Neo-Darwinian Principles Exemplified in Cancer Genomics.

Within the last two decades, the advent of next-generation sequencing accompanied by single-cell technologies has enabled cancer researchers to study in detail mutations and other genetic aberrations that transpire during transformation of cells to a neoplastic state. This article covers the insights gained through these extensive studies where neo-Darwinian principles can be inferred to play roles throughout neoplastic transformation. The cells promoted during cancer development exhibit cancer hallmarks combined with the related enabling characteristics as outlined by Hanahan and Weinberg, analogous to natural selection and survival of the fittest. Selection of driver mutations that inactivate proteins encoded by tumor suppressor genes differs in profound ways from mutations that activate tumor promoter proteins. In most cases, the later stages of cancer development are characterized by sudden, extensive damage to chromosomes in a process that is not Darwinian in nature. Nevertheless, cells that survive these cataclysmic events remain subject to Darwinian selection promoting clones exhibiting the greatest rates of progression. Duplications of chromosomal segments containing oncogenes, deletions of segments harboring tumor suppressor genes, or distinctive chromosomal rearrangements are often found in cells progressing into later stages of cancer. In summary, the technological developments in genome sequencing since the start of the century have given us clear insights into genomic alterations promoting tumor progression where neo-Darwinian mechanisms of clonal selection can be inferred to play a primary role.

Evaluation of the radiofrequency performance of a wide-bore 1.5 T positron emission tomography/magnetic resonance imaging body coil for radiotherapy planning.

BACKGROUND AND PURPOSE: The restricted bore diameter of current simultaneous positron emission tomography/magnetic resonance imaging (PET/MRI) systems can be an impediment to achieving similar patient positioning during PET/MRI planning and radiotherapy. Our goal was to evaluate the B1 transmit (B1 +) uniformity, B1 + efficiency, and specific absorption rate (SAR) of a novel radiofrequency (RF) body coil design, in which RF shielded PET detectors were integrated with the specific aim of enabling a wide-bore PET/MRI system. MATERIALS AND METHODS: We designed and constructed a wide-bore PET/MRI RF body coil to be integrated with a clinical MRI system. To increase its inner bore diameter, the PET detectors were positioned between the conductors and the RF shield of the RF body coil. Simulations and experiments with phantoms and human volunteers were performed to compare the B1 + uniformity, B1 + efficiency, and SAR between our design and the clinical body coil. RESULTS: In the simulations, our design achieved nearly the same B1 + field uniformity as the clinical body coil and an almost identical SAR distribution. The uniformity findings were confirmed by the physical experiments. The B1 + efficiency was 38% lower compared to the clinical body coil. CONCLUSIONS: To achieve wide-bore PET/MRI, it is possible to integrate shielding for PET detectors between the body coil conductors and the RF shield without compromising MRI performance. Reduced B1 + efficiency may be compensated by adding a second RF amplifier. This finding may facilitate the application of simultaneous whole-body PET/MRI in radiotherapy planning.

The Early Detection Research Network's Specimen reference sets: paving the way for rapid evaluation of potential biomarkers.

BACKGROUND: The mission of the National Cancer Institute's Early Detection Research Network (EDRN) is to identify and validate cancer biomarkers for clinical use. Since its inception, EDRN investigators have learned a great deal about the process of validating biomarkers for clinical use. Translational research requires a broad spectrum of research expertise, and coordinating collaborative activities can be challenging. The EDRN has developed a robust triage and validation system that serves the roles of both "facilitator" and "brake." CONTENT: The system consists of (a) establishing a reference set of specimens collected under PRoBE (Prospective Specimen Collection Retrospective Blinded Evaluation) design criteria; (b) using the reference set to prevalidate candidate biomarkers before committing to full-scale validation; (c) performing full-scale validation for those markers that pass prevalidation testing; and (d) ensuring that the reference set is sufficiently large in numbers and volumes of sample that it can also be used to study future candidate biomarkers. This system provides rigorous and efficient evaluation of candidate biomarkers and biomarker panels. Reference sets should also be constructed to enable high-quality biomarker-discovery research. SUMMARY: We describe the process of establishing our system in the hope that it will serve as an example of how to validate biomarkers for clinical application. We also hope that this description of the biospecimen reference sets available from the EDRN will encourage the biomarker research community--from academia or industry--to use this resource to advance biomarkers into clinical use.

