Intermediate-sized Molecules Research Articles

Cooperative control of intralayer and interlayer space in MOFs enables selective capture of intermediate-sized molecules

Adsorptive separation of the smallest or largest molecules from a mixture can be realized by the sieving effect; however, it is still an arduous task to specifically discriminate between the intermediate-sized component from a complicated multicomponent mixture. Here, we report a strategy via cooperative control of intralayer and interlayer space for selective adsorption of ethane from methane and propane on a 2D-layered MOF termed Ni(4-DPDS)2CrO4. The intralayer channels work as main adsorption sites, while interlayer channels are designed to achieve optimal discrepancy of kinetic diffusion rates. The restricted diffusion of C3H8 in the interlayer channels results in a dramatic inversed, equilibrium-kinetic, combined selectivity for C2H6/C3H8. Mixture breakthrough experiments manifest an efficient capture of C2H6 owing to the equilibrium-kinetic synergetic effect. The mechanism for selective gas adsorption is well supported by kinetic results and crystallography studies, demonstrating that fabrication of MOFs with multiple distinct controllable micropores enables selective capture of intermediate-sized molecules.

HyperBIRD: A Sensitivity‐Enhanced Approach to Collecting Homonuclear‐Decoupled Proton NMR Spectra

AbstractSamples prepared following dissolution dynamic nuclear polarization (DNP) enable the detection of NMR spectra from low‐γ nuclei with outstanding sensitivity, yet have limited use for the enhancement of abundant species like 1H nuclei. Small‐ and intermediate‐sized molecules, however, show strong heteronuclear cross‐relaxation effects: spontaneous processes with an inherent isotopic selectivity, whereby only the 13C‐bonded protons receive a polarization enhancement. These effects are here combined with a recently developed method that delivers homonuclear‐decoupled 1H spectra in natural abundance samples based on heteronuclear couplings to these same, 13C‐bonded nuclei. This results in the HyperBIRD methodology; a single‐shot combination of these two effects that can simultaneously simplify and resolve complex, congested 1H NMR spectra with many overlapping spin multiplets, while achieving 50–100 times sensitivity enhancements over conventional thermal counterparts.

HyperBIRD: a sensitivity-enhanced approach to collecting homonuclear-decoupled proton NMR spectra.

Samples prepared following dissolution dynamic nuclear polarization (DNP) enable the detection of NMR spectra from low-γ nuclei with outstanding sensitivity, yet have limited use for the enhancement of abundant species like (1)H nuclei. Small- and intermediate-sized molecules, however, show strong heteronuclear cross-relaxation effects: spontaneous processes with an inherent isotopic selectivity, whereby only the (13)C-bonded protons receive a polarization enhancement. These effects are here combined with a recently developed method that delivers homonuclear-decoupled (1)H spectra in natural abundance samples based on heteronuclear couplings to these same, (13)C-bonded nuclei. This results in the HyperBIRD methodology; a single-shot combination of these two effects that can simultaneously simplify and resolve complex, congested (1)H NMR spectra with many overlapping spin multiplets, while achieving 50-100 times sensitivity enhancements over conventional thermal counterparts.

The Multicompartmental p32/gClqR as a New Target for Antibody-based Tumor Targeting Strategies

Tumor-associated cell surface antigens and tumor-associated vascular markers have been used as a target for cancer intervention strategies. However, both types of targets have limitations due to accessibility, low and/or heterogeneous expression, and presence of tumor-associated serum antigen. It has been previously reported that a mitochondrial/cell surface protein, p32/gC1qR, is the receptor for a tumor-homing peptide, LyP-1, which specifically recognizes an epitope in tumor cells, tumor lymphatics, and tumor-associated macrophages/myeloid cells. Using antibody phage technology, we have generated an anti-p32 human monoclonal antibody (2.15). The 2.15 antibody, expressed in single-chain fragment variable and in trimerbody format, was then characterized in vivo using mice grafted subcutaneously with MDA-MB-231 human breast cancers cells, revealing a highly selective tumor uptake. The intratumoral distribution of the antibody was consistent with the expression pattern of p32 in the surface of some clusters of cells. These results demonstrate the potential of p32 for antibody-based tumor targeting strategies and the utility of the 2.15 antibody as targeting moiety for the selective delivery of imaging and therapeutic agents to tumors.

Ion Spectroscopy: Where Did It Come From; Where Is It Now; and Where Is It Going?

