Sculpting photoproducts with DNA origami.

Natural light-harvesting systems spatially organize densely packed dyes in different configurations to either transport excitons or convert them into charge photoproducts, with high efficiency. In contrast, artificial photosystems like organic solar cells and light-emitting diodes lack this fine structural control, limiting their efficiency. Thus, biomimetic multi-dye systems are needed to organize dyes with the sub-nanometer spatial control required to sculpt resulting photoproducts. Here, we synthesize 11 distinct perylene diimide (PDI) dimers integrated into DNA origami nanostructures and identify dimer architectures that offer discrete control over exciton transport versus charge separation. The large structural-space and site-tunability of origami uniquely provides controlled PDI dimer packing to form distinct excimer photoproducts, which are sensitive to interdye configurations. In the future, this platform enables large-scale programmed assembly of dyes mimicking natural systems to sculpt distinct photophysical products needed for a broad range of optoelectronic devices, including solar energy converters and quantum information processors.

3D RNA-scaffolded wireframe origami.

Hybrid RNA:DNA origami, in which a long RNA scaffold strand folds into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite its unique potential for biomedical delivery of mRNA, tertiary structure characterization of long RNAs, and fabrication of artificial ribozymes. Here, we investigate design principles of three-dimensional wireframe RNA-scaffolded origami rendered as polyhedra composed of dual-duplex edges. We computationally design, fabricate, and characterize tetrahedra folded from an EGFP-encoding messenger RNA and de Bruijn sequences, an octahedron folded with M13 transcript RNA, and an octahedron and pentagonal bipyramids folded with 23S ribosomal RNA, demonstrating the ability to make diverse polyhedral shapes with distinct structural and functional RNA scaffolds. We characterize secondary and tertiary structures using dimethyl sulfate mutational profiling and cryo-electron microscopy, revealing insight into both global and local, base-level structures of origami. Our top-down sequence design strategy enables the use of long RNAs as functional scaffolds for complex wireframe origami.

Nanoscale 3D spatial addressing and valence control of quantum dots using wireframe DNA origami.

Control over the copy number and nanoscale positioning of quantum dots (QDs) is critical to their application to functional nanomaterials design. However, the multiple non-specific binding sites intrinsic to the surface of QDs have prevented their fabrication into multi-QD assemblies with programmed spatial positions. To overcome this challenge, we developed a general synthetic framework to selectively attach spatially addressable QDs on 3D wireframe DNA origami scaffolds using interfacial control of the QD surface. Using optical spectroscopy and molecular dynamics simulation, we investigated the fabrication of monovalent QDs of different sizes using chimeric single-stranded DNA to control QD surface chemistry. By understanding the relationship between chimeric single-stranded DNA length and QD size, we integrated single QDs into wireframe DNA origami objects and visualized the resulting QD-DNA assemblies using electron microscopy. Using these advances, we demonstrated the ability to program arbitrary 3D spatial relationships between QDs and dyes on DNA origami objects by fabricating energy-transfer circuits and colloidal molecules. Our design and fabrication approach enables the geometric control and spatial addressing of QDs together with the integration of other materials including dyes to fabricate hybrid materials for functional nanoscale photonic devices.

Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami.

Wireframe DNA origami assemblies can now be programmed automatically from the top-down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (DX) edges. While these assemblies have numerous applications in nanoscale materials fabrication due to their nanoscale spatial addressability and high degree of customization, no easy-to-use graphical user interface software yet exists to deploy these algorithmic approaches within a single, standalone interface. Further, top-down sequence design of 3D DX-based objects previously enabled by DAEDALUS was limited to discrete edge lengths and uniform vertex angles, limiting the scope of objects that can be designed. Here, we introduce the open-source software package ATHENA with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami using DX or 6HB edges, including irregular, asymmetric DX-based polyhedra with variable edge lengths and vertices demonstrated experimentally, which significantly expands the set of possible 3D DNA-based assemblies that can be designed. ATHENA also enables external editing of sequences using caDNAno, demonstrated using asymmetric nanoscale positioning of gold nanoparticles, as well as providing atomic-level models for molecular dynamics, coarse-grained dynamics with oxDNA, and other computational chemistry simulation approaches.

Learning how to deliver bad and challenging news: Exploring the experience of trainee sonographers - A qualitative study.

