Changes In Molecular Distribution Research Articles

Design of a Brownian ratchet based on repetitive aggregation and dispersion of stimuli-responsive molecules.

We propose a Brownian ratchet for the unidirectional transport of stimuli-responsive molecules confined in a series of asymmetric geometries. It relies on repetitive cycles of aggregation and dispersion, which cause significant changes in molecular distribution within the confining geometry and enable the Brownian motion of the molecules to be ratcheted in a specific direction. To demonstrate the feasibility of the proposed Brownian ratchet, we conducted Brownian dynamics simulations where stimuli-responsive molecules were repeatedly aggregated and dispersed in a series of truncated conical tubes by altering intermolecular interactions. These simulations demonstrated the unidirectional transport of the molecules, indicating the efficacy of the proposed Brownian ratchet. Furthermore, we found that it becomes more effective with higher concentrations of molecules. This study suggests that, through the deliberate control of molecular assembly and disassembly by stimuli-responsive intermolecular interactions, it is possible to achieve directional and controlled molecular transport in various nanoscale applications.

Molecular Distributions and Compound-Specific Stable Carbon Isotopic Compositions of Plant Wax n-Alkanes in Marine Aerosols along a North–South Transect in the Arctic–Northwest Pacific Region

A geographical source of n-alkanes in marine aerosols was assessed along a North–South transect in the Arctic–Northwest Pacific region. Marine aerosol samples were collected during the ARA08 cruise with the R/V Araon between 28 August and 28 September 2017. We investigated molecular distributions of n-alkanes (homologous series of C16 to C34) and compound-specific stable carbon isotopes (δ13C) of n-C27, n-C29, and n-C31. Unresolved complex mixtures (UCM) showed a latitudinal trend from the Arctic Ocean to the northwest Pacific Ocean, highlighting an increasing influence of the plume of polluted air exported from East Asian countries. The anthropogenic input was further evidenced by high U/R ratios (>5) and low CPI17–23 (0.6–1.4). The occurrence of high molecular weight (HMW) n-alkanes with high CPI27–31 (>3) indicated the biogenic input of terrestrial higher plant leaf waxes in all studied samples. The δ13C of HMW n-alkanes was influenced by both the relative contributions from the C3/C4 plant sources and from fossil fuel combustions. The back-trajectory analyses provided evidence that changes in molecular distributions and δ13C of n-alkanes were due to the long-range atmospheric transport of anthropogenic and biogenic organic materials from North American and East Asian countries to the Arctic Ocean and the remote northwest Pacific Ocean, respectively.

Biomolecular Imaging of Regeneration of Zebrafish Caudal Fins Using High Spatial Resolution Ambient Mass Spectrometry.

We observed the molecular distribution changes that occurred during the regeneration of fresh zebrafish caudal fins using the recently developed ambient high-resolution mass spectrometry (MS) imaging technique of atmospheric pressure-nanoparticle and plasma-assisted laser desorption ionization (AP-nanoPALDI). AP-nanoPALDI analyses of fresh zebrafish caudal fins revealed that the small molecules, including neurotransmitters, amino acids, lipids, and metabolites of the regenerated area, were more evenly distributed throughout the bony rays and inter-ray mesenchymal tissues compared to the original area in the early stage. Zebrafish caudal fins of less than 200 μm thickness can be very useful for tissue regeneration studies using ambient MS imaging by providing sufficient biomolecular information at the molecular level for wound-healing studies. AP-nanoPALDI imaging was compared with a complementary MS imaging tool, surface sensitive time-of-flight secondary ion MS (ToF-SIMS).

