Identification of D-galactose-(1 → 7)-3-deoxy-d-manno-2-octulo-pyranosonate as component of the inner core region of escherichia coli EH 100 lipopolysaccharide

The dissaccharide D-galactosyl-3-deoxy-D-manno-2-octulosonic acid (Gal-KDO) from lipopolysaccharides (LPS) of the inner core region of the rough mutant EH100 of E. coli 0100 was isolated after mild acid hydrolysis of LPS by means of dialysis, ion-exchange chromatography, gelfiltration and high-voltage paper electrophresis. By chemical analysis galactose and KDO were identified in a molar ratio of approximately 1 : 1. ¹³C-NMR and ¹H-NMR studies, methylation analysis and GLC of the acetylated R.( – )-2-butyl-galactoside identified the structure .     

Cystine peptides: the intramolecular antiparallel beta-sheet conformation of a 20-membered cyclic peptide disulfide

A 20-membered cyclic peptide disulfide has been synthesized as a conformational model for disulfide loops of limited ring size. ¹H-nmr studies at 270 MHz establish the presence of three intramolecular hydrogen bonds involving the Leu, Val, and methylamide NH groups in CDCl₃. Evidence for peptide aggregation in CDCl₃ is also presented. A structural transition involving loosening of the hydrogen bond formed by the Val NH group is observed upon the measured addition of (CD₃)₂SO to CDCl₃. Hydrogen-bonding studies, together with unusually low field positions of the Cys(1) and Cys(6) C^αH resonances and high J values provide support for an intramolecular antiparallel β-sheet conformation, facilitated by a chain reversal at the Aib-Ala segment. Extensive nuclear Overhauser effect studies provide compelling evidence for the proposed conformation and also establish a type I′ β-turn at the Aib-Ala residues, the site of the chain reversal.     

Sigma receptor 1 activation attenuates release of inflammatory cytokines MIP1γ, MIP2, MIP3α, and IL12 (p40/p70) by retinal Müller glial cells

The high‐affinity sigma receptor 1 (σR1) ligand (+)‐pentazocine ((+)‐PTZ) affords profound retinal neuroprotection in vitro and in vivo by a yet‐unknown mechanism. A common feature of retinal disease is Müller cell reactive gliosis, which includes cytokine release. Here, we investigated whether lipopolysaccharide (LPS) stimulates cytokine release by primary mouse Müller cells and whether (+)‐PTZ alters release. Using a highly sensitive inflammatory antibody array we observed significant release of macrophage inflammatory proteins (MIP1γ, MIP2, MIP3α) and interleukin‐12 (IL12 (p40/p70)) in LPS‐treated cells compared to controls, and a significant decrease in secretion upon (+)‐PTZ treatment. Müller cells from σR1 knockout mice demonstrated increased MIP1γ, MIP2, MIP3α and IL12 (p40/p70) secretion when exposed to LPS compared to LPS‐stimulated WT cells. We investigated whether cytokine secretion was accompanied by cytosolic‐to‐nuclear NFκB translocation and whether endothelial cell adhesion/migration was altered by released cytokines. Cells exposed to LPS demonstrated increased NFκB nuclear location, which was reduced significantly in (+)‐PTZ‐treated cells. Media conditioned by LPS‐stimulated‐Müller cells induced leukocyte‐endothelial cell adhesion and endothelial cell migration, which was attenuated by (+)‐PTZ treatment. The findings suggest that release of certain inflammatory cytokines by Müller cells can be attenuated by σR1 ligands providing insights into the retinal neuroprotective role of this receptor.

