An open-source software analysis package for Microspheres with Ratiometric Barcode Lanthanide Encoding (MRBLEs)

Multiplexed bioassays, in which multiple analytes of interest are probed in parallel within a single small volume, have greatly accelerated the pace of biological discovery. Bead-based multiplexed bioassays have many technical advantages, including near solution-phase kinetics, small sample volume requirements, many within-assay replicates to reduce measurement error, and, for some bead materials, the ability to synthesize analytes directly on beads via solid-phase synthesis. To allow bead-based multiplexing, analytes can be synthesized on spectrally encoded beads with a 1:1 linkage between analyte identity and embedded codes. Bead-bound analyte libraries can then be pooled and incubated with a fluorescently-labeled macromolecule of interest, allowing downstream quantification of interactions between the macromolecule and all analytes simultaneously via imaging alone. Extracting quantitative binding data from these images poses several computational image processing challenges, requiring the ability to identify all beads in each image, quantify bound fluorescent material associated with each bead, and determine their embedded spectral code to reveal analyte identities. Here, we present a novel open-source Python software package (the mrbles analysis package) that provides the necessary tools to: (1) find encoded beads in a bright-field microscopy image; (2) quantify bound fluorescent material associated with bead perimeters; (3) identify embedded ratiometric spectral codes within beads; and (4) return data aggregated by embedded code and for each individual bead. We demonstrate the utility of this package by applying it towards analyzing data generated via multiplexed measurement of calcineurin protein binding to MRBLEs (Microspheres with Ratiometric Barcode Lanthanide Encoding) containing known and mutant binding peptide motifs. We anticipate that this flexible package should be applicable to a wide variety of assays, including simple bead or droplet finding analysis, quantification of binding to non-encoded beads, and analysis of multiplexed assays that use ratiometric, spectrally encoded beads.

A BaSiC tool for background and shading correction of optical microscopy images

Quantitative analysis of bioimaging data is often skewed by both shading in space and background variation in time. We introduce BaSiC, an image correction method based on low-rank and sparse decomposition which solves both issues. In comparison to existing shading correction tools, BaSiC achieves high-accuracy with significantly fewer input images, works for diverse imaging conditions and is robust against artefacts. Moreover, it can correct temporal drift in time-lapse microscopy data and thus improve continuous single-cell quantification. BaSiC requires no manual parameter setting and is available as a Fiji/ImageJ plugin.

Genetically encoded fluorescent tags

Genetically encoded fluorescent tags are protein sequences that can be fused to a protein of interest to render it fluorescent. These tags have revolutionized cell biology by allowing nearly any protein to be imaged by light microscopy at submicrometer spatial resolution and subsecond time resolution in a live cell or organism. They can also be used to measure protein abundance in thousands to millions of cells using flow cytometry. Here I provide an introduction to the different genetic tags available, including both intrinsically fluorescent proteins and proteins that derive their fluorescence from binding of either endogenous or exogenous fluorophores. I discuss their optical and biological properties and guidelines for choosing appropriate tags for an experiment. Tools for tagging nucleic acid sequences and reporter molecules that detect the presence of different biomolecules are also briefly discussed.

A quick guide to light microscopy in cell biology

Light microscopy is a key tool in modern cell biology. Light microscopy has several features that make it ideally suited for imaging biology in living cells: the resolution is well-matched to the sizes of subcellular structures, a diverse range of available fluorescent probes makes it possible to mark proteins, organelles, and other structures for imaging, and the relatively nonperturbing nature of light means that living cells can be imaged for long periods of time to follow their dynamics. Here I provide a brief introduction to using light microscopy in cell biology, with particular emphasis on factors to be considered when starting microscopy experiments.

