Activation of the Catalytic Activity of Thrombin for Fibrin Formation by Ultrasound

The regulation of enzyme activity is a method to control biological function. We report two systems enabling the ultrasound-induced activation of thrombin, which is vital for secondary hemostasis. First, we designed polyaptamers, which can specifically bind to thrombin, inhibiting its catalytic activity. With ultrasound generating inertial cavitation and therapeutic medical focused ultrasound, the interactions between polyaptamer and enzyme are cleaved, restoring the activity to catalyze the conversion of fibrinogen into fibrin. Second, we used split aptamers conjugated to the surface of gold nanoparticles (AuNPs). In the presence of thrombin, these assemble into an aptamer tertiary structure, induce AuNP aggregation, and deactivate the enzyme. By ultrasonication, the AuNP aggregates reversibly disassemble releasing and activating the enzyme. We envision that this approach will be a blueprint to control the function of other proteins by mechanical stimuli in the sonogenetics field.

Multicolor Mechanofluorophores for the Quantitative Detection of Covalent Bond Scission in Polymers

The fracture of polymer materials is a multiscale process starting with the scission of a single molecular bond advancing to a site of failure within the bulk. Quantifying the bonds broken during this process remains a big challenge yet would help to understand the distribution and dissipation of macroscopic mechanical energy. We here show the design and synthesis of fluorogenic molecular optical force probes (mechanofluorophores) covering the entire visible spectrum in both absorption and emission. Their dual fluorescent character allows to track non-broken and broken bonds in dissolved and bulk polymers by fluorescence spectroscopy and microscopy. Importantly, we develop an approach to determine the absolute number and relative fraction of intact and cleaved bonds with high local resolution. We anticipate that our mechanofluorophores in combination with our quantification methodology will allow to quantitatively describe fracture processes in materials ranging from soft hydrogels to high-performance polymers.

Light-Activation of DNA-Methyltransferases

5-Methylcytosine (5mC), the central epigenetic mark of mammalian DNA, plays fundamental roles in chromatin regulation. 5mC is written onto genomes by DNA methyltransferases (DNMT), and perturbation of this process is an early event in carcinogenesis. However, studying 5mC functions is limited by the inability to control individual DNMTs with spatiotemporal resolution in vivo. We report light-control of DNMT catalysis by genetically encoding a photocaged cysteine as a catalytic residue. This enables translation of inactive DNMTs, their rapid activation by light-decaging, and subsequent monitoring of de novo DNA methylation. We provide insights into how cancer-related DNMT mutations alter de novo methylation in vivo, and demonstrate local and tuneable cytosine methylation by light-controlled DNMTs fused to a programmable transcription activator-like effector domain targeting pericentromeric satellite-3 DNA. We further study early events of transcriptome alterations upon DNMT-catalyzed cytosine methylation. Our study sets a basis to dissect the order and kinetics of diverse chromatin-associated events triggered by normal and aberrant DNA methylation.

Mechanochemical Release of Non-Covalently Bound Guests from a Polymer-Decorated Supramolecular Cage

Supramolecular coordination cages show a wide range of useful properties including, but not limited to, complex molecular machine-like operations, confined space catalysis, and rich host-guest chemistries. Here we report the uptake and release of non-covalently encapsulated, pharmaceutically-active cargo from an octahedral Pd cage bearing polymer chains on each vertex. Six poly(ethylene glycol)-decorated bipyridine ligands are used to assemble an octahedral PdII6 (TPT)4 cage. The supramolecular container encapsulates progesterone and ibuprofen within its hydrophobic nanocavity and is activated by shear force produced by ultrasonication in aqueous solution entailing complete cargo release upon rupture, as shown by NMR and GPC analyses.

