Selective killing of nonreplicating mycobacteria

Antibiotics are typically more effective against replicating rather than nonreplicating bacteria. However, a major need in global health is to eradicate persistent or nonreplicating subpopulations of bacteria such as Mycobacterium tuberculosis (Mtb). Hence, identifying chemical inhibitors that selectively kill bacteria that are not replicating is of practical importance. To address this, we screened for inhibitors of dihydrolipoamide acyltransferase (DlaT), an enzyme required by Mtb to cause tuberculosis in guinea pigs and used by the bacterium to resist nitric oxide-derived reactive nitrogen intermediates, a stress encountered in the host. Chemical screening for inhibitors of Mtb DlaT identified select rhodanines as compounds that almost exclusively kill nonreplicating mycobacteria in synergy with products of host immunity, such as nitric oxide and hypoxia, and are effective on bacteria within macrophages, a cellular reservoir for latent Mtb. Compounds that kill nonreplicating pathogens in cooperation with host immunity could complement the conventional chemotherapy of infectious disease.     

Network 'small-world-ness': a quantitative method for determining canonical network equivalence

Background

Many technological, biological, social, and information networks fall into the broad class of ‘small-world’ networks: they have tightly interconnected clusters of nodes, and a shortest mean path length that is similar to a matched random graph (same number of nodes and edges). This semi-quantitative definition leads to a categorical distinction (‘small/not-small’) rather than a quantitative, continuous grading of networks, and can lead to uncertainty about a network''s small-world status. Moreover, systems described by small-world networks are often studied using an equivalent canonical network model – the Watts-Strogatz (WS) model. However, the process of establishing an equivalent WS model is imprecise and there is a pressing need to discover ways in which this equivalence may be quantified.

Methodology/Principal Findings

We defined a precise measure of ‘small-world-ness’ S based on the trade off between high local clustering and short path length. A network is now deemed a ‘small-world’ if S>1 - an assertion which may be tested statistically. We then examined the behavior of S on a large data-set of real-world systems. We found that all these systems were linked by a linear relationship between their S values and the network size n. Moreover, we show a method for assigning a unique Watts-Strogatz (WS) model to any real-world network, and show analytically that the WS models associated with our sample of networks also show linearity between S and n. Linearity between S and n is not, however, inevitable, and neither is S maximal for an arbitrary network of given size. Linearity may, however, be explained by a common limiting growth process.

Conclusions/Significance

We have shown how the notion of a small-world network may be quantified. Several key properties of the metric are described and the use of WS canonical models is placed on a more secure footing.     

Private specificities can dominate the humoral response to self-antigens in patients with cryptogenic fibrosing alveolitis

Background  

The pathogenetic mechanisms that underlie the interstitial lung disease cryptogenic fibrosing alveolitis (CFA) may involve an immunological reaction to unidentified antigens in the lung, resulting in tissue damage.     

Bicarbonate enhances peroxidase activity of Cu,Zn-superoxide dismutase. Role of carbonate anion radical and scavenging of carbonate anion radical by metalloporphyrin antioxidant enzyme mimetics.

Much evidence exists for the increased peroxidase activity of copper, zinc superoxide dismutase (SOD1) in oxidant-induced diseases. In this study, we measured the peroxidase activity of SOD1 by monitoring the oxidation of dichlorodihydrofluorescein (DCFH) to dichlorofluorescein (DCF). Bicarbonate dramatically enhanced DCFH oxidation to DCF in a SOD1/H(2)O(2)/DCFH system. Peroxidase activity could be measured at a lower H(2)O(2) concentration ( approximately 1 microm). We propose that DCFH oxidation to DCF is a sensitive index for measuring the peroxidase activity of SOD1 and familial amyotrophic lateral sclerosis SOD1 mutants and that the carbonate radical anion (CO(3)) is responsible for oxidation of DCFH to DCF in the SOD1/H(2)O(2)/bicarbonate system. Bicarbonate enhanced H(2)O(2)-dependent oxidation of DCFH to DCF by spinal cord extracts of transgenic mice expressing SOD1(G93A). The SOD1/H(2)O(2)/HCO(3)(-)-dependent oxidation was mimicked by photolysis of an inorganic cobalt carbonato complex that generates CO(3). Metalloporphyrin antioxidants that are usually considered as SOD1 mimetic or peroxynitrite dismutase effectively scavenged the CO(3) radical. Implications of this reaction as a plausible protective mechanism in inflammatory cellular damage induced by peroxynitrite are discussed.     