     

NMR‐based conformation and dynamics of a tetrasaccharide‐repeating sulfated fucan substituted by different counterions

The sulfated fucan from the sea urchin Lytechinus variegatus is composed of the repetitive sequence [‐3)‐α‐l ‐Fucp‐4( )‐(1‐3)‐α‐l ‐Fucp‐2,4‐di( )‐(1‐3)‐α‐l ‐Fucp‐2( )‐(1‐3)‐α‐l ‐Fucp‐2( )‐(1‐]_n. Conformation (of rings and chains) and dynamics of this tetrasaccharide‐repeating sulfated fucan substituted by Na⁺, Ca²⁺, and Li⁺ as counterions have been examined through experiments of liquid‐state nuclear magnetic resonance spectroscopy. Scalar coupling and nuclear Overhauser effect (NOE)‐based data have confirmed that all composing units occur as ¹C₄ chair conformer regardless of the cation type, unit position within the repeating sequence, and sulfation type. Chain conformation determined by NOE signal pattern assisted by molecular modeling for a theoretical octasaccharide has shown a similar linear 3D structure for the three differently substituted forms. Data derived from spin‐relaxation measurements have indicated a contribution of counterion type to dynamics. The calcium‐based preparation has shown the highest mobility while the sodiated one showed the lowest mobility. The set of results from this work suggests that counterion type can affect the physicochemical properties of the structurally well‐defined sulfated fucan. The counterion effect seems to impact more on the structural mobility than on average conformation of the studied sulfated glycan in solution.     

Das Gesetz der absoluten Geschwindigkeiten biologischer Prozesse

The dependency of the velocity of biological processes from the temperature is described by the “Law of absolute velocity of biological processes”, which has only the individual parameters energy of activation ΔE, and the universal constant C. The law holds for all biological processes and is expressed by the equation: where C is: .     

An Unbalanced Mixed Model with Random Effects Having Unequal Variances

Consider the mixed model where x_ijk's are known constants, β_k are unknown parameters and a_i, e_ij are random variables independently and normally distributed with zero means and variances σd_i and σ² respectively, where it is assumed that the d_i's are known (d_i >0). This paper presents procedures for estimating the variance components σ, σ², for testing the hypothesis σ = 0, and for making transformations to random variables with uncorrelated errors and constant variances in order to estimate as well as to test hypothesis concerning the β_k's in the model.     

Transfer function matrix of the continuous cultivation system of Morchella crassipes in ammonia base waste sulfite liquor

A continuous stirred tank fermentor (CSTF) used for cultivation of the fungus Morchella crassipes in ammonia base waste sulfite liquor (NH₃-WSL) was considered as a multivariable linear system around its operating point. Pulse testing on the inputs (inlet jacket temperature, inlet pH, inlet substrate concentration) and their responses at the outputs (biomass, outlet temperature, outlet jacket temperature, outlet pH, outlet substrate concentration) were used for numerical determination of the transfer function matrix:      

Serine racemase deficiency attenuates choroidal neovascularization and reduces nitric oxide and VEGF levels by retinal pigment epithelial cells

Choroidal neovascularization (CNV) is a leading cause of blindness in age‐related macular degeneration. Production of vascular endothelial growth factor (VEGF) and macrophage recruitment by retinal pigment epithelial cells (RPE) significantly contributes to the process of CNV in an experimental CNV model. Serine racemase (SR) is expressed in retinal neurons and glial cells, and its product, d ‐serine, is an endogenous co‐agonist of N‐methyl‐d ‐aspartate receptor. Activation of the receptor results in production of nitric oxide (^.NO), a molecule that promotes retinal and choroidal neovascularization. These observations suggest possible roles of SR in CNV. With laser‐injured CNV mice, we found that inactivation of SR‐coding gene (Srr_null) significantly reduced CNV volume, neovascular density, and invading macrophages. We exploited the underlying mechanism in vivo and ex vivo. RPE from wild‐type (WT) mice expressed SR. To explore the possible downstream target of SR inactivation, we showed that choroid/RPE homogenates extracted from laser‐injured Srr_null mice contained less inducible nitric oxide synthase and decreased phospho‐VEGFR2 compared to amounts in WT mice. In vitro, inflammation‐primed WT RPEs expressed more inducible NOS, produced more^.NO and VEGF than did inflammation‐primed Srr_null RPEs. When co‐cultured with inflammation‐primed Srr_null RPE, significantly fewer RF/6A‐a cell line of choroidal endothelial cell, migrated to the opposite side of the insert membrane than did cells co‐cultured with pre‐treated WT RPE. Altogether, SR deficiency reduces RPE response to laser‐induced inflammatory stimuli, resulting in decreased production of a cascade of pro‐angiogenic cytokines, including^.NO and VEGF, and reduced macrophage recruitment, which contribute synergistically to attenuated angiogenesis.