The ASMS conference on ion spectroscopy brought together at Asilomar on October 16-20, 2009 a large group of mass spectrometrists working in the area of ion spectroscopy. In this introduction to the field, we provide a brief history, its current state, and where it is going. Ion spectroscopy of intermediate size molecules began with photoelectron spectroscopy in the 1960s, while electronic spectroscopy of ions using the photodissociation "action spectroscopic" mode became active in the next decade. These approaches remained for many years the main source of information about ionization energies, electronic states, and electronic transitions of ions. In recent years, high-resolution laser techniques coupled with pulsed field ionization and sample cooling in molecular beams have provided high precision ionization energies and vibrational frequencies of small to intermediate sized molecules, including a number of radicals. More recently, optical parametric oscillator (OPO) IR lasers and free electron lasers have been developed and employed to record the IR spectra of molecular ions in either molecular beams or ion traps. These results, in combination with theoretical ab initio molecular orbital (MO) methods, are providing unprecedented structural and energetic information about gas-phase ions.

Computational dose predictions for combined treatment of hemofiltration with weekly hemodialysis

Hemodialysis (HD) has sufficient efficacy as a conventional diffusive treatment for removing small molecules, whereas hemofiltration (HF), which is a convective treatment, has an improved the clearance of intermediate-sized molecules. This paper reports a combined treatment (CT) which combines the diffusive and convective efficacies of HF several times weekly with HD weekly. CT modalities with various schedules and prescriptions are described mathematically using a variable-volume two-compartment kinetics model, and the kinetic parameters were obtained from previous clinical reports and a hemodialysis-related database. The blood concentration profiles of the three waste molecules for 52 weeks were calculated in order to compare the capability of removing small and intermediate-sized molecules to those of other renal treatments. The results by a computer simulation show that CT can reduce the frequency of sessions and the volume of replacement fluid compared with daily convective treatment, and achieve the adequate treatment efficiency with both small and intermediate-sized molecules for chronic renal failure patients.

BIRD (blackbody infrared radiative dissociation): evolution, principles, and applications.

Blackbody infrared radiative dissociation (BIRD) describes the observation of ion-dissociation reactions at essentially zero pressure by the ambient blackbody radiation field, which is usually studied in the ion-trapping ion cyclotron resonance (ICR) mass spectrometer. A brief summary of the historical context and evolution is provided. Focussing on the quantitative observation of the temperature dependence of BIRD rates, methods are developed for connecting BIRD observations with activation parameters and dissociation thermochemistry. Three regimes are differentiated and described, comprising large molecules, small molecules, and intermediate-sized molecules. The different approaches to interpreting BIRD kinetics in those three regimes are discussed. In less than a decade since its inception, this approach to studying gas-phase ions has spread over a wide variety of applications, which are surveyed. Some major areas of activity are: the characterization of solvent-molecule detachment from solvated ions; dissociation reactions of biomolecules (polypeptides, oligonucleotides, complexes involving polysaccharides) and the structural information to be deduced from them; and dissociations of proton-bound and metal-ion-containing complexes. Studies of blackbody-radiation-driven evaporation of water molecules from large water-cluster ions are surveyed briefly. Several techniques related to BIRD are noted, including collisional dissociation in the FT-ICR ion trap; high-pressure thermal dissociation in quadrupole ion traps and in heated inlet capillary regions; hot-filament-assisted dissociation; and infrared multiphoton dissociation (IRMPD).

Real-Time Imaging of Nuclear Permeation by EGFP in Single Intact Cells

The NPC is the portal for the exchange of proteins, mRNA, and ions between nucleus and cytoplasm. Many small molecules (<10 kDa) permeate the nucleus by simple diffusion through the pore, but molecules larger than 70 kDa require ATP and a nuclear localization sequence for their transport. In isolated Xenopus oocyte nuclei, diffusion of intermediate-sized molecules appears to be regulated by the NPC, dependent upon [Ca 2+] in the nuclear envelope. We have applied real-time imaging and fluorescence recovery after photobleaching to examine the nuclear pore permeability of 27-kDa EGFP in single intact cells. We found that EGFP diffused bidirectionally via the NPC across the nuclear envelope. Although diffusion is slowed ∼100-fold at the nuclear envelope boundary compared to diffusion within the nucleus or cytoplasm, this delay is expected for the reduced cross-sectional area of the NPCs. We found no evidence for significant nuclear pore gating or block of EGFP diffusion by depletion of perinuclear Ca 2+ stores, as assayed by a nuclear cisterna-targeted Ca 2+ indicator. We also found that EGFP exchange was not altered significantly during the cell cycle.

