Synergistic topological and supramolecular control of Diels-Alder reactivity based on a tunable self-complexing host-guest molecular switch.

Compartmentalization and binding-triggered conformational change regulate many metabolic processes in living matter. Here, we have synergistically combined these two biorelevant processes to tune the Diels-Alder (DA) reactivity of a synthetic self-complexing host-guest molecular switch CBPQT4+ -Fu, consisting of an electron-rich furan unit covalently attached to the electron-deficient cyclobis(paraquat-p-phenylene) tetrachloride (CBPQT4+ , 4Cl- ) host. This design allows CBPQT4+ -Fu to efficiently compartmentalize the furan ring inside its host cavity in water, thereby protecting it from the DA reaction with maleimide. Remarkably, the self-complexed CBPQT4+ -Fu can undergo a conformational change through intramolecular decomplexation upon the addition of a stronger binding molecular naphthalene derivative as a competitive guest, triggering the DA reaction upon addition of a chemical regulator. Remarkably, connecting the guest to a thermoresponsive lower critical solution temperature (LCST) copolymer regulator controls the DA reaction on command upon heating and cooling the reaction media beyond and below the cloud point temperature of the copolymer, representing a rare example of decreased reactivity upon increasing temperature. Altogether, this work opens up new avenues towards combined topological and supramolecular control over reactivity in synthetic constructs, enabling control over reactivity through molecular regulators or even mild temperature variations.

Systematic interaction network filtering identifies CRMP1 as a novel suppressor of huntingtin misfolding and neurotoxicity.

Assemblies of huntingtin (HTT) fragments with expanded polyglutamine (polyQ) tracts are a pathological hallmark of Huntington's disease (HD). The molecular mechanisms by which these structures are formed and cause neuronal dysfunction and toxicity are poorly understood. Here, we utilized available gene expression data sets of selected brain regions of HD patients and controls for systematic interaction network filtering in order to predict disease-relevant, brain region-specific HTT interaction partners. Starting from a large protein-protein interaction (PPI) data set, a step-by-step computational filtering strategy facilitated the generation of a focused PPI network that directly or indirectly connects 13 proteins potentially dysregulated in HD with the disease protein HTT. This network enabled the discovery of the neuron-specific protein CRMP1 that targets aggregation-prone, N-terminal HTT fragments and suppresses their spontaneous self-assembly into proteotoxic structures in various models of HD. Experimental validation indicates that our network filtering procedure provides a simple but powerful strategy to identify disease-relevant proteins that influence misfolding and aggregation of polyQ disease proteins.

Ultrafast Tailoring of Carbon Surfaces via Electrochemically Attached Triazolinediones.

The straightforward coupling between a triazolinedione (TAD) unit and citronellyl derivatives via an Alder-ene reaction has been exploited to tailor the physicochemical surface properties of glassy carbon (GC) surfaces in an ultrafast and additive-free manner. For this purpose, we first covalently grafted a TAD precursor onto GC via electrochemical reduction of an in situ generated diazonium salt, which was then electrochemically oxidized into the desired GC-bonded TAD unit. A kinetic study of the modification of this reactive layer with an electroactive ferrocene probe proved that a complete functionalization was obtained in merely 1 minute. Further modification experiments with a fluorinated probe demonstrated that the surface properties can be swiftly tailored on demand. The different modification steps, as well as the efficiency of this strategy, were investigated by electrochemistry, contact angle goniometry, and X-ray photoelectron spectroscopy analysis.

Superresolution imaging reveals structurally distinct periodic patterns of chromatin along pachytene chromosomes.

During meiosis, homologous chromosomes associate to form the synaptonemal complex (SC), a structure essential for fertility. Information about the epigenetic features of chromatin within this structure at the level of superresolution microscopy is largely lacking. We combined single-molecule localization microscopy (SMLM) with quantitative analytical methods to describe the epigenetic landscape of meiotic chromosomes at the pachytene stage in mouse oocytes. DNA is found to be nonrandomly distributed along the length of the SC in condensed clusters. Periodic clusters of repressive chromatin [trimethylation of histone H3 at lysine (Lys) 27 (H3K27me3)] are found at 500-nm intervals along the SC, whereas one of the ends of the SC displays a large and dense cluster of centromeric histone mark [trimethylation of histone H3 at Lys 9 (H3K9me3)]. Chromatin associated with active transcription [trimethylation of histone H3 at Lys 4 (H3K4me3)] is arranged in a radial hair-like loop pattern emerging laterally from the SC. These loops seem to be punctuated with small clusters of H3K4me3 with an average spread larger than their periodicity. Our findings indicate that the nanoscale structure of the pachytene chromosomes is constrained by periodic patterns of chromatin marks, whose function in recombination and higher order genome organization is yet to be elucidated.

