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Pathogenesis of venous thrombosis.

This brief review attempts to describe the present understanding of the pathogenesis of venous thrombosis in general with special reference to venous thromboembolism in spinal cord injury patients with paralysis. The component parts of Virchow's triad are examined. Most venous thrombi seem to originate in regions of slow blood flow, ie, the large venous sinuses of the calf and thigh or in valve cusp pockets. Decreased blood flow or even stasis due to lack of the pumping action of the large muscle packages in paralyzed patients is undoubtedly one of the major factors. As blood pools, activation products of the coagulation system accumulate locally leading potentially to local hypercoagulability. Activation products of clotting and fibrinolysis can induce endothelial damage which in turn leads to further activation of the hemostasis system. Endothelial damage may also result from distension of the vessel walls by the pooling blood. Blood flow is further decreased by hyperviscosity due to elevated fibrinogen levels and dehydration. Some spinal cord injury patients may sustain direct trauma to the legs; others may encounter vessel wall damage by the immobilized limbs. Shortly after injury, certain changes develop in the clotting system, especially increases in components of the von Willebrand factor macromolecular complex and increased platelet aggregability which could further contribute to hypercoagulability. Recently, an inhibition of the fibrinolytic system was suggested which also could add to a prothrombotic state. All of these interrelated processes clearly explain the high risk of venous thromboembolism in spinal cord injury patients with paralysis which has been clearly demonstrated by many investigators. It is hoped that intense thrombosis prophylaxis will reduce the incidence of this potentially devastating complication.

Blood Coagulation↗

The XIIth International Symposium on Recent Advances in Drug Delivery Systems.

The XIIth International Symposium on Recent Advances in Drug Delivery Systems was held from 21-24 February 2005 in Salt Lake City, UT, USA. Approximately 250 people attended this symposium dedicated to a broad variety of topics, ranging from recent advances in drug delivery systems to biomaterials and novel concepts in macromolecular therapeutics. A total of 33 people, all recognised specialists in the aforementioned fields, presented 30-min up-to-date reviews of these topics, as well as discussing recent results. In addition, the symposium included a poster session with approximately 100 displays highlighting various interesting data.

Animals↗

A new method for the analysis of the dynamics of the molecular genetic control systems. I. Description of the method of generalized threshold models.

In the molecular system of coding polymers and metabolites a control subsystem has been singled out that forms controlling variables showing the action of regulatory molecules and a controlled subsystem where, depending on the values of controlling variables controlled variables are formed, i.e. concentrations of DNA, m-RNA, proteins and metabolites. Relationships have been obtained which enable controlling variables to be found. Equations showing the dynamics of molecular genetic control systems' components have been obtained. A method of generalized threshold models that enables kinetic curves to be obtained by pure mathematical means for macromolecular components (DNA, RNA, proteins) of molecular genetic control systems of varying complexity is suggested.

Animals↗

Multi-slice MRI of rat brain perfusion during amphetamine stimulation using arterial spin labeling.

When a single coil is used to measure perfusion by arterial spin labeling, saturation of macromolecular protons occurs during the labeling period. Induced magnetization transfer contrast (MTC) effects decrease tissue water signal intensity, reducing the sensitivity of the technique. In addition, MTC effects must be properly accounted for in acquiring a control image. This forces the image to a single slice centered between the labeling plane and the control plane. In this work, a two-coil system is presented as a way to avoid saturation of macromolecular spins during arterial spin labeling. The system consists of one small surface coil for labeling the arterial water spins, and a head coil for MRI, actively decoupled from the labeling coil by using PIN diodes. It is shown that no signal loss occurs due to MTC effects when the two-coil system is used for MRI of rat brain perfusion, enabling three-dimensional perfusion imaging. Using the two-coil system, a multi-slice MRI sequence was used to study the regional effects of amphetamine on brain perfusion. Amphetamine causes significant increases in perfusion in many areas of the brain including the cortex, cingulate, and caudate putamen, in agreement with previous results using deoxyglucose uptake to monitor brain activation.

Amphetamine↗

Exaptation and torsion: toward a theory of natural information processing.