Radiolytic alteration of biopolymers in the Mulga Rock (Australia) uranium deposit

We investigated the effect of ionizing radiation on organic matter (OM) in the carbonaceous uranium (U) mineralization at the Mulga Rock deposit, Western Australia. Samples were collected from mineralized layers between 53 and 58.5m depths in the Ambassador prospect, containing <5300ppm U. Uranium bears a close spatial relationship with OM, mostly finely interspersed in the attrinite matrix and via enrichments within liptinitic phytoclasts (mainly sporinite and liptodetrinite). Geochemical analyses were conducted to: (i) identify the natural sources of molecular markers, (ii) recognize relationships between molecular markers and U concentrations and (iii) detect radiolysis effects on molecular marker distributions. Carbon to nitrogen ratios between 82 and 153, and Rock–Eval pyrolysis yields of 316–577mg hydrocarbon/g TOC (HI) and 70–102mg CO2/g TOC (OI) indicate a predominantly lipid-rich terrigenous plant OM source deposited in a complex shallow swampy wetland or lacustrine environment. Saturated hydrocarbon and ketone fractions reveal molecular distributions co-varying with U concentration. In samples with <1700ppm U concentrations, long-chain n-alkanes and alkanones (C27–C31) reveal an odd/even carbon preference indicative of extant lipids. Samples with ⩾1700ppm concentrations contain intermediate-length n-alkanes and alkanones, bearing a keto-group in position 2–10, with no carbon number preference. Such changes in molecular distributions are inconsistent with diagenetic degradation of terrigenous OM in oxic depositional environments and cannot be associated with thermal breakdown due to the relatively low thermal maturity of the deposits (Rr=0.26%). It is assumed that the intimate spatial association of high U concentrations resulted in breakdown via radiolytic cracking of recalcitrant polyaliphatic macromolecules (spores, pollen, cuticles, or algal cysts) yielding medium chain length n-alkanes (C13–C24). Reactions of n-alkenes with OH− radicals from water hydrolysis produced alcohols that dehydrogenated to alkanones or through carbonylation formed alkanones. Rapid reactions with hydroxyl radicals likely decreased the isomerization of n-alkenes and decreased alkanone diversity, such that the alkan-2-one isomer is predominant. This specific distribution of components generated by natural radiolysis enables their application as “radiolytic molecular markers”. Breaking of C–C bonds through radiolytic cracking at temperatures much lower than the oil window (<50°C) can have profound implications on initiation of petroleum formation, paleoenvironmental reconstructions, mineral exploration and in tracking radiolysis of OM.

Disentangling the Peak and Background Signals in Surface-Enhanced Raman Scattering

Understanding the complex relationship between peak enhancement and the underlying broad continuum (called the “background”) is crucial for developing reliable and quantitative applications of surface-enhanced Raman scattering (SERS). Here we use a gentle mechanochemical (“snow jet”) process to perturb molecules on a SERS active substrate to track the dynamics of the different contributions to SERS. By use of the snow jet process we are able to increase SERS signals on substrates by 500% or more while simultaneously increasing the peak:background intensity ratio. We identify components of the signal arising from changes in molecular distribution and surface morphology using a multiplexed time-varied exposure technique developed in-house. This allows us to distinguish between processes decaying over time and those decaying due to laser heating. Our study goes a long way toward disentangling the different contributions to SERS peak and background continuum signals and points to the different origins of these two co-occurring processes on nanostructured plasmonic substrates. This deeper understanding of the SERS process is crucial to allow SERS to reach its full potential.

Multiple changes in peptide and lipid expression associated with regeneration in the nervous system of the medicinal leech.

