Miracle-dz/UniFAR-FTUs huggingface dataset:
Determining the folding and binding free energy of DNA-based nanodevices and nanoswitches using urea titration curves

Abstract DNA nanotechnology takes advantage of the predictability of DNA interactions to build complex DNA-based functional nanoscale structures. However, when DNA functional and responsive units that are based on non-canonical DNA interactions are employed it becomes quite challenging to predict, understand and control their thermodynamics. In response to this limitation, here we demonstrate the use of isothermal urea titration experiments to estimate the free energy involved in a set of DNA-based systems ranging from unimolecular DNA-based nanoswitches to more complex DNA folds (e.g. aptamers) and nanodevices. We propose here a set of fitting equations that allow to analyze the urea titration curves of these DNA responsive units based on Watson–Crick and non-canonical interactions (stem-loop, G-quadruplex, triplex structures) and to correctly estimate their relative folding and binding free energy values under different experimental conditions. The results described herein will pave the way toward the use of urea titration experiments in the field of DNA nanotechnology to achieve easier and more reliable thermodynamic characterization of DNA-based functional responsive units. More generally, our results will be of general utility to characterize other complex supramolecular systems based on different biopolymers.
Can Doping Graphite Trigger Room Temperature Superconductivity? Evidence for Granular High‐Temperature Superconductivity in Water‐Treated Graphite Powder

Granular superconductivity in powders of small graphite grains (several tens of micrometers) is demonstrated after treatment with pure water. The temperature, magnetic field and time dependence of the magnetic moment of the treated graphite powder provides evidence for the existence of superconducting vortices with some similarities to high-temperature granular superconducting oxides but even at temperatures above 300 K. Room temperature superconductivity in doped graphite or at its interfaces appears to be possible.
Contrasts between adaptive coding and noncoding changes during human evolution

Changes in non–protein-coding regulatory DNA sequences have been proposed to play distinctive roles in adaptive evolution. We analyzed correlations between gene functions and evidence for positive selection in a common statistical framework across several large surveys of coding and noncoding sequences throughout the human genome. Strong correlations with both classifications in gene ontologies and measurements of gene expression indicate that neural development and function have adapted mainly through noncoding changes. In contrast, adaptation via coding changes is dominated by immunity, olfaction, and male reproduction. Genes with highly tissue-specific expression have undergone more adaptive coding changes, suggesting that pleiotropic constraints inhibit such changes in broadly expressed genes. In contrast, adaptive noncoding changes do not exhibit this pattern. Our findings underscore the probable importance of noncoding changes in the evolution of human traits, particularly cognitive traits.
Stability of an autoinhibitory interface in the structure of the tyrosine kinase ZAP-70 impacts T cell receptor response

The delivery of signals from the activated T cell antigen receptor (TCR) inside the cell relies on the protein tyrosine kinase ZAP-70 (ζ-associated protein of 70 kDa). A recent crystal structure of inactive full-length ZAP-70 suggests that a central interface formed by the docking of the two SH2 domains of ZAP-70 onto the kinase domain is crucial for suppressing catalytic activity. Here we validate the significance of this autoinhibitory interface for the regulation of ZAP-70 catalytic activity and the T cell response. For this purpose, we perform in vitro catalytic activity assays and binding experiments using ZAP-70 proteins purified from insect cells to examine activation of ZAP-70. Furthermore, we use cell lines stably expressing wild-type or mutant ZAP-70 to monitor proximal events in T cell signaling, including TCR-induced phosphorylation of ZAP-70 substrates, activation of the MAP kinase pathway, and intracellular Ca2+ levels. Taken together, our results directly correlate the stability of the autoinhibitory interface with the activation of these key events in the T cell response.
Carbon Dot‐Based Inorganic–Organic Nanosystem for Two‐Photon Imaging and Biosensing of pH Variation in Living Cells and Tissues

A carbon dot (C-Dot)-based two-photon fluorescent probe has been developed for the monitoring of pH changes across a broad range with high sensitivity and selectivity. The inorganic-organic probe also shows good biocompatibility and cell permeability, and thus can be successfully applied in bioimaging and biosensing of physiological pH in living cells, as well as living tissues at a depth of 65-185 μm.
Magnetizing DNA and Proteins Using Responsive Surfactants