     

Lipopolysaccharide induction of outward potassium current expression in human monocyte-derived macrophages: Lack of correlation with secretion

Summary Although an outwardly rectifying K⁺ conductance (I _K, A) is prominently expressed in human alveolar macrophages, the expression of this conductance in human monocyte-derived macrophages (HMDMs) is rare. We have analyzed the induction of the expression of I _K, A in voltage-clamped, in vitro differentiated HMDMs by a number of stimuli which produce either priming or activation of macrophages. Cultures were stimulated with lipopolysaccharide (LPS, 2 g/ml), interleukin 2 (IL-2, 100 U/ml), or combinations of LPS and either recombinant interferon-gamma (-IFN, 10 U/ml), phorbol myristate acetate (PMA, 0.01 or 1 g/ ml) and platelet activating factor (PAF, 20 ng/ml) for periods of up to 24 hr. Treatment of the cells with either LPS or IL-2 greatly enhanced the frequency of current expression. Treatment with either PMA or -IFN alone did not induce current expression; treatment of the cells with a combination of LPS and either PMA, -IFN, or PAF did not enhance current expression over that observed with LPS alone. The expression of the outwardly rectifying K⁺ current was observed in 36% (n=321) of the cells for cultures treated with LPS and 33% (n=55) of the cells for cultures treated with IL-2. The inactivating outward K⁺ current was absent in cells which were not treated with either LPS or IL-2. The kinetics of current activation and inactivation appeared identical to that previously described for the transient-inactivating outward current of the human alveolar macrophage. Cycloheximide (1 g/ml), an inhibitor of protein synthesis, completely suppressed LPS-induced current expression. No correlation was found between peak current amplitude and cell size in LPS-activated cells expressing the outwardly rectifying K⁺ current, indicating that current density was not held constant from cell to cell. The coupling of ion channel expression and secretion in individual HMDMs was studied using the reverse hemolytic plaque assay. Although an enhancement of K ⁺ current expression was observed following either LPS or IL-2 treatment, a quantitatively similar and uniform increase in the percentage of either IL-1 or lysozyme-secreting cells was not observed. The frequency of current expression in cells identified as secreting tumor necrosis factor- (TNF-), interleukin 1 (IL-1), or lysozyme was the same or decreased over that observed for nonsecreting cells. Thus, LPS treatment increases the number of K⁺ channels on HMDM membranes; however, K⁺ channel expression alone was not sufficient to give rise to enhanced secretion in LPS-activated macrophages. Enhanced K⁺ channel expression appears to be a part of the primary activation signal. K⁺-channel activation would hyperpolarize the membrane potential, potentially providing the driving force for calcium entry through voltage-independent pathways activated by the subsequent binding of soluble substances to membrane surface receptors, the secondary signal linked to secretion.This work was supported by NIH grant RO 1 GM36823.     

Tobacco mosaic virus, not just a single component virus anymore

Taxonomy: Tobacco mosaic virus (TMV) is the type species of the Tobamovirus genus and a member of the alphavirus-like supergroup. Historically, many tobamoviruses are incorrectly called strains of TMV, although they can differ considerably in sequence similarities and host range from each other and from TMV. Physical properties: TMV virions are 300 × 18 nm rods with a central hollow cavity ( Fig. 1 ) and are composed of 95% capsid protein (CP), and 5% RNA. Each CP subunit interacts with 3-nts in a helical arrangement around the RNA. Virions are stable for decades; infectivity in sap survives heating to 90 °C.

Figure 1 Open in figure viewer PowerPoint Electron micrograph of TMV virions stained with uranyl acetate. Courtesy of Dr J.N. Culver, University of Maryland Biotechnology Institute.     

