Bioorthogonal tools enable cell-type-specific proteomics, a prerequisite to understanding biological processes in multicellular organisms. Here we report two engineered aminoacyl-tRNA synthetases for mammalian bioorthogonal labeling: a tyrosyl ( ScTyrY43G) and a phenylalanyl ( MmPheT413G) tRNA synthetase that incorporate azide-bearing noncanonical amino acids specifically into the nascent proteomes of host cells. Azide-labeled proteins are chemoselectively tagged via azide-alkyne cycloadditions with fluorophores for imaging or affinity resins for mass spectrometric characterization. Both mutant synthetases label human, hamster, and mouse cell line proteins and selectively activate their azido-bearing amino acids over 10-fold above the canonical. ScTyrY43G and MmPheT413G label overlapping but distinct proteomes in human cell lines, with broader proteome coverage upon their coexpression. In mice, ScTyrY43G and MmPheT413G label the melanoma tumor proteome and plasma secretome. This work furnishes new tools for mammalian residue-specific bioorthogonal chemistry, and enables more robust and comprehensive cell-type-specific proteomics in live mammals.

Many signaling proteins consist of globular domains connected by flexible linkers that allow for substantial domain motion. Because these domains often serve as complementary functional modules, the possibility of functionally important domain motions arises. To explore this possibility, we require knowledge of the ensemble of protein conformations sampled by interdomain motion. Measurements of NMR residual dipolar couplings (RDCs) of backbone HN bonds offer a per-residue characterization of interdomain dynamics, as the couplings are sensitive to domain orientation. A challenge in reaching this potential is the need to interpret the RDCs as averages over dynamic ensembles of domain conformations. Here, we address this challenge by introducing an efficient protocol for generating conformational ensembles appropriate for flexible, multi-domain proteins. The protocol uses map-restrained self-guided Langevin dynamics simulations to promote collective, interdomain motion while restraining the internal domain motion to near rigidity. Critically, the simulations retain an all-atom description for facile inclusion of site-specific NMR RDC restraints. The result is the rapid generation of conformational ensembles consistent with the RDC data. We illustrate this protocol on human Pin1, a two-domain peptidyl-prolyl isomerase relevant for cancer and Alzheimer's disease. The results include the ensemble of domain orientations sampled by Pin1, as well as those of a dysfunctional variant, I28A-Pin1. The differences between the ensembles corroborate our previous spin relaxation results that showed weakened interdomain contact in the I28A variant relative to wild type. Our protocol extends our abilities to explore the functional significance of protein domain motions.

In the current study, twenty-two compounds based upon 3-hydroxy-3-(2-oxo-2-phenylethyl)indolin-2-one nucleus were designed, synthesized and in vitro evaluated for HIV-1 RT inhibition and anti-HIV-1 activity. Compounds 3d, 5c and 5e demonstrated encouraging potency against RT enzyme as well as HIV-1 in low micromolar to nanomolar concentration with good to excellent safety index. Structure activity relationship studies revealed that halogens such as bromo or chloro at 5th the position of oxindole ring remarkably enhanced the potency against RT. Moreover, methoxy or chloro groups at the ortho position of phenyl ring also significantly favored RT inhibition activity. Seven compounds (3b, 3c, 3d, 3e, 5b, 5c and 5e) with better anti-HIV-1 potency were tested against the mutant HIV-1K103N strain. The putative binding mode, as well as interaction patterns of the best active compound 5c with wild HIV-1 RT were studied via docking studies.

Although the dicarboxylic acid has been reported to react with nitrate for aged internally mixed aerosols in atmosphere, the quantitative nitrate depletion dependent upon composition in particles is still not well constrained. The chemical composition evolutions for malonic acid/sodium nitrate (MA/SN), malonic acid/magnesium nitrate (MA/MN) and malonic acid/calcium nitrate (MA/CN) particles with the organic to inorganic molar ratio (OIR) of 1:1 are investigated by vacuum Fourier transform infrared spectroscopy (FTIR). Upon dehydration, the intensity of the asymmetric stretching mode of COO- group (νas-COO-) increases, accompanying the decrease in OH feather band and COOH band and NO3- band. These band changes suggest malonate salts formation and HNO3 release. The quantitative NO3- depletion data shows that the reactivity of MA-MN is most and that of MA-SN is least. Analysis of the stretching mode of COO- indicates the different bond type between metal cation and carboxylate anion. In addition, water content in particles decreases at the constant RH, implying water loss with the chemical reaction. When the RH changes very quickly, water uptake delay during the humidification process reveals that water mass transport is limited below 37% RH.

