TGF-β-responsive CAR-T cells promote anti-tumor immune function.

A chimeric antigen receptor (CAR) that responds to transforming growth factor beta (TGF-β) enables the engineering of T cells that convert this immunosuppressive cytokine into a potent T-cell stimulant. However, clinical translation of TGF-β CAR-T cells for cancer therapy requires the ability to productively combine TGF-β responsiveness with tumor-targeting specificity. Furthermore, the potential concern that contaminating, TGF-β?producing regulatory T (Treg) cells may preferentially expand during TGF-β CAR-T cell manufacturing and suppress effector T (Teff) cells demands careful evaluation. Here, we demonstrate that TGF-β CAR-T cells significantly improve the anti-tumor efficacy of neighboring cytotoxic T cells. Furthermore, the introduction of TGF-β CARs into mixed T-cell populations does not result in the preferential expansion of Treg cells, nor do TGF-β CAR-Treg cells cause CAR-mediated suppression of Teff cells. These results support the utility of incorporating TGF-β CARs in the development of adoptive T-cell therapy for cancer

A high-throughput, quantitative cell-based screen for efficient tailoring of RNA device activity

Recent advances have demonstrated the use of RNA-based control devices to program sophisticated cellular functions; however, the efficiency with which these devices can be quantitatively tailored has limited their broader implementation in cellular networks. Here, we developed a high-efficiency, high-throughput and quantitative two-color fluorescence-activated cell sorting-based screening strategy to support the rapid generation of ribozyme-based control devices with user-specified regulatory activities. The high-efficiency of this screening strategy enabled the isolation of a single functional sequence from a library of over 106 variants within two sorting cycles. We demonstrated the versatility of our approach by screening large libraries generated from randomizing individual components within the ribozyme device platform to efficiently isolate new device sequences that exhibit increased in vitro cleavage rates up to 10.5-fold and increased in vivo activation ratios up to 2-fold. We also identified a titratable window within which in vitro cleavage rates and in vivo gene-regulatory activities are correlated, supporting the importance of optimizing RNA device activity directly in the cellular environment. Our two-color fluorescence-activated cell sorting-based screen provides a generalizable strategy for quantitatively tailoring genetic control elements for broader integration within biological networks

Activation of Wingless Targets Requires Bipartite Recognition of DNA by TCF

SummarySpecific recognition of DNA by transcription factors is essential for precise gene regulation. In Wingless (Wg) signaling in Drosophila, target gene regulation is controlled by T cell factor (TCF), which binds to specific DNA sequences through a high mobility group (HMG) domain [1]. However, there is considerable variability in TCF binding sites [2–5], raising the possibility that they are not sufficient for target location. Some isoforms of human TCF contain a domain, termed the C-clamp, that mediates binding to an extended sequence in vitro [6]. However, the significance of this extended sequence for the function of Wnt response elements (WREs) is unclear. In this report, we identify a cis-regulatory element that, to our knowledge, was previously unpublished. The element, named the TCF Helper site (Helper site), is essential for the activation of several WREs. This motif greatly augments the ability of TCF binding sites to respond to Wg signaling. Drosophila TCF contains a C-clamp that enhances in vitro binding to TCF-Helper site pairs and is required for transcriptional activation of WREs containing Helper sites. A genome-wide search for clusters of TCF and Helper sites identified two new WREs. Our data suggest that DNA recognition by fly TCF occurs through a bipartite mechanism, involving both the HMG domain and the C-clamp, which enables TCF to locate and activate WREs in the nucleus

Structure alignment based on coding of local geometric measures

BACKGROUND: A structure alignment method based on a local geometric property is presented and its performance is tested in pairwise and multiple structure alignments. In this approach, the writhing number, a quantity originating from integral formulas of Vassiliev knot invariants, is used as a local geometric measure. This measure is used in a sliding window to calculate the local writhe down the length of the protein chain. By encoding the distribution of writhing numbers across all the structures in the protein databank (PDB), protein geometries are represented in a 20-letter alphabet. This encoding transforms the structure alignment problem into a sequence alignment problem and allows the well-established algorithms of sequence alignment to be employed. Such geometric alignments offer distinct advantages over structural alignments in Cartesian coordinates as it better handles structural subtleties associated with slight twists and bends that distort one structure relative to another. RESULTS: The performance of programs for pairwise local alignment (TLOCAL) and multiple alignment (TCLUSTALW) are readily adapted from existing code for Smith-Waterman pairwise alignment and for multiple sequence alignment using CLUSTALW. The alignment algorithms employed a blocked scoring matrix (TBLOSUM) generated using the frequency of changes in the geometric alphabet of a block of protein structures. TLOCAL was tested on a set of 10 difficult proteins and found to give high quality alignments that compare favorably to those generated by existing pairwise alignment programs. A set of protein comparison involving hinged structures was also analyzed and TLOCAL was seen to compare favorably to other alignment methods. TCLUSTALW was tested on a family of protein kinases and reveal conserved regions similar to those previously identified by a hand alignment. CONCLUSION: These results show that the encoding of the writhing number as a geometric measure allow high quality structure alignments to be generated using standard algorithms of sequence alignment. This approach provides computationally efficient algorithms that allow fast database searching and multiple structure alignment. Because the geometric measure can employ different window sizes, the method allows the exploration of alignments on different, well-defined length scales