BackgroundThe adult medicinal leech central nervous system (CNS) is capable of regenerating specific synaptic circuitry after a mechanical lesion, displaying evidence of anatomical repair within a few days and functional recovery within a few weeks. In the present work, spatiotemporal changes in molecular distributions during this phenomenon are explored. Moreover, the hypothesis that neural regeneration involves some molecular factors initially employed during embryonic neural development is tested.ResultsImaging mass spectrometry coupled to peptidomic and lipidomic methodologies allowed the selection of molecules whose spatiotemporal pattern of expression was of potential interest. The identification of peptides was aided by comparing MS/MS spectra obtained for the peptidome extracted from embryonic and adult tissues to leech transcriptome and genome databases. Through the parallel use of a classical lipidomic approach and secondary ion mass spectrometry, specific lipids, including cannabinoids, gangliosides and several other types, were detected in adult ganglia following mechanical damage to connected nerves. These observations motivated a search for possible effects of cannabinoids on neurite outgrowth. Exposing nervous tissues to Transient Receptor Potential Vanilloid (TRPV) receptor agonists resulted in enhanced neurite outgrowth from a cut nerve, while exposure to antagonists blocked such outgrowth.ConclusionThe experiments on the regenerating adult leech CNS reported here provide direct evidence of increased titers of proteins that are thought to play important roles in early stages of neural development. Our data further suggest that endocannabinoids also play key roles in CNS regeneration, mediated through the activation of leech TRPVs, as a thorough search of leech genome databases failed to reveal any leech orthologs of the mammalian cannabinoid receptors but revealed putative TRPVs. In sum, our observations identify a number of lipids and proteins that may contribute to different aspects of the complex phenomenon of leech nerve regeneration, establishing an important base for future functional assays.

Live Imaging of Cell Motility and Actin Cytoskeleton of Individual Neurons and Neural Crest Cells in Zebrafish Embryos

The zebrafish is an ideal model for imaging cell behaviors during development in vivo. Zebrafish embryos are externally fertilized and thus easily accessible at all stages of development. Moreover, their optical clarity allows high resolution imaging of cell and molecular dynamics in the natural environment of the intact embryo. We are using a live imaging approach to analyze cell behaviors during neural crest cell migration and the outgrowth and guidance of neuronal axons.Live imaging is particularly useful for understanding mechanisms that regulate cell motility processes. To visualize details of cell motility, such as protrusive activity and molecular dynamics, it is advantageous to label individual cells. In zebrafish, plasmid DNA injection yields a transient mosaic expression pattern and offers distinct benefits over other cell labeling methods. For example, transgenic lines often label entire cell populations and thus may obscure visualization of the fine protrusions (or changes in molecular distribution) in a single cell. In addition, injection of DNA at the one-cell stage is less invasive and more precise than dye injections at later stages.Here we describe a method for labeling individual developing neurons or neural crest cells and imaging their behavior in vivo. We inject plasmid DNA into 1-cell stage embryos, which results in mosaic transgene expression. The vectors contain cell-specific promoters that drive expression of a gene of interest in a subset of sensory neurons or neural crest cells. We provide examples of cells labeled with membrane targeted GFP or with a biosensor probe that allows visualization of F-actin in living cells1.Erica Andersen, Namrata Asuri, and Matthew Clay contributed equally to this work.

Live Imaging of Cell Motility and Actin Cytoskeleton of Individual Neurons and Neural Crest Cells in Zebrafish Embryos

The zebrafish is an ideal model for imaging cell behaviors during development in vivo. Zebrafish embryos are externally fertilized and thus easily accessible at all stages of development. Moreover, their optical clarity allows high resolution imaging of cell and molecular dynamics in the natural environment of the intact embryo. We are using a live imaging approach to analyze cell behaviors during neural crest cell migration and the outgrowth and guidance of neuronal axons. Live imaging is particularly useful for understanding mechanisms that regulate cell motility processes. To visualize details of cell motility, such as protrusive activity and molecular dynamics, it is advantageous to label individual cells. In zebrafish, plasmid DNA injection yields a transient mosaic expression pattern and offers distinct benefits over other cell labeling methods. For example, transgenic lines often label entire cell populations and thus may obscure visualization of the fine protrusions (or changes in molecular distribution) in a single cell. In addition, injection of DNA at the one-cell stage is less invasive and more precise than dye injections at later stages. Here we describe a method for labeling individual developing neurons or neural crest cells and imaging their behavior in vivo. We inject plasmid DNA into 1-cell stage embryos, which results in mosaic transgene expression. The vectors contain cell-specific promoters that drive expression of a gene of interest in a subset of sensory neurons or neural crest cells. We provide examples of cells labeled with membrane targeted GFP or with a biosensor probe that allows visualization of F-actin in living cells1. Erica Andersen, Namrata Asuri, and Matthew Clay contributed equally to this work.