Previous studies reported that exposure to environmentally relevant concentrations of TDCIPP significantly decreased the number of cumulative eggs in zebrafish, but effects on the quantity of eggs and sperms remained unknown. Therefore, in this study, effects of TDCIPP on yolk diameter, surface morphology of eggs, sperm density and total motility were evaluated. First generation (F0) zebrafish larvae (Danio rerio) were exposed to 0, 50, 500 or 5000 ng/L tris(1,3-dichloro-2-propyl) phosphate (TDCIPP) from 14 days post fertilization (dpf) to 120 dpf. The F0 generation of zebrafish were paired and F1 generation of embryos were collected and continuously exposed to the same concentrations of TDCIPP until 150 dpf. TDCIPP bioconcentration in the whole body as well as effects on survival and fecundity were evaluated in F1 generation. Exposure to TDCIPP resulted in an accumulation of the chemical and decreased survival of F1 generation of zebrafish. TDCIPP decreased cumulative production and changed surface morphology of eggs in females. In males, TDCIPP decreased total motility of sperm but did not affect sperm density. These effects on quality of egg and sperm might be responsible for the decreased hatching rates observed in cross mating experiments. Furthermore, TDCIPP exposure resulted in down-regulated gene expression related to gonadal development and maturation of germ cells in females or/and males, and the down-regulation was correlated to decreased fecundity. Taken together, the results suggested that exposure to TDCIPP could decrease the quantity of eggs and sperms by down-regulating the expression of genes related to gonadal development and maturation of germ cells in zebrafish.

For the purpose of producing carbons with developed mesoporosity, a wood biochar was thermally treated at 600-800 °C in the air/nitrogen atmosphere. The mesopore development was observed when the air flux increased to 50-90 mL/min, and the carbon product having high mesopore surface area (316 m2/g) and mesopore pore volume (0.284 cm3/g) was produced at the treatment temperature of 700 °C. The mesopores were developed mainly in the temperature holding stage of thermal treatment, with size mainly ranged from 20 to 60 Å. The carbons' adsorption to the antibiotic tetracycline was enhanced by 5.5-9.2 folds when the air/nitrogen mixture was used instead of nitrogen atmosphere in thermal treatment, and the enhanced adsorption is positively related to the mesopore development. In general, this research provides a facile way to produce carbons with developed mesoporosity, so as to improve their adsorption to bulky organic molecules.

A novel Pd/CNTs-Ni foam composite catalyst was developed for catalytic hydrodechlorination of chlorophenols by using CNTs-Ni foam as support. Characterizations including FESEM, TEM/HRTEM, HAADF-STEM and element mapping revel that the composite catalyst with 2 wt.% Pd loading possesses high porous micro-network structure and high dispersed active Pd nanoparticles (5.81 nm) on CNTs surface. The HDC of chlorophenols over Pd/CNTs-Ni foam composite catalyst has been studied in continuous-flow packed bed reactor. This packed bed reactor system with Pd/CNTs-Ni foam composite catalyst, presented the very short reaction cycle (22-74 s), high efficiency (dechlorination > 99.95%) and excellent catalytic stability during HDC in continuous-flow, making it to be a promising candidate for the HDC of wastewater containing highly toxic chlorinated organic pollutants and other Pd catalyzed hydrogenation reactions.

The degradation of organophosphorous nerve agents is of primary concern due to the severe toxicity of these agents. Based on the active center of organophosphorus hydrolase (OPH), a bimetallic nuclear ligand, (5-vinyl-1,3-phenylene)bis(di(1H-imidazol-2-yl) methanol) (VPIM), was designed and synthesized, which contains four imidazole groups to mimic the four histidines at OPH active center. By grafting VPIM on graphene oxide (GO) surface via polymerization, the VPIM-polymer beads@GO was produced. The obtained OPH mimics has an impressive activity in dephosphorylation reactions (turnover frequency (TOF) towards paraoxon: 2.3 s-1). The synergistic catalytic effect of the bimetallic Zn2+ nuclear center and carboxyl groups on surface of GO possibly contributes to the high hydrolysis on organophosphate substrate. Thus, a biomimetic catalyst for efficient degradation of some organophosphorous nerve agent simulants, such as paraoxon and chlorpyrifos, was prepared by constructing catalytic active sites. The proposed mechanism and general synthetic strategy open new avenues for the engineering of functional GOs for biomimetic catalysts.

