Control of aggregation-induced emission by DNA hybridization

Aggregation-induced emission (AIE) was studied by hybridization of dialkynyl-tetraphenylethylene (DATPE) modified DNA strands. Molecular aggregation and fluorescence of DATPEs are controlled by duplex formation.

Molecular and Translational Classifications of DAMPs in Immunogenic Cell Death.

The immunogenicity of malignant cells has recently been acknowledged as a critical determinant of efficacy in cancer therapy. Thus, besides developing direct immunostimulatory regimens, including dendritic cell-based vaccines, checkpoint-blocking therapies, and adoptive T-cell transfer, researchers have started to focus on the overall immunobiology of neoplastic cells. It is now clear that cancer cells can succumb to some anticancer therapies by undergoing a peculiar form of cell death that is characterized by an increased immunogenic potential, owing to the emission of the so-called "damage-associated molecular patterns" (DAMPs). The emission of DAMPs and other immunostimulatory factors by cells succumbing to immunogenic cell death (ICD) favors the establishment of a productive interface with the immune system. This results in the elicitation of tumor-targeting immune responses associated with the elimination of residual, treatment-resistant cancer cells, as well as with the establishment of immunological memory. Although ICD has been characterized with increased precision since its discovery, several questions remain to be addressed. Here, we summarize and tabulate the main molecular, immunological, preclinical, and clinical aspects of ICD, in an attempt to capture the essence of this phenomenon, and identify future challenges for this rapidly expanding field of investigation.

Source apportionment and dynamic changes of carbonaceous aerosols during the haze bloom-decay process in China based on radiocarbon and organic molecular tracers

Fine carbonaceous aerosols (CAs) is the key factor influencing the currently filthy air in megacities in China, yet few studies simultaneously focus on the origins of different CAs species using specific and powerful source tracers. Here, we present a detailed source apportionment for various CAs fractions, including organic carbon (OC), water-soluble OC (WSOC), water-insoluble OC (WIOC), elemental carbon (EC) and secondary OC (SOC) in the largest cities of North (Beijing, BJ) and South China (Guangzhou, GZ), using the measurements of radiocarbon and anhydrosugars. Results show that non-fossil fuel sources such as biomass burning and biogenic emission make a significant contribution to the total CAs in Chinese megacities: 56±4 in BJ and 46±5% in GZ, respectively. The relative contributions of primary fossil carbon from coal and liquid petroleum combustions, primary non-fossil carbon and secondary organic carbon (SOC) to total carbon are 19, 28 and 54% in BJ, and 40, 15 and 46% in GZ, respectively. Non-fossil fuel sources account for 52 in BJ and 71% in GZ of SOC, respectively. These results suggest that biomass burning has a greater influence on regional particulate air pollution in North China than in South China. We observed an unabridged haze bloom-decay process in South China, which illustrates that both primary and secondary matter from fossil sources played a key role in the blooming phase of the pollution episode, while haze phase is predominantly driven by fossil-derived secondary organic matter and nitrate.

Dissolved organic matter molecular composition and concentrations from a large scale mesocosm study KOSMOS 2013 Kristineberg) on ocean acidification

Marine dissolved organic matter (DOM) represents one of the largest active carbon reservoirs on Earth. Changes in pool size or composition could have major impacts on the global carbon cycle. Ocean acidification is a potential driver for these changes because it influences marine primary production and heterotrophic respiration. Here we show that ocean acidification as expected for a 'business-as-usual' emission scenario in the year 2100 (900 µatm) does not affect the DOM pool with respect to its size and molecular composition. We applied ultrahigh-resolution mass spectrometry to monitor the production and turnover of 7,360 distinct molecular DOM features in an unprecedented long-term mesocosm study in a Swedish Fjord, covering a full cycle of marine production. DOM concentration and molecular composition did not differ significantly between present-day and year 2100 CO2 levels. Our findings are likely applicable to other coastal and productive marine ecosystems in general.