5-Hydroxymethyl-, 5-Formyl- and 5-Carboxydeoxycytidines as Oxidative Lesions and Epigenetic Marks

The four non-canonical nucleotides in the human genome 5-methyl-, 5-hydroxymethyl-, 5-formyl- and 5-carboxydeoxycytidine (mdC, hmdC, fdC and cadC) form a second layer of epigenetic information that contributes to the regulation of gene expression. Formation of the oxidized nucleotides hmdC, fdC and cadC requires oxidation of mdC by ten-eleven translocation (Tet) enzymes that require oxygen, Fe(II) and α-ketoglutarate as cosubstrates. Although these oxidized forms of mdC are widespread in mammalian genomes, experimental evidence for their presence in fungi and plants is ambiguous. This vagueness is caused by the fact that these oxidized mdC derivatives are also formed as oxidative lesions, resulting in unclear basal levels that are likely to have no epigenetic function. Here, we report the xdC levels in the fungus Amanita muscaria in comparison to murine embryonic stem cells (mESCs), HEK cells and induced pluripotent stem cells (iPSCs), to obtain information about the basal levels of hmdC, fdC and cadC as DNA lesions in the genome.

Pyrene-Based "Turn-Off" Probe with Broad Detection Range for Cu2+ , Pb2+ and Hg2+ Ions

Detection of metals in different environments with high selectivity and specificity is one of the prerequisites of the fight against environmental pollution with these elements. Pyrenes are well suited for the fluorescence sensing in different media. The applied sensing principle typically relies on the formation of intra- and intermolecular excimers, which is however limiting the sensitivity range due to masking of e. g. quenching effects by the excimer emission. Herein we report a highly selective, structurally rigid chemical sensor based on the monomer fluorescence of pyrene moieties bearing triazole groups. This sensor can quantitatively detect Cu2+ , Pb2+ and Hg2+ in organic solvents over a broad concentrations range, even in the presence of ubiquitous ions such as Na+ , K+ , Ca2+ and Mg2+ . The strongly emissive sensor's fluorescence with a long lifetime of 165 ns is quenched by a 1 : 1 complex formation upon addition of metal ions in acetonitrile. Upon addition of a tenfold excess of the metal ion to the sensor, agglomerates with a diameter of about 3 nm are formed. Due to complex interactions in the system, conventional linear correlations are not observed for all concentrations. Therefore, a critical comparison between the conventional Job plot interpretation, the method of Benesi-Hildebrand, and a non-linear fit is presented. The reported system enables the specific and robust sensing of medically and environmentally relevant ions in the health-relevant nM range and could be used e. g. for the monitoring of the respective ions in waste streams.

Impact of Segmented Magnetization on the Flagellar Propulsion of Sperm-Templated Microrobots

Technical design features for improving the way a passive elastic filament produces propulsive thrust can be understood by analyzing the deformation of sperm-templated microrobots with segmented magnetization. Magnetic nanoparticles are electrostatically self-assembled on bovine sperm cells with nonuniform surface charge, producing different categories of sperm-templated microrobots. Depending on the amount and location of the nanoparticles on each cellular segment, magnetoelastic and viscous forces determine the wave pattern of each category during flagellar motion. Passively propagating waves are induced along the length of these microrobots using external rotating magnetic fields and the resultant wave patterns are measured. The response of the microrobots to the external field reveals distinct flow fields, propulsive thrust, and frequency responses during flagellar propulsion. This work allows predictions for optimizing the design and propulsion of flexible magnetic microrobots with segmented magnetization.

Programmed Molecular Assembly of Abrupt Crystalline Organic/Organic Heterointerfaces Yielding Metal-Organic Framework Diodes with Large On-Off Ratios

Structurally well-defined, crystalline organic/organic heterojunctions between C60- and anthracene-based semiconductors are realized via layer-by-layer deposition of metal-organic framework, MOF, thin films. As demonstrated by X-ray diffraction, perfect epitaxy is achieved by adjusting the lattice constants of the two different MOFs. Deposition of top electrodes allows to fabricate p-n as well as n-p devices. Measurements of the electrical properties reveal the presence of high-performance diodes, with a current on/off ratio of up to 6 orders of magnitude and an ideality factor close to unity. The crystalline nature of the abrupt organic/organic heterojunction provides the basis for a rational, simulation-based optimization and tailoring of such organic semiconductor interfaces.

