Fibrous Cap Thickness Predicts Stable Coronary Plaque Progression: Early Clinical Validation of a Semiautomated OCT Technology.

Background: Imaging-based characteristics associated with the progression of stable coronary atherosclerotic lesions are poorly defined. Utilizing a combination of optical coherence tomography (OCT) and intravascular ultrasound (IVUS) imaging, we aimed to characterize the lesions prone to progression through clinical validation of a semiautomated OCT computational program. Methods: Patients with stable coronary artery disease underwent nonculprit vessel imaging with IVUS and OCT at baseline and IVUS at the 12-month follow-up. After coregistration of baseline and follow-up IVUS images, paired 5-mm segments from each patient were identified, demonstrating the greatest plaque progression and regression as measured by the change in plaque burden. Experienced readers identified plaque features on corresponding baseline OCT segments, and predictors of plaque progression were assessed by multivariable analysis. Each segment then underwent volumetric assessment of the fibrous cap (FC) using proprietary software. Results: Among 23 patients (70% men; median age, 67 years), experienced-reader analysis demonstrated that for every 100 µm increase in mean FC thickness, plaques were 87% less likely to progress (P = .01), which persisted on multivariable analysis controlling for baseline plaque burden (P = .05). Automated FC analysis (n = 17 paired segments) confirmed this finding (P = .01) and found thinner minimal FC thickness (P = .01) and larger FC surface area of <65 µm (P = .02) and <100 µm (P = .04) in progressing segments than in regressing segments. No additional imaging features predicted plaque progression. Conclusions: A semiautomated FC analysis tool confirmed the significant association between thinner FC and stable coronary plaque progression along entire vessel segments, illustrating the diffuse nature of FC thinning and suggesting a future clinical role in predicting the progression of stable coronary artery disease.

Immersive educational curriculum on intracoronary optical coherence tomography image analysis among naïve readers.

BACKGROUND: Optical coherence tomography (OCT) is an intravascular imaging modality for analysing coronary vessels. Image interpretation remains an obstacle for novice readers due to technical artefacts and uncertainty in tissue characterization. Despite an expanding clinical and research role for OCT, few training efforts exist, and there is an absence of a national standardized educational curriculum. We sought to determine whether an interactive, feedback-based OCT curriculum improved image interpretation among naive readers. METHODS: Naive OCT readers completed both a Standard curriculum, comprised of self-directed didactics and consensus statements, and an Augmented curriculum, which provided real-time digital feedback of feature identification and measurements. Modules were separated by a minimum one-week washout period. After each module, and blinded to the exam answers, subjects completed an identical expert-designed 413-item exam to assess technical knowledge and ability to identify and measure vessel features. Performances were compared using Exact Wilcoxon signed-rank tests. RESULTS: Among the 7 included subjects were 3 medical students, 3 internal medicine residents, and 1 cardiovascular medicine fellow with no prior OCT experience. The technical knowledge score (maximum 13) was significantly higher with the Augmented compared with the Standard curriculum (median 11 vs. 7, p = 0.03). After undergoing the Augmented curriculum, all 7 subjects were able to identify features of plaque rupture (Standard curriculum: 5/7 subjects, p = 0.5) and macrophages (Standard curriculum: 6/7 subjects, p = 0.99), differentiate the components between red and white thrombus (Standard curriculum: 6/7 subjects, p = 0.99), and characterize lipid plaque by attenuation, signal, homogeneity, and borders (Standard curriculum: 5/7 subjects, p = 0.5). Performances on the remaining exam portions did not differ between curricula. CONCLUSIONS: The need for standardized, effective training in OCT image interpretation is increasingly essential as the intravascular imaging modality becomes widely utilized among interventional cardiologists and trainees. A novel interactive OCT curriculum enhanced naive readers' technical knowledge and may supplement traditional self-learning in refining analytic skills.