InN/InGaN multiple quantum wells emitting at 1.5 mu m grown by molecular beam epitaxy

This work reports on the growth by molecular beam epitaxy and characterization of InN/InGaN multiple quantum wells (MQWs) emitting at 1.5 μm. X-ray diffraction (XRD) spectra show satellite peaks up to the second order. Estimated values of well (3 nm) and barrier (9 nm) thicknesses were derived from transmission electron microscopy and the fit between experimental data and simulated XRD spectra. Transmission electron microscopy and XRD simulations also confirmed that the InGaN barriers are relaxed with respect to the GaN template, while the InN MQWs grew under biaxial compression on the InGaN barriers. Low temperature (14 K) photoluminescence measurements reveal an emission from the InN MQWs at 1.5 μm. Measurements as a function of temperature indicate the existence of localized states, probably due to InN quantum wells’ thickness fluctuations as observed by transmission electron microscopy.

Internal quantum efficiency of III-nitride quantum dot superlattices grown by plasma-assisted molecular-beam epitaxy

We present a study of the optical properties of GaN/AlN and InGaN/GaN quantum dot (QD) superlattices grown via plasma-assisted molecular-beam epitaxy, as compared to their quantum well (QW) counterparts. The three-dimensional/two-dimensional nature of the structures has been verified using atomic force microscopy and transmission electron microscopy. The QD superlattices present higher internal quantum efficiency as compared to the respective QWs as a result of the three-dimensional carrier localization in the islands. In the QW samples, photoluminescence (PL) measurements point out a certain degree of carrier localization due to structural defects or thickness fluctuations, which is more pronounced in InGaN/GaN QWs due to alloy inhomogeneity. In the case of the QD stacks, carrier localization on potential fluctuations with a spatial extension smaller than the QD size is observed only for the InGaN QD-sample with the highest In content (peak emission around 2.76 eV). These results confirm the efficiency of the QD three-dimensional confinement in circumventing the potential fluctuations related to structural defects or alloy inhomogeneity. PL excitation measurements demonstrate efficient carrier transfer from the wetting layer to the QDs in the GaN/AlN system, even for low QD densities (~1010 cm-3). In the case of InGaN/GaN QDs, transport losses in the GaN barriers cannot be discarded, but an upper limit to these losses of 15% is deduced from PL measurements as a function of the excitation wavelength.

O 1s excitation and ionization processes in the CO2 molecule studied via detection of low-energy fluorescence emission

Oxygen 1s excitation and ionization processes in the CO2 molecule have been studied with dispersed and non-dispersed fluorescence spectroscopy as well as with the vacuum ultraviolet (VUV) photon?photoion coincidence technique. The intensity of the neutral O emission line at 845 nm shows particular sensitivity to core-to-Rydberg excitations and core?valence double excitations, while shape resonances are suppressed. In contrast, the partial fluorescence yield in the wavelength window 300?650 nm and the excitation functions of selected O+ and C+ emission lines in the wavelength range 400?500 nm display all of the absorption features. The relative intensity of ionic emission in the visible range increases towards higher photon energies, which is attributed to O 1s shake-off photoionization. VUV photon?photoion coincidence spectra reveal major contributions from the C+ and O+ ions and a minor contribution from C2+. No conclusive changes in the intensity ratios among the different ions are observed above the O 1s threshold. The line shape of the VUV?O+ coincidence peak in the mass spectrum carries some information on the initial core excitation

Smooth muscle myosin mutants containing a single tryptophan reveal molecular interactions at the actin-binding interface

