A rapid boiling method for the preparation of bacterial plasmids

Compounds separated on polyamide thin-layers and located in an appropriate manner can be introduced directly into the ion source of the mass spectrometer together with the chromatographic polyamide adsorbent. In spite of the large excess of polyamide, excellent mass spectra are obtained exhibiting low backgrounds. In this way, organic compounds can be rationally identified on a nanogram scale not requiring reference substances. The application of the procedure is described for selected compounds of different classes of substances, e.g., phenols, steroids, nucleosides, biogenic amines, and amino acids.     

Functional dyspepsia and nonerosive reflux disease: clinical interactions and their implications

Functional dyspepsia or nonulcer dyspepsia, and nonerosive reflux disease (NERD) or endoscopy-negative reflux disease, are common reasons for referral to a gastroenterologist. Although there is much confusion with regard to definition, recent research would suggest that these 2 conditions are linked and may represent components in the spectrum of the same disease entity, in terms of both symptoms and pathophysiology. Several theories have been proposed regarding the etiology of these disorders, including acid exposure, visceral hypersensitivity, impaired fundal accommodation, delayed gastric emptying, and Helicobacter pylori infection.     

The mode of host-parasite interaction shapes coevolutionary dynamics and the fate of host cooperation

Antagonistic coevolution between hosts and parasites can have a major impact on host population structures, and hence on the evolution of social traits. Using stochastic modelling techniques in the context of bacteria-virus interactions, we investigate the impact of coevolution across a continuum of host-parasite genetic specificity (specifically, where genotypes have the same infectivity/resistance ranges (matching alleles, MA) to highly variable ranges (gene-for-gene, GFG)) on population genetic structure, and on the social behaviour of the host. We find that host cooperation is more likely to be maintained towards the MA end of the continuum, as the more frequent bottlenecks associated with an MA-like interaction can prevent defector invasion, and can even allow migrant cooperators to invade populations of defectors.     

Activity-based protein profiling implicates urokinase activation as a key step in human fibrosarcoma intravasation

Entry of malignant cells into the vasculature (i.e. intravasation) requires proteolytic remodeling of the extracellular matrix so that tumor cells may pass through the local stroma and penetrate the vessel wall. The circulatory system then provides a means of transporting tumor cells to distant sites where they extravasate and establish metastatic lesions. This study utilizes activity-based protein profiling to compare the active serine hydrolase repertoire in high intravasating (HT-hi/diss) and low intravasating (HT-lo/diss) variants of the human fibrosarcoma HT-1080 cell line to determine which enzyme(s) play a role in intravasation. Activity-based protein profiling revealed multiple serine hydrolases with altered activity between HT-hi/diss and HT-lo/diss cells, with the largest difference being the activity of urokinase-type plasminogen activator (uPA). Levels of inactive uPA zymogen were similar between the two cell variants, but only HT-hi/diss conditioned medium contained active uPA, suggesting that uPA activation may contribute to the enhanced intravasation of HT-hi/diss cells. To analyze the role of uPA activity specifically in the process of intravasation, we grafted cells from the two HT-1080 variants onto the chorioallantoic membrane of chick embryos and measured levels of tumor cell intravasation in the distal chorioallantoic membrane using quantitative human-specific Alu PCR. Inhibition of uPA activity with natural (plasminogen activator inhibitor-1) or synthetic (amiloride) inhibitors diminished HT-hi/diss Matrigel invasion in vitro and intravasation and metastasis in vivo. Additionally, treatment of HT-lo/diss tumors with exogenous active uPA increased the number of intravasated cells in vivo. These results indicate that active uPA promotes tumor cell intravasation and that uPA activation appears to be a key step in tumor progression.     

