Porphyromonas gingivalis DPP-7 represents a novel type of dipeptidylpeptidase

A novel dipeptidylpeptidase (DPP-7) was purified from the membrane fraction of Porphyromonas gingivalis. This enzyme, with an apparent molecular mass of 76 kDa, has the specificity for both aliphatic and aromatic residues in the P1 position. Although it belongs to the serine class of peptidases, it does not resemble other known dipeptidylpeptidases. Interestingly, the amino acid sequence around the putative active site serine residue shows significant similarity to the C-terminal region of the Staphylococcus aureus V-8 endopeptidase. The genes encoding homologues of DPP-7 were found in genomes of Xylella fastidiosa, Shewanella putrefaciens, and P. gingivalis. It is likely that at least in P. gingivalis, DPP-7 and its homologue, in concert with other di- and tripeptidases, serve nutritional functions by providing dipeptides to this asaccharolytic bacterium.

Life in transition: balancing inertial and viscous forces by planktonic copepods

Copepods (1-10 mm aquatic crustaceans moving at 1-1000 mm s(-1)) live at Reynolds numbers that vary over 5 orders of magnitude, from 10(-2) to 10(3). Hence, they live at the interface between laminar and turbulent regimes and are subject to the physical constraints imposed by both viscous and inertial realms. At large scales, the inertially driven system enforces the dominance of physically derived fluid motion; plankton, advected by currents, adjust their life histories to the changing oceanic environment. At Kolmogorov scales, a careful interplay of evenly matched forces of biology and physics occurs. Copepods conform or deform the local physical environment for their survival, using morphological and behavioral adaptations to shift the balance in their favor. Examples of these balances and transitions are observed when copepods engage in their various survival tasks of feeding, predator avoidance, mating, and signaling. Quantitative analyses of their behavior give measures of such physical properties of their fluid medium as energy dissipation rates, molecular diffusion rates, eddy size, and eddy packaging. Understanding the micromechanics of small-scale biological-physical-chemical interactions gives insight into factors influencing large-scale dynamics of copepod distribution, patchiness, and encounter probabilities in the sea.

Emerging family of proline-specific peptidases of Porphyromonas gingivalis: purification and characterization of serine dipeptidyl peptidase, a structural and functional homologue of mammalian prolyl dipeptidyl peptidase IV

Porphyromonas gingivalis is an asaccharolytic and anaerobic bacterium that possesses a complex proteolytic system which is essential for its growth and evasion of host defense mechanisms. In this report, we show the purification and characterization of prolyl dipeptidyl peptidase IV (DPPIV) produced by this organism. The enzyme was purified to homogeneity, and its enzymatic activity and biochemical properties were investigated. P. gingivalis DPPIV, like its human counterpart, is able to cleave the N terminus of synthetic oligopeptides with sequences analogous to those of interleukins 1beta and 2. Additionally, this protease hydrolyzes biologically active peptides including substance P, fibrin inhibitory peptide, and beta-casomorphin. Southern blot analysis of genomic DNA isolated from several P. gingivalis strains reveal that a single copy of the DPPIV gene was present in all strains tested.

A fuzzy logic approach to identifying brain structures in MRI using expert anatomic knowledge

We report a novel computer method for automatic labeling of structures in 3D MRI data sets using expert anatomical knowledge that is coded in fuzzy sets and fuzzy rules. The method first identifies major structures and then uses spatial relationships to these landmarks to recognize other structures. This labeling process simulates the iterative process that we ourselves use to locate structures in images. We demonstrate its application in three data sets, labeling brain MRI by locating the longitudinal and lateral fissures and the central sulci and then determining boundaries for the frontal lobes. Our method is adaptable to the identification of other anatomical structures.

Potent dipeptidylketone inhibitors of the cysteine protease cathepsin K

Cathepsin K (EC 3.4.22.38) is a cysteine protease of the papain superfamily which is selectively expressed within the osteoclast. Several lines of evidence have pointed to the fact that this protease may play an important role in the degradation of the bone matrix. Potent and selective inhibitors of cathepsin K could be important therapeutic agents for the control of excessive bone resorption. Recently a series of peptide aldehydes have been shown to be potent inhibitors of cathepsin K. In an effort to design more selective and metabolically stable inhibitors of cathepsin K, a series of electronically attenuated alkoxymethylketones and thiomethylketones inhibitors have been synthesized. The X-ray co-crystal structure of one of these analogues in complex with cathepsin K shows the inhibitor binding in the primed side of the enzyme active site with a covalent interaction between the active site cysteine 25 and the carbonyl carbon of the inhibitor.