Several conundrums are provoked by attempts to provide algorithmic descriptions of natural phenomena. A characteristic feature of natural computation is a breakdown in the formal simulation relation. This is called hermeneutic torsion, and is formally the failure to commute of a diagram describing homomorphisms between dynamical systems. This torsion is a source of computational power. For example, it is deeply involved with phenomena such as exaptation, wherein an existing structure is recruited for a novel function. Exaptation occurs continually at the macromolecular level and is fundamentally nonalgorithmic; our system-theoretic models of computation deal with structural descriptions for which a functional semantics must be assigned in advance, and a natural system continually 'diagonalizes out' of this semantics. This perspective clarifies the nature of computing power and encourages consideration of a new kind of transcomputational complexity.

Algorithms↗

VQLM: a Visual Query Language for Macromolecular structural databases.

Databases of macromolecular structures allow researchers to identify general principles of molecular behavior. They do this by providing a variety of data obtained under a number of different experimental conditions. Many new tools have been developed recently to aid in exploratory analysis of structural data. However, some queries of interest still require considerable manual filtering of data. In particular, studies attempting to make generalizations about complex arrangements of atoms or building blocks in macromolecular structures cannot be approached directly with existing tools. Such studies are frequently carried out on only a few structures or else require a labor-intensive process. To address this problem, we have developed a visual language, VQLM (Visual Query Language for Macromolecules). A query is formulated in this language by drawing an abstract picture of substructures to be searched for in the database and specifying constraints on the objects in them. To illustrate the usefulness of our language, we show how to encode a number of queries that were found scientifically interesting in the published literature in molecular biology. VQLM relies on VQL, a new database language, as its underlying engine for database retrieval and computation. We believe that VQLM will make macromolecular structural data more accessible to scientists, enabling faster and deeper data analysis.

Animals↗

Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions.

Macromolecular interactions define many biological phenomena. Although genetic methods are available to identify novel protein-protein and DNA-protein interactions, no genetic system has thus far been described to identify molecules or mutations that dissociate known interactions. Herein, we describe genetic systems that detect such events in the yeast Saccharomyces cerevisiae. We have engineered yeast strains in which the interaction of two proteins expressed in the context of the two-hybrid system or the interaction between a DNA-binding protein and its binding site in the context of the one-hybrid system is deleterious to growth. Under these conditions, dissociation of the interaction provides a selective growth advantage, thereby facilitating detection. These methods referred to as the "reverse two-hybrid system" and "reverse one-hybrid system" facilitate the study of the structure-function relationships and regulation of protein-protein and DNA-protein interactions. They should also facilitate the selection of dissociator molecules that could be used as therapeutic agents.

Base Sequence↗

Quasi-elastic light scattering studies of native hepatic bile from the dog: comparison with aggregative behavior of model biliary lipid systems.

Using quasi-elastic light scattering ( QLS ), we have characterized the macromolecular components in hepatic bile obtained from the dog and compared these results with data from model bile solutions containing the bile salt (BS) sodium taurocholate (TC), egg lecithin (L), and cholesterol (Ch). Native bile samples were obtained by direct catheterization of the common bile duct in a previously cholecystectomized dog fitted with a Thomas duodenal cannula. Hepatic bile was sampled during three secretory states: (A) unstimulated "fasting" bile, (B) "stimulated" secretion during an intravenous TC infusion, and (C) "secretin-stimulated" secretion. All three samples had comparable molar ratios of L/BS (0.21 +/- 0.03) and Ch/L (0.027 +/- 0.006) but differed in the total lipid concentration (BS + L + Ch): (A) 13.1 +/- 0.8, (B) 6.7 +/- 0.8, and (C) 3.0 +/- 0.4 g/dL. From the QLS autocorrelation functions measured on samples B and C, three macromolecular components (denoted 1 alpha, 1 beta, and 2) were resolved. Component 1 alpha (hydrodynamic radius R1 alpha = 10 +/- 2 A) is comparable in size to the micellar aggregates of model systems. Component 1 beta (R1 beta = 67 +/- 7 A) appears to reflect an average of biliary proteins. Component 2 (R2 = 650 +/- 15 A) is a trace component whose size and sedimentation behavior are compatible with those of the canalicular membrane vesicles postulated to be present in bile [ Godfrey , P. P., Warner, M. J., & Coleman , R. (1981) Biochem. J. 196, 11]. Serial dilution of the B and C bile samples with Tris buffer (0.15 M NaCl, pH 8.0) showed a remarkable similarity in the behavior of the 1 alpha component as compared to the mean hydrodynamic radius Rh of similarly diluted model bile solutions. When a critical dilution factor, d gamma, is reached, Rh increases abruptly from approximately 30 to approximately 400 A. Above a second dilution factor, d alpha, it then decreases to a value of approximately 150 A. Similar results were obtained on sample A but were shifted to higher dilutions. Such behavior is consistent with the presence of "mixed disk" micelles [ Mazer , N. A., Benedek , G. B., & Carey, M. C. (1980) Biochemistry 19, 601] in native bile which undergo a micelle-to-vesicle transition upon dilution. From the d gamma and d alpha values, estimates of the intermicellar bile salt concentrations were made for all three samples (range 1.4-6.2 mM) which agree well with previous experimental results on model and native bile. These studies offer compelling evidence for the existence of micellar aggregates in native bile whose size, structure, and equilibria are similar to those found in model bile solutions.