Identification of novel, orally bioavailable spirohydantoin CGRP receptor antagonists

A rapid analogue approach to identification of spirohydantoin-based CGRP antagonists provided novel, low molecular weight leads. Modification of these leads afforded a series of nanomolar benzimidazolinone-based CGRP receptor antagonists. The oral bioavailability of these antagonists was inversely correlated with polar surface area, suggesting that membrane permeability was a key limitation to absorption. Optimization provided compound 12, a potent CGRP receptor antagonist (K_i = 21 nM) with good oral bioavailability in three species.     

A Novel Mode of Intervention with Serine Protease Activity: TARGETING ZYMOGEN ACTIVATION*

Serine proteases are secreted from cells as single-chain zymogens, typically having activities orders of magnitude lower than those of the mature two-chain enzymes. Activation occurs by a conformational change initiated by cleavage of a specific peptide bond. We have derived a monoclonal antibody (mAb-112) which binds with subnanomolar affinity to pro-uPA, the zymogen form of urokinase-type plasminogen activator (uPA). We mapped the epitope of the antibody to the autolysis loop, one of the structural elements known to change conformation during zymogen activation. A mechanistic evaluation with biophysical methods elucidated a novel bifunctional inhibitory mechanism whereby mAb-112 not only delays the proteolytic conversion of single-chain pro-uPA into the two-chain form but also subsequently averts the conformational transition to a mature protease by sequestering the two-chain form in a zymogen-like, noncatalytic state. Functional studies employing two variants of human HT-1080 cells, exhibiting high and low levels of dissemination in a chorioallantoic membrane assay, demonstrate that mAb-112 is an effective inhibitor of tumor cell intravasation. These findings show that pharmacological interference with zymogen activation is a plausible and robust means to regulate uPA activity and the downstream effects of plasminogen activation in the spread of cancer and other processes of pathological tissue remodeling. A strategy that targets regions related to pro-enzyme activation likely provide a unique inhibitor-protease interaction surface and is, thus, expected to enhance the chances of engineering high inhibitor specificity. Our results provide new information about the structural flexibility underlying the equilibrium between active and inactive forms of serine proteases.In nature a key mechanism for regulation of serine proteases with a trypsin-like fold is the activation of secreted zymogens or proenzymes, which typically have activities orders of magnitude lower than the mature enzymes. Zymogen activation is the central step in natural protease cascade regulation, allowing for rapid amplification of the activation signal. The catalytic activity of a zymogen relative to the mature protease can generally be thought of as a problem of equilibrium between active and inactive conformational states of the protease domain. Zymogen activation generally occurs by cleavage of the bond between amino acid residues 15 and 16.² The liberated amino terminus inserts into a hydrophobic binding cleft of the catalytic domain forming, in addition to hydrophobic interactions, a salt bridge to the side chain of Asp¹⁹⁴ which stabilizes the substrate binding pocket and oxyanion hole in a catalytically productive conformation. Conformational changes after cleavage involves four disordered regions of the activation domain, including the activation loop (residues 16-21), the autolysis loop (residues 142-152), the oxyanion stabilizing loop (residues 184-194), and the S1 entrance frame (residues 216-223) (Fig. 1A) (for reviews, see Refs. 1-3).Open in a separate windowFIGURE 1.Three-dimensional structure of uPA. A, overview of the three-dimensional structure of the serine protease domain of active uPA, displayed as ribbons. Depicted as sticks are the residues Ile¹⁶, Asp¹⁹⁴, and Ser¹⁹⁵. The activation domain, i.e. the activation loop (residues 16-21), the autolysis loop (residues 142-152), the oxyanion stabilizing loop (residues 184-193), and the S1 entrance frame (residues 216-223) are colored green. B, the epitope of mAb-112, displayed on a surface presentation of the serine protease domain of active uPA. Alanine substitution of residues depicted in red resulted in a significant change in the affinity to mAb-112, whereas alanine substitution of residues depicted in blue did not. C, a close up view of the autolysis loop (residues Gly¹⁴¹ to Lys¹⁵⁶) and residues implicated in the binding of mAb-112. All figures were constructed