Elucidation of the molecular details of the cyclic actomyosin interaction requires the ability to examine structural changes at specific sites in the actin-binding interface of myosin. To study these changes dynamically, we have expressed two mutants of a truncated fragment of chicken gizzard smooth muscle myosin, which includes the motor domain and essential light chain (MDE). These mutants were engineered to contain a single tryptophan at (Trp-546) or near (Trp-625) the putative actin-binding interface. Both 546- and 625-MDE exhibited actin-activated ATPase and actin-binding activities similar to wild-type MDE. Fluorescence emission spectra and acrylamide quenching of 546- and 625-MDE suggest that Trp-546 is nearly fully exposed to solvent and Trp-625 is less than 50% exposed in the presence and absence of ATP, in good agreement with the available crystal structure data. The spectrum of 625-MDE bound to actin was quite similar to the unbound spectrum indicating that, although Trp-625 is located near the 50/20-kDa loop and the 50-kDa cleft of myosin, its conformation does not change upon actin binding. However, a 10-nm blue shift in the peak emission wavelength of 546-MDE observed in the presence of actin indicates that Trp-546, located in the A-site of the lower 50-kDa subdomain of myosin, exists in a more buried environment and may directly interact with actin in the rigor acto-S1 complex. This change in the spectrum of Trp-546 constitutes direct evidence for a specific molecular interaction between residues in the A-site of myosin and actin.

Ammonia observations of the nearby molecular cloud MBM 12

We present NH_3(1,1) and (2,2) observations of MBM 12, the closest known molecular cloud (65-pc distance), aimed at finding evidence for on-going star formation processes, No local temperature (with a T_rot upper limit of 12 K) or linewidth enhancement is found, which suggests that the area of the cloud that we have mapped (∼ 15-arcmin size) is not currently forming stars. Therefore this nearby 'starless' molecular gas region is an ideal laboratory to study the physical conditions preceding new star formation. A radio continuum source has been found in Very Large Array archive data, close to but outside the NH_3 emission. This source is likely to be a background object.

[C II] and 12^CO(1-0) emission maps in HLSJ091828.6+514223: a strongly lensed interacting system AT z = 5.24

We present Submillimeter Array [C II] 158 μm and Karl G. Jansky Very Large Array 12^CO(1-0) line emission maps for the bright, lensed, submillimeter source at z = 5.2430 behind A 773: HLSJ091828.6+514223 (HLS0918). We combine these measurements with previously reported line profiles, including multiple 12^CO rotational transitions, [C I], water, and [N II], providing some of the best constraints on the properties of the interstellar medium in a galaxy at z > 5. HLS0918 has a total far-infrared (FIR) luminosity L_FIR(8–1000 μm) = (1.6 ± 0.1) × 10^14 L_☉ μ^–1, where the total magnification μ_total = 8.9 ± 1.9, via a new lens model from the [C II] and continuum maps. Despite a HyLIRG luminosity, the FIR continuum shape resembles that of a local LIRG. We simultaneously fit all of the observed spectral line profiles, finding four components that correspond cleanly to discrete spatial structures identified in the maps. The two most redshifted spectral components occupy the nucleus of a massive galaxy, with a source-plane separation <1 kpc. The reddest dominates the continuum map (demagnified L_FIR, component = (1.1 ± 0.2) × 10^13 L_☉) and excites strong water emission in both nuclear components via a powerful FIR radiation field from the intense star formation. A third star-forming component is most likely a region of a merging companion (ΔV ~ 500 km s^–1) exhibiting generally similar gas properties. The bluest component originates from a spatially distinct region and photodissociation region analysis suggests that it is lower density, cooler, and forming stars less vigorously than the other components. Strikingly, it has very strong [N II] emission, which may suggest an ionized, molecular outflow. This comprehensive view of gas properties and morphology in HLS0918 previews the science possible for a large sample of high-redshift galaxies once ALMA attains full sensitivity.