Herein, we constructed an ultrasensitive electrochemiluminescence (ECL) biosensor for detecting microRNA-21 (miR-21) based on in-situ generation of copper nanoclusters (Cu NCs) as luminophore and titanium dioxide (TiO2) as coreaction accelerator. First, numerous AT-rich double-stranded DNA (dsDNA) was produced from the conversion of a small amount of target miR-21 via the combination of exonuclease III (Exo III)-assisted amplification and hybridization chain reaction (HCR), which could reduce the aggregation-caused self-etching effect of Cu NCs and improve the emitting of Cu NCs. Simultaneously, the introduction of TiO2 in the sensing interface not just acted as the immobilizer of dsDNA-stabilized Cu NCs, more than acted as the coreaction accelerator to accelerate the reduction of the coreaction reagent (S2O82-) for significantly enhancing the ECL efficiency of Cu NCs. The biosensor showed an excellent linear relationship in the concentration range from 100 aM to 100 pM with the detection limit of 19.05 aM Impressively, the strategy not only opened up a novel and efficient preparation method for the Cu NCs, but expanded the application of Cu NCs in ultrasensitive biodetection owing to the addition of coreaction accelerator.

A series of sulfonated hydroxypropyl guar gum (SHG) samples with different degrees of substitution (DSs) were prepared, and the SHG solution and SHG fracturing fluid were prepared and analyzed. The SHG aqueous solutions with different DSs all exhibit shear thinning behavior, which is well correlated with the Ostwald-deWaele model. Owing to the electrostatic repulsion of SHG molecular chains, SHG solutions with a higher DS will exhibit weaker thixotropic performance and strong anti-salinity ability. In addition, the SHG fracturing fluids, which were formed by interactions between SHG and organic zirconium, exhibit good temperature- and shear-resistant properties, proppant suspension properties, and salt tolerance. Furthermore, SHG gel-breaking fluids show low interfacial and surface tensions, with low residue content and small core permeability damage. These results provide useful indicators for the applications of SHG in the oil field industry.

Star-shaped poly(2-(dimethylamino)ethyl methacrylate) based on β-cyclodextrin (β-CD-(PDMAEMA)7) was synthesized by means of atomic transfer radical polymerization (ATRP). Dual pH-sensitive supramolecular micelles were formed from β-CD-(PDMAEMA)7 and benzimidazole modified poly(ε-caprolactone) (BM-PCL) through the host-guest interactions between β-CD and benzimidazole. The supramolecular micelles have regular spherical structure with hydrophobic β-CD/BM-PCL as the core and pH-sensitive PDMAEMA as the shell. The hydrophobic PCL as well as the hydrophobic cavity of β-CD can efficiently encapsulate doxorubicin (DOX) with the drug-loading content and entrapment efficiency up to 40% and 86%. The drug release from micelles accelerated when the pH decreased from 7.0 to 2.0 and the temperature increased from 25 °C to 45 °C. MTT assay showed that drug loaded supramolecular micelles exhibited excellent anti-cancer activity than free DOX. These supramolecular micelles have promising potential applications as intelligent nanocarriers in drug delivery system.

Chronic social isolation causes severe psychological effects in humans, but their neural bases remain poorly understood. 2 weeks (but not 24 hr) of social isolation stress (SIS) caused multiple behavioral changes in mice and induced brain-wide upregulation of the neuropeptide tachykinin 2 (Tac2)/neurokinin B (NkB). Systemic administration of an Nk3R antagonist prevented virtually all of the behavioral effects of chronic SIS. Conversely, enhancing NkB expression and release phenocopied SIS in group-housed mice, promoting aggression and converting stimulus-locked defensive behaviors to persistent responses. Multiplexed analysis of Tac2/NkB function in multiple brain areas revealed dissociable, region-specific requirements for both the peptide and its receptor in different SIS-induced behavioral changes. Thus, Tac2 coordinates a pleiotropic brain state caused by SIS via a distributed mode of action. These data reveal the profound effects of prolonged social isolation on brain chemistry and function and suggest potential new therapeutic applications for Nk3R antagonists.