Electrophoretic mobility and molecular distribution studies of poly(amidoamine) dendrimers of defined charges

Generation 5 ethylenediamine (EDA)-cored poly(amidoamine) (PAMAM) dendrimers (E5, E denotes the EDA core and 5 the generation number) with different degrees of acetylation and carboxylation were synthesized and used as a model system to investigate the effect of charge and the influence of dendrimer surface modifications on electrophoretic mobility (EM) and molecular distribution. The surface-modified dendrimers were characterized by size-exclusion chromatography, 1H NMR, MALDI-TOF-MS, PAGE, and CE. The focus of our study was to determine how EM changes as a function of particle charge and molecular mass, and how the molecular distribution changes due to surface modifications. We demonstrate that partially modified dendrimers have much broader migration peaks than those of fully surface functionalized or unmodified E5 dendrimers due to variations in the substitution of individual dendrimer surfaces. EM decreased nonlinearly with increases in surface acetylation for both PAMAM acetamides and PAMAM succinamic acids, indicating a complex migration activity in CE separations that is not solely due to charge/mass ratio changes. These studies provide new insights into dendrimer properties under an electric field, as well as into the characterization of dendrimer-based materials being developed for medical applications.

Molecular mass distribution and degradation rate of xylan sonicated in acid and alkaline media

The molecular mass distribution of birch wood xylan sonicated in H 2SO 4 or KOH solution was investigated for elucidating the effect of medium on the change of molecular distribution. A recycling-style ultrasonic spray system, mainly composed of a 20 kHz frequency generator and a spraying nozzle, was used. Xylan was repeatedly sonicated for 0–15 cycles, and the molecular mass of xylan was determined by high-performance size-exclusion chromatography (HPSEC). Results indicated that the molecular mass of sonicated xylan decreased with increasing sonication cycle in alkaline solution, whereas no significant reduced in acid solution was observed. Moreover, the change of molecular mass of xylan treated with sonication in 2% KOH was higher than in 1% KOH solution. The degradation of xylan sonicated in alkaline solution was manifested by a decrease in weight ratio of higher molecular mass component. The changes on degradation rate constant ( k) and average-number of chain splitting ratio (ANCS) of sonicated xylan indicate that the molecule is rapidly degraded within the first 5 cycles of sonication in 2% KOH solution. However, occurrence of aggregation was observed in H 2SO 4 solution ( k<0). Results indicate that alkaline solution is a better medium than acid solution for xylan sonication.

Isolation of bovine plasma albumin by liquid chromatography and its polymerization for use in immunohematology.

The aim of the method described here is to remove hemoglobin, the major contaminant in the bovine plasma obtained from slaughterhouses, by adding a mixture of 19% cold ethanol and 0.6% chloroform, followed by fibrinogen and globulin precipitation by the Cohn method and nonspecific hemagglutinin by thermocoagulation. The experimental volume of bovine plasma was 2,000 ml per batch. Final purification was performed by liquid chromatography using the ion-exchange gel DEAE-Sepharose FF. The bovine albumin thus obtained presented > or =99% purity, a yield of 25.0 +/- 1.2 g/l plasma and >71.5% recovery. N-acetyl-DL-tryptophan (0.04 mmol/g protein) and sodium caprylate (0.04 mmol/g protein) were used as stabilizers and the final concentration of albumin was adjusted to 22.0% (w/v), pH 7.2 to 7.3. Viral inactivation was performed by pasteurization for 10 h at 60 degrees C. The bovine albumin for the hemagglutination tests used in immunohematology was submitted to chemical treatment with 0.06% (w/v) glutaraldehyde and 0.1% (w/v) formaldehyde at 37 degrees C for 12 h to obtain polymerization. A change in molecular distribution was observed after this treatment, with average contents of 56.0% monomers, 23.6% dimers, 12.2% trimers and 8.2% polymers. The tests performed demonstrated that this polymerized albumin enhances the agglutination of Rho(D)-positive red cells by anti-Rho(D) serum, permitting and improving visualization of the results.