A novel plasma etching and emission monitoring system (PEEMS) to assess protein and lipid spoilation for hydrogel contact lenses

The work presents a new method that combines plasma etching with extrinsic techniques to simultaneously measure matrix and surface protein and lipid deposits. The acronym for this technique is PEEMS - Plasma Etching and Emission Monitoring System. Previous work has identified the presence of proteinaceous and lipoidal deposition on the surface of contact lenses and highlighted the probability that penetration of these spoilants will occur. This technique developed here allows unambiguous identification of the depth of penetration of spoilants to be made for various material types. It is for this reason that the technique has been employed in this thesis. The technique is applied as a 'molecular' scalpel, removing known amounts of material from the target. In this case from both the anterior .and posterior surfaces of a 'soft' contact lens. The residual material is then characterised by other analytical techniques such as UV/visible .and fluorescence spectroscopy. Several studies have be.en carried out for both in vivo and in vitro spoilt materials. The analysis and identification of absorbed protein and lipid of the substrate revealed the importance of many factors in the absorption and adsorption process. The effect of the material structure, protein nature (in terms of size, shape and charge) and environment conditions were examined in order to determine the relative uptake of tear proteins. The studies were extended to real cases in order to study the. patient dependent factors and lipoidal penetration.

Investigating the origin of PM2.5 in Baltimore using highly time-resolved organic molecular markers measured during the Baltimore PM-supersite

The detailed organic composition of atmospheric fine particles with an aerodynamic diameter smaller than or equal to 2.5 micrometers (PM2.5) is an integral part of the knowledge needed in order to fully characterize its sources and transformation in the environment. For the study presented here, samples were collected at 3-hour intervals. This high time resolution allows gaining unique insights on the influence of short- and long-range transport phenomena, and dynamic atmospheric processes. A specially designed sequential sampler was deployed at the 2002-2003 Baltimore PM-Supersite to collect PM2.5 samples at a 3-hourly resolution for extended periods of consecutive days, during both summer and winter seasons. Established solvent-extraction and GC-MS techniques were used to extract and analyze the organic compounds in 119 samples from each season. Over 100 individual compounds were quantified in each sample. For primary organics, averaging the diurnal ambient concentrations over the sampled periods revealed ambient patterns that relate to diurnal emission patterns of major source classes. Several short-term releases of pollutants from local sources were detected, and local meteorological data was used to pinpoint possible source regions. Biogenic secondary organic compounds were detected as well, and possible mechanisms of formation were evaluated. The relationships between the observed continuous variations of the concentrations of selected organic markers and both the on-site meteorological measurements conducted parallel to the PM2.5 sampling, and the synoptic patterns of weather and wind conditions were also examined. Several one-to-two days episodes were identified from the sequential variation of the concentration observed for specific marker compounds and markers ratios. The influence of the meteorological events on the concentrations of the organic compounds during selected episodes was discussed. It was observed that during the summer, under conditions of pervasive influence of air masses originated from the west/northwest, some organic species displayed characteristics consistent with the measured PM2.5 being strongly influenced by the aged nature of these long-traveling background parcels. During the winter, intrusions from more regional air masses originating from the south and the southwest were more important.

Fluorescence Characteristics of Size-Fractionated Dissolved Organic Matter: Implications for a Molecular Assembly Based Structure?

Surface freshwater samples from Everglades National Park, Florida, were used to investigate the size distributions of natural dissolved organic matter (DOM) and associated fluorescence characteristics along the molecular weight continuum. Samples were fractionated using size exclusion chromatography (SEC) and characterized by spectroscopic means, in particular Excitation-Emission Matrix fluorescence modeled with parallel factor analysis (EEM-PARAFAC). Most of the eight components obtained from PARAFAC modeling were broadly distributed across the DOM molecular weight range, and the optical properties of the eight size fractions for all samples studied were quite consistent among each other. Humic-like components presented a similar distribution in all the samples, with enrichment in the middle molecular weight range. Some variability in the relative distribution of the different humic-like components was observed among the different size fractions and among samples. The protein like fluorescence, although also generally present in all fractions, was more variable but generally enriched in the highest and lowest molecular weight fractions. These observations are in agreement with the hypothesis of a supramolecular structure for DOM, and suggest that DOM fluorescence characteristics may be controlled by molecular assemblies with similar optical properties, distributed along the molecular weight continuum. This study highlights the importance of studying the molecular structure of DOM on a molecular size distribution perspective, which may have important implications in understanding the environmental dynamics such materials.