with Pymol on the basis of the coordinates given in the PDB entry 1C5W.Several proteases contribute to a variety of pathophysiological states, thus stimulating considerable interest in the design of specific inhibitors for pharmacological intervention. Nonetheless, classical development of small molecule inhibitors of serine proteases has proved a daunting task, with only limited success in engineering inhibitors with high affinity and specificity for related proteases possessing conserved active site architecture and P1³ specificity (4, 5). Thus far targeting zymogen activation instead of the mature protease has been a greatly under-exploited strategy in therapeutic regulation of protease activity. This approach provides an opportunity to target more unique interaction surfaces, thereby increasing inhibitor specificity, and ultimately offering novel inhibitory mechanisms. In addition, a more efficient inhibition is expected by targeting enzymes functioning high up in a catalytic cascade.A serine protease of particular relevance for pursuing therapeutic intervention is urokinase-type plasminogen activator (uPA),⁴ which catalyzes the conversion of plasminogen to the active protease plasmin, which in turn acts directly on the degradation of extracellular matrix proteins (6). Abnormal expression of uPA is implicated in tissue remodeling in several pathological conditions, including rheumatoid arthritis, allergic vasculitis, and xeroderma pigmentosum. In particular, uPA is central to the invasive capacity of malignant tumors (6). As with all trypsin-like proteases, uPA has a catalytic serine protease domain with surface-exposed loops around residues 37, 60, 97, 110, 170, and 185. Besides the catalytic domain, uPA has an amino-terminal extension consisting of a kringle domain and an epidermal growth factor domain. The latter domain functions in binding to the cell surface-anchored uPA receptor (uPAR) (6). Several proteases including plasmin (6), glandular kallikrein (7), matriptase (8), and hepsin (9) can catalyze the activation of the zymogen, pro-uPA.A number of inhibitors targeting the proteolytic activity of uPA have been developed, such as small organochemical molecules, peptides, and monoclonal antibodies, with a perspective on their use for elucidating the pathophysiological functions of its various molecular interactions and generating leads during drug development. The most specific inhibitors to date appear to be those derived from antibodies and peptidyl inhibitors, which utilize binding sites involving surface loops of uPA and extended exosite interactions to drive selectivity and specificity (for reviews, see Refs. 4 and 5).Here we present evidence that targeting zymogen activation is an effective means to regulate protease activity. This conclusion was realized through the development and biochemical analysis of an inhibitory monoclonal antibody, referred to as monoclonal antibody (mAb)-112, which not only delays cleavage of pro-uPA but acts to stabilize the activated two-chain protease in a non-catalytic conformation by restricting the conformational mobility of the activation domain. Characterization of mAb-112 further provides new insights into the flexibility of protease domains and uPA zymogen activation mechanisms. Moreover, mAb-112 was shown to efficiently inhibit human tumor cell intravasation, a step in the metastatic cascade in which activation of pro-uPA was previously implicated as a key event (10).     

Isolation of lactobacilli with probiotic properties from the human stomach

Aims: Recent evidence suggests that the human gastric microbiota is much more diverse than previously thought. The aim of this study was to assess the potential for isolating lactobacilli from the human stomach. Methods and Results: Lactobacilli were selectively cultured from gastric biopsies from 12 patients undergoing routine endoscopy. Lactobacilli were present in four of 12 biopsies. We isolated, in total 10 different strains representing five species (Lactobacillus gasseri, L. fermentum, L. vaginalis, L. reuteri and L. salivarius). The 10 isolates varied greatly in their ability to inhibit the growth of two Gram‐positive bacteria and two Gram‐negative bacteria. Furthermore, the acid and bile resistance profiles of the 10 isolates spanned a wide range. Conclusions: Five different Lactobacillus species were cultured from human gastric biopsies for the first time. Significance and Impact of the Study: Diverse Lactobacillus species are more prevalent in the human stomach than previously recognized, representing an untapped source of bacteria with beneficial probiotic and/or biotechnological properties.