Regulation of endocytic clathrin dynamics by cargo ubiquitination

VIDEO ABSTRACT

Some endocytic cargoes control clathrin-coated pit (CCP) maturation, but it is not known how such regulation is communicated. We found that μ-opioid neuropeptide receptors signal to their enclosing CCPs by ubiquitination. Nonubiquitinated receptors delay CCPs at an intermediate stage of maturation, after clathrin lattice assembly is complete but before membrane scission. Receptor ubiquitination relieves this inhibition, effectively triggering CCP scission and producing a receptor-containing endocytic vesicle. The ubiquitin modification that conveys this endocytosis-promoting signal is added to the receptor's first cytoplasmic loop, catalyzed by the Smurf2 ubiquitin ligase, and coordinated with activation-dependent receptor phosphorylation and clustering through Smurf2 recruitment by the endocytic adaptor beta-arrestin. Epsin1 detects the signal at the CCP and is required for ubiquitin-promoted scission. This cargo-to-coat communication system mediates a biochemical checkpoint that ensures appropriate receptor ubiquitination for later trafficking, and it controls specific receptor loading into CCPs by sensing when a sufficient quorum is reached.

Separase biosensor reveals that cohesin cleavage timing depends on phosphatase PP2A(Cdc55) regulation

In anaphase, sister chromatids separate abruptly and are then segregated by the mitotic spindle. The protease separase triggers sister separation by cleaving the Scc1/Mcd1 subunit of the cohesin ring that holds sisters together. Polo-kinase phosphorylation of Scc1 promotes its cleavage, but the underlying regulatory circuits are unclear. We developed a separase biosensor in Saccharomyces cerevisiae that provides a quantitative indicator of cohesin cleavage in single cells. Separase is abruptly activated and cleaves most cohesin within 1 min, after which anaphase begins. Cohesin near centromeres and telomeres is cleaved at the same rate and time. Protein phosphatase PP2A(Cdc55) inhibits cohesin cleavage by counteracting polo-kinase phosphorylation of Scc1. In early anaphase, the previously described separase inhibition of PP2A(Cdc55) promotes cohesin cleavage. Thus, separase acts directly on Scc1 and also indirectly, through inhibition of PP2A(Cdc55), to stimulate cohesin cleavage, providing a feedforward loop that may contribute to a robust and timely anaphase.

Merkel cell carcinoma in Western Australia: a population-based study of incidence and survival

BACKGROUND

Merkel cell carcinoma (MCC) is an uncommon but aggressive cutaneous skin cancer. Even with the appropriate treatment, MCC is prone to recurrence, and metastases are common. Exposure to ultraviolet radiation has been suggested as contributing towards the development of MCC. MCC has not been extensively investigated in Australia, even though Australia has the highest incidence of sun-related cancers in the world.

OBJECTIVES

To describe the demographics and determine trends of incidence and survival of MCC cases in Western Australia (WA).

METHODS

All reported invasive cases of MCC incident between 1 January 1993 and 31 December 2007 were extracted from the WA Cancer Registry. Age-adjusted incidence rates for MCC were calculated using direct standardization to the U.S. standard 2000 population. Cause-specific survival was investigated using Kaplan-Meier and Cox proportional hazards analysis. results: Two hundred and fifteen cases were confirmed by pathological review as being definite cases of MCC. Patients were mainly males (65%) and elderly (median age 77 years). Standardized age-adjusted incidence rates were higher in men (1·0/100,000) than in women (0·63/100,000) and higher in older ages (15·5/100,000 in the 85+year age group) than younger ages (0·1/100,000 in the 30-34 year age group). Five-year cause-specific survival was 64%.

CONCLUSIONS

Incidence of MCC in WA is the highest reported in the literature. In addition, MCC has worse survival than melanoma. The high rates and demographic and anatomical distribution are consistent with sun exposure playing a causal role.

Detection of Streptococcus pneumoniae carriage by the Binax NOW test with nasal and nasopharyngeal swabs in young children

The rapid detection of carriage of Streptococcus pneumoniae could assist in the management of pneumococcal infection, such as acute otitis media. We evaluated the reliability of the Binax NOW test in the exclusion and detection of pneumococcal carriage by nasal samples from 139 children and using nasopharyngeal samples from 250 children (aged 6-35 months) with respiratory infection with or without acute otitis media. The Binax NOW test results were compared with culture-based detection of carriage of S. pneumoniae. The Binax NOW test from the nasal samples had a sensitivity of 95%, a specificity of 78%, and the positive and negative predictive values were 83 and 93%, respectively; and for the nasopharyngeal samples the corresponding numbers were 88%, 95%, 96%, and 87%. When rapid knowledge of the carriage status of S. pneumoniae is needed, the Binax NOW test is a reliable method for the exclusion of carriage using nasal sampling, and in the detection of carriage using nasopharyngeal sampling.