Glutamate-induced excitotoxicity plays a vital role in neurodegenerative diseases. Neuroprotection against excitotoxicity has been considered as an effective experimental approach for preventing and/or treating excitotoxicity-mediated diseases. In the present study, six new sesquiterpenoids (1-6) and 26 known compounds of this type (7-32) were isolated and characterized from the whole plants of Chloranthus anhuiensis. Chlorantolide A (1) is the first example of a 5,6- seco-germacrane-type sesquiterpenoid, while phacadinane E (2) is a rare 4,5- seco-cadinane-type sesquiterpenoid. The structures of the new compounds were determined by spectroscopic analysis and by calculations of electronic circular dichroism (ECD) spectra. Their neuroprotective effects in mediating glutamate-induced PC12 cell apoptosis were evaluated. Compound 26 exhibited potent neuroprotective activity with an EC50 value of 3.3 ± 0.9 μM. Using Hoechst 33258 staining, a caspase-3 activity assay, and Western blot analysis it was demonstrated that this compound reduces the apoptosis of PC12 cells through inhibition of caspase-3 activity, while activating the Akt signaling pathway.

Telomerase is an RNA-protein complex (RNP) that extends telomeric DNA at the 3' ends of chromosomes using its telomerase reverse transcriptase (TERT) and integral template-containing telomerase RNA (TER). Its activity is a critical determinant of human health, affecting aging, cancer, and stem cell renewal. Lack of atomic models of telomerase, particularly one with DNA bound, has limited our mechanistic understanding of telomeric DNA repeat synthesis. We report the 4.8 Å resolution cryoelectron microscopy structure of active Tetrahymena telomerase bound to telomeric DNA. The catalytic core is an intricately interlocked structure of TERT and TER, including a previously structurally uncharacterized TERT domain that interacts with the TEN domain to physically enclose TER and regulate activity. This complete structure of a telomerase catalytic core and its interactions with telomeric DNA from the template to telomere-interacting p50-TEB complex provides unanticipated insights into telomerase assembly and catalytic cycle and a new paradigm for a reverse transcriptase RNP.

Genome-wide association studies have identified risk loci associated with the development of inflammatory bowel disease, while epidemiological studies have emphasized that pathogenesis likely involves host interactions with environmental elements whose source and structure need to be defined. Here, we identify a class of compounds derived from dietary, microbial, and industrial sources that are characterized by the presence of a five-membered oxazole ring and induce CD1d-dependent intestinal inflammation. We observe that minimal oxazole structures modulate natural killer T cell-dependent inflammation by regulating lipid antigen presentation by CD1d on intestinal epithelial cells (IECs). CD1d-restricted production of interleukin 10 by IECs is limited through activity of the aryl hydrocarbon receptor (AhR) pathway in response to oxazole induction of tryptophan metabolites. As such, the depletion of the AhR in the intestinal epithelium abrogates oxazole-induced inflammation. In summary, we identify environmentally derived oxazoles as triggers of CD1d-dependent intestinal inflammatory responses that occur via activation of the AhR in the intestinal epithelium.

A new solid-state NMR study determines the high-resolution hetero-amyloid structure of the RIPK1-RIPK3 signaling complex that is involved in mediating necroptosis. The structure demonstrates specific formation of hetero-amyloids over homo-amyloids and the structural basis for a functional amyloid to act as a platform to recruit and activate downstream partners in intracellular signaling.

We provide a comprehensive analysis of transcription in real time by T7 RNA Polymerase (RNAP) using single-molecule fluorescence resonance energy transfer by monitoring the entire life history of transcription initiation, including stepwise RNA synthesis with near base-pair resolution, abortive cycling, and transition into elongation. Kinetically branching pathways were observed for abortive initiation with an RNAP either recycling on the same promoter or exchanging with another RNAP from solution. We detected fast and slow populations of RNAP in their transition into elongation, consistent with the efficient and delayed promoter release, respectively, observed in ensemble studies. Real-time monitoring of abortive cycling using three-probe analysis showed that the initiation events are stochastically branched into productive and failed transcription. The abortive products are generated primarily from initiation events that fail to progress to elongation, and a majority of the productive events transit to elongation without making abortive products.

