Engineered binding to erythrocytes induces immunological tolerance to E. coli asparaginase.

Antigen-specific immune responses to protein drugs can hinder efficacy and compromise safety because of drug neutralization and secondary clinical complications. We report a tolerance induction strategy to prevent antigen-specific humoral immune responses to therapeutic proteins. Our modular, biomolecular approach involves engineering tolerizing variants of proteins such that they bind erythrocytes in vivo upon injection, on the basis of the premise that aged erythrocytes and the payloads they carry are cleared tolerogenically, driving the deletion of antigen-specific T cells. We demonstrate that binding the clinical therapeutic enzyme Escherichia coli l-asparaginase to erythrocytes in situ antigen-specifically abrogates development of antibody titers by >1000-fold and extends the pharmacodynamic effect of the drug 10-fold in mice. Additionally, a single pretreatment dose of erythrocyte-binding asparaginase tolerized mice to multiple subsequent doses of the wild-type enzyme. This strategy for reducing antigen-specific humoral responses may enable more effective and safer treatment with therapeutic proteins and drug candidates that are hampered by immunogenicity

Microfluidic assays for DNA manipulation based on a block copolymer immobilization strategy

Methods to manipulate and visualize isolated DNA and oligonucleotide strands are important for investigation of their biophysics as well as their interactions with proteins. Herein, we report such a method by combining a block copolymer surface functionalization strategy with microfluidics. The copolymer poly(L-lysine-graftpolyethylene glycol) (PLL-g-PEG) coated one surface of the microfluidic channels, rendering it passive to adsorption and thus minimizing any noise arising from nontargeted adsorbed molecules. Single λ-phage DNA molecules were immobilized and were extended by molecular combing. Their extension did not exceed their contour length, which we attribute to the low surface tension of the coated surface. To demonstrate further the applicability of our method, the anchored DNA was extended by hydrodynamic flow. We propose this method for exploring DNA-protein interactions due to the copolymer's enhanced capacity for single-molecule detection, stability under wet or dry conditions, hydrophilicity, full compatibility with microfluidics and simplicity being a one-step process. © 2010 American Chemical Society

Fiber density of collagen grafts impacts rabbit urethral regeneration.

There is a need for efficient and "off-the-shelf" grafts in urethral reconstructive surgery. Currently available surgical techniques require harvesting of grafts from autologous sites, with increased risk of surgical complications and added patient discomfort. Therefore, a cost-effective and cell-free graft with adequate regenerative potential has a great chance to be translated into clinical practice. Tubular cell-free collagen grafts were prepared by varying the collagen density and fiber distribution, thereby creating a polarized low fiber density collagen graft (LD-graft). A uniform, high fiber density collagen graft (HD-graft) was engineered as a control. These two grafts were implanted to bridge a 2 cm long iatrogenic urethral defect in a rabbit model. Histology revealed that rabbits implanted with the LD-graft had a better smooth muscle regeneration compared to the HD-graft. The overall functional outcome assessed by contrast voiding cystourethrography showed patency of the urethra in 90% for the LD-graft and in 66.6% for the HD-graft. Functional regeneration of the rabbit implanted with the LD-graft could further be demonstrated by successful mating, resulting in healthy offspring. In conclusion, cell-free low-density polarized collagen grafts show better urethral regeneration than high-density collagen grafts

The maximum entropy formalism and the idiosyncratic theory of biodiversity

Why does the neutral theory, which is based on unrealistic assumptions, predict diversity patterns so accurately? Answering questions like this requires a radical change in the way we tackle them. The large number of degrees of freedom of ecosystems pose a fundamental obstacle to mechanistic modelling. However, there are tools of statistical physics, such as the maximum entropy formalism (MaxEnt), that allow transcending particular models to simultaneously work with immense families of models with different rules and parameters, sharing only well-established features. We applied MaxEnt allowing species to be ecologically idiosyncratic, instead of constraining them to be equivalent as the neutral theory does. The answer we found is that neutral models are just a subset of the majority of plausible models that lead to the same patterns. Small variations in these patterns naturally lead to the main classical species abundance distributions, which are thus unified in a single framework

Production of Medical Radioisotopes with High Specific Activity in Photonuclear Reactions with γ\gamma Beams of High Intensity and Large Brilliance