Dynamics of chromatin accessibility and epigenetic state in response to UV damage.

Epigenetic mechanisms determine the access of regulatory factors to DNA during events such as transcription and the DNA damage response. However, the global response of histone modifications and chromatin accessibility to UV exposure remains poorly understood. Here, we report that UV exposure results in a genome-wide reduction in chromatin accessibility, while the distribution of the active regulatory mark H3K27ac undergoes massive reorganization. Genomic loci subjected to epigenetic reprogramming upon UV exposure represent target sites for sequence-specific transcription factors. Most of these are distal regulatory regions, highlighting their importance in the cellular response to UV exposure. Furthermore, UV exposure results in an extensive reorganization of super-enhancers, accompanied by expression changes of associated genes, which may in part contribute to the stress response. Taken together, our study provides the first comprehensive resource for genome-wide chromatin changes upon UV irradiation in relation to gene expression and elucidates new aspects of this relationship.

Reactive oxygen species and protein modifications in spermatozoa.

Cellular response to reactive oxygen species (ROS) includes both reversible redox signaling and irreversible nonenzymatic reactions which depend on the nature and concentration of the ROS involved. Changes in thiol/disulfide pairs affect protein conformation, enzymatic activity, ligand binding, and protein-protein interactions. During spermatogenesis and epididymal maturation, there are ROS-dependent modifications of the sperm chromatin and flagellar proteins.The spermatozoon is regulated by redox mechanisms to acquire fertilizing ability. For this purpose, controlled amounts of ROS are necessary to assure sperm activation (motility and capacitation). Modifications of the thiol groups redox status of sperm proteins are needed for spermatozoon to achieve fertilizing ability. However, when ROS are produced at high concentrations, the established oxidative stress promotes pathological changes affecting sperm function and leading to infertility. Sperm proteins are sensitive to high levels of ROS and suffer modifications that impact on motility, capacitation, and the ability of the spermatozoon to recognize and bind to the zona pellucida and damage of sperm DNA. Thiol oxidation, tyrosine nitration, and S-glutathionylation are highlighted in this review as significant redox-dependent protein modifications associated with impairment of sperm function and alteration of paternal genome leading to infertility. Peroxiredoxins, the primary antioxidant protection in spermatozoa, are affected by most of the protein modifications described in this review. They play a significant role in both physiological and pathological processes in mammalian spermatozoa.

Reversible Tethering of Polymers onto Catechol-Based Titanium Platforms.

In this article, we report on the reversible tethering of end-functionalized polymers onto catechol-based titanium platforms by exploiting the reversible Diels-Alder (DA) cycloaddition reaction. For this purpose, furan and maleimide end-functionalized polymers, prepared via reversible addition-fragmentation chain transfer polymerization, were covalently grafted through a DA reaction onto reactive titanium platforms elaborated from catechol-based anchors incorporating either the furan or the maleimide moiety. As a proof of concept, a hydrophilic poly(oligo(ethylene glycol)acrylate) (POEGA) and a hydrophobic poly(2,2,2-trifluoroethyl acrylate) (PTFEA) were grafted onto titanium surfaces and subsequently detached by exploiting the thermoreversible nature of the DA reaction [i.e., retro Diels-Alder (rDA)]. These polymers were interchanged by performing a second DA reaction, thereby allowing the titanium surface wettability to be switched from hydrophobic to hydrophilic on demand. The grafting of furan/maleimide end-functionalized polymers onto functionalized (maleimide/furan, respectively) catechol-based titanium platforms and the subsequent rDA/DA sequence used for switching the titanium surface were evidenced by attenuated total reflectance-Fourier transform-infrared spectroscopy, X-ray photoelectron spectroscopy, and contact angle measurements.

Bio++: efficient extensible libraries and tools for computational molecular evolution.

