Regulatory T cells require mammalian target of rapamycin signaling to maintain both homeostasis and alloantigen-driven proliferation in lymphocyte-replete mice

Rapamycin (Rapa), an immunosuppressive drug that acts through mammalian target of Rapa inhibition, broadly synergizes with tolerogenic agents in animal models of transplantation and autoimmunity. Rapa preferentially inhibits conventional CD4(+) Foxp3(-) T cells (Tconv) and promotes outgrowth of CD4(+)Foxp3(+) regulatory T cells (Treg) during in vitro expansion. Moreover, Rapa is widely perceived as augmenting both expansion and conversion of Treg in vivo. However, most quantitative studies were performed in lymphopenic hosts or in graft-versus-host disease models. We show in this study that in replete wild-type mice, Rapa significantly inhibits both homeostatic and alloantigen-induced proliferation of Treg, and promotes their apoptosis. Together, these lead to significant Treg depletion. Tconv undergo depletion to a similar degree, resulting in no change in the percent of Treg among CD4 cells. Moreover, in this setting, there was no evidence of conversion of Tconv into Treg. However, after withdrawal of Rapa, Treg recover Ag-induced proliferation more quickly than Tconv, leading to recovery to baseline numbers and an increase in the percent of Treg compared with Tconv. These findings suggest that the effects of Rapa on Treg survival, homeostasis, and induction, depend heavily on the cellular milieu and degree of activation. In vivo, the resistance of Treg to mammalian target of Rapa inhibition is relative and results from lymphopenic and graft-versus-host disease models cannot be directly extrapolated to settings more typical of solid organ transplantation or autoimmunity. Moreover, these results have important implications for the timing of Rapa therapy with tolerogenic agents designed to increase the number of Treg in vivo.     

Bringing Rad52 foci into focus

In 2007, we published the results of a genome-wide screen for ORFs that affect the frequency of Rad52 foci in yeast. That paper was published within the constraints of conventional online publishing tools, and it provided only a glimpse into the actual screen data. New tools in the JCB DataViewer now show how these data can—and should—be shared.