Visualization of electronic and vibrational polarizabilities and hyperpolarizabilities

At the molecular level of any observed nonlinear optical behavior, one finds the polarizability and hyperpolarizability tensors. These quantities are nowadays easily calculated for small- to intermediate-sized molecules. However, to gain further insight into these properties, pictorial approaches are valuable. Here we extend the work of Chopra et al. [J. Phys. Chem., 93, 7120 (1989)] to obtain a method that may be used in order to understand how average (hyper)polarizabilities are distributed over the molecular frame. The pictures obtained represent (hyper)polarizability moments and give a description of local contributions to the total electric property. Furthermore, the formal foundations of the proposed method are developed to be used to represent both the electronic and the vibrational components of the (hyper)polarizabilities. The theory is applied to a series of push–pull polyenes. One important conclusion is the lack of any similarity between the electronic and vibrational pictorializations of either the polarizability or the first hyperpolarizability. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 78: 348–377, 2000

Conformational Changes of the in Situ Nuclear Pore Complex

By bridging the double membrane separating the cell nucleus and cytoplasm, nuclear pore complexes (NPCs) are crucial pathways for the exchange of ions, proteins, and RNA between these two cellular compartments. A structure in the central lumen of the NPC, called the nuclear transport protein, central granule, or nuclear plug, appeared to gate diffusion of intermediate-sized molecules (10–40 kDa) across the nuclear membranes. Visualization of the NPC required drying and fixation of the specimen for electron and atomic force microscopy (AFM), a requirement that has raised doubts about the physiological relevance of the observation. Here we present AFM images of the outer nuclear membranes and NPCs of Xenopus laevis oocytes under more physiological conditions. Measured under a variety of Ca2+ depletion conditions, the central granule appeared to occupy and occlude the lumen of the pore in >80% of NPCs compared to <10% in controls. In a few instances images were obtained of the same NPCs as the solution was changed from control saline to store depletion conditions, and finally to store repletion conditions. We conclude that the central lumen of the nuclear pore complex undergoes a conformational change in response to depletion of nuclear cisternal Ca2+ levels.

Nuclear calcium and the regulation of the nuclear pore complex

In eukaryotic cells the nucleus and its contents are separated from the cytoplasm by the nuclear envelope. Macromolecules, as well as smaller molecules and ions, can cross the nuclear envelope through the nuclear pore complex. Molecules greater than approx. 60 kDa and containing a nuclear localization signal are actively transported across the nuclear membranes, but there has been little evidence for regulatory mechanisms for smaller molecules and ions. Recently, diffusion across the nuclear envelope has been observed to be regulated by nuclear cisternal Ca2+ concentrations. Following depletion of Ca2+ from the nuclear store by inositol 1,4,5-trisphosphate or Ca2+ chelators, a fluorescent 10 kDa marker molecule was no longer able to enter the nucleus. Distinct conformational states of the nuclear pore complexes depended on the Ca2+ filling state of the nuclear envelope, supporting the assumption that a switch in the conformation of the nuclear pore complex may control the transport of intermediate-sized molecules across the nuclear envelope. Thus nuclear Ca2+ stores may regulate the conformational state of the nuclear pore complex, and thereby passive diffusion of molecules between the cytosol and the nucleoplasm. The physiological significance of this finding is currently unknown.

Conformational States of the Nuclear Pore Complex Induced by Depletion of Nuclear Ca 2+ Stores

The nuclear pore complex (NPC) is essential for the transit of molecules between the cytoplasm and nucleoplasm of a cell and until recently was thought to allow intermediate-sized molecules (relative molecular mass of approximately 10,000) to diffuse freely across the nuclear envelope. However, the depletion of calcium from the nuclear envelope of Xenopus laevis oocytes was shown to regulate the passage of intermediate-sized molecules. Two distinct conformational states of the NPC were observed by field emission scanning electron microscopy and atomic force microscopy. A central plug occluded the NPC channel after nuclear calcium stores had been depleted and free diffusion of intermediate-sized molecules had been blocked. Thus, the NPC conformation appears to gate molecular movement across the nuclear envelope.