Insights into the physiological function of the β‐amyloid precursor protein: beyond Alzheimer's disease

The β‐amyloid precursor protein (APP) has been extensively studied for its role as the precursor of the β‐amyloid protein (Aβ) of Alzheimer's disease. However, the normal function of APP remains largely unknown. This article reviews studies on the structure, expression and post‐translational processing of APP, as well as studies on the effects of APP in vitro and in vivo. We conclude that the published data provide strong evidence that APP has a trophic function. APP is likely to be involved in neural stem cell development, neuronal survival, neurite outgrowth and neurorepair. However, the mechanisms by which APP exerts its actions remain to be elucidated. The available evidence suggests that APP interacts both intracellularly and extracellularly to regulate various signal transduction mechanisms.

     

In vivo NMR studies of regional cerebral energetics in MPTP model of Parkinson's disease: recovery of cerebral metabolism with acute levodopa treatment

In this study, we have evaluated cerebral atrophy, neurometabolite homeostasis, and neural energetics in 1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridin (MPTP) model of Parkinson's disease. In addition, the efficacy of acute l ‐DOPA treatment for the reversal of altered metabolic functions was also evaluated. Cerebral atrophy and neurochemical profile were monitored in vivo using MRI and ¹H MR Spectroscopy. Cerebral energetics was studied by ¹H‐[¹³C]‐NMR spectroscopy in conjunction with infusion of ¹³C labeled [1,6^‐13C₂]glucose or [2‐¹³C]acetate. MPTP treatment led to reduction in paw grip strength and increased level of GABA and myo‐inositol in striatum and olfactory bulb. ¹³C Labeling of glutamate‐C4 (1.93 ± 0.24 vs. 1.48 ± 0.06 μmol/g), GABA‐C2 (0.24 ± 0.04 vs. 0.18 ± 0.02 μmol/g) and glutamaine‐C4 (0.26 ± 0.04 vs. 0.20 ± 0.04 μmol/g) from [1,6‐¹³C₂]glucose was found to be decreased with MPTP exposure in striatum as well as in other brain regions. However, glutamine‐C4 labeling from [2‐¹³C]acetate was found to be increased in the striatum of the MPTP‐treated mice. Acute l ‐DOPA treatment failed to normalize the increased ventricular size and level of metabolites but recovered the paw grip strength and ¹³C labeling of amino acids from [1,6‐¹³C₂]glucose and [2‐¹³C]acetate in MPTP‐treated mice. These data indicate that brain energy metabolism is impaired in Parkinson's disease and acute l ‐DOPA therapy could temporarily recover the cerebral metabolism.

     

Derepressive effect of NH on hydrogen production by deleting the glnA1 gene in Rhodobacter sphaeroides

Purple non‐sulfur (PNS) bacteria produce hydrogen by photofermentation of organic acids in wastewater. However, NH in wastewater may inhibit hydrogen synthesis by repressing the expression and activity of nitrogenase, the enzyme catalyzing hydrogen production in PNS bacteria. In this study, the Rhodobacter sphaeroides 6016 glnA gene encoding glutamine synthetase (GS) was knocked out by homologous recombination, and the effects on hydrogen production and nitrogenase activity were examined. Using 3 mM glutamine as the nitrogen source, hydrogen production (1,245–1,588 mL hydrogen/L culture) and nitrogenase activity were detected in the mutant in the presence of relatively high NH concentrations (15–40 mM), whereas neither was detected in the wild‐type strain under the same conditions. Further analysis indicated that high NH concentrations greatly inhibited the expression of nifA and nitrogenase gene in the wild‐type strain but not in the glnA1^? mutant. These observations suggest that GS is essential to NH repression of nitrogenase and that deletion of glnA1 results in the complete derepression of nitrogenase by preventing NH assimilation in vivo, thus relieving the inhibition of nifA and nitrogenase gene expression. Knocking out glnA1 therefore provides an efficient approach to removing the inhibitory effects of ammonium ions in R. sphaeroides and possibly in other hydrogen‐producing PNS bacteria. Biotechnol. Bioeng. 2010;106: 564–572. © 2010 Wiley Periodicals, Inc.     