Efficient algorithms and programs for the analysis of the ever-growing amount of biological sequence data are strongly needed in the genomics era. The pace at which new data and methodologies are generated calls for the use of pre-existing, optimized-yet extensible-code, typically distributed as libraries or packages. This motivated the Bio++ project, aiming at developing a set of C++ libraries for sequence analysis, phylogenetics, population genetics, and molecular evolution. The main attractiveness of Bio++ is the extensibility and reusability of its components through its object-oriented design, without compromising the computer-efficiency of the underlying methods. We present here the second major release of the libraries, which provides an extended set of classes and methods. These extensions notably provide built-in access to sequence databases and new data structures for handling and manipulating sequences from the omics era, such as multiple genome alignments and sequencing reads libraries. More complex models of sequence evolution, such as mixture models and generic n-tuples alphabets, are also included.

Impact of the polymer dispersity on the properties of curcumin/polyvinylpyrrolidone amorphous solid dispersions.

Amorphous solid dispersions (ASD) are known to enhance the absorption of poorly water-soluble drugs. In this work we synthesise well-defined Polyvinylpyrrolidone (PVP) to establish the impact of dispersity and chain-end functionality on the physical properties of Curcumin (CUR)/PVP ASD. Thermodynamic characterisation of synthesised PVP emphasises a strong effect of the dispersity on the glass transition temperature (Tg), 50 °C higher for synthesised PVP than for commercial PVP K12 of same molar mass. This increase of Tg affects the thermodynamic properties of CUR/PVP ASD successfully formulated up to 70 wt% of CUR by milling or solvent evaporation. The evolution of both the Tg and CUR solubility values versus CUR content points out the development of fairly strong CUR-PVP interactions that strengthen the antiplasticising effect of PVP on the Tg of ASD. However, for ASD formulated with commercial PVP this effect is counterbalanced at low CUR content by a plasticising effect due to the shortest PVP chains. Moreover, the overlay of the phase and state diagrams highlights the strong impact of the polymer dispersity on the stability of CUR/PVP ASD. ASD formulated with low dispersity PVP are stable on larger temperature and concentration ranges than those formulated with PVP K12.

Mitotic bookmarking redundancy by nuclear receptors in pluripotent cells.

Mitotic bookmarking transcription factors (TFs) are thought to mediate rapid and accurate reactivation after mitotic gene silencing. However, the loss of individual bookmarking TFs often leads to the deregulation of only a small proportion of their mitotic targets, raising doubts on the biological significance and importance of their bookmarking function. Here we used targeted proteomics of the mitotic bookmarking TF ESRRB, an orphan nuclear receptor, to discover a large redundancy in mitotic binding among members of the protein super-family of nuclear receptors. Focusing on the nuclear receptor NR5A2, which together with ESRRB is essential in maintaining pluripotency in mouse embryonic stem cells, we demonstrate conjoint bookmarking activity of both factors on promoters and enhancers of a large fraction of active genes, particularly those most efficiently reactivated in G1. Upon fast and simultaneous degradation of both factors during mitotic exit, hundreds of mitotic targets of ESRRB/NR5A2, including key players of the pluripotency network, display attenuated transcriptional reactivation. We propose that redundancy in mitotic bookmarking TFs, especially nuclear receptors, confers robustness to the reestablishment of gene regulatory networks after mitosis.

AI-Powered Biomolecular-Specific and Label-Free Multispectral Imaging Rapidly Detects Malignant Neoplasm in Surgically Excised Breast Tissue Specimens.

CONTEXT.­: Repeated surgery is necessary for 20% to 40% of breast conservation surgeries owing to the unavailability of any adjunctive, accurate, and objective tool in the surgeon's hand for real-time margin assessment to achieve the desired balance of oncologic and cosmetic outcomes. OBJECTIVE.­: To assess the feasibility of using a multispectral autofluorescence imaging device for discriminating malignant neoplasm from normal breast tissue in pathology as a critical step in the development of a device for intraoperative use, and to demonstrate the device's utility for use in processing and prioritizing specimens during frozen section and in the pathology grossing room. DESIGN.­: We performed a preliminary assessment of our device, called the TumorMAP system, on 172 fresh tissue blocks from 115 patients obtained from lumpectomy specimens at the time of initial gross examination and compared the device results with gold standard pathology evaluation. RESULTS.­: The preliminary results demonstrate the potential of our device in detecting breast cancer in fresh tissue samples with a sensitivity of 82%, a specificity of 91%, a positive predictive value of 84%, and a negative predictive value of 89%. CONCLUSIONS.­: Our results suggest that the TumorMAP system is suitable for the detection of malignant neoplasm in freshly excised breast specimens and has the potential to evaluate resection margins in real time.