Investigating the origin of PM2.5 in Baltimore using highly time-resolved organic molecular markers measured during the Baltimore PM-supersite

The detailed organic composition of atmospheric fine particles with an aerodynamic diameter smaller than or equal to 2.5 micrometers (PM 2.5) is an integral part of the knowledge needed in order to fully characterize its sources and transformation in the environment. For the study presented here, samples were collected at 3-hour intervals. This high time resolution allows gaining unique insights on the influence of short- and long-range transport phenomena, and dynamic atmospheric processes. A specially designed sequential sampler was deployed at the 2002-2003 Baltimore PM Supersite to collect PM2.5 samples at a 3-hourly resolution for extended periods of consecutive days, during both summer and winter seasons. Established solvent-extraction and GC-MS techniques were used to extract and analyze the organic compounds in 119 samples from each season. Over 100 individual compounds were quantified in each sample. For primary organics, averaging the diurnal ambient concentrations over the sampled periods revealed ambient patterns that relate to diurnal emission patterns of major source classes. Several short-term releases of pollutants from local sources were detected, and local meteorological data was used to pinpoint possible source regions. Biogenic secondary organic compounds were detected as well, and possible mechanisms of formation were evaluated. The relationships between the observed continuous variations of the concentrations of selected organic markers and both the on-site meteorological measurements conducted parallel to the PM2.5 sampling, and the synoptic patterns of weather and wind conditions were also examined. Several one-to-two days episodes were identified from the sequential variation of the concentration observed for specific marker compounds and markers ratios. The influence of the meteorological events on the concentrations of the organic compounds during selected episodes was discussed. It was observed that during the summer, under conditions of pervasive influence of air masses originated from the west/northwest, some organic species displayed characteristics consistent with the measured PM2.5 being strongly influenced by the aged nature of these long-traveling background parcels. During the winter, intrusions from more regional air masses originating from the south and the southwest were more important.

The Synthesis of Novel N-Heterocyclic Scaffolds and Diazirine-Based Molecular Tags

N-Heterocycles are ubiquitous in biologically active natural products and pharmaceuticals. Yet, new syntheses and modifications of N-heterocycles are continually of interest for the purposes of expanding chemical space, finding quicker synthetic routes, better pharmaceuticals, and even new handles for molecular labeling. There are several iterations of molecular labeling; the decision of where to place the label is as important as of which visualization technique to emphasize.

Piperidine and indole are two of the most widely distributed N-heterocycles and thus were targeted for synthesis, functionalization, and labeling. The major functionalization of these scaffolds should include a nitrogen atom, while the inclusion of other groups will expand the utility of the method. Towards this goal, ease of synthesis and elimination of step-wise transformations are of the utmost concern. Here, the concept of electrophilic amination can be utilized as a way of introducing complex secondary and tertiary amines with minimal operations.

Molecular tags should be on or adjacent to an N-heterocycle as they are normally the motifs implicated at the binding site of enzymes and receptors. The labeling techniques should be useful to a chemical biologist, but should also in theory be useful to the medical community. The two types of labeling that are of interest to a chemist and a physician would be positron emission tomography (PET) and magnetic resonance imaging (MRI).

Coincidentally, the 3-positions of both piperidine and indole are historically difficult to access and modify. However, using electrophilic amination techniques, 3-functionalized piperidines can be synthesized in good yields from unsaturated amines. In the same manner, 3-labeled piperidines can be obtained; the piperidines can either be labeled with an azide for biochemical research or an 18F for PET imaging research. The novel electrophiles, N-benzenesulfonyloxyamides, can be reacted with indole in one of two ways: 3-amidation or 1-amidomethylation, depending on the exact reaction conditions. Lastly, a novel, hyperpolarizable 15N2-labeled diazirine has been developed as an exogenous and versatile tag for use in magnetic resonance imaging.