Design of adsorptive columns for specific pathogen removal: application to staphylococcal enterotoxin B

The removal of pathogens such as toxins, viruses, bacteria, and prions in human blood, mammalian cell culture media, fermentation broths, food items, and water streams has gained increasing importance in ensuring product safety and in combatting acts of terrorism. Adsorption processes can play an important role in removing such pathogens from solution without affecting other desirable components. Adsorptive columns that can remove specific families of pathogens would need to achieve a reduction of several logs in pathogen concentration. This requirement is much more stringent than the normal yield requirements associated with adsorptive separations aimed at product recovery and purification in a process stream. This paper considers the design of an adsorptive column aimed at reducing the concentration of infectious agents from a known volume of solution by several logs in a fixed amount of time. The general rate (GR) model of chromatography is used in the analysis, including all major transport and kinetic steps in the adsorption process. The theory, with no adjustable parameters, is shown to predict with great accuracy the effect of residence time on the log removal of staphylococcal enterotoxin B (SEB) from solution using an affinity resin with a small peptide (YYWLHH) that has been found to bind specifically to this toxin.     

Ubiquitin hubs in oncogenic networks

Ubiquitin is an important regulator of diverse biological functions including cell cycle progression, apoptosis, cell proliferation, and DNA damage responses. Crucial proteins involved in the control of such diverse functions are modified by ubiquitin and are frequently altered during oncogenesis. Here, we define such proteins as key-nodes regulated by ubiquitin, discuss examples of their oncogenic aberrations, and indicate how pharmacologic manipulation of such molecular hubs might improve anticancer therapy.     

Genetic relations among basil taxa (Ocimum L.) based on molecular markers, nuclear DNA content, and chromosome number

Twenty-eight basil accessions including six Ocimum species and six botanical varieties or cultivars of O. basilicum were studied using molecular markers, nuclear DNA content, and chromosome counting. This is the first study reporting the nuclear DNA content in the genus Ocimum. The results supported the existence of more infrageneric groups within the genus. The section Ocimum was further divided into two separate clades. The first clade contained the accessions belonging to different botanical varieties and cultivars of O. basilicum as well as O. minimum, indicating that the separate species rank of O. minimum was not justified. The second clade, comprising O. americanum, O. africanum, and two O. basilicum var. purpurascens accessions, could represent a set of allopolyploid species sharing some common parental genomes. O. tenuiflorum was the most divergent species according to genetic distance; it had the smallest genome size, organized in small chromosomes, and the lowest chromosome number. Chromosome data obtained in our research could indicate that the basic chromosome number for species belonging to section Ocimum is x = 12. This suggestion implies that species belonging to O. basilicum clade are tetraploids, while species belonging to O. americanum clade are hexaploids. It seems that the basic chromosome number for O. gratissimum could be x = 10 and for O. tenuiflorum x = 9. The differences in genome size and chromosome number among Ocimum species indicate that evolution of their genomes was accompanied by both sequence deletion/amplification and chromosome rearrangements and polyploidization.     

Multiplex RT-PCR with broad-range primers and an exogenous internal amplification control for the detection of honeybee viruses in bumblebees

Bumblebees are commercially reared and transported worldwide mainly for pollination of greenhouse tomatoes. Three honeybee viruses have been reported in bumblebees: Acute bee paralysis virus, Kashmir bee virus and Deformed wing virus. We developed a multiplex RT-PCR with primers designed on highly conserved regions of the RNA-dependent RNA polymerase in order to detect a maximum range of viral variants. Rearing facilities and governmental organizations can now thoroughly screen bumblebee colonies with a cost-effective technique with an integrated internal amplification control (IAC) implementable in laboratories that strive for International Organization for Standardization (ISO) certification.     

Automated tracking of unmarked cells migrating in three-dimensional matrices applied to anti-cancer drug screening

In oncology, combating the spread of tumor cells is a clinical need which currently remains unsatisfied. Identifying anti-migratory compounds usually requires in vitro screening of a large number of molecules. Efficient and realistic (i.e., preferably 3D) in vitro tests are thus required in order to quantify the anti-migratory effects of anti-cancer drugs. To remain compatible with high-throughput screening, we focus on assays where unlabeled cells are migrating in 3D transparent gels and are observed under time-lapse 3D phase-contrast microscopy. In this context, we present a method for automatically tracking cells that combines a template matching preprocessing step with a mean-shift process. The preprocessing step consists in performing a correlation of a cell template with each observed volume in order to provide a phase-contrast artifact-free volume where the cells appear as correlation peaks surrounded by smooth gradients. This transformation enables the cells to be efficiently tracked by a mean-shift process. Robustness and efficiency of this approach are qualitatively and quantitatively shown in various experiments. Finally, we successfully applied our method to the quantitative characterization of the anti-migratory impact of cytochalasin-D on cancer cells. In conclusion, our method can efficiently be used for drug screening aiming to evidence drug-induced effects on cell migration in 3D transparent environments, such as matrix gels.     

Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes

Since determining the crystallographic structure of all peptide-MHC complexes is infeasible, an accurate prediction of the conformation is a critical computational problem. These models can be useful for determining binding energetics, predicting the structures of specific ternary complexes with T-cell receptors, and designing new molecules interacting with these complexes. The main difficulties are (1) adequate sampling of the large number of conformational degrees of freedom for the flexible peptide, (2) predicting subtle changes in the MHC interface geometry upon binding, and (3) building models for numerous MHC allotypes without known structures. Whereas previous studies have approached the sampling problem by dividing the conformational variables into different sets and predicting them separately, we have refined the Biased-Probability Monte Carlo docking protocol in internal coordinates to optimize a physical energy function for all peptide variables simultaneously. We also imitated the induced fit by docking into a more permissive smooth grid representation of the MHC followed by refinement and reranking using an all-atom MHC model. Our method was tested by a comparison of the results of cross-docking 14 peptides into HLA-A*0201 and 9 peptides into H-2K(b) as well as docking peptides into homology models for five different HLA allotypes with a comprehensive set of experimental structures. The surprisingly accurate prediction (0.75 A backbone RMSD) for cross-docking of a highly flexible decapeptide, dissimilar to the original bound peptide, as well as docking predictions using homology models for two allotypes with low average backbone RMSDs of less than 1.0 A illustrate the method's effectiveness. Finally, energy terms calculated using the predicted structures were combined with supervised learning on a large data set to classify peptides as either HLA-A*0201 binders or nonbinders. In contrast with sequence-based prediction methods, this model was also able to predict the binding affinity for peptides to a different MHC allotype (H-2K(b)), not used for training, with comparable prediction accuracy.     

Induction of peripheral T cell tolerance by antigen-presenting B cells. II. Chronic antigen presentation overrules antigen-presenting B cell activation

Ag presentation in the absence of danger signals and Ag persistence are the inductive processes of peripheral T cell tolerization proposed so far. Nevertheless, it has never been definitively shown that chronic Ag presentation per se can induce T cell tolerance independent of the state of activation of APCs. In the present work, we investigated whether chronic Ag presentation by either resting or activated B cells can induce tolerance of peripheral Ag-specific T cells. We show that CD4(+) T cells that re-encounter the Ag for a prolonged period, presented either by resting or activated Ag-presenting B cells, become nonfunctional and lose any autoimmune reactivity. Thus, when the main APCs are B cells, the major mechanism responsible for peripheral T cell tolerization is persistent Ag exposure, independent of the B cell activation state.