PDBpaint, a visualization webservice to tag protein structures with sequence annotations.

SUMMARY: Protein features are often displayed along the linear sequence of amino acids that make up that protein, but in reality these features occupy a position in the folded protein's 3D space. Mapping sequence features to known or predicted protein structures is useful when trying to deduce the function of those features and when evaluating sequence or structural predictions. To facilitate this goal, we developed PDBpaint, a simple tool that displays protein sequence features gathered from bioinformatics resources on top of protein structures, which are displayed in an interactive window (using the Jmol Java viewer). PDBpaint can be used either with existing protein structures or with novel structures provided by the user. The current version of PDBpaint allows the visualization of annotations from Pfam, ARD (detection of HEAT-repeats), UniProt, TMHMM2.0 and SignalP. Users can also add other annotations manually. AVAILABILITY AND IMPLEMENTATION: PDBpaint is accessible at http://cbdm.mdc-berlin.de/~pdbpaint. Code is available from http://sourceforge.net/projects/pdbpaint. The website was implemented in Perl, with all major browsers supported. CONTACT: david.fournier@mdc-berlin.de.

Highly efficient ring-opening reaction of azlactone-based copolymer platforms for the design of functionalized materials.

Azlactone-based homopolymers and copolymers were successfully synthesized using the reversible addition-fragmentation chain transfer (RAFT) process. The functional monomer 2-styryl-4,4-dimethylazlactone (SDA) was first homopolymerized in bulk then copolymerized with styrene, leading to (co)polymers with low polydispersity indices (PDI = 1.10-1.20). The reactive azlactone rings, located along the backbone of the copolymers were subjected to highly efficient ring-opening reactions with functionalized primary amine derivatives incorporating a fluorescent (naphthalene) or an electrochemical (ferrocene) probes, a biological fragment (glutathione), a sugar unit (ß-cyclodextrin), or an oligomeric fluorinated moiety, leading to materials with various interesting properties.

Simultaneous detection of single molecules and singulated ensembles of molecules enables immunoassays with broad dynamic range.

We report a method for combining the detection of single molecules (digital) and an ensemble of molecules (analog) that is capable of detecting enzyme label from 10(-19) M to 10(-13) M, for use in high sensitivity enzyme-linked immunosorbent assays (ELISA). The approach works by capturing proteins on microscopic beads, labeling the proteins with enzymes using a conventional multistep immunosandwich approach, isolating the beads in an array of 50-femtoliter wells (Single Molecule Array, SiMoA), and detecting bead-associated enzymatic activity using fluorescence imaging. At low concentrations of proteins, when the ratio of enzyme labels to beads is less than ∼1.2, beads carry either zero or low numbers of enzymes, and protein concentration is quantified by counting the presence of "on" or "off" beads (digital regime). (1) At higher protein concentrations, each bead typically carries multiple enzyme labels, and the average number of enzyme labels present on each bead is quantified from a measure of the average fluorescence intensity (analog regime). Both the digital and analog concentration ranges are quantified by a common unit, namely, average number of enzyme labels per bead (AEB). By combining digital and analog detection of singulated beads, a linear dynamic range of over 6 orders of magnitude to enzyme label was achieved. Using this approach, an immunoassay for prostate specific antigen (PSA) was developed. The combined digital and analog PSA assay provided linear response over approximately four logs of concentration ([PSA] from 8 fg/mL to 100 pg/mL or 250 aM to 3.3 pM). This approach extends the dynamic range of ELISA from picomolar levels down to subfemtomolar levels in a single measurement.

Fifth-generation digital immunoassay for prostate-specific antigen by single molecule array technology.