A Modular Fluorescent Probe for Viscosity and Polarity Sensing in DNA Hybrid Mesostructures

There exists a critical need in biomedical molecular imaging and diagnostics for molecular sensors that report on slight changes to their local microenvironment with high spatial fidelity. Herein, a modular fluorescent probe, termed StyPy, is rationally designed which features i) an enormous and tunable Stokes shift based on twisted intramolecular charge transfer (TICT) processes with no overlap, a broad emission in the far-red/near-infrared (NIR) region of light and extraordinary quantum yields of fluorescence, ii) a modular applicability via facile para-fluoro-thiol reaction (PFTR), and iii) a polarity- and viscosity-dependent emission. This renders StyPy as a particularly promising molecular sensor. Based on the thorough characterization on the molecular level, StyPy reports on the viscosity change in all-DNA microspheres and indicates the hydrophilic and hydrophobic compartments of hybrid DNA-based mesostructures consisting of latex beads embedded in DNA microspheres. Moreover, the enormous Stokes shift of StyPy enables one to detect multiple fluorophores, while using only a single laser line for excitation in DNA protocells. The authors anticipate that the presented results for multiplexing information are of direct importance for advanced imaging in complex soft matter and biological systems.

Wavelength-Gated Adaptation of Hydrogel Properties via Photo-Dynamic Multivalency in Associative Star Polymers

Responsive materials, such as switchable hydrogels, have been largely engineered for maximum changes between two states. In contrast, adaptive systems target distinct functional plateaus between these maxima. Here, we demonstrate how the photostationary state (PSS) of an E/Z-arylazopyrazole photoswitch can be tuned by the incident wavelength across a wide color spectrum, and how this behavior can be exploited to engineer the photo-dynamic mechanical properties of hydrogels based on multivalent photoswitchable interactions. We show that these hydrogels adapt to the wavelength-dependent PSS and the number of arylazopyrazole units by programmable relationships. Hence, our material design enables the facile adjustment of the mechanical properties without laborious synthetic efforts. The concept goes beyond the classical switching from state A to B, and demonstrates pathways for a truly wavelength-gated adaptation of hydrogel properties potentially useful to engineer cell fate or in soft robotics.

A context analysis of bobbing and fin-flicking in a small marine benthic fish

Most antipredator strategies increase survival of individuals by signaling to predators, by reducing the chances of being recognized as prey, or by bewildering a predator's perception. In fish, bobbing and fin-flicking are commonly considered as pursuit-deterrent behaviors that signal a predator that it has been detected and thus lost its surprise-attack advantage. Yet, very few studies assessed whether such behavioral traits are restricted to the visual presence of a predator. In this study, we used the yellow black-headed triplefin Tripterygion delaisi to investigate the association between these behaviors and the visual exposure to (a) a black scorpionfish predator (Scorpaena porcus), (b) a stone of a size similar to that of S. porcus, (c) a conspecific, and (d) a harmless heterospecific combtooth blenny (Parablennius sanguinolentus). We used a laboratory-controlled experiment with freshly caught fish designed to test for differences in visual cues only. Distance kept by the focal fish to each stimulus and frequency of bobbing and fin-flicking were recorded. Triplefins kept greater distance from the stimulus compartment when a scorpionfish predator was visible. Bobbing was more frequent in the visual presence of a scorpionfish, but also shown toward the other stimuli. However, fin flicks were equally abundant across all stimuli. Both behaviors decreased in frequency over time suggesting that triplefin become gradually comfortable in a nonchanging new environment. We discuss why bobbing and fin-flicking are not exclusive pursuit-deterrent behaviors in this species, and propose additional nonexclusive functions such as enhancing depth perception by parallax motion (bobbing) or signaling vigilance (fin-flicking).

Controlling Optical and Catalytic Activity of Genetically Engineered Proteins by Ultrasound

Ultrasound (US) produces cavitation-induced mechanical forces stretching and breaking polymer chains in solution. This type of polymer mechanochemistry is widely used for synthetic polymers, but not biomacromolecules, even though US is biocompatible and commonly used for medical therapy as well as in vivo imaging. The ability to control protein activity by US would thus be a major stepping-stone for these disciplines. Here, we provide the first examples of selective protein activation and deactivation by means of US. Using GFP as a model system, we engineer US sensitivity into proteins by design. The incorporation of long and highly charged domains enables the efficient transfer of force to the protein structure. We then use this principle to activate the catalytic activity of trypsin by inducing the release of its inhibitor. We expect that this concept to switch "on" and "off" protein activity by US will serve as a blueprint to remotely control other bioactive molecules.

