Antibacterial substances from marine algae isolated from Jeddah coast of Red sea,Saudi Arabia

Marine algae are known to produce a wide variety of bioactive secondary metabolites and several compounds have been derived from them for prospective development of novel drugs by the pharmaceutical industries. However algae of the Red sea have not been adequately explored for their potential as a source of bioactive substances. In this context Ulva reticulata, Caulerpa occidentalis, Cladophora socialis, Dictyota ciliolata, and Gracilaria dendroides isolated from Red sea coastal waters of Jeddah, Saudi Arabia, were evaluated for their potential for bioactivity. Extracts of the algae selected for the study were prepared using ethanol, chloroform, petroleum ether and water, and assayed for antibacterial activity against Escherichia coli ATCC 25322, Pseudomonas aeruginosa ATCC 27853, Stapylococcus aureus ATCC 29213, and Enterococcus faecalis ATCC 29212. It was found that chloroform was most effective followed by ethanol, petroleum ether and water for the preparation of algal extract with significant antibacterial activities, respectively. Results also indicated that the extracts of red alga G. dendroides were more efficient against the tested bacterial strains followed by green alga U. reticulata, and brown algae D. ciliolata. Chemical analyses showed that G. dendroides recorded the highest percentages of the total fats and total proteins, followed by U. reticulata, and D. ciliolate. Among the bioflavonoids determined Rutin, Quercetin and Kaempherol were present in high percentages in G. dendroides, U. reticulata, and D. ciliolate. Estimation of saturated and unsaturated fatty acids revealed that palmitic acid was present in highest percentage in all the algal species analyzed. Amino acid analyses indicated the presence of free amino acids in moderate contents in all the species of algae. The results indicated scope for utilizing these algae as a source of antibacterial substances.     

Extraction and physicochemical characterization of Sargassum vulgare alginate from Brazil

Alginate fractions from Sargassum vulgare brown seaweed were characterized by (1)H NMR and fluorescence spectroscopy and by rheological measurements. The alginate extraction conditions were investigated. In order to carry out the structural and physicochemical characterization, samples extracted for 1 and 5h at 60 degrees C were further purified by re-precipitation with ethanol and denoted as SVLV (S. vulgare low viscosity) and SVHV (S. vulgare high viscosity), respectively. The M/G ratio values for SVLV and SVHV were 1.56 and 1.27, respectively, higher than the ratio for most Sargassum spp. alginates (0.19-0.82). The homopolymeric blocks F(GG) and F(MM) of these fractions characterized by (1)H NMR spectroscopy were 0.43 and 0.55 for SVHV and 0.36 and 0.58 for SVLV samples, respectively, these values typically being within 0.28-0.77 and 0.07-0.41, respectively. Therefore, the alginate samples from S. vulgare are much richer in mannuronic block structures than those from other Sargassum species. Values of M(w) for alginate samples were also calculated using intrinsic viscosity data. The M(w) value for SVLV (1.94 x 10(5)g/mol) was lower than that for SVHV (3.3 x 10(5)g/mol). Newtonian behavior was observed for a solution concentration as high as 0.7% for SVLV, while for SVHV the solutions behaved as a Newtonian fluid up to 0.5%. The optimal conditions for obtaining the alginates from S. vulgare were 60 degrees C and 5h extraction. Under these conditions, a more viscous alginate in higher yield was extracted from the seaweed biomass.     

Effect of inorganic and organic nutrient addition on coral–algae assemblages from the Northern Red Sea

Previous studies in fringing reefs of the Northern Red Sea demonstrated that the in-situ competition of corals and algae in natural assemblages is highly variable between seasons displaying fast overgrowth of corals by benthic reef algae in fall that follows close to equilibrium between both groups of organisms in summer. This may be caused by up to 5-fold higher inorganic nutrient and 6-fold higher organic nutrient concentrations in fall and winter, thereby potentially promoting algae and cyanobacteria growth with concomitant phase shift. A long term mesocosm experiment (duration: 90 days) was conducted in order to study the effect of dissolved inorganic (ammonium, phosphate, nitrate, and mix of all three) and organic (glucose) nutrient addition onto the competitive process in the dominant coral–algae assemblages of the Northern Red Sea involving branching corals of the genus Acropora and a typical consortium of benthic turf algae. Nutrients were added in 3-fold higher concentrations compared to the annual averages, and the parameters algal growth, extension of bleached area on corals, tissue colour change and chlorophyll a concentrations were monitored at regular intervals over experimental duration. This revealed that elevated ammonium concentrations and elevated organic nutrient concentrations stimulate algal growth, while coral tissue pigmentation and chlorophyll a content were significantly decreased. But only in the elevated organic nutrient treatment all effects on corals were significantly pronounced when assembled with benthic turf algae. Supplementary logger measurements revealed that O₂ water concentrations were significantly lower in the elevated organic nutrient mesocosm compared to all other treatments, confirming side-effects on microbial activity. These findings indicate that organic nutrient input into coral reefs can affect physiology and metabolism of both corals and benthic turf algae. Reinforcing interaction between both groups of organisms along with involvement of microbes may facilitate phase shifts in coral reef ecosystems.     