Diffusion Across the Nuclear Envelope Inhibited by Depletion of the Nuclear Ca 2+ Store

Intact, isolated nuclei and a nuclear membrane (ghost) preparation were used to study regulation of the movement of small molecules across the Xenopus laevis oocyte nuclear membrane. In contrast to models of the nuclear pore complex, which assume passive bidirectional diffusion of molecules less than 70 kilodaltons, diffusion of intermediate-sized molecules was regulated by the nuclear envelope calcium stores. After depletion of nuclear store calcium by inositol 1,4,5-trisphosphate or calcium chelators, fluorescent molecules conjugated to 10-kilodalton dextran were unable to enter the nucleus. Dye exclusion after calcium store depletion was not dependent on the nuclear matrix because it occurred in nuclear ghosts lacking nucleoplasm. Smaller molecules and ions (500-dalton Lucifer yellow and manganese) diffused freely into the core of the nuclear ghosts and intact nuclei even after calcium store depletion. Thus, depletion of the nuclear calcium store blocks diffusion of intermediate-sized molecules.

Partially N-Deacetylated Chitin Fragments are Strong Elicitors for (+)-Pisatin Induction in Epicotyls of Pea

Abstract Chitosan derivatives classed into three groups according to their molecular size were examined for the relationships between degree of N -acetylation and phytoalexin (+)-pisatin-inducing activity in pea epicotyl assay. Partially N-deacetylated chitin with degree of N-acetylation 56% (DAC 56%) was the most potent inducer of (+)-pisatin among sparingly water-soluble polysaccharides including chitosan (degree of N -acetylation 0%), DAC 32%, and chitin. Among the intermediate-sized molecules obtained from degradation of the chitosan and the DACs by NaNO2, the chitosan fragment was the most powerful elicitor for (+)-pisatin induc­tion. The NaNO2-degraded DAC 56% exhibited a com parable activity to the NaNO2 -degrad-ed chitosan at low concentrations. The NaNO2-degraded fragments as well as the native poly­mer induced a relatively high amount of (+)-pisatin, while the acetone precipitate of chitosan oligomers from the HCl-catalyzed hydrolysate and their partially N-acetylated derivatives ex­hibited a moderate (+)-pisatin-inducing activity. These findings suggest the possibility that partially N-deacetylated chitin fragments could be one of the most promising elicitors in the pea system.

Elevation of rat intestinal permeability by enterotoxigenic Escherichia coli in comparison to non-toxigenic E. coli and Salmonella typhimurium. Application of fluorescent dextran 3000 as permeability probe

The effect of bacterial enterotoxins on rat intestinal permeability properties was studied by comparing the effect of toxin-positive and toxin-negative Escherichia coli and Salmonella typhimurium inoculated into a segment of rat small intestine. Fluoresceinated dextran 3000 (FITC-D3; Mr 3000) was applied as permeability marker. The E. coli strain C922a-1 producing heat-labile (LT) and heat-stable (ST) enterotoxins and colonising factor CFA/II increased the transmural passage of the dextran probe into portal blood. In contrast, its plasmid-negative variant, a non-toxin producer lacking CFA, caused permeability changes indistinguishable from the bacteria-free nutrient broth control. Another pair of enterotoxigenic E. coli strains, 1628–14 (LT+, ST+, CFA/I+) and 1628–15 (LT+, ST− and CFA/I−) both increased the intestinal permeability. The observations indicate that the LT+-only E. coli strain 1628–15 has the ability to promote permeability of rat intestine. The toxin-negative, rough S. typhimurium 395MR10 bacteria had a very small effect on the permeability, which was also achieved with culture filtrate only. It is concluded that enterotoxigenic E. coli (ETEC) can alter the properties of the mucosal barrier towards intermediate-sized molecules that could be of antigenic significance, or which could play a crucial role in the nutritional status of the host organism.

Elevation of rat intestinal permeability by enterotoxigenicEscherichia coliin comparison to non-toxigenicE. coliandSalmonella typhimurium. Application of fluorescent dextran 3000 as permeability probe

The effect of bacterial enterotoxins on rat intestinal permeability properties was studied by comparing the effect of toxin-positive and toxin-negativeEscherichia coli andSalmonella typhimurium inoculated into a segment of rat small intestine. Fluoresceinated dextran 3000 (FITC-D3; Mr 3000) was applied as permeability marker. TheE. coli strain C922a-1 producing heat-labile (LT) and heat-stable (ST) enterotoxins and colonising factor CFA/II increased the transmural passage of the dextran probe into portal blood. In contrast, its plasmid-negative variant, a non-toxin producer lacking CFA, caused permeability changes indistinguishable from the bacteria-free nutrient broth control. Another pair of enterotoxigenicE. coli strains, 1628-14 (LT+, ST+, CFA/I+) and 1628-15 (LT+, ST− and CFA/I−) both increased the intestinal permeability. The observations indicate that the LT+-onlyE. coli strain 1628-15 has the ability to promote permeability of rat intestine. The toxin-negative, roughS. typhimurium 395MR10 bacteria had a very small effect on the permeability, which was also achieved with culture filtrate only. It is concluded that enterotoxigenicE. coli (ETEC) can alter the properties of the mucosal barrier towards intermediate-sized molecules that could be of antigenic significance, or which could play a crucial role in the nutritional status of the host organism.

