Sequence Determinants of Circadian Gene Expression Phase in Cyanobacteria

The cyanobacterium Synechococcus elongatus PCC 7942 exhibits global biphasic circadian oscillations in gene expression under constant-light conditions. Class I genes are maximally expressed in the subjective dusk, whereas class II genes are maximally expressed in the subjective dawn. Here, we identify sequence features that encode the phase of circadian gene expression. We find that, for multiple genes, an ∼70-nucleotide promoter fragment is sufficient to specify class I or II phase. We demonstrate that the gene expression phase can be changed by random mutagenesis and that a single-nucleotide substitution is sufficient to change the phase. Our study provides insight into how the gene expression phase is encoded in the cyanobacterial genome.Chemistry and Chemical BiologyMolecular and Cellular Biolog

Circadian Gene Expression in Cyanobacteria

Cyanobacteria are photosynthetic prokaryotes that live in aquatic environments. The cyanobacterium Synechococcus elongatus PCC 7942, (hereafter S. elongatus) coordinates its day and night behaviors via a circadian clock. The clock is entrained by light/dark cycles but continues to run in constant light conditions. The core circadian clock in S. elongatus is encoded by post-translational modifications of three Kai proteins, but the extent and mechanism of circadian gene expression are unknown. We provide the first unbiased characterization of circadian gene expression in S. elongatus, demonstrating that $\sim 65\%$ of genes display oscillation in continuous light conditions, with some genes peaking in expression at subjective dawn and others at subjective dusk. We next sought to identify the mechanism by which such a large fraction of the genome could be rhythmically controlled. Through bioinformatic, correlative, and perturbation experiments, we find that circadian changes in chromosome topology/supercoiling are sufficient to drive rhythmic expression (Chapter 2). To further investigate how chromosome topology can control gene expression we performed a high resolution characterization of transcripts and RNA polymerase across the S. elongatus genome (Chapter 3). Bioinformatic analysis of transcription start sites suggests that the AT/GC content a particular region of the promoter is informative in defining the phase at which a transcript is maximally expressed. We find that these sequences are sufficient to drive circadian gene expression at a particular phase and that mutation of single nucleotides in this region can reverse the expression phase of a transcript (Chapter 4). To understand the role of chromosome dynamics in circadian gene expression and cyanobacterial physiology, we tagged and followed chromosomes over multiple cell divisions. We find that S. elongatus cells harbor multiple ordered copies of a single chromosome, and the organization of chromosomes in the cytoplasm facilitates equal segregation of chromosomes to daughter cells (Chapter 5)

Oscillations in Supercoiling Drive Circadian Gene Expression in Cyanobacteria

The cyanobacterium Synechococcus elongatus PCC 7942 exhibits oscillations in mRNA transcript abundance with 24-h periodicity under continuous light conditions. The mechanism underlying these oscillations remains elusive—neither cis nor trans-factors controlling circadian gene expression phase have been identified. Here, we show that the topological status of the chromosome is highly correlated with circadian gene expression state. We also demonstrate that DNA sequence characteristics of genes that appear monotonically activated and monotonically repressed by chromosomal relaxation during the circadian cycle are similar to those of supercoiling-responsive genes in Escherichia coli. Furthermore, perturbation of superhelical status within the physiological range elicits global changes in gene expression similar to those that occur during the normal circadian cycle.Molecular and Cellular Biolog

A high resolution map of a cyanobacterial transcriptome

Background: Previous molecular and mechanistic studies have identified several principles of prokaryotic transcription, but less is known about the global transcriptional architecture of bacterial genomes. Here we perform a comprehensive study of a cyanobacterial transcriptome, that of Synechococcus elongatus PCC 7942, generated by combining three high-resolution data sets: RNA sequencing, tiling expression microarrays, and RNA polymerase chromatin immunoprecipitation sequencing. Results: We report absolute transcript levels, operon identification, and high-resolution mapping of 5' and 3' ends of transcripts. We identify several interesting features at promoters, within transcripts and in terminators relating to transcription initiation, elongation, and termination. Furthermore, we identify many putative non-coding transcripts. Conclusions: We provide a global analysis of a cyanobacterial transcriptome. Our results uncover insights that reinforce and extend the current views of bacterial transcription.Molecular and Cellular Biolog

A comparison of covered vs bare expandable stents for the treatment of aortoiliac occlusive disease