BACKGROUND: Measurement of prostate-specific antigen (PSA) in prostate cancer patients following radical prostatectomy (RP) has been hindered by the limit of quantification of available assays. Because radical prostatectomy removes the tissue responsible for PSA production, postsurgical PSA is typically undetectable with current assay methods. Evidence suggests, however, that more sensitive determination of PSA status following RP could improve assessment of patient prognosis and response to treatment and better target secondary therapy for those who may benefit most. We developed an investigational digital immunoassay with a limit of quantification 2 logs lower than current ultrasensitive third-generation PSA assays. METHODS: We developed reagents for a bead-based ELISA for use with high-density arrays of femtoliter-volume wells. Anti-PSA capture beads with immunocomplexes and associated enzyme labels were singulated within the wells of the arrays and interrogated for the presence of enzymatic product. We characterized analytical performance, compared its accuracy with a commercially available test, and analyzed longitudinal serum samples from a pilot study of 33 RP patients. RESULTS: The assay exhibited a functional sensitivity (20% interassay CV) <0.05 pg/mL, total imprecision <10% from 1 to 50 pg/mL, and excellent agreement with the comparator method. All RP samples were well within the assay measurement capability. PSA concentrations following surgery were found to be predictive of prostate cancer recurrence risk over 5 years. CONCLUSIONS: The robust 2-log improvement in limit of quantification relative to current ultrasensitive assays and the validated analytical performance of the assay allow for accurate assessment of PSA status after RP.

Tetrathiafulvalene end-functionalized poly(N-isopropylacrylamide): a new class of amphiphilic polymer for the creation of multistimuli responsive micelles.

In this article, we report the formation of micelles from a tetrathiafulvalene (TTF) end-functionalized poly(N-isopropylacrylamide) (poly(NIPAM)) derivative (1). We have determined the critical aggregation concentration (CAC) and average diameter of the micelles using fluorescence spectroscopy and dynamic light scattering experiments, respectively. We have exploited the NIPAM backbone of the polymer to thermally transform the swollen hydrophilic poly(NIPAM) derivative to a more globular hydrophobic state at the lower critical solution temperature (LCST). Finally, we have shown that we can exploit the chemical oxidation and complexation properties of the TTF unit to disrupt the micelle architecture to release the hydrophobic dye Nile Red from the interior of the micelle.

Separation between low-energy hole dynamics and spin dynamics in a frustrated magnet.

An angle-resolved photoemission spectroscopy (ARPES) study is reported on a Mott insulator NiGa2S4 in which Ni2+ (S=1) ions form a triangular lattice and the Ni spins do not order even in its ground state. The first ARPES study on the two-dimensional spin-disordered system shows that low-energy hole dynamics at high temperatures is characterized by wave vectors Q(E) which are different from wave vectors Q(M) dominating low-energy spin excitations at low temperatures. The unexpected difference between Q(E) and Q(M) is deeply related to charge fluctuation across the Mott gap in the frustrated lattice and is a key issue to understand the spin-disordered ground states in Mott insulators.

Solvent-resistant nanofiltration for product purification and catalyst recovery in click chemistry reactions.

The quickly developing field of "click" chemistry would undoubtedly benefit from the availability of an easy and efficient technology for product purification to reduce the potential health risks associated with the presence of copper in the final product. Therefore, solvent-resistant nanofiltration (SRNF) membranes have been developed to selectively separate "clicked" polymers from the copper catalyst and solvent. By using these solvent-stable cross-linked polyimide membranes in diafiltration, up to 98 % of the initially present copper could be removed through the membrane together with the DMF solvent, the polymer product being almost completely retained. This paper also presents the first SRNF application in which the catalyst permeates through the membrane and the reaction product is retained.

A "clickable" titanium surface platform.

A straightforward functionalization of a titanium surface using "click" chemistry is reported. A "clickable" titanium surface platform was prepared by the immobilization of an azide-functionalized electroactive catechol anchor and was subsequently derivatized with an electroactive or fluorinated probe via the CuAAC (copper-catalyzed azide-alkyne cycloaddition) reaction. The course of the reaction was investigated by contact angle, XPS, and electrochemical measurements.

Star-Shaped Polyacrylates: Highly Functionalized Architectures via CuAAC Click Conjugation.

Well-defined functional star-shaped polymer structures with up to 29 arms have been successfully synthesized by the combination of atom transfer radical polymerization (ATRP) and click chemistry. First, azide end-functionalized poly(isobornyl acrylate) (PiBA) star-shaped polymers were prepared by successive ATRP and bromine substitution. Subsequently, alkyne end-functionalized molecules and polymers were introduced onto the star-shaped PiBA bearing pendant azide moieties by copper-catalyzed azide-alkyne cycloaddition (CuAAC). The possibilities and limits for the CuAAC on such highly branched polyacrylates are described.