Applying analytical ultracentrifugation to nanocrystal suspensions.

While applied frequently in physical biochemistry to the study of protein complexes, the quantitative use of analytical ultracentrifugation (AUC) for nanocrystal analysis is relatively rare. Its application in nanoscience is potentially very powerful as it provides a measure of nanocrystal density, size and structure directly in the solution phase. Towards that end, this paper examines the best practices for applying data collection and analysis methods for AUC, geared towards the study of biomolecules, to the unique problems of nanoparticle analysis. Using uniform nanocrystals of cadmium selenide, we compared several schemes for analyzing raw sedimentation data. Comparable values of the mean sedimentation coefficients (s-value) were found using several popular analytical approaches; however, the distribution in sample s-values is best captured using the van Holde-Weischt algorithm. Measured s-values could be reproducibly collected if sample temperature and concentration were controlled; under these circumstances, the variability for average sedimentation values was typically 5%. The full shape of the distribution in s-values, however, is not easily subjected to quantitative interpretation. Moreover, the selection of the appropriate sedimentation speed is crucial for AUC of nanocrystals as the density of inorganic nanocrystals is much larger than that of solvents. Quantitative analysis of sedimentation properties will allow for better agreement between experimental and theoretical models of nanocrystal solution behavior, as well as providing deeper insight into the hydrodynamic size and solution properties of nanomaterials.

Standard operating procedures for serum and plasma collection: early detection research network consensus statement standard operating procedure integration working group.

Specimen collection is an integral component of clinical research. Specimens from subjects with various stages of cancers or other conditions, as well as those without disease, are critical tools in the hunt for biomarkers, predictors, or tests that will detect serious diseases earlier or more readily than currently possible. Analytic methodologies evolve quickly. Access to high-quality specimens, collected and handled in standardized ways that minimize potential bias or confounding factors, is key to the "bench to bedside" aim of translational research. It is essential that standard operating procedures, "the how" of creating the repositories, be defined prospectively when designing clinical trials. Small differences in the processing or handling of a specimen can have dramatic effects in analytical reliability and reproducibility, especially when multiplex methods are used. A representative working group, Standard Operating Procedures Internal Working Group (SOPIWG), comprised of members from across Early Detection Research Network (EDRN) was formed to develop standard operating procedures (SOPs) for various types of specimens collected and managed for our biomarker discovery and validation work. This report presents our consensus on SOPs for the collection, processing, handling, and storage of serum and plasma for biomarker discovery and validation.

Size-dependent sedimentation properties of nanocrystals.

Centrifugation is an increasingly important technique for nanomaterial processing. Here, we examine this process for gold, cadmium selenide, and iron oxide nanocrystals using an analytical ultracentrifuge. Such data provide an accurate measure of the sedimentation coefficients for these materials, and we find that this parameter has a significant dependence on the size and surface coating. Conventional models for particle sedimentation cannot capture the behavior of these nanocrystals unless the density of the nanocrystals is described by a size-dependent term that accounts for both the inorganic core and the organic coating. Using this modification in the particle sedimentation framework, it is possible to estimate sedimentation coefficients from information about the nanocrystal core and surface coating dimensions. Such data are useful in choosing the speeds for a centrifugation process and are particularly important when bimodal nanocrystal distributions are present.

Characterization of nanocrystalline CdSe by size exclusion chromatography.

High-performance size exclusion chromatography (HPSEC) is a powerful tool for probing the size and size distribution of complex materials. Here we report its application to the analysis of cadmium selenide nanocrystals produced in organic solvents. If nanocrystal-column interactions are minimized, this method provides an accurate measure of nanocrystal hydrodynamic diameter directly in solution; such information is complementary to TEM in that it can measure the thickness of various capping agents. While the resolution of single-pass HPSEC is limited to 1 nm, we show here that recycling size exclusion chromatography can be applied to assess the fine details of a sample's distribution. Finally, semiconductor nanocrystals can be made a variety of shapes whose optical characteristics are difficult to distinguish. HPSEC can be applied to the general problem of shape separations which we demonstrate with a tetrapod material.