Incorporating qualitative knowledge in enzyme kinetic models using fuzzy logic

Modeling of metabolic pathway dynamics requires detailed kinetic equations at the enzyme level. In particular, the kinetic equations must account for metabolite effectors that contribute significantly to the pathway regulation in vivo. Unfortunately, most kinetic rate laws available in the literature do not consider all the effectors simultaneously, and much kinetic information exists in a qualitative or semiquantitative form. In this article, we present a strategy to incorporate such information into the kinetic equation. This strategy uses fuzzy logic-based factors to modify algebraic rate laws that account for partial kinetic characteristics. The parameters introduced by the fuzzy factors are then optimized by use of a hybrid of simplex and genetic algorithms. The resulting model provides a flexible form that can simulate various kinetic behaviors. Such kinetic models are suitable for pathway modeling without complete enzyme mechanisms. Three enzymes in Escherichia coli central metabolism are used as examples: phosphoenolpyruvate carboxylase; phosphoenolpyruvate carboxykinase; and pyruvate kinase I. Results show that, with fuzzy logic-augmented models, the kinetic data can be much better described. In particular, complex behavior, such as allosteric inhibition, can be captured using fuzzy rules. The resulting models, even though they do not provide additional physical meaning in enzyme mechanisms, allow the model to incorporate semiquantitative information in metabolic pathway models.

Short-term cell/substrate contact dynamics of subconfluent endothelial cells following exposure to laminar flow

The manner in which fluid stresses are transmitted from the apical to the basal surface of the endothelium will influence the dynamics of cell/substrate contacts. Such dynamics could be important in the design of synthetic vascular grafts to promote endothelial cell adhesion. To examine whether the initial response of cell/substrate contact sites to flow depends on the magnitude of the applied shear stress, subconfluent monolayers of endothelial cells were exposed to flow at 10, 20, and 30 dyn cm-2 wall shear stresses for 20 min. Cell/substrate contact sites were visualized with total internal reflection fluorescence microscopy. Flow induced a rapid fluctuation in the membrane topography, which was reflected in dynamic changes in cell/substrate contacts. Exposure to flow caused marked changes in contact area. Contact movement occurred normal and parallel to the direction of flow. Contact sites demonstrated significant variability in contact area at 30 dyn cm-2 during the experiment but no significant movement of the contact sites in flow direction after 20 min of flow. Mean square displacements of the contact center of mass were described in terms of a directed diffusion model. Prior to onset of flow, contact movement was random. Flow induced a significant convective component to contact movement for 300-600 s, followed by reestablishment of diffusive growth and movement of contacts. These results suggest that fluid stresses are rapidly transmitted from the apical to the basal surface of the cell via the cytoskeleton.

Following the invisible trail: kinematic analysis of mate-tracking in the copepod Temora longicornis

We have analysed the fine-scale kinematics of movement of male and female copepods, Temora longicornis, to resolve how these small animals find their mates. Location of the trail initially involves rapid random turning and high rates of directional change. Males subsequently increase their rate of movement as they follow the trail, and execute a regular pattern of counter turns in both x,z and y,z planes to stay near or within the central axis of the odour field. Pursuit behaviour of males is strongly associated with female swimming behaviour, suggesting that quantifiable variations in the structure of the odour signal released by females affects male tracking. The behavioural components of mate tracking in Temora are very similar to those of other animals that employ chemically mediated orientation in their search for mates and food, and we conclude that male Temora find their mates using chemoperception. The kinematic analysis indicates both sequential and simultaneous taxis mechanisms are used by Temora to follow the odour signal. This, in turn, indicates that rather than responding to a diffuse plume, males are following a signal more accurately characterized as a chemical trail, and copepods appear to use mechanisms that are similar to those employed by trail-following terrestrial insects such as ants. While Temora expresses similar behaviours to those of a variety of chemosensory organisms, the ability to track a three-dimensional odour trail appears unique, and possibly depends on the persistence of fluid-borne odour signals created in low Reynolds number hydrodynamic regimes.

