Cryo-soft-X-ray tomography is being increasingly used in biological research to study the morphology of cellular compartments and how they change in response to different stimuli, such as viral infections. Segmentation of these compartments is limited by time-consuming manual tools or machine learning algorithms that require extensive time and effort to train. Here we describe Contour, a new, easy-to-use, highly automated segmentation tool that enables accelerated segmentation of tomograms to delineate distinct cellular compartments. Using Contour, cellular structures can be segmented based on their projection intensity and geometrical width by applying a threshold range to the image and excluding noise smaller in width than the cellular compartments of interest. This method is less laborious and less prone to errors from human judgement than current tools that require features to be manually traced, and it does not require training datasets as would machine-learning driven segmentation. We show that high-contrast compartments such as mitochondria, lipid droplets, and features at the cell surface can be easily segmented with this technique in the context of investigating herpes simplex virus 1 infection. Contour can extract geometric measurements from 3D segmented volumes, providing a new method to quantitate cryo-soft-X-ray tomography data. Contour can be freely downloaded at github.com/kamallouisnahas/Contour.

This Technical Research Communication describes a new method by which thermally treated Coxiella in milk products may be grown in a liquid growth medium and quantitated using an MPN-PCR assay. Coxiella is generally not used in studies on thermal and non-thermal processing of milk due to the need for specialized and highly laborious techniques such as animal assays and tissue culture for determining viability. Recently, a liquid growth medium (ACCM-2) and modified atmosphere were used to grow Coxiella from pure cultures, infected mouse tissues, and clinical samples, however, the ability to grow Coxiella from a food such as milk has not been shown. The potential ability to enrich Coxiella directly from contaminated milk presents a new avenue for conducting pasteurization research in which the viability of heat-treated or injured cultures could be more easily determined through direct enrichment of Coxiella in ACCM-2. ACCM-2 medium allowed enrichment of Coxiella from bovine whole milk and cream, whole goat, and whole camel milks but not whole water buffalo milk. Enrichment was possible from whole bovine milk containing as few as 6 Coxiella ge/ml of milk. The applicability of this ACCM-2 enrichment method was shown when using an MPN-PCR assay to quantitate the number of viable Coxiella remaining in whole bovine milk after 64 °C thermal treatment for up to 10 min.

The obligate intracellular pathogen Coxiella burnetii has long been considered the most heat resistant pathogen in raw milk, making it the reference pathogen for determining pasteurisation conditions for milk products. New milk formulations and novel non-thermal processes require validation of effectiveness which requires a more practical method for analysis than using the currently used animal model for assessing Coxiella survival. Also, there is an interest in better characterising thermal inactivation of Coxiella in various milk formulations. To avoid the use of the guinea pig model for evaluating Coxiella survival, an Integrated Cell Culture-PCR (ICC-PCR) method was developed for determining Coxiella viability in milk. Vero cell cultures were directly infected from Coxiella-contaminated milk in duplicate 24-well plates. Viability of the Coxiella in milk was shown by a ≥0·5 log genome equivalent (ge)/ml increase in the quantity of IS111a gene from the baseline post-infection (day 0) level after 9–11 d propagation. Coxiella in skim, 2%, and whole milk, and half and half successfully infected Vero cells and increased in number by at least 2 logs using a 48-h infection period followed by 9-d propagation time. As few as 125 Coxiella ge/ml in whole milk was shown to infect and propagate at least 2 logs in the optimised ICC-PCR assay, though variable confirmation of propagation was shown for as low as 25 Coxiella ge/ml. Applicability of the ICC-PCR method was further proven in an MPN format to quantitate the number of viable Coxiella remaining in whole milk after 60 °C thermal treatment at 0, 20, 40, 60 and 90 min.