Mechanisms of Selective Impairment of Nitric Oxide-Mediated Endothelium-Dependent Vasodilation Following Ionizing Irradiation

The endothelium is the main target in the vascular wall for ionizing radiation; an irradiation-induced impairment leads to the loss of endothelium-dependent vasodilation. Recent studies showed that gamma irradiation causes selective impairment of nitric oxide (NO)-mediated vasodilation, but little is known about the underlying mechanisms. The goal of our study was to identify mechanisms underlying the impairment of NO-mediated endothelium-dependent vasodilation after whole-body irradiation with a cobalt⁶⁰ source. We compared vasodilation and NO release induced by acetylcholine (ACh), as well as relaxations induced by exogenous NO, in the thoracic aorta from healthy and irradiated rabbits. It was shown that despite the loss of relaxation the apparent release of NO induced by ACh and detected by chemiluminescence assay remained unaltered in irradiated tissue, as compared with that of healthy rabbits. At the same time, it was evident that while in healthy vessels relaxation increased with increasing NO concentration;, this relationship was lost in irradiated vessels. Endothelium-denuded aortic smooth muscles from irradiated rabbits retained the same sensitivity to NO gas solution as healthy denuded vessels. When non-denuded vascular tissues were used, irradiated aortas demonstrated an increased sensitivity, as compared with non-irradiated vascular tissue. α-Tocopherol acetate and phosphatidylcholine liposomes, when administered to rabbits 1 h after irradiation, effectively restored the NO-mediated endothelium-dependent relaxation and normalized the relationship between NO release and relaxation and also the sensitivity of the vessels to inhibition by N^ω-nitro-L-arginine (L-NA). Taken together, these data allow us to hypothesize that inhibition of an EDRF/NO-dependent component of vascular relaxation in irradiated rabbits may be due to at least two possible reasons: (i) intensified inactivation of endothelium-derived NO by oxygen free radicals, and (ii) abnormalities in diffusion of NO in the irradiated endothelium and subendothelial layer. Both these effects may lead to a decrease in the bioavailability of NO.     

Instability and complex dynamic behaviour in population models with long time delays

Some of the properties of the delay-differential equation $\text{dX(t)}\text{dt}\text{= R(X(t ? τ)) ? D(X(t))}$, where R and D represent the rates of recruitment to, and death from, an adult population of size X, with maturation period τ are examined. The biological constraints upon these recruitment and death functions are specified, and they are used to establish results on stability, boundedness, and persistent fluctuations of limit cycle type. The relationship between models based on delay-differential and difference equations is then explored, and it is shown how well-established results on period-doubling and chaotic behaviour in the latter can yield insight into the qualitative dynamics of the former. Using numerical studies of two population models with differing forms of recruitment function, we show how, by making use of our results, it is possible to simplify the analysis of delay-differential equation population models.     

Restricted heterogeneity of antibody to gp120 and p24 in AIDS

Neurologic complications and cerebrospinal fluid (CSF) abnormalities are common in AIDS. We found that a substantial number of AIDS patients with neurologic involvement had oligoclonal IgG bands in CSF and sera by IEF. Using an IEF-Ag overlay technique, anti-gp120 antibody activity was demonstrated more frequently than anti-p24 antibody activity. These antibody activities exhibited restricted heterogeneity of their IEF pattern; this restriction may contribute to the relatively low titers of neutralizing antibody found in AIDS sera. None of the CSF and serum oligoclonal bands showed anti-HIV antibody activity, suggesting that they are directed against opportunistic agents or result from immunodysregulation.     

3-Acrylamide-4-aryloxyindoles: Synthesis,biological evaluation and metabolic stability of potent and selective EP3 receptor antagonists

A series of potent and selective EP₃ receptor antagonists are described. Utilizing a pharmacophore model developed for the EP₃ receptor, a series of 3,4-disubstituted indoles were found to be efficient ligands for this target. These compounds showed high selectivity over IP, FP and other EP receptors. An optimized molecule 7c featured a sound profile and potency in the functional rat and human platelet aggregation assays.     

A biologically plausible model of early visual motion processing II: Psychophysical application

We test the model of early visual processing introduced in the companion paper by simulating a range of psychophysical phenomena. We present new data concerning our ability to discriminate the speed of drifting gratings when spatiotemporally apertured in a variety of ways. We shall investigate the role played by the aperture in modifying the grating's behaviour from its idealisation as a pure Fourier component and show that this is not negligible. Other phenomena which we simulate and explain relate to the way perceived velocity is influenced by contrast and spatial frequency. Many of our explanations are couched in terms of the relative number of cells occurring within each locale of the Fourier domain. This use of the cell density map is a unifying concept and avoids the necessity for a range of separate mechanisms. We argue that a neurophysiologically detailed model is necessary in order to explain psychophysical data (Weber fractions) which vary over less than an order of magnitude, and small deviations from veridical encoding of velocity.     

Subcellular location of polypeptides that react with anti-Sm and anti-RNP antibodies

Whole nuclear and cytoplasmic fractions from HeLa cells were analyzed in protein gel blots probed with either monoclonal anti-Sm or polyclonal anti-(U1)RNP antibodies. The cells were fractionated by a nonaqueous procedure, to minimize proteolysis and artifactual leakage of nuclear components to the cytoplasmic fraction. Unexpectedly, more reactive proteins were detected in the nucleus than shown earlier in partially purified small nuclear ribonucleoprotein particles (snRNPs). In addition, reactive polypeptides were now found in the cytoplasm. These results are discussed in reference to the possibility that the nucleus and cytoplasm of adult somatic human cells may have a more complex than anticipated set of populations of polypeptides bearing Sm or RNP antigenic determinants, including some proteins that might not be in snRNP form.