The fluid physics of signal perception by mate-tracking copepods

Within laboratory-induced swarms of the marine copepod Temora longicornis, the male exhibits chemically mediated trail-following behaviour, concluding with fluid mechanical provocation of the mate-capture response. The location and structure of the invisible trail were determined by examining the specific behaviour of the female copepods creating the signal, the response of the male to her signal, and the fluid physics of signal persistence. Using the distance of the mate-tracking male from the ageing trail of the female, we estimated that the molecular diffusion coefficient of the putative pheromonal stimulant was 2.7 x 10(-5) cm2 s-1, or 1000 times slower than the diffusion of momentum. Estimates of signal strength levels, using calculations of diffusive properties of odour trails and attenuation rates of fluid mechanical signals, were compared to the physiological and behavioural threshold detection levels. Males find trails because of strong across-plume chemical gradients; males sometimes go the wrong way because of weak along-plume gradients; males lose the trail when the female hops because of signal dilution; and mate-capture behaviour is elicited by suprathreshold flow signals. The male is stimulated by the female odour to accelerate along the trail to catch up with her, and the boundary layer separating the signal from the chemosensitive receptors along the copepod antennule thins. Diffusion times, and hence reaction times, shorten and behavioural orientation responses can proceed more quickly. While 'perceptive' distance to the odour signal in the trail or the fluid mechanical signal from the female remains within 1-2 body lengths (< 5 mm), the 'reactive' distance between males and females was an order of magnitude larger. Therefore, when nearest-neighbour distances are 5 cm or less, as in swarms of 10(4) copepods m-3, mating events are facilitated. The strong similarity in the structure of mating trails and vortex tubes (isotropic, millimetre-centimetre scale, 10:1 aspect ratio, 10s persistence), indicates that these trails are constrained by the same physical forces that influence water motion in a low Reynolds number fluid regime, where viscosity limits forces to the molecular scale. The exploratory reaches of mating trails appear inscribed within Kolmogorov eddies and may represent a measure of eddy size. Biologically formed mating trails, however, are distinct in their flow velocity and chemical composition from common small-scale turbulent features; and mechanoreceptive and chemoreceptive copepods use their senses to discriminate these differences. Zooplankton are not aimless wanderers in a featureless environment. Their ambit is replete with clues that guide them in their efforts for survival in the ocean.

Human placental norepinephrine transporter mRNA: expression and correlation with fetal condition at birth

The purpose of this study was to determine the primary form of human placental norepinephrine transporter (hNET) mRNA expressed in the human placenta and to compare the level of expression in normal pregnancies and in pregnancies complicated by drug exposure or other forms of physiological derangement. We used the hNET cDNA to measure RNA extracted from placenta and examined placental RNA following complicated and uncomplicated pregnancies. To compare transporter expression and its relation to fetal condition at birth, umbilical arterial plasma catecholamine levels, umbilical arterial blood gases and placental transporter mRNA level were compared by linear regression analysis. Uncomplicated pregnancies had a higher level of placental norepinephrine transporter mRNA than complicated pregnancies. An inverse relationship between umbilical cord norepinephrine level and transporter expression was demonstrated. We conclude that placental transporter expression represents an important and newly described metabolic function of the placenta. Placental catecholamine clearance mediated via the placental NET may be important in the pathophysiology of disorders associated with placental dysfunction, impaired placental blood flow or intrauterine growth retardation. This may also explain the adverse effects of drugs, such as cocaine, which block catecholamine transport.

A clinical phase I/II study of recombinant human interleukin-1 receptor in glucocorticoid-resistant graft-versus-host disease

Graft-versus-host disease (GVHD) is the major complication of allogeneic bone marrow transplantation. GVHD is accompanied by the release of inflammatory cytokines, including interleukin (IL)-1, and previous work has demonstrated that IL-1 participates in the pathogenesis of GVHD. The recombinant human IL-1 receptor (rhuIL-1R) is the soluble form of the type I IL-1 receptor that can bind to IL-1 and prevent cellular activation. We report a phase I/II trial utilizing the rhuIL-1R in the treatment of allogeneic bone narrow transplant patients not improving with glucocorticoid therapy. RhuIL-R was given at four dose levels for 21 days to 14 patients with progressive or persistent acute GVHD. The study drug had no clinical or persistent hematopoiesis and the treatment was tolerated by patients without toxicity at all dose levels. Eight of 14 patients (57%) had an improvement of GVHD after rhuIL-1R therapy. Improvement in GVHD was noted at each dose level, although a dose-response effect for rhuIL-1R treatment was not observed. This work supports the concept that IL-1 plays a role in the inflammation associated with acute GVHD. A controlled study of the rhuIL-1R for treatment of prophylaxis of GVHD is warranted.

Survival factors in 186 patients younger than 40 years old with colorectal adenocarcinoma

BACKGROUND

We sought to determine the clinical factors and tumor characteristics associated with the reported poor prognosis in young patients with carcinoma of the colon and rectum.

STUDY DESIGN

A retrospective review was performed of 186 patients younger than 40 years of age who were treated for primary colorectal adenocarcinoma. The median age was 34.3 years, and the median follow-up period was 9.4 years. Clinical and tumor histopathologic parameters were analyzed.