BACKGROUND: Previous studies suggest there is a need to improve the delivery of bad and challenging news in obstetric ultrasound settings. However, no research has explored the experiences of trainee sonographers when learning how to deliver challenging news. Understanding this could identify gaps in current provision and inform future training interventions. AIMS: To explore the experiences of trainee sonographers when learning how to deliver challenging news. METHODS: Semi-structured interviews were conducted with trainee sonographers (n = 7) from four training centres to explore their experiences and preferences for news delivery training. RESULTS: Learning how to deliver difficult news was a journey where trainees developed their confidence over time. Most learning occurred in clinical settings, but classroom teaching complemented this. Trainees appreciated the opportunity to observe clinical practice and to hear from patient representatives. However, quality of teaching varied between centres and trainees reported uncertainty regarding the specific language and behaviours they should use. They described building their own personal protocol for news delivery through the course of their training. DISCUSSION: An ultrasound-specific news delivery protocol which details the words and behaviours sonographers can employ could help reduce uncertainty in trainees. Trainees may also benefit from receiving structured feedback on their news delivery performance.

Programming Structured DNA Assemblies to Probe Biophysical Processes.

Structural DNA nanotechnology is beginning to emerge as a widely accessible research tool to mechanistically study diverse biophysical processes. Enabled by scaffolded DNA origami in which a long single strand of DNA is weaved throughout an entire target nucleic acid assembly to ensure its proper folding, assemblies of nearly any geometric shape can now be programmed in a fully automatic manner to interface with biology on the 1-100-nm scale. Here, we review the major design and synthesis principles that have enabled the fabrication of a specific subclass of scaffolded DNA origami objects called wireframe assemblies. These objects offer unprecedented control over the nanoscale organization of biomolecules, including biomolecular copy numbers, presentation on convex or concave geometries, and internal versus external functionalization, in addition to stability in physiological buffer. To highlight the power and versatility of this synthetic structural biology approach to probing molecular and cellular biophysics, we feature its application to three leading areas of investigation: light harvesting and nanoscale energy transport, RNA structural biology, and immune receptor signaling, with an outlook toward unique mechanistic insight that may be gained in these areas in the coming decade.

Quantification of aging effects upon global knee inflammation by 18F-FDG-PET.

OBJECTIVE: The goal of this study was to quantify aging effects upon the global knee joint and surrounding capsule and soft tissue inflammation using fluorine-18 fluorodeoxyglucose (18F-FDG) PET imaging. METHODS: This reanalysis of a prospective study included 64 patients who had undergone 18F-FDG-PET for evaluation of hip joint prostheses, and whose scans included the knee joints in the field of view. Mean patient age was 53 years (range: 33-84 years). A fixed-sized three-dimensional region of interest was placed around each knee joint, paying close attention to exclude the popliteal vessels. 18F-FDG-avid regions in each knee joint were then segmented using an adaptive contrast-oriented thresholding method, and metabolically active volume (MAV), mean standardized uptake value (SUV mean), partial volume-corrected SUV mean (cSUV mean), and partial volume-corrected mean metabolic volumetric product (cMVP mean = cSUV mean × MAV) of the segmented regions were calculated. Finally, global knee inflammation (GKI) for each knee joint was calculated as the sum of cMVP mean in all segmented regions. Association of GKI with age was assessed with Pearson's correlation and linear regression methods, and GKI was compared between patients at different ages - between patients younger than 55 years and those older than 55 years - using the unpaired t-test. RESULTS: The correlation coefficient of GKI with advancing age was 0.57 (P = 0.02). In the linear regression model, considering GKI as the dependent variable and age and sex as independent covariates, the ß coefficient of age was 2.1 (95% confidence interval: 1.1-3.2). For patients aged younger than 55 years versus those aged older than 55 years, the mean GKI was 157 and 190 cm3, respectively (P = 0.01). CONCLUSION: Through the use of novel quantitative techniques, we were able to calculate GKI and demonstrate a significant increase in the entity of joint inflammation with advancing age. As degenerative disease is age-related and inflammation is implicated in its pathogenesis, our findings further support this association. These preliminary data suggest that this approach can potentially provide a means to objectively quantify the degree of inflammation in various joint disorders, and possibly in other knee degenerative/inflammatory diseases.

Increased 18F-FDG uptake suggests synovial inflammatory reaction with osteoarthritis: preliminary in-vivo results in humans.