Sequence-dependent sorting of recycling proteins by actin-stabilized endosomal microdomains

The functional consequences of signaling receptor endocytosis are determined by the endosomal sorting of receptors between degradation and recycling pathways. How receptors recycle efficiently, in a sequence-dependent manner that is distinct from bulk membrane recycling, is not known. Here, in live cells, we visualize the sorting of a prototypical sequence-dependent recycling receptor, the beta-2 adrenergic receptor, from bulk recycling proteins and the degrading delta-opioid receptor. Our results reveal a remarkable diversity in recycling routes at the level of individual endosomes, and indicate that sequence-dependent recycling is an active process mediated by distinct endosomal subdomains distinct from those mediating bulk recycling. We identify a specialized subset of tubular microdomains on endosomes, stabilized by a highly localized but dynamic actin machinery, that mediate this sorting, and provide evidence that these actin-stabilized domains provide the physical basis for a two-step kinetic and affinity-based model for protein sorting into the sequence-dependent recycling pathway.

Spinning-disk confocal microscopy of yeast

Spinning-disk confocal microscopy is an imaging technique that combines the out-of-focus light rejection of confocal microscopy with the high sensitivity of wide-field microscopy. Because of its unique features, it is well suited to high-resolution imaging of yeast and other small cells. Elimination of out-of-focus light significantly improves the image contrast and signal-to-noise ratio, making it easier to resolve and quantitate small, dim structures in the cell. These features make spinning-disk confocal microscopy an excellent technique for studying protein localization and dynamics in yeast. In this review, I describe the rationale behind using spinning-disk confocal imaging for yeast, hardware considerations when assembling a spinning-disk confocal scope, and methods for strain preparation and imaging. In particular, I discuss choices of objective lens and camera, choice of fluorescent proteins for tagging yeast genes, and methods for sample preparation.

Determination of bending-induced strain in optical fibers by use of quantitative phase imaging

Quantitative phase microscopy with polarized light has been used to determine the change in refractive index introduced into an optical fiber when the fiber is bent through a constant radius of curvature. By obtaining phase images for two orthogonal directions of the polarization of the incident light, one can infer the induced axial strain profile within the fiber. Radii of curvature from 1 to 8 cm were considered, and in each case excellent agreement, within lambda/100, was obtained between experimental results and theory.

Hepatitis C: the lurking dragon

Hepatitis C virus (HCV) is the most common chronic blood-borne infection in the United States. An estimated 3.9 million Americans (1.4%) are infected with HCV. The 10th leading cause of death in U.S. adults is chronic liver disease (CLD), which accounts for 25,000 deaths annually. Approximately 40% of all CLD is related to HCV, causing 8000 to 10,000 deaths annually. In addition, approximately 60% of people with HIV are believed to be coinfected with HCV, which hastens their progression to AIDS.

Elemental Distributions in Marine Bivalve Shells as Measured by Synchrotron X-Ray Fluorescence

The concentrations of elements from Mn to Pb in the shells of Mercenaria mercenaria, Mya arenaria, and Argopecten irradians were measured using synchrotron x-ray fluorescence. This technique provides sensitivity as low as 1 ppm and resolution of 8 {mu}m. Elements were heterogeneously distributed, both on a large scale (several millimeters) and on a small scale (tens of micrometers). Large-scale variations were observed in the compositions of shell layers and in seasonal variations in strontium concentration. Small-scale changes in composition included elevated iron levels at the boundary between the prismatic and inner homogeneous shell of the hard clam, Mercenaria mercenaria. Variations in strontium concentrations were seen over time spans of several months, suggesting that this technique can be used to determine historical water temperatures. Elemental maps with a resolution of less than 10 {mu}m were produced.