oxidative stress. Cumulative evidence has shown that oxidative stress plays a key role in the pathogenesis of Alzheimer's disease (AD). Previous animal and clinical studies had observed decreased expression of Nrf2 in AD. However, the underlying regulation mechanisms of Nrf2 in AD remain unclear. Here, we used the DNA methyltransferases (Dnmts) inhibitor 5-aza-2′-deoxycytidine (5-Aza) to test whether Nrf2 expression was regulated by methylation in N2a cells characterizing by expressing human Swedish mutant amyloid precursor protein (N2a/APPswe). We found 5-Aza treatment increased Nrf2 at both mRNA and protein levels via down-regulating the expression of Dnmts and DNA demethylation. In addition, 5-Aza mediated upregulation of Nrf2 expression was concomitant with increased nuclear translocation of Nrf2 and higher expression of Nrf2 downstream target gene NAD(P)H:quinone oxidoreductas (NQO1). Our study showed that DNA demethylation promoted the Nrf2 cell signaling pathway, which may enhance the antioxidant system against AD development