The Arabidopsis epitranscriptome

The most prevalent internal modification of plant messenger RNAs, N6-methyladenosine (m6A), was first discovered in the 1970s, then largely forgotten. However, the impact of modifications to eukaryote mRNA, collectively known as the epitranscriptome, has recently attracted renewed attention. mRNA methylation is required for normal Arabidopsis development and the first methylation maps reveal that thousands of Arabidopsis mRNAs are methylated. Arabidopsis is likely to be a model of wide utility in understanding the biological impacts of the epitranscriptome. We review recent progress and look ahead with questions awaiting answers to reveal an entire layer of gene regulation that has until recently been overlooked

The effect of ambient temperature on cold start urban traffic emissions for a real world SI car

The influence of ambient temperature on exhaust emissions for an instrumented Euro 1 SI car was determined. A real world test cycle was used, based on an urban drive cycle that was similar to the ECE urban drive cycle. It was based on four laps of a street circuit and an emissions sample bag was taken for each lap. The bag for the first lap was for the cold start emissions. An in-vehicle direct exhaust dual bag sampling technique was used to simultaneously collect exhaust samples upstream and downstream of the three-way catalyst (TWC). The cold start tests were conducted over a year, with ambient temperatures ranging from – 2°C to 32°C. The exhaust system was instrumented with thermocouples so that the catalyst light off temperature could be determined. The results showed that CO emissions for the cold start were reduced by a factor of 8 downstream of catalyst when ambient temperature rose from -2°C to 32°C, the corresponding hydrocarbon emissions were reduced by a factor of 4. There was no clear relationship between NOx emissions and ambient temperature. For subsequent laps of the test circuit the reduction of CO and HC emissions as a function of ambient temperature was lower. The time for catalyst light off increased by 50% as the ambient temperature was reduced. The results show that the vehicle used is unlikely to meet the new – 7oC cold start CO emission regulations

Crystal structure of the SPOC domain of the <i>Arabidopsis</i> flowering regulator FPA

The Arabidopsis protein FPA controls flowering time by regulating the alternative 3'-end processing of the FLOWERING LOCUS (FLC) antisense RNA. FPA belongs to the split ends (SPEN) family of proteins, which contain N-terminal RNA recognition motifs (RRMs) and a SPEN paralog and ortholog C-terminal (SPOC) domain. The SPOC domain is highly conserved among FPA homologs in plants, but the conservation with the domain in other SPEN proteins is much lower. We have determined the crystal structure of Arabidopsis thaliana FPA SPOC domain at 2.7 Å resolution. The overall structure is similar to that of the SPOC domain in human SMRT/HDAC1 Associated Repressor Protein (SHARP), although there are also substantial conformational differences between them. Structural and sequence analyses identify a surface patch that is conserved among plant FPA homologs. Mutations of two residues in this surface patch did not disrupt FPA functions, suggesting that either the SPOC domain is not required for the role of FPA in regulating RNA 3'-end formation or the functions of the FPA SPOC domain cannot be disrupted by the combination of mutations, in contrast to observations with the SHARP SPOC domain

Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification

Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification. We adapted nanopore direct RNA sequencing to examine RNA from a wild-type accession of the model plant Arabidopsis thaliana and a mutant defective in mRNA methylation (m6A). Here we show that m6A can be mapped in full-length mRNAs transcriptome-wide and reveal the combinatorial diversity of cap-associated transcription start sites, splicing events, poly(A) site choice and poly(A) tail length. Loss of m6A from 3’ untranslated regions is associated with decreased relative transcript abundance and defective RNA 30 end formation. A functional consequence of disrupted m6A is a lengthening of the circadian period. We conclude that nanopore direct RNA sequencing can reveal the complexity of mRNA processing and modification in full-length single molecule reads. These findings can refine Arabidopsis genome annotation. Further, applying this approach to less well-studied species could transform our understanding of what their genomes encode

Two zinc finger proteins with functions in m6A writing interact with HAKAI

The methyltransferase complex (m6A writer), which catalyzes the deposition of N6-methyladenosine (m6A) in mRNAs, is highly conserved across most eukaryotic organisms, but its components and interactions between them are still far from fully understood. Here, using in vivo interaction proteomics, two HAKAI-interacting zinc finger proteins, HIZ1 and HIZ2, are discovered as components of the Arabidopsis m6A writer complex. HAKAI is required for the interaction between HIZ1 and MTA (mRNA adenosine methylase A). Whilst HIZ1 knockout plants have normal levels of m6A, plants in which it is overexpressed show reduced methylation and decreased lateral root formation. Mutant plants lacking HIZ2 are viable but have an 85% reduction in m6A abundance and show severe developmental defects. Our findings suggest that HIZ2 is likely the plant equivalent of ZC3H13 (Flacc) of the metazoan m6A-METTL Associated Complex

Abrupt closure: The CAVEAT I experience

Objectives.This study sought to assess the incidence and consequences of abrupt closure in a series of patients undergoing directional coronary atherectomy versus percutaneous coronary angioplasty.Background.Abrupt closure with coronary angioplasty has been associated with adverse outcome. The results from the Coronary Angioplasty Versus Excisional Atherectomy Trial (CAVEAT) I, a randomized trial of coronary angioplasty versus directional coronary atherectomy, were analyzed.Method.This multicenter trial enrolled 1,012 patients from 1991 to 1992. All records from patients with abrupt closure, which was coded as a discrete complication, were reviewed.Results.Abrupt closure occurred in 60 patients (5.9%) and was associated with a significantly longer hospital stay (median 8 vs. 3 days). Severe proximal target vessel tortuosity was more common in patients with abrupt closure (20.3% vs. 11.6%, p = 0.046), as was preexistent coronary artery thrombus (30.5% vs. 18.3%, p = 0.02). Abrupt closure was associated with a marked increase in subsequent complications (myocardial infarction 46.7% vs. 2.1%, emergency bypass surgery 383% vs. 0.32%, death 33% vs. 0%) and occurred more frequently in the directional coronary atherectomy group (8.0% vs. 3.8%, p = 0.005). In the coronary angioplasty group, the occlusion usually occurred at the target lesion (91%), presumably related to the effects of barotrauma. In the directional coronary atherectomy group, the site of the occlusion was the target lesion in only 58% (p = 0.045). The remaining occlusions related to problems with the technique (guide catheter or nose cone trauma), reflecting the fact that directional coronary atherectomy is a more complex procedure.Conclusions.Abrupt closure remains the principal determinant of adverse outcome after percutaneous procedures for the treatment of coronary artery disease. Although abrupt closure is more common with directional atherectomy than angioplasty, the sequelae are similar

Fano Resonances in Electronic Transport through a Single Electron Transistor

We have observed asymmetric Fano resonances in the conductance of a single electron transistor resulting from interference between a resonant and a nonresonant path through the system. The resonant component shows all the features typical of quantum dots, but the origin of the non-resonant path is unclear. A unique feature of this experimental system, compared to others that show Fano line shapes, is that changing the voltages on various gates allows one to alter the interference between the two paths.Comment: 8 pages, 6 figures. Submitted to PR