The use of heat transfer fluids in the synthesis of high-quality CdSe quantum dots, core/shell quantum dots, and quantum rods.

Fluorescent semiconductor nanoparticles, or quantum dots, have potential uses as an optical material, in which the optoelectronic properties can be tuned precisely by particle size. Advances in chemical synthesis have led to improvements in size and shape control, cost, and safety. A limiting step in large-scale production is identified to be the raw materials cost, in which a common synthesis solvent, octadecene, accounts for most of the materials cost for a batch of CdSe quantum dots. Thus, less expensive solvents are needed. In this paper, we identify heat transfer fluids, a class of organic liquids commonly used in chemical process industries to transport heat between unit operations, as alternative solvents for quantum dot synthesis. We specifically show that two heat transfer fluids can be used successfully in the synthesis of CdSe quantum dots with uniform particle sizes. We show that the synthesis chemistry for CdSe/CdS core/shell quantum dots and CdSe quantum rods can also be performed in heat transfer fluids. With the aid of a population balance model, we interpret the effect of different HT fluids on QD growth kinetics in terms of solvent effects, i.e., solvent viscosity, CdSe bulk solubility in the solvent, and surface free energy.

Recycling size exclusion chromatography for the analysis and separation of nanocrystalline gold.

Recycling size exclusion chromatography (RSEC) provides a high-resolution technique for the analysis and separation of materials based on size. We show here the application of this method to gold nanocrystals stabilized by thiols. Alternate recycling is more effective at separating nanomaterials as compared to closed-loop recycling because of its improved efficiency and high resolution. With the use of this technique, we find the resolution ratio of nanocrystal separation increases with the square root of the cycle number, in good agreement with theory. The increased resolution of the size exclusion chromatograms permits the use of RSEC in the baseline separation of nanocrystals which differ by only 6 A in size. In addition to separations, RSEC is valuable as an analytical tool. For example, after recycling processes an initially broad and chromatographic feature from a gold nanocrystal solution resolves into three distinct peaks. Transmission electron microscopy of collected fractions reveals that these peaks correspond to distinct populations of gold nanoparticles with narrowly defined sizes.

Deletion of the NOT4 gene impairs hyphal development and pathogenicity in Candida albicans.

The Candida albicans NOT4 gene was disrupted in order to investigate the role of Not4p in growth, morphogenesis and pathogenicity. Heterozygote (NOT4/not4), null (not4/not4) and reconstructed heterozygote ([NOT4]/not4) strains of C. albicans, as well as CAF2-1, the parental strain, were grown under conditions that promote hyphal formation. When cultured in liquid medium 199 the heterozygote, reconstructed and wild-type strains began the yeast-to-hyphal transition within 3 h and continued hyphal growth for the duration of experiments. The null mutant also began hyphal growth within 3-5 h but hyphae tended to be shorter and distorted. Subsequently, hyphal growth was arrested and growth returned predominantly to the yeast form. Similar differences were observed when strains were grown on solid Spider medium and medium 199. The parental, heterozygote and reconstructed strains formed normal filamentous networks emanating from colonies. In contrast, the null mutant failed to form hyphae on all solid media tested. The ability of the NOT4 null strain to form biofilms was also investigated, and it was observed that biofilm development does not readily occur for this strain. Virulence of each strain was examined utilizing the mouse model of systemic candidiasis. Mice infected with CAF2-1 succumbed to infection within 3-7 days. All mice infected with the null strain survived for the duration of experiments, while the heterozygote and reconstructed heterozygote strains showed an intermediate level of virulence. These findings suggest that NOT4 may play a role in affecting strain pathogenicity, possibly by regulating expression of certain genes that effect cellular morphogenesis and virulence.