DNA chains and their movement in solvent may now be controlled simply by surfactant binding and the switching "on" and "off" of a magnetic field adding a new paradigm to the study and control, condensation and manipulation of DNA (and other biomolecules). Such control is essential for biotechnological applications such as transfection and the regulation of gene suppression, as well as in materials science concerning soft molecular self-assemblies.
Synchronized switching of multiple toxin–antitoxin modules by (p)ppGpp fluctuation

Abstract Toxin–antitoxin (TA) loci are widespread in bacteria including important pathogenic species. Recent studies suggest that TA systems play a key role in persister formation. However, the persistence phenotype shows only weak dependence on the number of TA systems, i.e. they are functionally redundant. We use a mathematical model to investigate the interaction of multiple TA systems in the switching between growth and persistence. We explore two scenarios: (i) TA systems are bistable and each TA system experiences its own noise and (ii) the noise in the level of common stress signal (e.g. (p)ppGpp) coordinates all TA systems simultaneously. We find that in the first scenario the exit from the persister state strongly depends on the number of TA systems. However in the second case, we could reproduce the weak dependence. The duration of the high (p)ppGpp state was found to be the key parameter for persistence. The (p)ppGpp-driven synchronized transition of all TA systems results in the redundancy.
Sustainability and substitution of exhaustible natural resources. How structural change affects long-term R&D-investments

We study long-run growth in a multi-sector economy with non-renewable resource use and endogenous innovations. Unlike recent capital resource models, we find that poor input substitution need not be detrimental for sustainable growth; on the contrary, combined with resource depletion it fosters structural change, which helps to sustain research investments. We derive the properties of the transition path, show which sectors survive in the long run, and discuss whether the economy approximates a steady state with or without a scale effect. The results continue to hold when some sectors exhibit perfect competition.
Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation

Two major goals of regenerative medicine are to reproducibly transform adult somatic cells into a pluripotent state and to control their differentiation into specific cell fates. Progress toward these goals would be greatly helped by obtaining a complete picture of the RNA isoforms produced by these cells due to alternative splicing (AS) and alternative promoter selection (APS). To investigate the roles of AS and APS, reciprocal exon–exon junctions were interrogated on a genome-wide scale in differentiating mouse embryonic stem (ES) cells with a prototype Affymetrix microarray. Using a recently released open-source software package named AltAnalyze, we identified 144 genes for 170 putative isoform variants, the majority (67%) of which were predicted to alter protein sequence and domain composition. Verified alternative exons were largely associated with pathways of Wnt signaling and cell-cycle control, and most were conserved between mouse and human. To examine the functional impact of AS, we characterized isoforms for two genes. As predicted by AltAnalyze, we found that alternative isoforms of the gene Serca2 were targeted by distinct microRNAs (miRNA-200b, miRNA-214), suggesting a critical role for AS in cardiac development. Analysis of the Wnt transcription factor Tcf3, using selective knockdown of an ES cell-enriched and characterized isoform, revealed several distinct targets for transcriptional repression (Stmn2, Ccnd2, Atf3, Klf4, Nodal, and Jun) as well as distinct differentiation outcomes in ES cells. The findings herein illustrate a critical role for AS in the specification of ES cells with differentiation, and highlight the utility of global functional analyses of AS.
Elongated fibrillar structure of a streptococcal adhesin assembled by the high-affinity association of α- and PPII-helices