Animals↗

Characterization of protein behavior in high-performance capillary electrophoresis using a novel capillary system.

Original calculations of over a million theoretical plate efficiency for macromolecular solutes in the open tubular high-performance capillary electrophoresis experiment considered axial diffusion to be the efficiency limiting factor. In practice, interactions of biopolymers, such as proteins, with the capillary wall has had a significant impact on readily achieving high efficiencies for a wide variety of proteins. This paper reports a capillary system in which protein-surface interactions have been minimized, resulting in high efficiencies (greater than or equal to 300,000 theoretical plates). This system allows the analysis of a set of protein standards over a wide pI range at neutral pH and moderate ionic strength. The characterization of the behavior of those protein standards in this capillary system is described.

Drug Storage↗

Bromobenzene epoxidation leading to binding on macromolecular protein sites.

Bromobenzene is metabolized via the hepatic mixed-function oxygenase system to reactive intermediates; i.e., 2,3- and 3,4-bromobenzene epoxides. These metabolites presumably bind to tissue macromolecules evoking cytotoxicity. However, the specific sites of macromolecular proteins are not known and this was investigated using microsomal protein and hemoglobin. The results indicate that 2,3- and 3,4-epoxide bind to macromolecules at different rates. The 3,4-epoxide is more reactive, binding covalently to microsomal protein at the site of its synthesis, whereas bromobenzene 2,3-epoxide is more stable, leaving the microsomal protein compartment and binding covalently to soluble protein, i.e., the hemoglobin beta chain. Structural analysis with fingerprint mapping of the hemoglobin beta chain after pretreatment with cysteine and histidine blocking agents such as p-nitrophenacyl bromide, 2-bromoethylamine hydrobromide and diethylprocarbonate indicated that the 2,3-epoxide preferentially binds to the cysteinyl residue, whereas the 3,4-epoxide binds to the histidinyl residue. This difference in binding of the 2,3- and 3,4-bromobenzene epoxides may be an important factor in determining the degree of their cytotoxicity.

Animals↗

Comparison of the temperature sensitivity of protein synthesis by cell-free systems from liver of rat and skate (Raja ocellata).

Studies were undertaken to determine the component(s) responsible for the temperature optimum characteristic of the protein-synthesizing system from skate and rat. 1. The macromolecular constituents of rat and skate liver ribosomes are compared. The number of ribosomal proteins is similar in the two species, although most proteins display different electrophoretic mobilities on polyacrylamide gels. The RNAs from the small subunit of skate and rat have similar sedimentation coefficients; however, the RNA from the large subunit of skate ribosomes appeared to be slight smaller than the comparable RNA from the rat. 2. Ribosomes from either rat or skate were capable of supporting poly(U)dependent polyphenylalanine synthesis with soluble factors from either species. 3. Maximal leucine incorporation directed by endogenous mRNA occurred at 35--40 degrees C with post-mitochondrial supernatant from the rat liver and at 20--30 degrees C with that from skate liver. 4. The characteristic temperature sensitivity of protein synthesis was dependent upon the source of cell sap and independent of the source of ribosomes. 5. Elongation factor 1 from both the rat and skate exhibited maximum activity at approx. 30 degrees C. 6. Phenylalanyl-tRNA synthetase from skate liver showed maximum activity at 30 degrees C while that from rat was maximally active at 37 degrees C. The rat enzyme, however, was active at 0--10 degrees C, at which temperature protein synthesis in the reconstructed rat system is virtually absent. 7. The protein-synthesizing capacity of the reconstituted system at various temperatures was closely correlated with the activity of Elongation factor 2 (translocase). Elongation factor 2 from rat liver displayed an optimum at 30 degrees C and lost all activity below 10 degrees C, while this same factor from skate liver showed an optimum at 20 degrees C and significant activity below 10 degrees C. At this low temperature the reconstituted skate liver system continued to exhibit the ability to synthesize protein. These studies suggest that Elongation factor 2 is the component responsible for determining the temperature at which the protein-synthesizing system displays its characteristic maximum activity.