Differential responses of two wetland graminoids to high ammonium at different pH values

Enhanced soil ammonium () concentrations in wetlands often lead to graminoid dominance, but species composition is highly variable. Although is readily taken up as a nutrient, several wetland species are known to be sensitive to high concentrations or even suffer toxicity, particularly at low soil pH. More knowledge about differential graminoid responses to high availability in relation to soil pH can help to better understand vegetation changes. The responses of two wetland graminoids, Juncus acutiflorus and Carex disticha, to high (2 mmol·l^?1) versus control (20 μmol·l^?1) concentrations were tested in a controlled hydroponic set up, at two pH values (4 and 6). A high concentration did not change total biomass for these species at either pH, but increased C allocation to shoots and increased P uptake, leading to K and Ca limitation, depending on pH treatment. More than 50% of N taken up by C. disticha was invested in N‐rich amino acids with decreasing C:N ratio, but only 10% for J. acutiflorus. Although both species appeared to be well adapted to high loadings in the short term, C. disticha showed higher classic detoxifying responses that are early warning indicators for decreased tolerance in the long term. In general, the efficient aboveground biomass allocation, P uptake and N detoxification explain the competitive strength of wetland graminoids at the expense of overall biodiversity at high loading. In addition, differential responses to enhanced affect interspecific competition among graminoids and lead to a shift in vegetation composition.     

Dynamic light scattering as a probe of superhelical DNA-intercalating agent interaction

Polarized dynamic light-scattering measurements on superhelical pBR322-plasmid DNA solutions in 0.2M NaCl, 2 mM NaPi, pH 7.0, 2 mM EDTA result in a translational diffusion coefficient D = (3.77 ± 0.10) × 10^?8 cm²/s for the native molecule. Modeling the DNA, in the simplest approximation, as a 10 × 440-nm effective hydrodynamic rigid rod yields a good fit to the apparent diffusion coefficient angular-dependence data up to 70°; the model fails at higher angles, probably due to the effects of flexibility or branching of the rod. Diffusion coefficient titration experiments with a platinum complex intercalating agent (PtTS) result in a titratable superhelix density of σ = ?0.079 ± 0.008 under our experimental conditions, corresponding to about 34 superhelical turns in the native DNA. The DNA contour length predicted by our two independent results, the rod dimensions and the number of superhelical turns, is in excellent agreement with the contour length calculated from the number of base pairs, supporting the hydrodynamic approximation of an effective rodlike structure for this small DNA molecule in solution.     

Characterization of a biofilm membrane reactor and its prospects for fine chemical synthesis

Biofilms are known to be robust biocatalysts. Conventionally, they have been mainly applied for wastewater treatment, however recent reports about their employment for chemical synthesis are increasingly attracting attention. Engineered Pseudomonas sp. strain VLB120ΔC biofilm growing in a tubular membrane reactor was utilized for the continuous production of (S)‐styrene oxide. A biofilm specific morphotype appeared in the effluent during cultivation, accounting for 60–80% of the total biofilm irrespective of inoculation conditions but with similar specific activities as the original morphotype. Mass transfer of the substrate styrene and the product styrene oxide was found to be dependent on the flow rate but was not limiting the epoxidation rate. Oxygen was identified as one of the main parameters influencing the biotransformation rate. Productivity was linearly dependent on the specific membrane area and on the tube wall thickness. On average volumetric productivities of 24 g L day^?1 with a maximum of 70 g L day^?1 and biomass concentrations of 45 g_BDW L have been achieved over long continuous process periods (≥50 days) without reactor downtimes. Biotechnol. Bioeng. 2010. 105: 705–717. © 2009 Wiley Periodicals, Inc.     