Abundance of Crabs and Predation on Hemigrapsis oregonensis in Tiscornia Marsh, San Francisco Bay

With a carapace width ranging up to 35 mm for adult males and 29 mm for adult females, Hemigrapsis oregonensis is a native shore crab typically found in the rocky intertidal zone along the Northern Pacific coast. Although this habitat provides protection against desiccation as well as changes in temperature, it may also expose H. oregonensis to predators who prefer the same habitat. The goal of this research was to investigate both the predation on H. oregonensis and the abundance of various crabs of Tiscornia Marsh in San Francisco Bay. We hypothesize that the largest predation will occur in the mud with no vegetation habitat, followed by the mud with Spartina foliosa habitat, then the rock with no vegetation habitat and rock with Spartina foliosa habitat will have equal rates of predation. In regards to the abundance of crabs, we hypothesize that the rock with no vegetation and rock with Spartina foliosa habitats will have an equal abundance of crabs, followed by the mud with Spartina foliosa, and finally the mud with no vegetation having the least amount of crabs. At each of these four different habitat types, 20 tethers were set out to monitor predation rates over a 24 hour period. Then, 10 traps were used at each habitat to record the abundance of crabs every 24 hours spanning three days, for a total of 30 traps. Results supported the hypothesis that the largest amount of crabs would be found in the rocks with no vegetation, however, the results did not support the hypothesis that the largest predation rate would occur in the mud habitat. Instead, the most predation on H. oregonensis was found in the rock with Spartina foliosa habitat. Based on these results, more research needs to be conducted to determine if the distribution throughout the different habitats of H. oregonensis is due to the presence of Spartina Foliosa, predators, or another factor

Small scale rotational disorder observed in epitaxial graphene on SiC(0001)

Interest in the use of graphene in electronic devices has motivated an explosion in the study of this remarkable material. The simple, linear Dirac cone band structure offers a unique possibility to investigate its finer details by angle-resolved photoelectron spectroscopy (ARPES). Indeed, ARPES has been performed on graphene grown on metal substrates but electronic applications require an insulating substrate. Epitaxial graphene grown by the thermal decomposition of silicon carbide (SiC) is an ideal candidate for this due to the large scale, uniform graphene layers produced. The experimental spectral function of epitaxial graphene on SiC has been extensively studied. However, until now the cause of an anisotropy in the spectral width of the Fermi surface has not been determined. In the current work we show, by comparison of the spectral function to a semi-empirical model, that the anisotropy is due to small scale rotational disorder ($\sim\pm$ 0.15$^{\circ}$) of graphene domains in graphene grown on SiC(0001) samples. In addition to the direct benefit in the understanding of graphene's electronic structure this work suggests a mechanism to explain similar variations in related ARPES data.Comment: 5 pages, 4 figure

Highly p-doped graphene obtained by fluorine intercalation

We present a method for decoupling epitaxial graphene grown on SiC(0001) by intercalation of a layer of fluorine at the interface. The fluorine atoms do not enter into a covalent bond with graphene, but rather saturate the substrate Si bonds. This configuration of the fluorine atoms induces a remarkably large hole density of p \approx 4.5 \times 1013 cm-2, equivalent to the location of the Fermi level at 0.79 eV above the Dirac point ED .Comment: 4 pages, 2 figures, in print AP

Defining the clinical genomic landscape for real-world precision oncology

Through the delivery of large international projects including ICGC and TCGA, knowledge of cancer genomics is reaching saturation point. Enabling this to improve patient outcomes now requires embedding comprehensive genomic profiling into routine oncology practice. Towards this goal, this study defined the biologically and clinically relevant genomic features of adult cancer through detailed curation and analysis of large genomic datasets, accumulated literature and biomarker-driven therapeutics in clinic and development. The characteristics and prevalence of these features were then interrogated in 2348 whole genome sequences, covering 21 solid tumour types, generated by the PCAWG project. This analysis highlights the predominant contribution of copy number alterations and identifies a critical role for disruptive structural variants in the inactivation of clinically important tumour suppressor genes, including PTEN and RB1, which are not currently captured by diagnostic assays. This study defines a set of essential genomic features for the characterisation of common adult cancers