Streptococcus mutans antigen I/II (AgI/II) is a cell surface-localized protein adhesin that interacts with salivary components within the salivary pellicle. AgI/II contributes to virulence and has been studied as an immunological and structural target, but a fundamental understanding of its underlying architecture has been lacking. Here we report a high-resolution (1.8 Å) crystal structure of the A3VP1 fragment of S. mutans AgI/II that demonstrates a unique fibrillar form (155 Å) through the interaction of two noncontiguous regions in the primary sequence. The A3 repeat of the alanine-rich domain adopts an extended α-helix that intertwines with the P1 repeat polyproline type II (PPII) helix to form a highly extended stalk-like structure heretofore unseen in prokaryotic or eukaryotic protein structures. Velocity sedimentation studies indicate that full-length AgI/II that contains three A/P repeats extends over 50 nanometers in length. Isothermal titration calorimetry revealed that the high-affinity association between the A3 and P1 helices is enthalpically driven. Two distinct binding sites on AgI/II to the host receptor salivary agglutinin (SAG) were identified by surface plasmon resonance (SPR). The current crystal structure reveals that AgI/II family proteins are extended fibrillar structures with the number of alanine- and proline-rich repeats determining their length.
mRNA cap analogues substituted in the tetraphosphate chain with CX2: identification of O-to-CCl2 as the first bridging modification that confers resistance to decapping without impairing translation

Abstract Analogues of the mRNA 5′-cap are useful tools for studying mRNA translation and degradation, with emerging potential applications in novel therapeutic interventions including gene therapy. We report the synthesis of novel mono- and dinucleotide cap analogues containing dihalogenmethylenebisphosphonate moiety (i.e. one of the bridging O atom substituted with CCl2 or CF2) and their properties in the context of cellular translational and decapping machineries, compared to phosphate-unmodified and previously reported CH2-substituted caps. The analogues were bound tightly to eukaryotic translation initiation factor 4E (eIF4E), with CCl2-substituted analogues having the highest affinity. When incorporated into mRNA, the CCl2-substituted dinucleotide most efficiently promoted cap-dependent translation. Moreover, the CCl2-analogues were potent inhibitors of translation in rabbit reticulocyte lysate. The crystal structure of eIF4E in complex with the CCl2-analogue revealed a significantly different ligand conformation compared to that of the unmodified cap analogue, which likely contributes to the improved binding. Both CCl2- and CF2- analogues showed lower susceptibility to hydrolysis by the decapping scavenger enzyme (DcpS) and, when incorporated into RNA, conferred stability against major cellular decapping enzyme (Dcp2) to transcripts. Furthermore, the use of difluoromethylene cap analogues was exemplified by the development of 19F NMR assays for DcpS activity and eIF4E binding.
RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data

RNA structures are hierarchically organized. The secondary structure is articulated around sophisticated local 3D motifs shaping the full 3D architecture of the molecule. Recent contributions have identiﬁed and organized recurrent local 3D motifs, but applications of this knowledge for predictive purposes is still in its infancy. We recently developed a computational framework, named RNA-MoIP (RNA Motifs over Integer Programming), to reconcile RNA secondary structure and local 3D motif information available in databases. In this paper, we introduce a web service using our software for predicting RNA hybrid 2D-3D structures from sequence data only. Optionally, it can be used for (i) local 3D motif prediction or (ii) the reﬁnement of user-deﬁned secondary structures. Importantly, our web-server automatically generates a script for the MC-Sym software, which can be immediately used to quickly predict all-atom RNA 3D models. Theweb-server
BSAVA Manual of Canine and Feline Wound Management and Reconstruction

The chapter is an interesting introduction to the field but does not contain enough material to be truly useful, and some of the information is somewhat peripheral to the field of anesthesia. Who should purchase this book? There are many practical suggestions for veterinarians in practice, but the book also includes a great deal of theoretical discussion that is probably of more interest to students than to busy practitioners. With the exception of the chapter on clinical techniques, the level of discussion seems inappropriate to veterinary technicians unless they have a particular interest in anesthesia. Overall, however, there is much useful information (and even more important, a good presentation of current philosophy) contained in this small and reasonably priced book.
Design of embedded chimeric peptide nucleic acids that efficiently enter and accurately reactivate gene expression in vivo