Characterization of O-acetyl-(4-O-methylglucurono)xylan isolated from birch and beech

The structures of water-soluble birch and beech xylans, extracted from holocellulose using dimethyl sulfoxide, were determined employing 1H and 13C NMR spectroscopy together with chemical analysis. These polysaccharides were found to be O-acetyl-(4-O-methylglucurono)xylans containing one 4-O-methylglucuronic acid substituent for approximately every 15 D-xylose residues. The average degree of acetylation of the xylose residues in these polymers was 0.4. The presence of the structural element -->4)[4-O-Me-alpha-D-GlcpA-(1-->2)][3-O-Ac]-beta-D-Xylp-(1--> was demonstrated. Additional acetyl groups were present as substituents at C-2 and/or C-3 of the xylopyranosyl residues. Utilizing size-exclusion chromatography in combination with mass spectroscopy, the weight-average molar masses (and polydispersities) were shown to be 8000 (1.09) and 11,100 (1.08) for birch and beech xylan, respectively.     

Complete 1H, 13C and 15N NMR assignments and secondary structure of the 269-residue serine protease PB92 from Bacillus alcalophilus

Summary The ¹H, ¹³C and ¹⁵N NMR resonances of serine protease PB92 have been assigned using 3D tripleresonance NMR techniques. With a molecular weight of 27 kDa (269 residues) this protein is one of the largest monomeric proteins assigned so far. The side-chain assignments were based mainly on 3D H(C)CH and 3D (H)CCH COSY and TOCSY experiments. The set of assignments encompasses all backbone carbonyl and CH_n carbons, all amide (NH and NH₂) nitrogens and 99.2% of the amide and CH_n protons. The secondary structure and general topology appear to be identical to those found in the crystal structure of serine protease PB92 [Van der Laan et al. (1992) Protein Eng., 5, 405–411], as judged by chemical shift deviations from random coil values, NH exchange data and analysis of NOEs between backbone NH groups.Abbreviations 2D/3D/4D two-/three-/four-dimensional - HSQC heteronuclear single-quantum coherence - HMQC heteronuclear multiple-quantum coherence - COSY correlation spectroscopy - TOCSY total correlation spectroscopy - NOE nuclear Overhauser enhancement (connectivity) - NOESY 2D NOE spectroscopy Experiment nomenclature (H(C)CH, etc.) follows the conventions used elsewhere [e.g. Ikura et al. (1990) Biochemistry, 29, 4659–4667].     

Conformational studies of a novel cationic glycolipid,glyceroplasmalopsychosine, from bovine brain by NMR spectroscopy

A novel glycosphingolipid containing a long chain aldehyde conjugated to galactose and glycerol, Gro1(3)-O-CH((CH(2))(n)CH(3))-O-6Galbeta-sphingosine (glyceroplasmalopsychosine) has been studied by NMR spectroscopy (Hikita et al. J. Biol. Chem. 2001, 276, 23084-23091). We further report here on the conformation showing the galactose and the glycerol at the end of two parallel hydrophobic chains, i.e. the sphingosine and the fatty aldehyde. This is proposed based on the interproton distances derived from ROESY experiments and 3 J (H,H) coupling constants. The absence of any intraresidual NOEs between protons in the glycerol residue suggested that the C-C-2 and C-C-3 bonds in the glycerol may be rotating freely, supporting the proposed conformation in which the unique terminal glycerol is in an environment with a minimal steric hindrance. The present study proposes a conformation of glyceroplasmalopsychosine greatly different from the two conventional plasmalopsychosines possessing a fatty aldehyde chain oriented in an opposite direction to the sphingosine.     