Analysis of replicating vaccinia DNA in interferon-treated, virus-infected cells.

The effect of interferon (IFN) on the replication of vaccinia DNA has been examined. Studies were carried out in infected mouse L cells grown in monolayer cultures. We examined discontinuous synthesis of small DNA fragments, ligation of the small fragments to form intermediate-sized DNA molecules, completion of unit-length DNA molecules, and introduction of crosslinks at each end of the newly replicated DNA molecules late in infection. We measured by pulse-label and pulse-chase experiments the extent of incorporation of 3H-thymidine into DNA and the conversion of small size DNA into mature and cross-linked viral DNA molecules. Interferon inhibited the initiation of viral DNA and this correlated with an overall inhibition of protein synthesis. Interferon inhibited elongation of viral DNA but this did not correlate with an inhibition of protein synthesis. The effect on elongation was not the result of increased degradation of newly synthesized DNA. It is suggested that the effects of IFN on initiation and elongation of vaccinia DNA may be the result of a decrease in the availability of enzymes or factors involved in the regulation of viral DNA synthesis.

Composite separation units and their application in dialysis for the isolation of intermediate-sized molecules

Composite separation units (i.e. assemblages of similar elementary separation units) are studied. Dialysis is used as an example of a basic unit. The overall input-output response of a composite group made up of a system of interconnected dialyzers is developed in relation to the system configuration. In certain flow configurations, a composite dialyzer has the permeability characteristics of a band-pass filter. Since the selectivity of composite dialyzer systems can be amplified by repeating the units in a cascading manner, a specific solute of intermediate permeability can, in principle, be extracted from a complex multicomponent solution.

Localisation of an Endonuclease Specific for Double‐Stranded RNA within the Nucleolus and Its Implication in Processing Ribosomal Transcripts

Nucleoli of both chick embryos and mouse Ehrlich ascites cells contain an enzymatic activity that is very similar to RNase DII, an enzyme isolated from total chick embryos for its ability to degrade double-stranded RNA. The enzyme can be extracted by low salt/EDTA from nucleoli and is associated with pre-ribosomal 80-S and 55-S particles. Under ionic conditions which are inhibitory for the nucleolytic activity the transcript in vitro of nucleoli is not processed and sediments around 45 S. Under salt conditions which are optimal for the nucleolar enzyme the nucleolar transcripts are cleaved to distinct intermediate-sized molecules. Addition of the chicken RNase DII or RNase III to the nucleolar transcription system results in a similar shift of the chain length of the RNA molecules. It is concluded that a nucleolar RNase recognizing double-stranded regions in the pre-ribosomal RNA is involved in the maturation of ribosomal RNA.

PATHOGENESIS OF MEMBRANOUS GLOMERULONEPHRITIS

It is suggested that the morphological differences between various types of immune-complex nephritis (e.g., systemic lupus erythematosus, membranous glomerulonephritis) can be explained by differential filtration effects in the glomerulus. Low-molecular-weight compounds, such as horseradish peroxidase (40,000), show negligible concentration effects. Intermediate-sized molecules, such as myeloperoxidase (molecular weight 160,000), are concentrated slightly in the lumen, more in the mesangium, and markedly below the epithelial-foot processes. High-molecular-weight compounds, such as ferritin (400,000), enter the membrane in only low concentration but accumulate in the mesangium. When an antigen is of low molecular weight, it will behave like horseradish peroxidase; IgG and IgA antibody will behave like myeloperoxidase; and small complexes and high-molecular-weight antigen will behave like ferritin. Membranous glomerulonephritis will be produced by a pronounced excess of a low or high molecular-weight antigen, equivalence occurring only in the subepithelial zone. Mesangial deposition will occur with moderate excess of low-molecular-weight antigen, where the precipitation is favoured by the concentration of antibody and small complexes. It will also be seen with high-molecular-weight antigen in antibody excess when antigen and complexes accumulate at that site. Subendothelial deposits will result from near equivalence, especially with reduced renal blood-flow.