Pharmacological treatments designed to reactivate fetal γ-globin can lead to an effective and successful clinical outcome in patients with hemoglobinopathies. However, new approaches remain highly desired because such treatments are not equally effective for all patients, and toxicity issues remain. We have taken a systematic approach to develop an embedded chimeric peptide nucleic acid (PNA) that effectively enters the cell and the nucleus, binds to its target site at the human fetal γ-globin promoter, and reactivates this transcript in adult transgenic mouse bone marrow and human primary peripheral blood cells. In vitro and in vivo DNA-binding assays in conjunction with live-cell imaging have been used to establish and optimize chimeric PNA design parameters that lead to successful gene activation. Our final molecule contains a specific γ-promoter-binding PNA sequence embedded within two amino acid motifs: one leads to efficient cell/nuclear entry, and the other generates transcriptional reactivation of the target. These embedded PNAs overcome previous limitations and are generally applicable to the design of in vivo transcriptional activation reagents that can be directed to any promoter region of interest and are of direct relevance to clinical applications that would benefit from such a need.
Anisotropic Topological Surface States on High‐Index Bi2Se3 Films

A high-index topological insulator thin film, Bi2 Se3 (221), is grown on a faceted InP(001) substrate by molecular-beam epitaxy (see model in figure (a)). Angle-resolved photoemission spectroscopy measurement reveals the Dirac cone structure of the surface states on such a surface (figure (b)). The Fermi surface is elliptical (figure (c)), suggesting an anisotropy along different crystallographic directions. Transport studies also reveal a strong anisotropy in Hall conductance.
Novel cell surface luciferase reporter for high-throughput yeast one-hybrid screens

Abstract Gene-centered yeast one-hybrid (Y1H) screens provide a powerful and effective strategy to identify transcription factor (TF)-promoter interactions. While genome-wide TF ORFeome clone collections are increasingly available, screening protocols have limitations inherent to the properties of the enzymatic reaction used to identify interactions and to the procedure required to perform the assay in a high-throughput format. Here, we present the development and validation of a streamlined strategy for quantitative and fully automated gene-centered Y1H screens using a novel cell surface Gaussia luciferase reporter.
p53 controls expression of the DNA deaminase APOBEC3B to limit its potential mutagenic activity in cancer cells

Abstract Cancer genome sequencing has implicated the cytosine deaminase activity of apolipoprotein B mRNA editing enzyme catalytic polypeptide-like (APOBEC) genes as an important source of mutations in diverse cancers, with APOBEC3B (A3B) expression especially correlated with such cancer mutations. To better understand the processes directing A3B over-expression in cancer, and possible therapeutic avenues for targeting A3B, we have investigated the regulation of A3B gene expression. Here, we show that A3B expression is inversely related to p53 status in different cancer types and demonstrate that this is due to a direct and pivotal role for p53 in repressing A3B expression. This occurs through the induction of p21 (CDKN1A) and the recruitment of the repressive DREAM complex to the A3B gene promoter, such that loss of p53 through mutation, or human papilloma virus-mediated inhibition, prevents recruitment of the complex, thereby causing elevated A3B expression and cytosine deaminase activity in cancer cells. As p53 is frequently mutated in cancer, our findings provide a mechanism by which p53 loss can promote cancer mutagenesis.
Two‐Dimensional CdSe Nanosheets and their Interaction with Stabilizing Ligands

Single layer two-dimensional CdSe nanosheets are explored theoretically, highlighting the role of the coordinating (and stabilizing) ligands. Four isomeric CdSe single sheets bonded to H atoms are studied (CdSeH(2) ), as are four similar sheets with NH(3) coordinated to the Cd atoms. These are quite corrugated, unlike the pristine sheets, and have a different stability order from their graphane analogs.
Prognosis of Lung Cancer Mortality in West Germany: A Case Study in Bayesian Prediction. (REVISED, January 2000)

We apply a generalized Bayesian age-period-cohort (APC) model to a dataset on lung cancer mortality in West Germany, 1952-1996. Our goal is to predict future deaths rates until the year 2010, separately for males and females. Since age and period is not measured on the same grid, we propose a generalized APC-model where consecutive cohort parameters represent strongly overlapping birth cohorts. This approach results in a rather large number of parameters, where standard algorithms for statistical inference by Markov chain Monte Carlo (MCMC) methods turn out to be computationally intensive. We propose a more efficient implementation based on ideas of block sampling from the time series literature. We entertain two different formulations, penalizing either first or second differences of age, period and cohort parameters. To assess the predictive quality of both formulations, we first forecast the rates for the period 1987-1996 based on data until 1986. A comparison with the actual observed rates is made based on quantities related to the predictive deviance. Predictions of lung cancer mortality until 2010 both for males and females are finally reported.
Endogenous cannabinoid signaling is essential for stress adaptation

