A relational database for cryoEM: experience at one year and 50 000 images

For the past year we have been using a relational database as part of an automated data collection system for cryoEM. The database is vital for keeping track of the very large number of images collected and analyzed by the automated system and essential for quantitatively evaluating the utility of methods and algorithms used in the data collection. The database can be accessed using a variety of tools including specially developed Web-based interfaces that enable a user to annotate and categorize images using a Web-based form.     

Investigation on lipid asymmetry using lipid probes: Comparison between spin-labeled lipids and fluorescent lipids

Synthetic lipids with a nitroxide or a fluorescent probe have been extensively used during the last 30 years to determine the transmembrane diffusion of phospholipids in artificial or biological membranes. However, the relevance of data obtained with these modified lipids has sometimes been questioned. Beside possible artefacts introduced by the reporter probe, synthetic lipids used in cells often contain a short fatty acid chain in the sn-2 position, which gives them higher water solubility than naturally occurring lipids. In the present review, we have attempted to give a critical appraisal. Main strategies are recalled and important discoveries obtained with lipid probes on transmembrane lipid traffic in eukaryotic cells are briefly summarized. Examples of artefacts caused by lipid probes are given. Comparisons between data obtained by different techniques such as ESR and fluorescence allow us to emphasize the complementary character of the two approaches and more generally show the necessity to use several probes before drawing conclusions concerning endogenous lipids. In spite of these pitfalls, overall, lipid probes have provided a wealth of useful information that, to date, cannot be obtained with unlabeled lipids.     

Towards automated screening of two-dimensional crystals

Screening trials to determine the presence of two-dimensional (2D) protein crystals suitable for three-dimensional structure determination using electron crystallography is a very labor-intensive process. Methods compatible with fully automated screening have been developed for the process of crystal production by dialysis and for producing negatively stained grids of the resulting trials. Further automation via robotic handling of the EM grids, and semi-automated transmission electron microscopic imaging and evaluation of the trial grids is also possible. We, and others, have developed working prototypes for several of these tools and tested and evaluated them in a simple screen of 24 crystallization conditions. While further development of these tools is certainly required for a turn-key system, the goal of fully automated screening appears to be within reach.     

Cyto-immunological study of the Pleurodele pituitary gland]

In the pituitary of an Amphibian (Urodela), various cell types were localized by cytoimmunological techniques: corticotrophs located in a rostral zone near the median eminence, ventral orangeophilic cells secreting a prolactin-like hormone and erythrosinophilic cells in a more dorso-caudal situation secreting growth hormone. Alpha-MSH and beta-MSH produceng cell were identified in the intermediate lobe; these cells were also labelled with antibodies against 1-24 ACTH and 17-39 ACTH. These data are in accordance with results obtained after an experimental study of the prolactin cells.     

Specific hybridization of a synthetic oligonucleotide in rat hypothalamic neurons immunoreactive to immune serum against salmon melanin-concentrating hormone

An oligonucleotide probe corresponding to the 9 C-terminal residues encoded by a complementary DNA of a rat peptide related to salmon melanin concentrating hormone (MCH) was synthetized. It specifically hybridized to the neurons stained by antisera to MCH in the rat posterior hypothalamus, as seen by coupling in situ hybridization and immunocytochemical methods. This result validates our sequence determination. This oligonucleotide will be useful to establish the complete sequence of the rat MCH precursor molecule. It will also constitute a valuable tool to study physiological or experimentally-induced changes in the expression of the rat MCH gene.     

Toolkit for evaluating genes required for proliferation and survival using tetracycline-regulated RNAi

Short hairpin RNAs (shRNAs) are versatile tools for analyzing loss-of-function phenotypes in vitro and in vivo. However, their use for studying genes involved in proliferation and survival, which are potential therapeutic targets in cancer and other diseases, is confounded by the strong selective advantage of cells in which shRNA expression is inefficient. We therefore developed a toolkit that combines Tet-regulated miR30-shRNA technology, robust transactivator expression and two fluorescent reporters to track and isolate cells with potent target knockdown. We demonstrated that this system improves the study of essential genes and was sufficiently robust to eradicate aggressive cancer in mice by suppressing a single gene. Further, we applied this system for in vivo negative-selection screening with pooled shRNAs and propose a streamlined, inexpensive workflow that will facilitate the use of RNA interference (RNAi) for the identification and evaluation of essential therapeutic targets.     

Automated cryoEM data acquisition and analysis of 284742 particles of GroEL

One of the goals in developing our automated electron microscopy data acquisition system, Leginon, was to improve both the ease of use and the throughput of the process of acquiring low dose images of macromolecular specimens embedded in vitreous ice. In this article, we demonstrate the potential of the Leginon system for high-throughput data acquisition by describing an experiment in which we acquired images of more than 280,000 particles of GroEL in a single 25 h session at the microscope. We also demonstrate the potential for an automated pipeline for molecular microscopy by showing that these particles can be subjected to completely automated procedures to reconstruct a three-dimensional (3D) density map to a resolution better than 8 A. In generating the 3D maps, we used a variety of metadata associated with the data acquisition and processing steps to sort and select the particles. These metadata provide a number of insights into factors that affect the quality of the acquired images and the resulting reconstructions. In particular, we show that the resolution of the reconstructed 3D density maps improves with decreasing ice thickness. These data provide a basis for assessing the capabilities of high-throughput macromolecular microscopy.     

Estimation du taux d’aneuploïdies des spermatozoïdes épididymaires prélevés en vue d’ICSI chez des hommes à caryotype normal

Over the last ten years, fluorescent in situ hybridization in decondensed sperm nuclei has been used to study the chromosomal constitution of human spermatozoa. Studies have estimated that the disomy rate per chromosomal pairs is between 0.15% and 0.3%. The aim of this study was to evaluate the aneuploidy rate of human epididymal spermatozoa extracted from five men with obstructive azoospermia undergoing IVF. Genetic studies (karyotypes, Y micodeletion syndrome and mutation of the CFTR gene) did not reveal any abnormality. Disomy frequencies were determined by X-Y-8 multicolour fluorescence in situ hybridisation on 18,013 epididymal spermatozoa and 20,000 spermatozoa from healthy donors (control group). No significant difference was found between epididymal and ejaculated samples. However, isolated non-significant differences were observed between one of the patients and the control group. In conclusion, the present findings suggests that there is no increased risk for de novo chromosomal aberrations after IVF therapy with epididymal spermatozoa of men with obstructive azoospermia.