In Vivo Entombment of Bacteria and Fungi during Calcium Oxalate, Brushite, and Struvite Urolithiasis.

Background: Human kidney stones form via repeated events of mineral precipitation, partial dissolution, and reprecipitation, which are directly analogous to similar processes in other natural and manmade environments, where resident microbiomes strongly influence biomineralization. High-resolution microscopy and high-fidelity metagenomic (microscopy-to-omics) analyses, applicable to all forms of biomineralization, have been applied to assemble definitive evidence of in vivo microbiome entombment during urolithiasis. Methods: Stone fragments were collected from a randomly chosen cohort of 20 patients using standard percutaneous nephrolithotomy (PCNL). Fourier transform infrared (FTIR) spectroscopy indicated that 18 of these patients were calcium oxalate (CaOx) stone formers, whereas one patient formed each formed brushite and struvite stones. This apportionment is consistent with global stone mineralogy distributions. Stone fragments from seven of these 20 patients (five CaOx, one brushite, and one struvite) were thin sectioned and analyzed using brightfield (BF), polarization (POL), confocal, super-resolution autofluorescence (SRAF), and Raman techniques. DNA from remaining fragments, grouped according to each of the 20 patients, were analyzed with amplicon sequencing of 16S rRNA gene sequences (V1-V3, V3-V5) and internal transcribed spacer (ITS1, ITS2) regions. Results: Bulk-entombed DNA was sequenced from stone fragments in 11 of the 18 patients who formed CaOx stones, and the patients who formed brushite and struvite stones. These analyses confirmed the presence of an entombed low-diversity community of bacteria and fungi, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Aspergillus niger. Bacterial cells approximately 1 µm in diameter were also optically observed to be entombed and well preserved in amorphous hydroxyapatite spherules and fans of needle-like crystals of brushite and struvite. Conclusions: These results indicate a microbiome is entombed during in vivo CaOx stone formation. Similar processes are implied for brushite and struvite stones. This evidence lays the groundwork for future in vitro and in vivo experimentation to determine how the microbiome may actively and/or passively influence kidney stone biomineralization.

An optical coherence tomography comparison of coronary arterial plaque calcification in patients with end-stage renal disease and diabetes mellitus.

BACKGROUND: Coronary arterial plaques in patients with end-stage renal disease (ESRD) are assumed to have increased calcification due to underlying renal disease or initiation of dialysis. This relationship may be confounded by comorbid type 2 diabetes mellitus (DM). METHODS: From a single-center OCT registry, 60 patients were analyzed. Twenty patients with ESRD and diabetes (ESRD-DM) were compared to 2 groups of non-ESRD patients: 20 with and 20 without diabetes. In each patient, one 20 mm segment within the culprit vessel was analyzed. RESULTS: ESRD-DM patients exhibited similar calcium burden, arc, and area compared to patients with diabetes alone. When compared to patients without diabetes, patients with diabetes exhibited a greater summed area of calcium (DM: Median 9.0, IQR [5.3-28] mm2 vs Non-DM: 3.5 [0.1-14] mm2, p = 0.04) and larger calcium deposits by arc (DM: Mean 45 ± SE 6.2° vs Non-DM: 21 ± 6.2°, p = 0.01) and area (DM: 0.58 ± 0.10 mm2 vs Non-DM: 0.26 ± 0.10 mm2, p = 0.03). Calcification deposits in ESRD-DM patients (0.14 ± 0.02 mm) and patients with diabetes (0.14 ± 0.02 mm) were more superficially located relative to patients without diabetes (0.21 ± 0.02 mm), p = 0.01 for both. CONCLUSIONS: Coronary calcification in DM and ESRD-DM groups exhibited similar burden, deposit size, and depth within the arterial wall. The increase in coronary calcification and cardiovascular disease events seen in ESRD-DM patients may not be secondary to ESRD and dialysis, but instead due to a combination of declining renal function and diabetes.