Secretion of glucocorticoid hormones during stress produces an array of physiological changes that are adaptive and beneficial in the short term. In the face of repeated stress exposure, however, habituation of the glucocorticoid response is essential as prolonged glucocorticoid secretion can produce deleterious effects on metabolic, immune, cardiovascular, and neurobiological function. Endocannabinoid signaling responds to and regulates the activity of the hypothalamic–pituitary–adrenal (HPA) axis that governs the secretion of glucocorticoids; however, the role this system plays in adaptation of the neuroendocrine response to repeated stress is not well characterized. Herein, we demonstrate a divergent regulation of the two endocannabinoid ligands, N-arachidonylethanolamine (anandamide; AEA) and 2-arachidonoylglycerol (2-AG), following repeated stress such that AEA content is persistently decreased throughout the corticolimbic stress circuit, whereas 2-AG is exclusively elevated within the amygdala in a stress-dependent manner. Pharmacological studies demonstrate that this divergent regulation of AEA and 2-AG contribute to distinct forms of HPA axis habituation. Inhibition of AEA hydrolysis prevented the development of basal hypersecretion of corticosterone following repeated stress. In contrast, systemic or intra-amygdalar administration of a CB1 receptor antagonist before the final stress exposure prevented the repeated stress-induced decline in corticosterone responses. The present findings demonstrate an important role for endocannabinoid signaling in the process of stress HPA habituation, and suggest that AEA and 2-AG modulate different components of the adrenocortical response to repeated stressor exposure.
Electrolyte‐Gated Organic Field‐Effect Transistor Sensors Based on Supported Biotinylated Phospholipid Bilayer

Anchored, biotinylated phospholipids forming the capturing layers in an electrolyte-gated organic field-effect transistor (EGOFET) allow label-free electronic specific detection at a concentration level of 10 nM in a high ionic strength solution. The sensing mechanism is based on a clear capacitive effect across the PL layers involving the charges of the target molecules.
Electric‐Field Screening in Atomically Thin Layers of MoS2: the Role of Interlayer Coupling

This work was supported by MICINN/MINECO (Spain) through the programs MAT2011-25046 and CONSOLIDER-INGENIO-2010 “Nanociencia Molecular” CSD-2007-00010, Comunidad de Madrid through program Nanobiomagnet S2009/MAT-1726 and the European Union (FP7) through the programs RODIN and ELFOS. E.C. acknowledges a Marie Curie Grant, PIEF-GA-2009-251904.
A Highly Tunable Biocompatible and Multifunctional Biodegradable Elastomer

Biodegradable elastomers have emerged as promising materials for their potential to mimic the viscoelastic properties of several tissues and exhibit compliance with dynamic environments without damaging the surrounding tissue. [1, 2] Several elastomers have been recently proposed;[3–8] however, the development of highly tunable biodegradable elastomers that can effectively and controllably present biological and physical signals and withstand repeated cycles of physiologic loads, has remained elusive. Such materials should be useful for a broad range of clinically-relevant applications, such as cardiac therapy. For example, following myocardial infarction, the local controlled delivery of bioactive cues[9] or the physical support of the left ventricle wall[10] have been shown to improve cardiac function. The synergistic therapeutic effect of biochemical and biophysical cues has not yet been explored using degradable materials given the absence of materials that can simultaneously deliver bioactive cues and maintain mechanical integrity in a dynamic environment such as the beating heart. Here, we describe a novel biocompatible and mechanically tunable elastomer, poly(glycerol sebacate urethane) (PGSU), suitable for efficient encapsulation and controlled delivery of bioactive macromolecules and with the potential to be applied to cardiac drug delivery.