A polymer fibril assembly can dictate the morphology framework, in forming a network structure, which is highly advantageous in bulk heterojunction (BHJ) organic solar cells (OSCs). A fundamental understanding of how to manipulate such a fibril assembly and its influence on the BHJ morphology and device performance is crucially important. Here, a series of donor-acceptor polymers, PBT1-O, PBT1-S, and PBT1-C, is used to systematically investigate the relationship between molecular structure, morphology, and photovoltaic performance. The subtle atom change in side chains is found to have profound effect on regulating electronic structure and self-assembly of conjugated polymers. Compared with PBT1-O and PBT1-S, PBT1-C-based OSCs show much higher photovoltaic performance with a record fill factor (FF) of 80.5%, due to the formation of optimal interpenetrating network morphology. Such a fibril network strategy is further extended to nonfullerene OSCs using a small-molecular acceptor, which shows a high efficiency of 12.7% and an FF of 78.5%. The results indicate the formation of well-defined fibrillar structure is a promising approach to achieving a favorable morphology in BHJ OSCs.

Within the liver a single Plasmodium parasite transforms into thousands of blood-infective forms to cause malaria. Here, we use RNA-sequencing to identify host genes that are upregulated upon Plasmodium berghei infection of hepatocytes with the hypothesis that host pathways are hijacked to benefit parasite development. We found that expression of aquaporin-3 (AQP3), a water and glycerol channel, is significantly induced in Plasmodium-infected hepatocytes compared to uninfected cells. This aquaglyceroporin localizes to the parasitophorous vacuole membrane, the compartmental interface between the host and pathogen, with a temporal pattern that correlates with the parasite's expansion in the liver. Depletion or elimination of host AQP3 expression significantly reduces P. berghei parasite burden during the liver stage and chemical disruption by a known AQP3 inhibitor, auphen, reduces P. falciparum asexual blood stage and P. berghei liver stage parasite load. Further use of this inhibitor as a chemical probe suggests that AQP3-mediated nutrient transport is an important function for parasite development. This study reveals a previously unknown potential route for host-dependent nutrient acquisition by Plasmodium which was discovered by mapping the transcriptional changes that occur in hepatocytes throughout P. berghei infection. The dataset reported may be leveraged to identify additional host factors that are essential for Plasmodium liver stage infection and highlights Plasmodium's dependence on host factors within hepatocytes.

Fungal cells change shape in response to environmental stimuli, and these morphogenic transitions drive pathogenesis and niche adaptation. For example, dimorphic fungi switch between yeast and hyphae in response to changing temperature. The basidiomycete Cryptococcus neoformans undergoes an unusual morphogenetic transition in the host lung from haploid yeast to large, highly polyploid cells termed Titan cells. Titan cells influence fungal interaction with host cells, including through increased drug resistance, altered cell size, and altered Pathogen Associated Molecular Pattern exposure. Despite the important role these cells play in pathogenesis, understanding the environmental stimuli that drive the morphological transition, and the molecular mechanisms underlying their unique biology, has been hampered by the lack of a reproducible in vitro induction system. Here we demonstrate reproducible in vitro Titan cell induction in response to environmental stimuli consistent with the host lung. In vitro Titan cells exhibit all the properties of in vivo generated Titan cells, the current gold standard, including altered capsule, cell wall, size, high mother cell ploidy, and aneuploid progeny. We identify the bacterial peptidoglycan subunit Muramyl Dipeptide as a serum compound associated with shift in cell size and ploidy, and demonstrate the capacity of bronchial lavage fluid and bacterial co-culture to induce Titanisation. Additionally, we demonstrate the capacity of our assay to identify established (cAMP/PKA) and previously undescribed (USV101) regulators of Titanisation in vitro. Finally, we investigate the Titanisation capacity of clinical isolates and their impact on disease outcome. Together, these findings provide new insight into the environmental stimuli and molecular mechanisms underlying the yeast-to-Titan transition and establish an essential in vitro model for the future characterization of this important morphotype.