THE EFFECT OF SOFT SELECTION ON THE VARIABILITY OF A QUANTITATIVE TRAIT

The equilibrium phenotypic variance of a normally distributed quantitative character P under soft selection is studied. This character is assumed to undergo Gaussian stabilizing selection W(p, x) = exp[–(p – x)²/2w²]. The environmentally determined optimum (x) is a normal variable with variance s². A stable equilibrium with is found, so that increases both with increasing environmental heterogeneity and with increasing local intensity of stabilizing selection. It is shown that both genetic and environmental components of the variance are selected until this equilibrium is reached. Habitat selection, supposed to be normal (with variance H²) around the optimum, also increases the value. Nevertheless, relatively intense local stabilizing selection (w < s) and accurate habitat choice (H < s) are required for the initial spread and the evolutionary stability of this habitat selection.     

Dual effects of formylpeptides on the adhesion of endotoxin-primed human neutrophils

Neutrophils, treated with sequential additions of bacterial products such as endotoxin (E. Coli lipopolysaccharide, LPS) and the chemotactic peptide N-formyl-methionyl-leucyl-phenylalanine (fMLP), undergo to metabolic activation and express membrane-anchoring proteins that promote adhesion to serum-coated culture wells. By investigating the dose–response relationships of these phenomena, we have found that: (a) resting neutrophils do not produce a significant amount of superoxide (O) and show only minimal adhesion to serum-coated plastic surfaces; (b) fully activatory doeses (> 5 × 10^?8 M ) of fMLP induce the release of O and a significant increase of the cell adhesion; (c) pretreatment of the cells for 1 h with LPS augments cell adhesion to serum-coated culture wells in the absence of further stimulation and primes the neutrophils to enhanced fMLP-dependent O release; (d) addition of low, substimulatory doses of fMLP (from 10^?10 M to 5 × 10^?9 M ) inhibits and reverses the adhesion of LPS-treated cells, (e) high fMLP doses (> 10^?7 M ) are additive to LPS in promoting adhesion. Phorbol-myristate acetate (> 10^?9M) increased adhesion in both normal and LPS-treated neutrophils, but low doses of this stimulant did not inhibit adhesion. Low doses (10^?9 M ) of fMLP increased intracellular cyclic AMP in both normal and LPS-treated neutrophils, suggesting that stimulus-induced rises in cAMP may be the negative signal responsible for down-modulation of adhesion. Low (5 × 10^?9 M ) and high (5 × 10^?7 M ) fMLP doses induced the same increase of expression of CD11/CD18 integrins, indicating that the inhibition of adhesion caused by low doses is not due to quantitative down-regulation of integrins. These findings may provide an in vitro model of the complex biological events involved in the regulation of neutrophil adhesion.     

Conformational analysis of acetyl-L-phenylalanine p-acetyl and p-valeryl anilides

Empirical force-field calculations and ir and ¹H-nmr spectra indicate that five-membered (C₅) and seven-membered (C) hydrogen-bonded rings are the preferred conformations of acetyl-L -Phe p-acetyl and p-valeryl anilides in nonpolar media. The C₅/C ratio was found to be dependent on the dryness of the solute and the solvent. This fact and the results from conformational-energy calculations suggest that a molecule of water participates in the stabilization of the C conformation.     

Effective size of density‐dependent populations in fluctuating environments

Reliable estimates of effective population size are of central importance in population genetics and evolutionary biology. For populations that fluctuate in size, harmonic mean population size is commonly used as a proxy for (multi‐) generational effective size. This assumes no effects of density dependence on the ratio between effective and actual population size, which limits its potential application. Here, we introduce density dependence on vital rates in a demographic model of variance effective size. We derive an expression for the ratio in a density‐regulated population in a fluctuating environment. We show by simulations that yearly genetic drift is accurately predicted by our model, and not proportional to as assumed by the harmonic mean model, where N is the total population size of mature individuals. We find a negative relationship between and N. For a given N, the ratio depends on variance in reproductive success and the degree of resource limitation acting on the population growth rate. Finally, our model indicate that environmental stochasticity may affect not only through fluctuations in N, but also for a given N at a given time. Our results show that estimates of effective population size must include effects of density dependence and environmental stochasticity.