Evaluation of chemiluminescent estradiol conjugates by using a surface plasmon resonance detector

A series of chemiluminescent 17beta-estradiol probes were synthesized. Relative equilibrium dissociation constants (K(D)) for the interaction of an anti-E(2) Fab fragment for the probes in solution were evaluated using a single E(2)-analog biosensor surface on a BIAcore surface plasmon resonance instrument. The results show the antibody fragment binds all chemiluminescent conjugates tested with high affinity showing only minor preferences for site of substitution (C6 versus C7), stereochemistry (alpha versus beta), or linker moiety.     

Mobile larynx in Mongolian gazelle: Retraction of the larynx during rutting barks in male Mongolian gazelle (Procapra gutturosa Pallas, 1777)

This study provides the first evidence of pronounced temporary laryngeal descent in a bovid species. An elaborate acoustic display is prominent in male courtship behavior of polygynous Mongolian gazelle. During rut, rounding up of females is accompanied by continuous head‐up barking by dominant males. Throughout the rut their evolutionarily enlarged larynx descends to a low mid‐neck resting position. In the course of each bark the larynx is additionally retracted toward the sternum by 30% of the resting vocal tract length. A geometric model of active larynx movements was constructed by combining results of video documentation, dissection, skeletonization, and behavioral observation. The considerable distance between resting position and maximal laryngeal descent suggests a backward tilting of the hyoid apparatus and an extension of the thyrohyoid connection during the retraction phase. Return to the resting position is effected by strap muscles and by the elastic recoil of the pharynx and the thyrohyoid connection. An intrapharyngeal inflation of the peculiar palatinal pharyngeal pouch of adult males is inferred from a short‐time expansion of the ventral neck region rostral to the laryngeal prominence. The neck of adult dominant males is accentuated by long gray guard hairs during the rut. The passive swinging of the heavy larynx of adult males during locomotion gives the impression of a handicap imposed on rutting males. Apparently, this disadvantage becomes outweighed by the profits for reproductive success. J. Morphol., 2008. © 2008 Wiley‐Liss, Inc.     

Integration of multidimensional chromatographic protein separations with a combined "top-down" and "bottom-up" proteomic strategy

In this paper, we present a combined top-down/bottom-up proteomic analysis workflow for the characterization of proteomic samples. This workflow combines protein fractionation (multidimensional chromatographic separation) with parallel online ESI-TOF-MS intact protein analysis, and fraction collection. Collected fractions were digested and protein identifications were produced using MALDI Q-TOF-MS analysis. These identifications were then linked with corresponding ESI-TOF-MS intact protein mass data to permit full protein characterization. This methodology was applied to an E. coli cytosolic protein fraction, and enabled the identification and characterization of proteins exhibiting co-translational processing, post-translational modification, and proteolytic processing events. The approach also provided the ability to distinguish between closely related protein isoforms. The summary of results from this study indicated that roughly one-third of all detected components generated corresponding data from both top-down and bottom-up analyses, and that significant and novel information can be derived from this application of the hybrid analytical methodology.     

Increased Ca++ or mg++ concentration reduces relative tight-junction permeability to Na+ in the cortical thick ascending limb of Henle's loop of rabbit kidney

We have tested whether increased Ca++ and Mg++ concentrations have an effect on transepithelial voltage (PDte) and transepithelial resistance (Rte) in isolated perfused cortical thick ascending limbs (cTAL) of rabbit kidney. The divalent cations added at 2.5, 5.0 and 10.0 mmol.l-1 to the lumen or peritubular bath perfusate led to a concentration-dependent increase in Rte. The maximal response in Rte was observed between 5 and 10 mmol.l-1. No significant change in active transepithelial potential difference (PDte) was observed. The increase in Rte still occurred when the transcellular current was reduced by Ba++ (3 mmol.l-1) added to the lumen perfusate. This suggests that the increase in Rte caused by Ca++ and Mg++ is due to a modification of the paracellular shunt pathway. In the absence of active transport, i.e. when furosemide (5.10(-5) mol.l-1) was added to the lumen perfusate. Ca++ and Mg++ reduced the transepithelial diffusion potential generated by a NaCl gradient established across the epithelium, and thus produced a reduction of the relative permeability for Na+ over Cl- (PNa+/PCl-) of the paracellular shunt pathway. This indicates that divalent cations increase Rte by reducing the sodium permeability of the tight junctions. The observed Ca++ and Mg++ induced reduction of the sodium permeability of the paracellular pathway corresponds to a decrease in net Na+ reabsorption by 5-10%. Since it has been demonstrated that peptide hormones such as parathyrin (PTH) modulate divalent cation and NaCl reabsorptions, in a second series of experiments we tested the effects of PTH (2-20 USP.l-1) and dbcAMP (10(-3) mol.l-1) on PDte and Rte of isolated perfused cTAL segments of rabbit nephron. Neither Rte nor PDte were affected by PTH or dbcAMP.     

Reversed-phase ion-pair liquid chromatography analysis and purification of small interfering RNA

Small interfering RNA (siRNA)-induced gene silencing shows great promise in genomic research and therapeutic applications. siRNA duplexes are typically assembled from complementary synthetic oligonucleotides. High-purity single-stranded species are required for in vivo applications. Methods for separation, characterization, and purification of short RNA strands have been developed based on reversed-phase ion-pair liquid chromatography. The purification strategies were developed for both single-stranded and duplex RNA species. The method of duplex purification uses on-column annealing of complementary RNA strands, followed by separation of the target duplex from truncated duplexes and single-stranded RNA forms. The proposed method significantly reduces the purification time of synthetic siRNA.     