One of the most routine uses of fluorescence microscopy is colocalization, i.e., the demonstration of a relationship between pairs of biological molecules. Frequently this is presented simplistically by the use of overlays of red and green images, with areas of yellow indicating colocalization of the molecules. Colocalization data are rarely quantified and can be misleading. Our results from both synthetic and biological datasets demonstrate that the generation of Pearson's correlation coefficient between pairs of images can overestimate positive correlation and fail to demonstrate negative correlation. We have demonstrated that the calculation of a thresholded Pearson's correlation coefficient using only intensity values over a determined threshold in both channels produces numerical values that more accurately describe both synthetic datasets and biological examples. Its use will bring clarity and accuracy to colocalization studies using fluorescent microscopy.

The focus of this review is on trace-element quantitation of microstructures in solids. This review is aimed at the nonspecialist who wants to know how secondary ion mass spectrometry (SIMS) quantitation is achieved. Despite 35 years of SIMS research and applications, SIMS quantitation remains a fundamentally empirical enterprise and is based on standards. The most used standards are “bulk standards”—solids with a homogeneous distribution of a trace element—and ion-implanted solids. The SIMS systematics of bulk standards and ion-implanted solids are reviewed.

The gap junction (GJ) is an aggregate of intercellular channels that facilitates cytoplasmic interchange of ions, second messengers, and other molecules of less than 1000 Da between cells. In excitable organs such as heart and brain, GJs configure extended intercellular pathways for stable and long-term propagation of action potential. In a previous study in adult rat heart, we have shown that the Drosophila disks-large related protein ZO-1 shows low to moderate colocalization at myocyte borders with the GJ protein Cx43. In the present study, we detail a protocol for characterizing the pattern and level of colocalization of ZO-1 with Cx43 in cultures of neonatal myocytes at the level of individual GJ plaques. The data indicate that ZO-1 shows on average a partial 26.6% overlap (SD = 11.3%) with Cx43 GJ plaques. There is a strong positive correlation between GJ plaque size and area of ZO-1 colocalization, indicating that the level of associated ZO-1 scales with the area of the GJ plaque. Qualitatively, the most prominent colocalization occurs at the plaque perimeter. These studies may provide insight into the presently unknown biological function of ZO-1 interaction with Cx43.

Low-voltage energy-dispersive X-ray microanalysis has a number of distinct advantages for measuring the concentration of light elements (Z = 11−20) in a largely organic matrix. Between 10 and 4 kV, there is a 50-fold decrease in the size of the incident beam-specimen interaction volume which enables discrete subcel-lular compartments to be analyzed. Experiments with mineral and organic samples of known chemical composition show that two of the most widely used analytical algorithms are capable of providing quantitative data at accelerating voltages as low as 5 kV. This technique is used at 5 kV to analyze frozen hydrated fracture faces of leaves of the tea plant which are known to contain aluminium. Higher levels of aluminium are found in the cell walls and are associated with increased levels of silicon and magnesium. The advantages and disadvantages of the experimental approach are discussed in relation to analysis carried out at higher voltages.

Colloidal gold, conjugated to ligands or antibodies, is routinely used as a label for the detection of cell structures by light (LM) and electron microscopy (EM). To date, several methods to count the number of colloidal gold labels have been employed with limited success. Instrumental neutron activation analysis (INAA), a physical method for the analysis of the elemental composition of materials, can be used to provide a quantitative index of gold accumulation in bulk specimens. Given that gold is not naturally found in biological specimens in any substantial amount and that colloidal gold and ligand conjugates can be prepared to yield uniform bead sizes, the amount of label can be calculated in bulk biological samples by INAA. Here we describe the use of INAA, LM, transmission EM, and X-ray microanalysis (EDX) in a model to determine both distribution (localization) and amount of colloidal gold at the organ, tissue, cellular, and ultrastructural levels in whole animal systems following administration. In addition, the sensitivity for gold in biological specimens by INAA is compared with that of inductively coupled plasma-mass spectrometry (ICP-MS). The correlative use of INAA, LM, TEM, and EDX can be useful, for example, in the quantitative and qualitative tracking of various labeled molecular species following administration in vivo.