The genomic and transcriptomic landscape of HeLa cells

HeLa is and always has been the most widely used model cell line for studying human cellular and molecular biology, and has thus defined our current understanding of human cells. However, no genomic or transcriptomic references exist for this cell line, and studies thus far have relied on the undoubtedly different human reference genome. This knowledge is essential to guide the increasing number of molecular and genetic studies being done in this cell line, both for design and interpretation. During my doctoral work, I performed deep DNA and RNA sequencing of a HeLa-Kyoto cell line and analyzed its mutational portfolio and gene expression profile. We generated a comprehensive description of the genomic and transcriptomic landscape of this cell line. A segmentation of the genome according to copy number revealed an astonishingly high level of aneuploidy and numerous large structural variations at unprecedented resolution. Remnants of catastrophic chromosome shattering, known as chromothripsis, were evident. Comparison of the HeLa expression profile to the physiological range of human gene expression reveals that several pathways, including cell cycle and DNA repair mechanisms, are 'abnormally' expressed. These results provide the first detailed account of the extent of variations in the HeLa genome, yielding insight into their impact on gene expression, cellular function, and their origins during the evolution of this cell line. This study demonstrates the importance of accounting for the strikingly aberrant characteristics of HeLa cells when designing and interpreting experiments. The important resources provided will help to reevaluate the way HeLa is used to model human biology

Field Experiments on Anchoring of Economic Valuations

A pillar of behavioral research is the view that preferences are constructed during the value elicitation process, but it is unclear whether, and to what extent, such biases influence real market equilibria. This paper examines the “anchoring” phenomenon in the field. The first experiment produces evidence that inexperienced consumers can be anchored in the value elicitation process, yet there is little evidence that experienced agents are influenced by anchors. The second experiment finds that anchors have only transient effects on prices and quantities traded: aggregate market outcomes converge to the intersection of supply and demand after a few market periods.field experiment, anchoring, valuation, experience

Exploring simulation design for mental health practice preparation: a pilot study with learners and preceptors

The purpose of this exploratory pilot study was to determine the feasibility of delivering mental health practice simulations for occupational therapy learners, and whether different debriefing approaches yielded performance differences over successive simulations. Five clinical preceptors and nine first year MScOT students participated in this mixed-method study. In week one simulations, one student group received preceptor facilitated debriefing while the other group used self-debriefing. Both groups used the same scripted questions informed by an advocacy-inquiry approach. In the second week, both groups received the preceptor-led debriefing. Preceptors rated student performances while students self-rated their confidence, competence screen, and satisfaction using standardized tools. Ratings of simulation performance revealed gaps in practice knowledge and the process of practice. Preceptor-led debriefing for both groups resulted in greater depth of reflection and insight into learning gaps and opportunities for continued improvement. The self-debriefing group reported feeling less confident in the simulations. Preceptors reported the scripted advocacy inquiry debriefing approach helped draw out clinical reasoning that could not be observed from performance alone. Simulation may be an effective teaching tool for developing core practice competencies. Design and debriefing styles appear to impact preceptor feedback and the depth of learner critical reflection. Further study is required for generalization

Prolactin in man: a tale of two promoters

The pituitary hormone prolactin (PRL) is best known for its role in the regulation of lactation. Recent evidence furthermore indicates PRL is required for normal reproduction in rodents. Here, we report on the insertion of two transposon-like DNA sequences in the human prolactin gene, which together function as an alternative promoter directing extrapituitary PRL expression. Indeed, the transposable elements contain transcription factor binding sites that have been shown to mediate PRL transcription in human uterine decidualised endometrial cells and lymphocytes. We hypothesize that the transposon insertion event has resulted in divergent (pituitary versus extrapituitary) expression of prolactin in primates, and in differential actions of pituitary versus extrapituitary prolactin in lactation versus pregnancy respectively. Importantly, the TE insertion might provide a context for some of the conflicting results obtained in studies of PRL function in mice and man. BioEssays 28: 1051–1055, 2006. © 2006 Wiley Periodicals, Inc

Fabrication and characterization of a multimodal 3D printed mouse phantom for ionoacoustic quality assurance in image-guided pre-clinical proton radiation research

Objective. Image guidance and precise irradiation are fundamental to ensure the reliability of small animal oncology studies. Accurate positioning of the animal and the in-beam monitoring of the delivered radio-therapeutic treatment necessitate several imaging modalities. In the particular context of proton therapy with a pulsed beam, information on the delivered dose can be retrieved by monitoring the thermoacoustic waves resulting from the brief and local energy deposition induced by a proton beam (ionoacoustics). The objective of this work was to fabricate a multimodal phantom (x-ray, proton, ultrasound, and ionoacoustics) allowing for sufficient imaging contrast for all the modalities. Approach. The phantom anatomical parts were extracted from mouse computed tomography scans and printed using polylactic acid (organs) and a granite/polylactic acid composite (skeleton). The anatomical pieces were encapsulated in silicone rubber to ensure long term stability. The phantom was imaged using x-ray cone-beam computed tomography, proton radiography, ultrasound imaging, and monitoring of a 20 MeV pulsed proton beam using ionoacoustics. Main results. The anatomical parts could be visualized in all the imaging modalities validating the phantom capability to be used for multimodal imaging. Ultrasound images were simulated from the x-ray cone-beam computed tomography and co-registered with ultrasound images obtained before the phantom irradiation and low-resolution ultrasound images of the mouse phantom in the irradiation position, co-registered with ionoacoustic measurements. The latter confirmed the irradiation of a tumor surrogate for which the reconstructed range was found to be in reasonable agreement with the expectation. Significance. This study reports on a realistic small animal phantom which can be used to investigate ionoacoustic range (or dose) verification together with ultrasound, x-ray, and proton imaging. The co-registration between ionoacoustic reconstructions of the impinging proton beam and x-ray imaging is assessed for the first time in a pre-clinical scenario

Development of integration mode proton imaging with a single CMOS detector for a small animal irradiation platform

A novel irradiation platform for preclinical proton therapy studies foresees proton imaging for accurate setup and treatment planning. Imaging at modern synchrocyclotron-based proton therapy centers with high instantaneous particle flux is possible with an integration mode setup. The aim of this work is to determine an object’s water-equivalent thickness (WET) with a commercially available large-area CMOS sensor. Image contrast is achieved by recording the proton energy deposition in detector pixels for several incoming beam energies (here, called probing energies) and applying a signal decomposition method that retrieves the water-equivalent thickness. A single planar 114 mm × 65 mm CMOS sensor (49.5 µm pixel pitch) was used for this study, aimed at small-animal imaging. In experimental campaigns, at two isochronous cyclotron-based facilities, probing energies suitable for small-animal-sized objects were produced once with built-in energy layer switching and the other time, using a custom degrader wheel. To assess water-equivalent thickness accuracy, a micro-CT calibration phantom with 10 inserts of tissue-mimicking materials was imaged at three phantom-to-detector distances: 3 mm, 13 mm, and 33 mm. For 3 mm and 13 mm phantom-to-detector distance, the average water-equivalent thickness error compared to the ground truth was about 1 and the spatial resolution was 0.16(3) mm and 0.47(2) mm, respectively. For the largest separation distance of 33 mm air gap, proton scattering had considerable impact and the water-equivalent thickness relative error increased to 30, and the spatial resolution was larger than 1.75 mm. We conclude that a pixelated CMOS detector with dedicated post-processing methods can enable fast proton radiographic imaging in a simple and compact setup for small-animal-sized objects with high water-equivalent thickness accuracy and spatial resolution for reasonable phantom-to-detector distances