Prebiotic Nucleoside Synthesis: The Selectivity of Simplicity

Ever since the discovery of nucleic acids 150 years ago,[1] major achievements have been made in understanding and decrypting the fascinating scientific questions of the genetic code.[2] However, the most fundamental question about the origin and the evolution of the genetic code remains a mystery. How did nature manage to build up such intriguingly complex molecules able to encode structure and function from simple building blocks? What conditions were required? How could the precursors survive the unhostile environment of early Earth? Over the past decades, promising synthetic concepts were proposed providing clarity in the field of prebiotic nucleic acid research. In this Minireview, we show the current status and various approaches to answer these fascinating questions.

Prebiotically Plausible Organocatalysts Enabling a Selective Photoredox α-Alkylation of Aldehydes on the Early Earth

Organocatalysis is a powerful approach to extend and (enantio-) selectively modify molecular structures. Adapting this concept to the Early Earth scenario offers a promising solution to explain their evolution into a complex homochiral world. Herein, we present a class of imidazolidine-4-thione organocatalysts, easily accessible from simple molecules available on an Early Earth under highly plausible prebiotic reaction conditions. These imidazolidine-4-thiones are readily formed from mixtures of aldehydes or ketones in presence of ammonia, cyanides and hydrogen sulfide in high selectivity and distinct preference for individual compounds of the resulting catalyst library. These organocatalysts enable the enantioselective α-alkylation of aldehydes under prebiotic conditions and show activities that correlate with the selectivity of their formation. Furthermore, the crystallization of single catalysts as conglomerates opens the pathway for symmetry breaking.

Amphiphilic Polyphenylene Dendron Conjugates for Surface Remodeling of Adenovirus 5

Amphiphilic surface groups play an important role in many biological processes. The synthesis of amphiphilic polyphenylene dendrimer branches (dendrons), providing alternating hydrophilic and lipophilic surface groups and one reactive ethynyl group at the core is reported. The amphiphilic surface groups serve as biorecognition units that bind to the surface of adenovirus 5 (Ad5), which is a common vector in gene therapy. The Ad5/dendron complexes showed high gene transduction efficiencies in coxsackie-adenovirus receptor (CAR)-negative cells. Moreover, the dendrons offer incorporation of new functions at the dendron core by in situ post-modifications, even when bound to the Ad5 surface. Surfaces coated with these dendrons were analyzed for their blood-protein binding capacity, which is essential to predict their performance in the blood stream. A new platform for introducing bioactive groups to the Ad5 surface without chemically modifying the virus particles is provided.

Cyclotriphosphate: A Brief History, Recent Developments, and Perspectives in Synthesis

There has been a recent upsurge in the study and application of approaches utilizing cyclotriphosphate 1 (cyclo-TP, also known as trimetaphosphate, TMP) and/or proceeding through its analogues in synthetic chemistry to access modified oligo- and polyphosphates. This is especially useful in the area of chemical nucleotide synthesis, but by no means restricted to it. Enabled by new high yielding and easy-to-implement methodologies, these approaches promise to open up an area of research that has previously been underappreciated. Additionally, refinements of concepts of prebiotic phosphorylation chemistry have been disclosed that ultimately rely on cyclo-TP 1 as a precursor, placing it as a potentially central compound in the emergence of life. Given the importance of such concepts for our understanding of prebiotic chemistry in combination with the need to readily access modified polyphosphates for structural and biological studies, this paper will discuss selected recent developments in the field of cyclo-TP chemistry, briefly touch on ultraphosphate chemistry, and highlight areas in which further developments can be expected.

Hybrid Plasmonic-Aerogel Materials as Optical Superheaters with Engineered Resonances

Solar radiation is a versatile source of energy, convertible to different forms of power. A direct path to exploit it is the generation of heat, for applications including passive building heating, but it can also drive secondary energy-conversion steps. We present a novel concept for a hybrid material which is both strongly photo-absorbing and with superior characteristics for the insulation of heat. The combination of that two properties is rather unique, and make this material an optical superheater. To realize such a material, we are combining plasmonic nanoheaters with alumina aerogel. The aerogel has the double function of providing structural support for plasmonic nanocrystals, which serve as nanoheaters, and reducing the diffusion rate of the heat generated by them, resulting in large local temperature increases under a relatively low radiation intensity. This work includes theoretical discussion on the physical mechanisms impacting the system's balanced thermal equilibrium.