Characterizing biostructures and cellular events in 2D/3D [using wide-field and confocal optical sectioning microscopy

Cellular structures are made up of a very interesting puzzle of components, whose changes in molecular distribution are believed to underlie a wide range of cellular functions. For example, the cell cycle of mammalian cells is characterised by a series of ordered biochemical events. The availability of several specific probes has led to a renewed interest in optical microscopy as a very powerful tool in cell and molecular biology. This has led to the development of methods for studying the relationship between the 3D structure of specific cellular constituents and the cell function. Within this framework, several methods have been developed and applied. In the authors' study, wide-field optical sectioning microscopy and confocal scanning laser microscopy have been utilised, demonstrating the feasibility of a 3D reconstruction of biostructures imaged by an optical microscope.

Three-dimensional molecular distribution in single cells analysed using the digital imaging microscope

Cellular changes in molecular distribution are believed to underly a wide range of cell functions. In order to investigate changes in molecular distribution in single cells utilizing fluorescent probes we have developed a digital imaging microscope. The system, consisting of both hardware and software, automatically acquires 3-D data sets consisting of optical sections and then processes such data to facilitate the analysis of molecular distribution in single cells. The first major step in processing reverses distortion introduced principally by the optics of the fluorescent microscope. Various procedures for accomplishing this task are compared and a method based on regularization theory is shown to give superior results for several different 3-D images. Following this step features of interest are automatically extracted from 3-D images utilizing an artificial 3-D visual system. This artificial visual system utilize a system of spatial filters to identify regional characteristics of images, the information obtained from these filters being used to identify and characterize clusters of molecules within the image. This information is then utilized to construct a 3-D graphical model of molecular distribution in single cells. Such models are displayed in 3-D and may further analysed utilizing interactive 3-D computer graphics. These methods are illustrated by results obtained regarding alpha-actinin distribution in single smooth muscle cells.

Conversion of sedimentary fatty acids from extractable (unbound + bound) to tightly bound form during mild heating

Prolonged heating (1–248 days) of a recent sediment was conducted under mild conditions (65 and 83°C) to understand the thermal behavior of extractable (unbound and bound) fatty acids (C 12C 32 ). In the course of the heating, the concentrations of saturated and monounsaturated fatty acids first decreased, and then increased. This indicates that extractable fatty acids can be converted to a tightly bound form upon heating, before fatty acids are extensively released from sediment matrices. Changes in molecular distributions of extractable fatty acids upon heating were also observed. The higher molecular weight fatty acids (⩾C 20) are more likely to become tightly bound than are lower molecular weight (<C 20). Monounsaturated fatty acids (C 16:1 and C 18:1) are more easily converted to the tightly bound form than polyunsaturated fatty acids (C 18:2 and C 18:3). These differences probably reflect their mode of occurrence in sediments, which are closely related to their origin.

Use of Porphyrins as a Maturity Parameter for Oils and Sediments

Summary There is considerable interest at present in the use of biological markers, both as maturity parameters for oils and sediments, and oil-oil and oil-source rock correlations. Earlier work on biomarkers concentrated on the distribution of steranes and triterpanes; but with new analytical techniques becoming available other biomarker classes are under investigation, such as aromatics, sulphur compounds and porphyrins. Porphyrins in oils and sediments are probably derived from chlorophylls in algae or photosynthetic bacteria. Until recently, little was known about the structure of geological porphyrins, but now several compounds have been isolated, purified and characterized. Two main types of porphyrins are present, DPEP and ETIO, and it has been shown that with increasing thermal maturity the relative concentration of ETIO-porphyrins increases with respect to DPEP-porphyrins. Thus a measure of ratio (1) in sediments and oils should reveal the thermal maturity of these samples. A suite of oils and related source rocks have been examined, and their porphyrin distributions recorded. Porphyrins show large changes in ratio (1), ranging from 0.8, in the least mature oils, to zero in the most mature oils. Changes in molecular distribution were similar in the sediment extracts, and porphyrins seem to be useful maturation parameters in the range %Ro 0.3 to 0.8; after which they are thermally destroyed.