Complete screen data

https://doi.org/10.1083/jcb.201108095.dv The Rad52 protein has pivotal functions in double strand break repair and homologous recombination. The activity of Rad52 is often monitored by the subnuclear foci that it forms spontaneously in S phase or after DNA damage (Lisby et al., 2001). In mammals, the functions of yeast Rad52 may be divided between human RAD52 and the tumor suppressor BRCA2 (Feng et al., 2011). The full host of molecular players that govern Rad52 focus formation and maintenance was not well known when we initiated our screen. Using a high-content, image-based assay, we assessed the proportion of cells containing spontaneous Rad52-YFP foci in 4,805 viable Saccharomyces cerevisiae deletion strains (Alvaro et al., 2007). Starting with 96-well arrays of a deletion strain library, we created hybrid diploid strains (homozygous for the deletions) using systematic hybrid loss of heterozygosity (SHyLOH; Alvaro et al., 2006). We then manually and sequentially examined each strain using epifluorescence microscopy for the presence of Rad52-YFP foci. All of our image analysis was performed manually.As is often the case, our screen was published showing only a couple of representative images and providing data tables to summarize the findings. Tomes of data that could not be included in the published paper were relegated to supplemental Excel tables, typical of genome-wide screens. Also, the raw image data were sequestered in the laboratory on DVDs. With considerable help from JCB and Glencoe Software, we are delighted that the raw data from our Rad52 screen are now freely available online through the JCB DataViewer. A new interface within the JCB DataViewer brings presentation and preservation of high-content, multidimensional image-based screening data to a whole new level. To facilitate the development of this new interface, JCB required a dataset that was not time sensitive, and we were happy to provide our previously published Rad52 data. In the future, this new interface will be used to present high-content screening (HCS) datasets linked to published JCB papers. Indeed, the first publication of this sort appears in this issue of JCB (Rohn et al., 2011).The presentation of our data in the JCB DataViewer clearly shows the many benefits of this new publishing resource for the scientific community. Users now can view the complete collection of 3D image data across the entire screen, not just the two images in our original publication (Alvaro et al., 2007). Additionally, detailed information on image acquisition parameters, locus identities, and more is easily accessible (Fig. 1). Phenotypic scoring results can be visualized in interactive chart formats (Fig. 1), and search (Fig. 2) and database-linking tools (Fig. 1) allow extensive mining of the data for genes and phenotypes of interest. These tools provide an unprecedented view into HCS data in their entirety, as well as a means for authors to share and archive their data. This kind of accessibility to the direct visualization of the entire set of original screening data, on a scale previously only available to the scientists performing the screen, allows users to understand the full context of the image data analyzed in a screen. Furthermore, it is only through full access to the raw images and associated metadata that this information can be of maximum use to the community for large-scale data mining.Open in a separate windowFigure 1.The HCS interface of the JCB DataViewer provides interactive tools for the analysis of complete datasets from image-based screens. The miniviewer (top left) provides information for each gene in the screen through a zoomable and scrollable display of original multidimensional image data. It contains detailed metadata and a gene ontology (GO) summary, a link to a relevant external database (e.g., the Saccharomyces Genome Database [SGD]; top right), and a link to phenotypic scoring data for the complete screen in the chart view (bottom right). Within the chart view, hits designated by the screen authors are shown in blue, and the strain currently on display in the miniviewer is shown in red. The plate view (bottom left) shows the position of the strain of interest (red box) relative to other strains screened.Open in a separate windowFigure 2.The HCS interface of the JCB DataViewer provides search tools for the mining of complete datasets from image-based screens. (A) Users can search screen data by gene name or keywords (e.g., DNA repair). (B) Users can pick candidates for further analysis from the phenotypic scoring information in the chart view.As in all large-scale screens, the real data are variable; e.g., some strains provide a clear Rad52 focus phenotype, whereas others are more ambiguous. For our particular screen, images were not collected using automated technology but were acquired manually, strain by strain, over a period of months, leading to different levels of fluorescence intensity of Rad52-YFP as a result of, for example, changes in the intensity of our mercury arc lamp. Differences also exist in the number of fields and z stacks captured for each strain. In the absence of automated image collection, images from the primary screen in a few cases were not archived with the others and thus for all intents and purposes have been lost. In addition, our Rad52 screen only assayed nonessential genes, and some mutants are refractory to the SHyLOH methodology. Knowing all of this information allows users to view the data in a realistic manner and further highlights the importance of providing a central repository to archive HCS data.When published through conventional publication media, many important imaging details are known only to the original screeners. The new HCS interface of the JCB DataViewer shines a light on screening data as metadata become freely accessible, allowing any user to ask novel questions of the dataset. For example, the plate view for images (Fig. 1) allows users to assess whether neighboring colonies played any role in determining the phenotype and to delve deeper into why that might be. For example, are any “hits” a result of contamination from adjacent strains, resulting in clusters of positives? In the context of an automated screen, how were control and experimental samples arrayed across a plate during data collection? Did the controls on a particular plate behave as expected? Because our screen used a novel chromosome-specific loss of the heterozygosity method, users can ask whether mutations on specific chromosomes share features of Rad52 foci levels. The global resolution of the dataset provided through this new interface puts users of the dataset as close to the seat of the original screening scientist as possible, allowing them to ask, “what did the authors really see?”Presenting HCS data in the JCB DataViewer holds immense potential value to the scientific community. Through this new interface, users can access powerful interactive tools for analyzing scored phenotypes across the entire dataset (Fig. 1). Each gene ID can be charted against the phenotypic parameters scored in the original screen (e.g., the percentage of cells with Rad52 foci) and compared with all other loci (Fig. 1). Users can take our data and create their own list of hits based on their criteria, create a gallery of thumbnails for their selections (Fig. 2), and seamlessly move between their list of hits and the original data in the plate display format (Fig. 1). Users can also compare their candidates with our list (Fig. 2). The ability to visualize these data for comparative analyses creates a whole new perspective. The HCS interface of the JCB DataViewer allows users to look for their favorite gene, compare related genes, and discover new genes they never anticipated were involved in a given process.In summary, these new features of the JCB DataViewer will allow users to access the primary data from large-scale screens and to look at the full dataset to see what all of the images really look like. The ability to mine these data opens up whole new dimensions in data sharing and transparency. In the future, we anticipate that it will be possible to search many genome-wide screens, such as our Rad52 dataset, to identify commonalities in protein localization, concentration, cell morphology, etc. However, this will only occur if image data are archived and made freely available to the scientific community. We wholeheartedly support the efforts of JCB and hope that groups that use image-based HCS will increasingly make their images available using tools such as the JCB DataViewer.     