We study the production of radioisotopes for nuclear medicine in $(\gamma,x{\rm n}+y{\rm p})$ photonuclear reactions or ($\gamma,\gamma'$) photoexcitation reactions with high flux [($10^{13}-10^{15}$)$\gamma$/s], small diameter $\sim (100 \, \mu$m$)^2$ and small band width ($\Delta E/E \approx 10^{-3}-10^{-4}$) $\gamma$ beams produced by Compton back-scattering of laser light from relativistic brilliant electron beams. We compare them to (ion,$x$n$+ y$p) reactions with (ion=p,d,$\alpha$) from particle accelerators like cyclotrons and (n,$\gamma$) or (n,f) reactions from nuclear reactors. For photonuclear reactions with a narrow $\gamma$ beam the energy deposition in the target can be managed by using a stack of thin target foils or wires, hence avoiding direct stopping of the Compton and pair electrons (positrons). $(\gamma,\gamma')$ isomer production via specially selected $\gamma$ cascades allows to produce high specific activity in multiple excitations, where no back-pumping of the isomer to the ground state occurs. We discuss in detail many specific radioisotopes for diagnostics and therapy applications. Photonuclear reactions with $\gamma$ beams allow to produce certain radioisotopes, e.g. $^{47}$Sc, $^{44}$Ti, $^{67}$Cu, $^{103}$Pd, $^{117m}$Sn, $^{169}$Er, $^{195m}$Pt or $^{225}$Ac, with higher specific activity and/or more economically than with classical methods. This will open the way for completely new clinical applications of radioisotopes. For example $^{195m}$Pt could be used to verify the patient's response to chemotherapy with platinum compounds before a complete treatment is performed. Also innovative isotopes like $^{47}$Sc, $^{67}$Cu and $^{225}$Ac could be produced for the first time in sufficient quantities for large-scale application in targeted radionuclide therapy.Comment: submitted to Appl. Phys.

Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75247/1/j.1461-0248.2007.01094.x.pd

Background rejection in NEXT using deep neural networks

[EN] We investigate the potential of using deep learning techniques to reject background events in searches for neutrinoless double beta decay with high pressure xenon time projection chambers capable of detailed track reconstruction. The differences in the topological signatures of background and signal events can be learned by deep neural networks via training over many thousands of events. These networks can then be used to classify further events as signal or background, providing an additional background rejection factor at an acceptable loss of efficiency. The networks trained in this study performed better than previous methods developed based on the use of the same topological signatures by a factor of 1.2 to 1.6, and there is potential for further improvement.The NEXT Collaboration acknowledges support from the following agencies and institutions: the European Research Council (ERC) under the Advanced Grant 339787-NEXT; the Ministerio de Economia y Competitividad of Spain and FEDER under grants CONSOLIDER-Ingenio 2010 CSD2008-0037 (CUP), FIS2014-53371-C04 and the Severo Ochoa Program SEV-2014-0398; GVA under grant PROMETEO/2016/120. Fermilab is operated by Fermi Research Alliance, LLC under Contract No. DE-AC02-07CH11359 with the United States Department of Energy. JR acknowledges support from a Fulbright Junior Research Award.Renner, J.; Farbin, A.; Muñoz Vidal, J.; Benlloch-Rodríguez, J.; Botas, A.; Ferrario, P.; Gómez-Cadenas, J.... (2017). Background rejection in NEXT using deep neural networks. Journal of Instrumentation. 12. https://doi.org/10.1088/1748-0221/12/01/T01004S1

Statistical Mechanics of Horizontal Gene Transfer in Evolutionary Ecology

The biological world, especially its majority microbial component, is strongly interacting and may be dominated by collective effects. In this review, we provide a brief introduction for statistical physicists of the way in which living cells communicate genetically through transferred genes, as well as the ways in which they can reorganize their genomes in response to environmental pressure. We discuss how genome evolution can be thought of as related to the physical phenomenon of annealing, and describe the sense in which genomes can be said to exhibit an analogue of information entropy. As a direct application of these ideas, we analyze the variation with ocean depth of transposons in marine microbial genomes, predicting trends that are consistent with recent observations using metagenomic surveys.Comment: Accepted by Journal of Statistical Physic