Nucleic Acid Catalysis under Potential Prebiotic Conditions

Catalysis by nucleic acids is indispensable for extant cellular life, and it is widely accepted that nucleic acid enzymes were crucial for the emergence of primitive life 3.5-4 billion years ago. However, geochemical conditions on early Earth must have differed greatly from the constant internal milieus of today's cells. In order to explore plausible scenarios for early molecular evolution, it is therefore essential to understand how different physicochemical parameters, such as temperature, pH, and ionic composition, influence nucleic acid catalysis and to explore to what extent nucleic acid enzymes can adapt to non-physiological conditions. In this article, we give an overview of the research on catalysis of nucleic acids, in particular catalytic RNAs (ribozymes) and DNAs (deoxyribozymes), under extreme and/or unusual conditions that may relate to prebiotic environments.

Tunable Thermoelastic Anisotropy in Hybrid Bragg Stacks with Extreme Polymer Confinement

Controlling thermomechanical anisotropy is important for emerging heat management applications such as thermal interface and electronic packaging materials. Whereas many studies report on thermal transport in anisotropic nanocomposite materials, a fundamental understanding of the interplay between mechanical and thermal properties is missing, due to the lack of measurements of direction-dependent mechanical properties. In this work, exceptionally coherent and transparent hybrid Bragg stacks made of strictly alternating mica-type nanosheets (synthetic hectorite) and polymer layers (polyvinylpyrrolidone) were fabricated at large scale. Distinct from ordinary nanocomposites, these stacks display long-range periodicity, which is tunable down to angstrom precision. A large thermal transport anisotropy (up to 38) is consequently observed, with the high in-plane thermal conductivity (up to 5.7 W m-1  K-1 ) exhibiting an effective medium behavior. The unique hybrid material combined with advanced characterization techniques allows correlating the full elastic tensors to the direction-dependent thermal conductivities. We, therefore, provide a first analysis on how the direction-dependent Young's and shear moduli influence the flow of heat.

Machine learning with the hierarchy-of-hypotheses (HoH) approach discovers novel pattern in studies on biological invasions

Research synthesis on simple yet general hypotheses and ideas is challenging in scientific disciplines studying highly context-dependent systems such as medical, social, and biological sciences. This study shows that machine learning, equation-free statistical modeling of artificial intelligence, is a promising synthesis tool for discovering novel patterns and the source of controversy in a general hypothesis. We apply a decision tree algorithm, assuming that evidence from various contexts can be adequately integrated in a hierarchically nested structure. As a case study, we analyzed 163 articles that studied a prominent hypothesis in invasion biology, the enemy release hypothesis. We explored if any of the nine attributes that classify each study can differentiate conclusions as classification problem. Results corroborated that machine learning can be useful for research synthesis, as the algorithm could detect patterns that had been already focused in previous narrative reviews. Compared with the previous synthesis study that assessed the same evidence collection based on experts' judgement, the algorithm has newly proposed that the studies focusing on Asian regions mostly supported the hypothesis, suggesting that more detailed investigations in these regions can enhance our understanding of the hypothesis. We suggest that machine learning algorithms can be a promising synthesis tool especially where studies (a) reformulate a general hypothesis from different perspectives, (b) use different methods or variables, or (c) report insufficient information for conducting meta-analyses.

Reactivity of ZrO(MFP) and ZrO(RP) Nanoparticles with LnCl3 for Solvatochromic Luminescence Modification and pH-Dependent Optical Sensing

The luminescence of the inorganic-organic hybrid nanoparticles ZrO(MFP) (MFP=methylfluorescein phosphate) and ZrO(RP) (RP=resorufin phosphate) was modified by addition of different rare earth halides LnCl3 . The resulting composite materials form dispersible nanoparticles that exhibit modified nanoparticle fluorescence depending on the rare earth ion. The resulting chromaticity of the luminescence is further variable by the employment of different solvents for ZrO(MFP)-based composite systems. The strong solvatochromic effect of the MFP chromophore leads to different luminescence chromaticities of the composite materials between green, yellow, and blue in THF, toluene, and dichloromethane, respectively. The luminescence of ZrO(RP)-based composite particles can be modified between the red and blue spectral regions in dependence on the applied reaction temperature. Beside a luminescence shift that is derived from nanoparticle modification by LnCl3 , a strong turn-on effect of ZrO(RP) particles results after contact with different Brønsted acids and bases in combination with a respective chromaticity shift. Both effects enable the potential employment of such particles as highly sensitive optical pH sensors.