RESULTS

Regional lymph node metastases, distant metastases, or both, were seen at first examination in 65.6 percent of young patients. Histopathologic indicators of more aggressive tumor biology were present at a significantly higher frequency in young patients compared with patients older than 40 years (p < 0.001). Poorly differentiated tumor grade was present in 41.0 percent, signet-ring cell tumors were found in 11.1 percent, and infiltrating tumor leading edges were present in 69.0 percent of young patients. Among young patients with stage II disease, vascular invasion was a significant negative prognostic variable (p < 0.05).

CONCLUSIONS

We have demonstrated an increased incidence of three biological indicators of aggressive and potentially metastatic tumor biology in 186 young patients with carcinoma of the colon and rectum: signet-ring cell carcinoma, infiltrating tumor edges, and aggressive histologic grade in the primary adenocarcinoma. The increased incidence of these three histologic measures of more aggressive carcinoma of the colon and rectum in part accounts for the higher rate of advanced disease at presentation in patients younger than 40.

Transformation by FosB requires a trans-activation domain missing in FosB2 that can be substituted by heterologous activation domains

Two functionally distinct proteins derived from the FosB gene by alternative splicing have recently been described. FosB protein transforms fibroblasts efficiently, whereas FosB2 protein, a carboxy-terminally truncated form of FosB, does not, despite the fact that both proteins can participate in high-affinity, sequence-specific DNA binding as part of a heterodimeric complex with c-Jun protein. We show here that the functional difference between these proteins is the result of the presence of a potent proline-rich transcriptional activation domain in the carboxy-terminal amino acids unique to FosB. This conclusion is supported by three lines of evidence: (1) Mutations in the carboxy-terminal region of FosB that impair transcriptional activation also reduce transforming potential, despite the fact that DNA binding as part of a complex with c-Jun is not affected; (2) the carboxy-terminal region unique to FosB functions as an activation domain when fused to the DNA-binding domain of GAL4; and (3) transforming potential can be conferred on FosB2 by fusing any of several different well-characterized trans-activation domains. These results identify an additional functional requirement for transformation by Fos proteins and have implications for the mechanism(s) of mitogenic signaling by the AP-1 transcription complex.

An alternative spliced form of FosB is a negative regulator of transcriptional activation and transformation by Fos proteins

Two forms of FosB transcript and their products can be identified in mouse NIH 3T3 cells following serum induction. The larger RNA codes for a 338-amino acid protein, whereas the smaller RNA results from the removal of an additional 140 nucleotides from FosB mRNA by alternative splicing. This alternative splicing event places a stop codon following the "leucine zipper" region and results in a shorter protein (FosB2) of 237 amino acids that lacks 101 amino acids at the carboxyl terminus. FosB2 is able to form heterodimers with c-Jun and bind to an AP-1 site but is not able to activate the transcription of promoters containing AP-1 sites. Furthermore, FosB2 can not only suppress the transcriptional activation by c-Fos and c-Jun of promoters containing an AP-1 site but also interferes with the transforming potential of viral and cellular Fos proteins. We propose that FosB2 protein functions as a trans-negative regulator.

A rapid in vitro cytotoxicity assay for the detection of tumor necrosis factor on human BT-20 cells

This report describes a rapid, reproducible in vitro bioassay to quantitate the cytotoxic activity of human tumor necrosis factor-alpha using a human rather than murine cell line in the absence of metabolic inhibitors. The target cells are BT-20 (breast carcinoma) cultured at 39 degrees C in the presence of recombinant human tumor necrosis factor-alpha (rHuTNF-alpha) in 96-well microtiter plates for 2 days. Cytotoxicity is measured by the crystal violet dye uptake of the remaining viable cells. This bioassay is sensitive to 1.5 ng/ml of rHuTNF-alpha, with an assay range to 130 ng/ml. Samples spiked into human plasma are measurable from 0.5 to 150 ng/ml. The specificity of this cytotoxic effect on the BT-20 cell line was demonstrated using rHuTNF-alpha neutralizing antibodies. A panel of cytokines including interferons, interleukins, and tumor necrosis factors was also analyzed using this assay system. Of the cytokines assayed, only recombinant murine tumor necrosis factor-alpha and recombinant human tumor necrosis factor-beta demonstrated measurable cytotoxic activity when assayed independently, while recombinant human interferon-gamma was the only cytokine to demonstrate greater than additive activity in combination with rHuTNF-alpha. The simplicity and reproducibility of this assay on a human cell line makes it useful for the routine determination of the biological activity of human tumor necrosis factor-alpha.