(Tissue) P Systems with Vesicles of Multisets

We consider tissue P systems working on vesicles of multisets with the very simple operations of insertion, deletion, and substitution of single objects. With the whole multiset being enclosed in a vesicle, sending it to a target cell can be indicated in those simple rules working on the multiset. As derivation modes we consider the sequential mode, where exactly one rule is applied in a derivation step, and the set maximal mode, where in each derivation step a non-extendable set of rules is applied. With the set maximal mode, computational completeness can already be obtained with tissue P systems having a tree structure, whereas tissue P systems even with an arbitrary communication structure are not computationally complete when working in the sequential mode. Adding polarizations (-1, 0, 1 are sufficient) allows for obtaining computational completeness even for tissue P systems working in the sequential mode.Comment: In Proceedings AFL 2017, arXiv:1708.0622

Utilizing TAPBPR to promote exogenous peptide loading onto cell surface MHC I molecules.

The repertoire of peptides displayed at the cell surface by MHC I molecules is shaped by two intracellular peptide editors, tapasin and TAPBPR. While cell-free assays have proven extremely useful in identifying the function of both of these proteins, here we explored whether a more physiological system could be developed to assess TAPBPR-mediated peptide editing on MHC I. We reveal that membrane-associated TAPBPR targeted to the plasma membrane retains its ability to function as a peptide editor and efficiently catalyzes peptide exchange on surface-expressed MHC I molecules. Additionally, we show that soluble TAPBPR, consisting of the luminal domain alone, added to intact cells, also functions as an effective peptide editor on surface MHC I molecules. Thus, we have established two systems in which TAPBPR-mediated peptide exchange on MHC class I can be interrogated. Furthermore, we could use both plasma membrane-targeted and exogenous soluble TAPBPR to display immunogenic peptides on surface MHC I molecules and consequently induce T cell receptor engagement, IFN-γ secretion, and T cell-mediated killing of target cells. Thus, we have developed an efficient way to by-pass the natural antigen presentation pathway of cells and load immunogenic peptides of choice onto cells. Our findings highlight a potential therapeutic use for TAPBPR in increasing the immunogenicity of tumors in the future

3C in maize and arabidopsis

With Chromosome Conformation Capture (3C), the relative interaction frequency of one chromosomal fragment with another can be determined. The technique is especially suited for unraveling the 3D organization of specific loci when focusing on aspects such as enhancer–promoter interactions or other topological conformations of the genome. 3C has been extensively used in animal systems, among others providing insight into gene regulation by distant cis-regulatory elements. In recent years, the 3C technique has been applied in plant research. However, the complexity of plant tissues prevents direct application of existing protocols from animals. Here, we describe an adapted protocol suitable for plant tissues, especially Arabidopsis thaliana and Zea mays

A cautionary note on the use of chromosome conformation capture in plants

Background: The chromosome conformation capture (3C) technique is a method to study chromatin interactions at specific genomic loci. Initially established for yeast the 3C technique has been adapted to plants in recent years in order to study chromatin interactions and their role in transcriptional gene regulation. As the plant scientific community continues to implement this technology, a discussion on critical controls, validations steps and interpretation of 3C data is essential to fully benefit from 3C in plants. Results: Here we assess the reliability and robustness of the 3C technique for the detection of chromatin interactions in Arabidopsis. As a case study, we applied this methodology to the genomic locus of a floral integrator gene SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), and demonstrate the need of several controls and standard validation steps to allow a meaningful interpretation of 3C data. The intricacies of this promising but challenging technique are discussed in depth. Conclusions: The 3C technique offers an interesting opportunity to study chromatin interactions at a resolution infeasible by microscopy. However, for interpretation of 3C interaction data and identification of true interactions, 3C technology demands a stringent experimental setup and extreme caution

Tissue- and Expression Level–Specific Chromatin Looping at Maize b1 Epialleles[W]

This work examines the involvement of chromatin looping in the transcriptional regulation of two epialleles of the maize (Zea mays) b1 gene, B-I and B'. These two epialleles are tissue-specifically regulated and are involved in paramutation. B-I and B' are expressed at high and low levels, respectively. A hepta-repeat ∼100 kb upstream of the transcription start site (TSS) is required for both paramutation and high b1 expression. Using chromosome conformation capture, we show that the hepta-repeat physically interacts with the TSS region in a tissue- and expression level–specific manner. Multiple repeats are required to stabilize this interaction. High b1 expression is mediated by a multiloop structure; besides the hepta-repeat, other sequence regions physically interact with the TSS as well, and these interactions are epiallele- and expression level–specific. Formaldehyde-assisted isolation of regulatory elements uncovered multiple interacting regions as potentially regulatory