Animals↗

Glycosaminoglycan components in duodenum with advancing age and in patients with progressive systemic sclerosis.

The glycosaminoglycan (GAG) components in normal human duodenal tissue and in duodenal GAGs of patients with progressive systemic sclerosis (PSS) were characterized at the macromolecular level by electrophoresis combined with various GAG-specific digestion. High-performance liquid chromatographic assay quantified various unsaturated disaccharides derived from chondroitin sulfate and dermatan sulfate isomers (DS). The data obtained showed that on average, the total GAG content was 1.02 mg as uronic acid/g dry tissue weight, and the main GAGs were DS (33% of total GAGs), and heparan sulfates (HS, 27%), followed by hyaluronic acid (HA, 14%) and over-sulfated DS (10%), and small amounts of chondroitin, chondroitin-4- and -6-sulfates (C-4S and C-6S, totally 16%). With advancing age, the proportion of DS, HS and oversulfated DS increased, while HA, chondroitin and C-4S decreased. The composition of duodenal GAGs in PSS patients was similar to that in the aged: a higher proportion of DS isomers and HS and a lower proportion of HA and chondroitin. As the structure of sulfated GAGs differs with advancing age and in patients with PSS, GAGs may have a role in duodenal function and metabolism.

Adult↗

[Correlation between the organ blood flow, substrate absorption from blood, the activity of transport into mammary gland secretory cells and formation milk components in cow].

Epithelial cells of mammary alveoles may he considered as a bioreactor that works being monitored by regulatory system maintaining balance between blood substrate supply and rate of macromolecular synthesis. In the trial performed on lactating cows assigned to feeding regimen with temporally altered level of nutrition, functioning of this system in the course of a transition period was studied. The earliest sign of adaptation was a decrease in volume blood flow through mammary gland provoking decline in uptake of water soluble substrates (glucose, amino N, P-hydroxybutyrate) with increase in arterio-venous difference across mammary gland and extraction efficiency. At the end of deprivation period, an activity of transport into the cell decreased for amino N from 7.5 to 4.5; l/min (p < 0.05), for P-hydroxyhutyrate from 16.0 to 13.8 l/min; activity of glucose transport was not changed. The data obtained indicate existence of defined points in the system monitoring organ blood supply and transport of substrates into the cell being adjusted during adaptation to alteration in the level of nutrition.

Adaptation, Physiological↗

Subunit separation in reversed micelle system reveals the existence of active centers both on light and heavy gamma-glutamyltransferase subunits.

Regulation of supra-macromolecular composition and catalytic activity of a heterodimeric enzyme, gamma-glutamyltransferase, in the system of Aerosol OT (sodium bis(2-ethylhexyl) sulfosuccinate) reversed micelles in octane were studied. Variation of the surfactant hydration degree (parameter, determining dimensions of the polar inner cavity of the micelle) causes a reversible dissociation of the enzyme to light and heavy subunits. Both enzyme subunits possess catalytic activity. The light and heavy subunits of the enzyme were separated on a preparative scale in a reversed micelle system using ultracentrifugation. The active centers of gamma-glutamyltransferase were studied using its irreversible inhibitor--AT-125 (L-(alpha S, 5S)-alpha-amino-3-chloro-4,5-dihydro-5-isoxazoleacetic acid). Separation of the gamma-glutamyltransferase subunits results in the 'opening' of a new active center located at the heavy subunit. In the dimer form of the enzyme this center is masked and it is not accessible to both substrate and inhibitor molecules.

Binding Sites↗

Increased nitric oxide excretion in patients with severe acute pancreatitis: evidence of an endotoxin mediated inflammatory response?