A Click-Chemistry-Based Enrichable Crosslinker for Structural and Protein Interaction Analysis by Mass Spectrometry

Mass spectrometry is the method of choice for the characterisation of proteomes. Most proteins operate in protein complexes, in which their close association modulates their function. However, with standard MS analysis, information on protein–protein interactions is lost and no structural information is retained. To gain structural and interactome data, new crosslinking reagents are needed that freeze inter‐ and intramolecular interactions. Herein, the development of a new reagent, which has several features that enable highly sensitive crosslinking MS, is reported. The reagent enables enrichment of crosslinked peptides from the majority of background peptides to facilitate efficient detection of low‐abundant crosslinked peptides. Due to the special cleavable properties, the reagent can be used for MS² and potentially for MS³ experiments. Thus, the new crosslinking reagent, in combination with high‐end MS, should enable sensitive analysis of interactomes, which will help researchers to obtain important insights into cellular states in health and diseases.

Development and feasibility of the computerized Turkish edition of the Composite International Diagnostic Interview [DIA-X/CIDI version 2.8(TR)]

The Composite International Diagnostic Interview (CIDI), which has been widely applied in epidemiological research, is a standardized, clinically structured interview that enables the diagnosis of mental disorders based on DSM and ICD criteria. The computerized DIA-X CIDI Version 2.8 investigated in this study is an adaptation of the German DIA-X/Munich CIDI, which was translated in a multi-step process into Turkish and used to survey the prevalence of mental disorders in individuals with Turkish migration backgrounds in Germany (N = 662). The bilingual lay interviewers were intensively trained and supervised during the data collection. The survey was accompanied by further quality measures, including editing and documenting. To investigate the instrument's feasibility, quality criteria were used based on the following data sources: (1) socio-demographic sample characteristics; (2) interviewer assessments and (3) quantitative measures (interview duration, non-response items, error items). The results indicated that quality differences between the German and Turkish DIA-X/CIDI are associated with age, educational level and socio-economic status and not with the CIDI version itself. In short, the Turkish DIA-X/CIDI Version 2.8 has comparatively good quality and feasibility relative to its German counterpart.

Permian scorpions from the Petrified Forest of Chemnitz, Germany

BACKGROUND

Paleozoic scorpions (Arachnida: Scorpiones) have been widely documented from the Carboniferous Period; which hosts a remarkable assemblage of more than sixty species including both putative stem- and crown-group fossils. By contrast the succeeding Permian Period is almost completely devoid of records, which are currently restricted to a trace fossil from the early Permian of New Mexico, USA and some limb fragments from the late Permian of the Vologda Region, Russia.

RESULTS

?Opsieobuthus tungeri sp. nov. from the Petrified Forest of Chemnitz, Germany represents the first complete body fossils of scorpions from the Permian. Explosive volcanism preserved these remarkable specimens in situ as part of the palaeosol horizon and bedrock of the Petrified Forest, immediately beneath the Zeisigwald tuff horizon. This dates to the early Permian (Sakmarian) or ca. 291 Ma. Intriguingly, the specimens were obtained from a palaeosol horizon with a compacted network of different-sized woody roots and thus have been preserved in situ in their likely life position, even within their original burrows. Differences in the structure of the comb-like pectines in the two fossils offer evidence for sexual dimorphism, and permit further inferences about the ecology and perhaps even the reproductive biology of these animals.

CONCLUSIONS

As putative members of a Coal Measures genus, these fossils suggest that at least some Carboniferous scorpion lineages extended their range further into the Permian. This contributes towards a picture of scorpion evolution in which both basal and derived (orthostern) forms coexisted for quite some time; probably from the end of the Carboniferous through to at least the mid Triassic.