OBJECTIVE: The aim of this prospective study was to compare the metabolic activity of the knee joints of a group of patients with painful knees clinically (such as recurrent joint pain, joint instability, and functional limitations) consistent with osteoarthritis and those of another group of patients without such complaints, using [F]-2-fluoro-2-deoxy-D-glucose (F-FDG)-PET imaging. METHODS: A total of 97 patients who participated in either painful joint prosthesis or diabetic foot research studies involving F-FDG-PET scans were asked to complete a knee pain questionnaire. The patients were asked whether they experienced pain in any joint, and if so, which joints were affected. RESULTS: A total of 18 knee joints without prosthesis were reported to be painful. The maximum standardized uptake values (SUVmax) of the middle joint space and lateral synovial tissue of these 18 knees were measured and compared with those of a set of patients with control asymptomatic knees. The average SUVmax of the middle part of the joint space in the painful knees was 1.35±0.59 compared with an average SUVmax value of 0.86±0.14 in the control group (P=0.0176). The average SUVmax of the synovium in the lateral part of the painful joints was 1.17±0.49 compared with 0.73±0.31 in the control group (P=0.0161). CONCLUSION: These data indicate that increased F-FDG uptake is associated with knee pain in osteoarthritis patients and that there is a positive relationship between the two parameters.

Appearance of untreated bone metastases from breast cancer on FDG PET/CT: importance of histologic subtype.

PURPOSE: To determine if the histology of a breast malignancy influences the appearance of untreated osseous metastases on FDG PET/CT. METHODS: This retrospective study was performed under IRB waiver. Our Hospital Information System was screened for breast cancer patients who presented with osseous metastases, who underwent FDG PET/CT prior to systemic therapy or radiotherapy from 2009 to 2012. Patients with invasive ductal carcinoma (IDC), invasive lobular carcinoma (ILC), or mixed ductal/lobular (MDL) histology were included. Patients with a history of other malignancies were excluded. PET/CT was evaluated, blinded to histology, to classify osseous metastases on a per-patient basis as sclerotic, lytic, mixed lytic/sclerotic, or occult on CT, and to record SUVmax for osseous metastases on PET. RESULTS: Following screening, 95 patients who met the inclusion criteria (74 IDC, 13 ILC, and 8 MDL) were included. ILC osseous metastases were more commonly sclerotic and demonstrated lower SUVmax than IDC metastases. In all IDC and MDL patients with osseous metastases, at least one was FDG-avid. For ILC, all patients with lytic or mixed osseous metastases demonstrated at least one FDG-avid metastasis; however, in only three of seven patients were sclerotic osseous metastases apparent on FDG PET. CONCLUSION: The histologic subtype of breast cancer affects the appearance of untreated osseous metastases on FDG PET/CT. In particular, non-FDG-avid sclerotic osseous metastases were more common in patients with ILC than in patients with IDC. Breast cancer histology should be considered when interpreting non-FDG-avid sclerotic osseous lesions on PET/CT, which may be more suspicious for metastases (rather than benign lesions) in patients with ILC.

FDG PET for diagnosing infection in hip and knee prostheses: prospective study in 221 prostheses and subgroup comparison with combined (111)In-labeled leukocyte/(99m)Tc-sulfur colloid bone marrow imaging in 88 prostheses.

PURPOSE: This study aims to assess and compare the value of FDG PET with combined In-labeled leukocyte/Tc-sulfur colloid bone marrow (WBC/BM) imaging for diagnosing infection in hip and knee prostheses. METHODS: In this prospective study, patients with painful hip or knee arthroplasty, who were scheduled to undergo clinical and diagnostic evaluation for prosthesis revision, were included. They have been studied by using FDG PET and WBC/BM scan. This study was institutional review board approved and Health Insurance Portability and Accountability Act compliant. All patients provided written informed consent. RESULTS: A total of 134 hip and 87 knee prostheses, suspected of being either infected or noninfectious loosening, were evaluated. All 221 prostheses underwent FDG PET, whereas both WBC/BM imaging and FDG PET were performed in 88 prostheses. The initial analysis of data from the WBC/BM images demonstrated somewhat suboptimal results compared with those of FDG PET scans on 88 patients. In addition, some patients were not willing to undergo both procedures and therefore participate in this study. Therefore, a decision was made to eliminate WBC/BM imaging from the procedures for the remainder of this research study. This decision was reached partly because of the significant radiation dose delivered from labeled WBC and safety issues related to preparing these labeled cells. Final diagnosis was based on microbiological examinations of the surgical specimens in 125 prostheses and joint aspirations combined with the clinical follow-up of 6 months or more in 86 prostheses. The sensitivity, specificity, positive predictive value, and negative predictive value of FDG PET in hip prostheses were 81.8%, 93.1%, 79.4%, and 94.0%, respectively, and in knee prostheses were 94.7%, 88.2%, 69.2%, and 98.4%, respectively. The sensitivity, specificity, positive predictive value, and negative predictive value of WBC/BM imaging in hip prostheses were 38.5%, 95.7%, 71.4%, and 84.6%, respectively, and in knee prostheses were 33.3%, 88.5%, 25.0%, and 92.0%, respectively. In those cases that underwent both FDG PET and WBC/BM imaging, there was a trend (P = 0.0625) toward a higher sensitivity for FDG PET in hip prostheses, whereas other comparisons did not show any significant differences between the 2 imaging modalities. CONCLUSIONS: Based on this study, the diagnostic performance of FDG PET scan in detecting infection in painful hip and knee prostheses is optimal for routine clinical application. Considering the complexity and costs of WBC/BM imaging and related safety issues associated with this preparation, FDG PET seems to be an appropriate alternative for assessing these patients.