Ligand binding sites in proteins are often localized to deeply buried cavities, inaccessible to bulk solvent. Yet, in many cases binding of cognate ligands occurs rapidly. An intriguing system is presented by the L99A cavity mutant of T4 Lysozyme (T4L L99A) that rapidly binds benzene (~106 M-1s-1). Although the protein has long served as a model system for protein thermodynamics and crystal structures of both free and benzene-bound T4L L99A are available, the kinetic pathways by which benzene reaches its solvent-inaccessible binding cavity remain elusive. The current work, using extensive molecular dynamics simulation, achieves this by capturing the complete process of spontaneous recognition of benzene by T4L L99A at atomistic resolution. A series of multi-microsecond unbiased molecular dynamics simulation trajectories unequivocally reveal how benzene, starting in bulk solvent, diffuses to the protein and spontaneously reaches the solvent inaccessible cavity of T4L L99A. The simulated and high-resolution X-ray derived bound structures are in excellent agreement. A robust four-state Markov model, developed using cumulative 60 μs trajectories, identifies and quantifies multiple ligand binding pathways with low activation barriers. Interestingly, none of these identified binding pathways required large conformational changes for ligand access to the buried cavity. Rather, these involve transient but crucial opening of a channel to the cavity via subtle displacements in the positions of key helices (helix4/helix6, helix7/helix9) leading to rapid binding. Free energy simulations further elucidate that these channel-opening events would have been unfavorable in wild type T4L. Taken together and via integrating with results from experiments, these simulations provide unprecedented mechanistic insights into the complete ligand recognition process in a buried cavity. By illustrating the power of subtle helix movements in opening up multiple pathways for ligand access, this work offers an alternate view of ligand recognition in a solvent-inaccessible cavity, contrary to the common perception of a single dominant pathway for ligand binding.

Raman spectra of large graphene bubbles showed size-dependent oscillations in spectral intensity and frequency, which originate from optical standing waves formed in the vicinity of the graphene surface. At a high laser power, local heating can lead to oscillations in the Raman frequency and also create a temperature gradient in the bubble. Based on Raman data, the temperature distribution within the graphene bubble was calculated, and it is shown that the heating effect of the laser is reduced when moving from the center of a bubble to its edge. By studying graphene bubbles, both the thermal conductivity and chemical reactivity of graphene were assessed. When exposed to hydrogen plasma, areas with bubbles are found to be more reactive than flat graphene.

The structure of deformed neutron-rich nuclei in the rare-earth region is of significant interest for both the astrophysics and nuclear structure fields. At present, a complete explanation for the observed peak in the elemental abundances at A∼160 eludes astrophysicists, and models depend on accurate quantities, such as masses, lifetimes, and branching ratios of deformed neutron-rich nuclei in this region. Unusual nuclear structure effects are also observed, such as the unexpectedly low energies of the first 2^{+} levels in some even-even nuclei at N=98. In order to address these issues, mass and β-decay spectroscopy measurements of the ^{160}Eu_{97} and ^{162}Eu_{99} nuclei were performed at the Californium Rare Isotope Breeder Upgrade radioactive beam facility at Argonne National Laboratory. Evidence for a gap in the single-particle neutron energies at N=98 and for large deformation (β_{2}∼0.3) is discussed in relation to the unusual phenomena observed at this neutron number.

The development of porous composite materials is of great significance for their potentially improved performance over those of individual components and extensive applications in separation, energy storage, and heterogeneous catalysis. Now mesoporous metal-organic frameworks (MOFs) with macroporous melamine foam (MF) have been integrated using a one-pot process, generating a series of MOF/MF composite materials with preserved crystallinity, hierarchical porosity, and increased stability over that of melamine foam. The MOF nanocrystals were threaded by the melamine foam networks, resembling a ball-and-stick model overall. The resulting MOF/MF composite materials were employed as an effective heterogeneous catalyst for the epoxidation of cholesteryl esters. Combining the advantages of interpenetrative mesoporous and macroporous structures, the MOF/melamine foam composite has higher dispersibility and more accessibility of catalytic sites, exhibiting excellent catalytic performance.