Orenia metallireducens sp. nov. Strain Z6, a Novel Metal-Reducing Member of the Phylum Firmicutes from the Deep Subsurface.

A novel halophilic and metal-reducing bacterium, Orenia metallireducens strain Z6, was isolated from briny groundwater extracted from a 2.02 km-deep borehole in the Illinois Basin, IL. This organism shared 96% 16S rRNA gene similarity with Orenia marismortui but demonstrated physiological properties previously unknown for this genus. In addition to exhibiting a fermentative metabolism typical of the genus Orenia, strain Z6 reduces various metal oxides [Fe(III), Mn(IV), Co(III), and Cr(VI)], using H2 as the electron donor. Strain Z6 actively reduced ferrihydrite over broad ranges of pH (6 to 9.6), salinity (0.4 to 3.5 M NaCl), and temperature (20 to 60°C). At pH 6.5, strain Z6 also reduced more crystalline iron oxides, such as lepidocrocite (γ-FeOOH), goethite (α-FeOOH), and hematite (α-Fe2O3). Analysis of X-ray absorption fine structure (XAFS) following Fe(III) reduction by strain Z6 revealed spectra from ferrous secondary mineral phases consistent with the precipitation of vivianite [Fe3(PO4)2] and siderite (FeCO3). The draft genome assembled for strain Z6 is 3.47 Mb in size and contains 3,269 protein-coding genes. Unlike the well-understood iron-reducing Shewanella and Geobacter species, this organism lacks the c-type cytochromes for typical Fe(III) reduction. Strain Z6 represents the first bacterial species in the genus Orenia (order Halanaerobiales) reported to reduce ferric iron minerals and other metal oxides. This microbe expands both the phylogenetic and physiological scopes of iron-reducing microorganisms known to inhabit the deep subsurface and suggests new mechanisms for microbial iron reduction. These distinctions from other Orenia spp. support the designation of strain Z6 as a new species, Orenia metallireducens sp. nov. IMPORTANCE: A novel iron-reducing species, Orenia metallireducens sp. nov., strain Z6, was isolated from groundwater collected from a geological formation located 2.02 km below land surface in the Illinois Basin, USA. Phylogenetic, physiologic, and genomic analyses of strain Z6 found it to have unique properties for iron reducers, including (i) active microbial iron-reducing capacity under broad ranges of temperatures (20 to 60°C), pHs (6 to 9.6), and salinities (0.4 to 3.5 M NaCl), (ii) lack of c-type cytochromes typically affiliated with iron reduction in Geobacter and Shewanella species, and (iii) being the only member of the Halanaerobiales capable of reducing crystalline goethite and hematite. This study expands the scope of phylogenetic affiliations, metabolic capacities, and catalytic mechanisms for iron-reducing microbes.

Tepidibacillus decaturensis sp. nov., a microaerophilic, moderately thermophilic iron-reducing bacterium isolated from 1.7 km depth groundwater.

A Gram-stain-negative, microaerophilic rod-shaped organism designated as strain Z9T was isolated from groundwater of 1.7 km depth from the Mt. Simon Sandstone of the Illinois Basin, Illinois, USA. Cells of strain Z9T were rod shaped with dimensions of 0.3×(1-10) µm and stained Gram-negative. Strain Z9T grew within the temperature range 20-60 °C (optimum at 30-40 °C), between pH 5 and 8 (optimum 5.2-5.8) and under salt concentrations of 1-5 % (w/v) NaCl (optimum 2.5 % NaCl). In addition to growth by fermentation and nitrate reduction, this strain was able to reduce Fe(III), Mn(IV), Co(III) and Cr(VI) when H2 or organic carbon was available as the electron donor, but did not actively reduce oxidized sulfur compounds (e.g. sulfate, thiosulfate or S0). The G+C content of the DNA from strain Z9T was 36.1 mol%. Phylogenetic analysis of the 16S rRNA gene from strain Z9T showed that it belongs to the class Bacilli and shares 97 % sequence similarity with the only currently characterized member of the genus Tepidibacillus, T.fermentans. Based on the physiological distinctness and phylogenetic information, strain Z9T represents a novel species within the genus Tepidibacillus, for which the name Tepidibacillus decaturensis sp. nov. is proposed. The type strain is Z9T (=ATCC BAA-2644T=DSM 103037T).