Promising Roles of PET in Management of Arthroplasty-Associated Infection.

A number of diagnostic tests is often necessary to differentiate aseptic loosening from periprosthetic infection in most clinical settings. The accuracy of [(18)F]Fluorodeoxyglucose examined with positron emission tomography imaging (FDG PET) in diagnosing periprosthetic infection has been determined by a number of investigations. In general, Images are considered positive for infection if they demonstrate increased FDG activity at the bone-prosthesis interface of the prostheses. Based on the large number of reports in the literature the sensitivity and specificity for FDG PET are about 85-90%. The overall accuracy of this non-invasive imaging modality is superior to the other existing imaging techniques. Therefore, FDG PET appears a very promising and accurate diagnosing tool for distinguishing septic from aseptic painful hip prostheses.

Evaluation of thyroid FDG uptake incidentally identified on FDG-PET/CT imaging.

OBJECTIVES: To characterize the prevalence and malignancy of thyroid F-flurodeoxyglucose (FDG) uptake incidentally identified on FDG-PET/computed tomography (CT) scan in a relatively large population. METHODS: Two thousand five hundred and ninety-four cases of FDG-PET/CT performed at our institute in the past 1 year and a half were retrospectively reviewed. Images with incidental focal or diffuse thyroid FDG uptake were identified. Data of the PET findings, thyroid functional assay, and pathological diagnosis were collected and analyzed. Incidental thyroid FDG uptake was defined as a new thyroid lesion initially identified on PET scan in a patient without a previous known history of thyroid disease. RESULTS: The prevalence of incidental thyroid FDG uptake (including both focal and diffuse lesions) was 3.8% (99 of 2594) on FDG-PET/CT, of which 1.8% (46 of 2594) were diffuse and 2.0% (53/2594) were focal. Of the 46 cases with diffuse uptake, 21 had thyroid functional assay and/or ultrasound study, and a diagnosis of chronic thyroiditis was made in all of the 21 cases. Eleven of the 53 patients with focal uptake had fine-needle aspiration or postsurgical pathological diagnosis, four benign lesions (four of 11=36.4%: two thyroid adenomas and two hyperplastic lesions); seven malignancies (seven of 11=63.6%: three papillary carcinomas, two follicular carcinoma, and two metastases). There was overlapping of the lesion SUVmax between the benign and malignant cases, with no statistical difference of the mean SUVmax between the two groups. CONCLUSION: Thyroid FDG uptake incidentally identified on FDG-PET/CT occurred at a frequency of 3.8%, with about half of focal and half of diffuse lesions. The risk of thyroid malignancy was 63.6% in lesions with focal uptake, whereas the majority of diffuse uptake cases represents chronic thyroiditis. More data are needed to elucidate the role of SUV in the differentiation of benign and malignant lesions.

Clinical Significance of Incidental Focal Versus Diffuse Thyroid Uptake on FDG-PET Imaging.

The number of incidentally detected thyroid lesions found with (18)F-fluorodeoxyglucose positron emission tomography is increasing. Malignant cases incidentally found with this technique are mainly primary thyroid cancers, particularly papillary thyroid carcinoma, which tend to harbor a higher rate of unfavorable prognostic features than routinely diagnosed primary thyroid cancers. The significance of standardized uptake values in predicting malignancy of incidental thyroid fluorodeoxyglucose uptake is controversial, and more studies are needed to establish its role in differentiating benign and malignant incidental thyroid fluorodeoxyglucose uptake. In this article, we review recent publications regarding incidental thyroid lesions found on fluorodeoxyglucose positron emission tomography and their differential diagnosis, including the risk for malignancy.