ObjectiveThis trial was conducted to determine if covered stents offer a patency advantage over bare-metal stents in the treatment of aortoiliac arterial occlusive disease.MethodsThe Covered Versus Balloon Expandable Stent Trial (COBEST), a prospective, multicenter, randomized controlled trial, was performed involving 168 iliac arteries in 125 patients with severe aortoiliac occlusive disease who were randomly assigned to receive a covered balloon-expandable stent or bare-metal stent. Patient demographic data, clinical signs and symptoms, TransAtlantic Inter-Society Consensus (TASC) classification, and preprocedure and postprocedure ankle-brachial index measurements were recorded. The primary end points included freedom from binary restenosis and stent occlusion of the treated area, as determined by ultrasound imaging or quantitative visual angiography, or both. Postprocedural follow-up was at 1, 6, 12, and 18 months.ResultsAortoiliac lesions treated with a covered stent were significantly more likely to remain free from binary restenosis than those that were treated with a bare-metal stent (hazard ratio [HR], 0.35; 95% confidence interval (CI), 0.15-0.82; P = .02). Freedom from occlusion was also higher in lesions treated with covered stents than in those treated with a bare-metal stent (HR, 0.28; 95% CI, 0.07-1.09); however, this did not reach statistical significance (P = .07). Subgroup analyses demonstrated a significant difference in freedom from binary restenosis for covered stents in TASC C and D lesions compared with a bare stent (HR, 0.136; 95% CI, 0.042-0.442). This difference was not demonstrated for TASC B lesions (HR, 0.748; 95% CI, 0.235-2.386).ConclusionsCOBEST demonstrates covered and bare-metal stents produce similar and acceptable results for TASC B lesions. However, covered stents perform better for TASC C and D lesions than bare stents in longer-term patency and clinical outcome

Incidence and prognosis of vascular complications after transcatheter aortic valve implantation

ObjectiveTranscatheter aortic valve implantation (TAVI) has gained increasing global popularity as a minimally invasive option for high-risk cardiac patients. However, this operation is not without risk, particularly of significant vascular complications that increase the morbidity, mortality, and overall cost of the procedure. We aim to present our experience of TAVI-related vascular complications, including the morbidity and cost impacts of these events.MethodsA case-series study was performed for all patients undergoing TAVI at our center. Vascular complications were defined according to the 2011 Valve Academic Research Consortium standardized end points. The data were prospectively collected from February 2009 to April 2012, and the outcomes were entered into a database and cross-checked with the hospital notes.ResultsTAVI was performed on 100 patients in our center during the study period, and the 30-day mortality was 6%. Access approaches included 81 transfemoral, 18 transapical, and one trans-subclavian access. The average patient age was 84.9 years, and 65% of the patients were male. Among the transfemoral procedures, there were 16 vascular access-related complications (VAC), including nine major and seven minor complications. The major complications included aortic dissection, iliac arterial rupture, femoral dissection, false aneurysms, and distal embolization, all of which required surgical or endovascular repair. An apical false aneurysm and an apical tear were major VAC of the transapical group, with the latter resulting in death. Patients with VAC had higher blood transfusion requirements (4.1 ± 4.5 units vs 0.9 ± 2.2 units; P = .004), greater length of hospital stay (16.4 ± 10.7 days vs 6.5 ± 5.1 days; P = .001), and increased cost (A$93,448 ± 21,435 vs A$69,932 ± 15,007; P = .002) compared with the non-VAC group. The predictors of vascular complications using multivariate analysis included European System for Cardiac Operative Risk Evaluation (odds ratio, 1.06; 95% confidence interval, 1.02-1.10; P = .001) and diabetes mellitus (odds ratio, 5.07; 95% confidence interval, 1.17-21.88; P = .03). Occurrence of major VAC did not affect in-hospital or 30-day mortality rates and was not associated with poorer survival.ConclusionsVascular complications affect perioperative management and outcomes following TAVI. Our findings show that these complications often require urgent surgical or endovascular repair and result in increased blood transfusions, greater length of hospital stay, and significantly increased costs. Diabetes mellitus and logistic European System for Cardiac Operative Risk Evaluation may be predictive of VAC and should be considered during TAVI patient selection

CAD files for high throughput egg-laying choice chambers

CAD files for high throughput egg-laying choice chambers.</p

CAD files for sloped ceiling egg-laying chamber

CAD files for sloped ceiling egg-laying chamber.</p

Plasmid Maps

Plasmid Maps for Kir2.1* and Kir2.1*Mut.</p