Proteomic Analysis of a Poplar Cell Suspension Culture Suggests a Major Role of Protein S-Acylation in Diverse Cellular Processes.

S-acylation is a reversible post-translational modification of proteins known to be involved in membrane targeting, subcellular trafficking, and the determination of a great variety of functional properties of proteins. The aim of this work was to identify S-acylated proteins in poplar. The use of an acyl-biotin exchange method and mass spectrometry allowed the identification of around 450 S-acylated proteins, which were subdivided into three major groups of proteins involved in transport, signal transduction, and response to stress, respectively. The largest group of S-acylated proteins was the protein kinase superfamily. Soluble N-ethylmaleimide-sensitive factor-activating protein receptors, band 7 family proteins and tetraspanins, all primarily related to intracellular trafficking, were also identified. In addition, cell wall related proteins, including cellulose synthases and other glucan synthases, were found to be S-acylated. Twenty four of the identified S-acylated proteins were also enriched in detergent-resistant membrane microdomains, suggesting S-acylation plays a key role in the localization of proteins to specialized plasma membrane subdomains. This dataset promises to enhance our current understanding of the various functions of S-acylated proteins in plants.

ProteinShader: illustrative rendering of macromolecules.

BACKGROUND: Cartoon-style illustrative renderings of proteins can help clarify structural features that are obscured by space filling or balls and sticks style models, and recent advances in programmable graphics cards offer many new opportunities for improving illustrative renderings. RESULTS: The ProteinShader program, a new tool for macromolecular visualization, uses information from Protein Data Bank files to produce illustrative renderings of proteins that approximate what an artist might create by hand using pen and ink. A combination of Hermite and spherical linear interpolation is used to draw smooth, gradually rotating three-dimensional tubes and ribbons with a repeating pattern of texture coordinates, which allows the application of texture mapping, real-time halftoning, and smooth edge lines. This free platform-independent open-source program is written primarily in Java, but also makes extensive use of the OpenGL Shading Language to modify the graphics pipeline. CONCLUSION: By programming to the graphics processor unit, ProteinShader is able to produce high quality images and illustrative rendering effects in real-time. The main feature that distinguishes ProteinShader from other free molecular visualization tools is its use of texture mapping techniques that allow two-dimensional images to be mapped onto the curved three-dimensional surfaces of ribbons and tubes with minimum distortion of the images.

Identification of a phylogenetically conserved activin-responsive enhancer in the Zic3 gene.

Multiple signaling pathways are involved in the induction of the organizer, a major center controlling vertebrate body plan formation. To study these signals, we have focused on the regulation of the Zic3 gene, which codes for a zinc finger transcription factor expressed in the organizer region at the beginning of gastrulation. We searched for DNA regulatory elements in the Zic3 promoter by testing their ability to drive reporter gene expression in early embryos. By this approach, we identified an activin responsive enhancer (Zic3-ARE), which was located in the Zic3 first intron and was essential for dorsal activation of the reporter. The Zic3-ARE was stimulated by activin and Nodal ligands, but not by a dominant negative bone morphogenetic protein (BMP) receptor. The Zic3-ARE contains a repeating consensus homeodomain binding sequence, CTAATTAAA, suggesting involvement of a homeodomain transcription factor(s). Mutations in this motif abolished enhancer activity in dorsal marginal zone and its response to activin in animal pole explants. Inhibition of either Wnt/beta-catenin or activin/Nodal signaling suppressed Zic3-ARE activity in dorsal blastomeres, further illustrating the importance of these pathways in activation of organizer genes.