PyJAMAS: open-source, multimodal segmentation and analysis of microscopy images

SUMMARY

Our increasing ability to resolve fine details using light microscopy is matched by an increasing need to quantify images in order to detect and measure phenotypes. Despite their central role in cell biology, many image analysis tools require a financial investment, are released as proprietary software, or are implemented in languages not friendly for beginners, and thus are used as black boxes. To overcome these limitations, we have developed PyJAMAS, an open-source tool for image processing and analysis written in Python. PyJAMAS provides a variety of segmentation tools, including watershed and machine learning-based methods; takes advantage of Jupyter notebooks for the display and reproducibility of data analyses; and can be used through a cross-platform graphical user interface or as part of Python scripts via a comprehensive application programming interface.

AVAILABILITY AND IMPLEMENTATION

PyJAMAS is open-source and available at https://bitbucket.org/rfg_lab/pyjamas.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Enucleated cells reveal differential roles of the nucleus in cell migration, polarity, and mechanotransduction

The nucleus has long been postulated to play a critical physical role during cell polarization and migration, but that role has not been defined or rigorously tested. Here, we enucleated cells to test the physical necessity of the nucleus during cell polarization and directed migration. Using enucleated mammalian cells (cytoplasts), we found that polarity establishment and cell migration in one dimension (1D) and two dimensions (2D) occur without the nucleus. Cytoplasts directionally migrate toward soluble (chemotaxis) and surface-bound (haptotaxis) extracellular cues and migrate collectively in scratch-wound assays. Consistent with previous studies, migration in 3D environments was dependent on the nucleus. In part, this likely reflects the decreased force exerted by cytoplasts on mechanically compliant substrates. This response is mimicked both in cells with nucleocytoskeletal defects and upon inhibition of actomyosin-based contractility. Together, our observations reveal that the nucleus is dispensable for polarization and migration in 1D and 2D but critical for proper cell mechanical responses.

Science and regulation. Probiotics: finding the right regulatory balance

Some products marketed as drugs should be excused from Phase I trials, but safety and efficacy claims for dietary supplements should be more tightly regulated.

Consent to the use of stored DNA for genetics research: a survey of attitudes in the Jewish population

The use of anonymized stored tissue is a routine practice in genetic research. Investigators who utilize stored samples are neither required nor able to obtain informed consent before each use. Many genetic studies, however, are conducted on specific ethnic populations (e.g., Ashkenazi Jews). The results in these cases, although individually anonymous, are not anonymous with respect to the ethnicity of the participants. This lack of group anonymity has led to concern about the possibility of stigmatization and discrimination based on the results of the genetic research. In the present study we surveyed Jewish individuals about their attitudes regarding the practice of using stored DNA samples for genetic research. Specifically, we were interested in whether attitudes about informed consent and willingness to participate in genetics research using stored DNA would depend on the circumstances in which the material was collected (i.e., clinical setting vs. research setting) and the characteristics of the disease or trait under investigation. Overall, most respondents reported that written informed consent should be required and that they would be willing to provide such consent. Participants were most willing to provide consent, however, when the sample had been collected in a research rather than clinical setting. Further, participants were more likely to endorse the need for obtaining consent when the sample was collected in a clinical setting. Finally, participants were significantly less willing to participate in research that examined stereotypical or potentially stigmatizing traits as opposed to research that examined medical or mental illnesses.

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The use of genetic information in the workplace poses societal risks that have an impact on employment possibilities, health insurance, and privacy. Individuals who might otherwise believe they can benefit from genetic testing may decline it because of their fear of employment discrimination and lack of privacy in the workplace. As a consequence, the future of research on the benefits and risks of predictive genetic testing may also be compromised. Thus, policy-makers need to evaluate legislative and regulatory strategies to address these concerns. This paper analyzes state and federal legislative approaches to genetic information in the workplace and concludes with a discussion of policy considerations and recommendation.

The determination of antibody to Streptococcus mutans serotypes in saliva for children ages 3 to 7 years

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