Characterization of therapeutic oligonucleotides using liquid chromatography with on-line mass spectrometry detection

A method for the analysis and characterization of therapeutic and diagnostic oligonucleotides has been developed using a combination of liquid chromatography and mass spectrometry (LC-MS). The optimized ion-pairing buffers permit a highly efficient separation of native and chemically modified antisense oligonucleotides (AS-ODNs) from their metabolites or failure synthetic products. The mobile phases were MS compatible, allowing for direct and sensitive analysis of components eluting from the column. The method was applied for the quantitation and characterization of AS-ODNs, including phosphorothioates and 2'-O-methyl-modified phosphorothioates. Tandem LC-MS analysis confirmed the identity of the oligonucleotide metabolites, failure products, the presence of protection groups not removed after synthesis, and the extent of depurination or phosphorothioate backbone oxidation.     

Region-selective labeling of antibodies as determined by electrospray ionization-mass spectrometry (ESI-MS)

The electrospray ionization-mass spectrometry (ESI-MS) analysis of three sets of monoclonal antibody-acridinium-9-carboxamide conjugates is described. The conjugates (nine total) were enzymatically digested using papain and the resulting fragments [Fc heavy chain, Fab, or F(ab')(2)] were analyzed using liquid chromatography/ESI-MS. The average number of labels per fragment were calculated using Sigma nx%, where n is the number of acridinium molecules covalently bound to the fragment and x% is the percent relative area of the corresponding peaks in the mass spectrum. When these values were normalized against the molecular weight of their respective region, antibody-dependent labeling patterns were observed. For antibodies T (anti-L-T(4)) and F (anti-FITC), there was a preference for conjugation of the Fab region over the Fc region. For antibody B (anti-biotin), the trend was reversed.     

A chemoselective method for site-specific immobilization of peptides via aminooxy group

Site-specific modification of peptides and proteins is an important area of basic research for preparation of well-defined biosensors and probes. The unique properties of aminooxy group present an opportunity for chemoselective site-specific immobilization of peptides to prepare well-defined biosensors. We have prepared FLAG peptide derivatives containing L-epsilon-aminooxylysine (L-epsilon-AOLys, 1a) and L-lysine units in their sequence at the C- and N-terminals via solid-phase synthesis. Site-specific modification of peptides through aminooxy group was demonstrated in the preparation of biosensors and selective conjugation in the preparation of biotinylated probes. Effect of the incorporation of L-epsilon-AOLys (1a) into the peptide sequence and its subsequent labeling on the FLAG epitopic character was measured using a surface plasmon resonance detector. It was found that incorporation of L-epsilon-AOLys (1a) into the FLAG peptide and site-specific immobilization through aminooxy group preserved the integrity of FLAG epitope.     

Artificial neural network modelling of macrophyte indices based on physico-chemical characteristics of water

The study focused on modelling of macropyte indices against physico-chemical parameters of waters by artificial neural networks. Several macrophyte diversity indices were analysed (species richness—N, the Shannon index—H′, the Simpson index—D, and the Pielou index—J) as well as the ecological status index (the Macrophyte Index for Rivers—MIR). The aim of the study was to verify knowledge about potential application of macrophytes in the environmental monitoring. A Multi-Layer Perceptron type of network was used in the analyses. The study included 260 river sites located throughout Poland. Alkalinity, conductivity, pH, nitrate and ammonium nitrogen, reactive and total phosphorus, and biochemical oxygen demand were used as the explanatory variables. The quality of the constructed models was assessed using calculated errors (RMSE and NRMSE) and r Pearson’s linear correlation coefficient. The neural network for the MIR index was characterised by the highest quality. Neural networks for other diversity indices (N, H′, D, and J) did not provide adequate results for modelling, which shows their ineffectiveness biological monitoring. Sensitivity analysis revealed the influence of each variable to the models. It indicated that modelled values of MIR are most strongly influenced by total phosphorus and alkalinity.     

Glu-537, not Glu-461, is the nucleophile in the active site of (lac Z) beta-galactosidase from Escherichia coli.

The covalent intermediate formed during catalysis by the lac Z beta-galactosidase from Escherichia coli can be trapped by reaction of the enzyme with 2',4'-dinitrophenyl 2-deoxy-2-fluoro-beta-D-galactopyranoside, thereby inactivating the enzyme. Kinetic parameters for this inactivation process with the holo- and apo-enzymes have been determined. The intermediate so formed turns over only very slowly (t1/2 = 11.5 h) resulting in reactivation of the enzyme. The nucleophilic amino acid involved has been identified as Glu-537 by using a tritium-labeled inactivator to label the enzyme, then cleaving the labeled protein into peptides and purifying and sequencing the labeled peptide. This residue is conserved in five homologous beta-galactosidases and is different from that (Glu-461) proposed to be the nucleophile (Herrchen, M., and Legler, G. (1984) Eur. J. Biochem. 138, 527-531) on the basis of affinity labeling studies with conduritol C cis-epoxide. A role for glutamic acid residue 461 as the acid/base catalyst is proposed and justified.