BACKGROUND AND AIMS: Nitric oxide represents a potential key mediator of the local and systemic manifestations of acute pancreatitis (AP) in experimental models but its role in human disease is uncertain. We therefore sought to assess if systemic nitric oxide (NO) production is elevated in severe AP and determine whether this is a reflection of biochemical severity or endotoxin exposure. PATIENTS AND METHODS: Patients were recruited within 72 hours of pain onset. NO derived nitrite excretion determined from a 24 hour sterile urine collection was correlated with intestinal macromolecular permeability (polyethylene glycol excretion ratio), markers of systemic endotoxin exposure (IgG:IgM endotoxin core antibody (EndoCAb) ratio), disease severity, and the magnitude of systemic inflammation (peak C reactive protein (CRP) and Acute Physiology and Chronic Health Evaluation score II (APACHE-II)). RESULTS: In patients with a severe attack (n=20), nitrite excretion was increased significantly compared with patients with a mild attack (n=45, 20.6 micro g v 15.65 micro g; p<0.00) and the latter with healthy controls (n=20, p=0.004). Nitrite excretion correlated strongly with both intestinal permeability (r=0.7, p=0.006) and EndoCAb ratio (r=0.7, p<0.01) but not with CRP or APACHE-II scores (p>0.1). CONCLUSIONS: Total urinary nitrite excretion is increased in patients with severe AP, and may not be simply a reflection of systemic inflammation, but potentially a consequence of endotoxin mediated upregulation of inducible NO synthase activity.

Acute Disease↗

Transport of fluid and macromolecules in tumors. II. Role of heterogeneous perfusion and lymphatics.

We have recently developed a general theoretical framework for transvascular exchange and extravascular transport of fluid and macromolecules in tumors. The model was applied to a homogeneous, alymphatic tumor with no extravascular binding. For this simplified system, the interstitial pressure was found to be a major contributing factor to the heterogeneous distribution of macromolecules within solid tumors. A steep pressure gradient was predicted at the periphery of the tumor. Our recent experiments have verified these predicted profiles. The purpose of this investigation was to apply this theoretical framework to the more realistic case of a nonuniformly perfused tumor. The role of lymphatics for macromolecular transport was also studied using the model. The uptake and distribution of IgG and its fragment, Fab, were simulated. The novel result from this work is that necrosis does not reduce the central interstitial pressure in a tumor. Other results showed that (i) macromolecules do not penetrate a necrotic core at early times after injection; (ii) at longer time periods after a bolus injection (days for Fab, months for IgG in a tumor of radius approximately 1cm) a "reservoir" of material may be formed in the necrotic core; (iii) continuous infusion or repeated injections should maintain a higher interstitial concentration of macromolecules; and (iv) lymphatics, if present in a tumor, would rapidly remove material and result in much lower concentration levels. The model is also used to explain some previous experimental data in the literature on antibody distribution.

Animals↗

Spontaneous entrapment of polynucleotides upon electrostatic interaction with ethanol-destabilized cationic liposomes.

This study describes the effect of ethanol and the presence of poly(ethylene) glycol (PEG) lipids on the interaction of nucleotide-based polyelectrolytes with cationic liposomes. It is shown that preformed large unilamellar vesicles (LUVs) containing a cationic lipid and a PEG coating can be induced to entrap polynucleotides such as antisense oligonucleotides and plasmid DNA in the presence of ethanol. The interaction of the cationic liposomes with the polynucleotides leads to the formation of multilamellar liposomes ranging in size from 70 to 120 nm, only slightly bigger than the parent LUVs from which they originated. The degree of lamellarity as well as the size and polydispersity of the liposomes formed increases with increasing polynucleotide-to-lipid ratio. A direct correlation between the entrapment efficiency and the membrane-destabilizing effect of ethanol was observed. Although the morphology of the liposomes is still preserved at the ethanol concentrations used for entrapment (25-40%, v/v), entrapped low-molecular-weight solutes leak rapidly. In addition, lipids can flip-flop across the membrane and exchange rapidly between liposomes. Furthermore, there are indications that the interaction of the polynucleotides with the cationic liposomes in ethanol leads to formation of polynucleotide-cationic lipid domains, which act as adhesion points between liposomes. It is suggested that the spreading of this contact area leads to expulsion of PEG-ceramide and triggers processes that result in the formation of multilamellar systems with internalized polynucleotides. The high entrapment efficiencies achieved at high polyelectrolyte-to-lipid ratios and the small size and neutral character of these novel liposomal systems are of utility for liposomal delivery of macromolecular drugs.

Cations↗