The visceral pericardium: macromolecular structure and contribution to passive mechanical properties of the left ventricle

Much attention has been focused on the passive mechanical properties of the myocardium, which determines left ventricular (LV) diastolic mechanics, but the significance of the visceral pericardium (VP) has not been extensively studied. A unique en face three-dimensional volumetric view of the porcine VP was obtained using two-photon excitation fluorescence to detect elastin and backscattered second harmonic generation to detect collagen, in addition to standard light microscopy with histological staining. Below a layer of mesothelial cells, collagen and elastin fibers, extending several millimeters, form several distinct layers. The configuration of the collagen and elastin layers as well as the location of the VP at the epicardium providing a geometric advantage led to the hypothesis that VP mechanical properties play a role in the residual stress and passive stiffness of the heart. The removal of the VP by blunt dissection from porcine LV slices changed the opening angle from 53.3 +/- 10.3 to 27.3 +/- 5.7 degrees (means +/- SD, P < 0.05, n = 4). In four porcine hearts where the VP was surgically disrupted, a significant decrease in opening angle was found (35.5 +/- 4.0 degrees ) as well as a rightward shift in the ex vivo pressure-volume relationship before and after disruption and a decrease in LV passive stiffness at lower LV volumes (P < 0.05). These data demonstrate the significant and previously unreported role that the VP plays in the residual stress and passive stiffness of the heart. Alterations in this layer may occur in various disease states that effect diastolic function.     

A mutation in NLA, which encodes a RING-type ubiquitin ligase, disrupts the adaptability of Arabidopsis to nitrogen limitation

Abundant nitrogen is required for the optimal growth and development of plants, while numerous biotic and abiotic factors that consume soil nitrogen frequently create a nitrogen limitation growth condition. To cope with this, plants have evolved a suite of adaptive responses to nitrogen limitation. However, the molecular mechanism governing the adaptability of plants to nitrogen limitation is totally unknown because no reported mutant defines this trait. Here we isolated an Arabidopsis mutant, nla (nitrogen limitation adaptation), and identified the NLA gene as an essential component in this molecular mechanism. Supplied with insufficient inorganic nitrogen (nitrate or ammonium), the nla mutant failed to develop the essential adaptive responses to nitrogen limitation, but senesced much earlier and more rapidly than did the wild type. Under other stress conditions including low phosphorus nutrient, drought and high temperature, the nla mutant did not show this early senescence phenotype, but closely resembled the wild type in growth and development. Map-based cloning of NLA revealed that this gene encodes a RING-type ubiquitin ligase, and nla is a deletion mutation which does not code for the RING domain in the NLA protein. The NLA protein is localized to the nuclear speckles, where this protein interacts with the Arabidopsis ubiquitin conjugase 8 (AtUBC8). In the nla mutant, the deletion of the RING domain from NLA altered its subcellular localization, disrupted the interaction between NLA and AtUBC8 and caused the early senescence phenotype induced by low inorganic nitrogen. All the results indicate that NLA is a positive regulator for the development of the adaptability of Arabidopsis to nitrogen limitation.     

Factors related to Helicobacter pylori prevalence in an adult population in Brazil

Background: The prevalence of Helicobacter pylori is higher in developing countries. Sanitary facilities, crowding and ethnic group are some of the factors related to H. pylori infection. The aim of this study was to investigate in blood donors, free of dyspeptic symptoms, the prevalence and factors influencing H. pylori infection. Materials and Methods: This study was conducted in São Paulo, a city known to have a mixed population coming from all over the country. A total of 1008 blood donors were initially included in the study. After a final revision of all the questionnaires, 993 were included in the final analysis (746 males). H. pylori status was checked by an ELISA test. The following associations to infection were analyzed: sex, age, ethnic group, previous upper gastrointestinal (GI) endoscopy, smoking, alcoholism, drug addiction, type of drinking water, crowding, sanitary facilities, and family income. Results: Infection was observed in 496 of 746 male (66.5%) and in 156 of 247 female (63.2%) blood donors. Infection prevalence increased according to age group, regardless of sex. Prevalence was lower in White population than in non‐White. No relationship was observed between infection and smoking, drug addiction, and alcohol. A positive relation was observed between infection and previous upper GI endoscopy, and type of drinking water, regardless if currently or during childhood. Crowding and lack of toilet in the house during childhood resulted in a higher infection rate. Lower familial income and educational level showed a positive association to infection. Conclusions: Prevalence of H. pylori is higher in non‐White population, independent of gender. A positive association was observed in aging, previous upper GI endoscopy, crowding, type of drinking water, lack of toilet during childhood, lower family income, and lower educational level.     

Effects of lipid environment on the conformational changes of an ABC importer

In order to shuttle substrates across the lipid bilayer, membrane proteins undergo a series of conformation changes that are influenced by protein structure, ligands, and the lipid environment. To test the effect of lipid on conformation change of the ABC transporter MolBC, EPR studies were conducted in lipids and detergents of variable composition. In both a detergent and lipid environment, MolBC underwent the same general conformation changes as detected by site-directed EPR spectroscopy. However, differences in activity and the details of the EPR analysis indicate conformational rigidity that is dependent on the lipid environment. From these observations, we conclude that native-like lipid mixtures provide the transporter with greater activity and conformational flexibility as well as technical advantages such as reconstitution efficiency and protein stability.