A Metabolomic Study of Brain Tissues from Aged Mice with Low Expression of the Vesicular Monoamine Transporter 2 (VMAT2) Gene

The vesicular monoamine transporter 2 (VMAT2) sequesters monoamines into synaptic vesicles in preparation for neurotransmission. Samples of cerebellum, cortex, hippocampus, substantia nigra and striatum from VMAT2-deficient mice were compared to age-matched control mice. Multivariate statistical analyses of ¹H NMR spectral profiles separated VMAT2-deficient mice from controls for all five brain regions. Although the data show that metabolic alterations are region- and age-specific, in general, analyses indicated decreases in the concentrations of taurine and creatine/phosphocreatine and increases in glutamate and N-acetyl aspartate in VMAT2-deficient mouse brain tissues. This study demonstrates the efficacy of metabolomics as a functional genomics phenotyping tool for mouse models of neurological disorders, and indicates that mild reductions in the expression of VMAT2 affect normal brain metabolism. Special issue article in honor of Dr. Frode Fonnum.     

Spring time production of bottom ice algae in the landfast sea ice zone at Barrow, Alaska

The primary production of bottom ice algae is an important food source for sympagic, pelagic and benthic organisms in the Arctic Ocean as well as Antarctic Ocean. Using ¹³C-¹⁵N isotope tracers, the recent ice algal production at Barrow during the spring season was lower in 2003 than three decades ago, although the maximum chlorophyll-a concentration for the bottom ice algae was similar to the values from previous studies. Estimated recent new and total production rates of the ice algae were 0.8 g C m^- 2 yr^- 1 and 2.0 g C m^- 2 yr^- 1 respectively, while the rates of water column phytoplankton were 0.2 g C m^- 2 yr^- 1 and 0.7 g C m^- 2 yr^- 1 for the spring sampling period in 2003. The ice algae contributed 74% of the pelagic primary production under the landfast sea ice at Barrow before the phytoplankton spring bloom. At the end of the season in 2003, a high carbon allocation of lipids in the ice algae was found. Three possible explanations- nutrient depletion, increasing light, and/or changes in species composition- were suggested for the high carbon incorporation into lipids. This high lipid synthesis of the bottom ice algae might be significant to zooplankton and benthic fauna grazers because lipids are the most energy dense biomolecules.     

Spectroscopic characterization of extracts from humic and fulvic fractions: IR and1H NMR spectra

Summary Infrared and proton resonance spectra have been used to characterize fraction extracted sequentially from humic and fulvic acids by diethylether, acetone, dioxane, tetrahydrofuran, pyridine and dimethylformamide. The results showed that the same solvents extracted structurally similar components from both humic and fulvic acids. On the other hand, the spectra showed solvent-dependent differences, some being characteristic for a preponderance of aliphatic structures, others for aromatic structures.     

1,5-Anhydroxylitol from leaves of Olea europaea

1,5-Anhydroxylitol, a compound never found previously in the vegetal kingdom was obtained from Olea europaea leaves in approximately 0.5-1% yield.     

Oxytocin solution structure changes upon protonation of the N-terminus in dimethyl sulfoxide

Summary With the combined use of various two-dimensional (2D) NMR techniques, a complete assignment of the ¹H and ¹³C resonances of oxytocin, , for two molecular states, protonated and unprotonated at the N-terminal group, was performed in dimethyl sulfoxide. A small but distinct change in the backbone conformation of the six-residue cyclic moiety, associated with the protonation, was first suggested from those NMR parameters relevant to conformation, such as change with temperature in the chemical shifts of the peptide amide protons and changes in chemical shifts and homonuclear as well as heteronuclear three-bond coupling constants. The solution structures of oxytocin for the protonated and unprotonated forms were then calculated using distance analysis in dihedral-angle space, based on a relaxation matrix evaluated from quantitative NOE intensities at different mixing times. Total amounts of 93 and 105 distances were determined for the protonated and the unprotonated forms, respectively. There were 25 interresidue distances relevant to the structure of the cyclic moiety for the protonated form of oxytocin and 43 for the unprotonated form. Overall structures with the lowest target penalty function were similar between the two forms, having a -turn structure at the endocyclic residues of the Tyr-Ile-Gln-Asn moiety. The local backbone conformations near the N-terminus, however, were significantly different between the two forms. This was found to be due to a change in the dihedral angle of the disulfide bridge (^ss around C-S-S-C), which closes the ring in the cyclic peptide. The dihedral angle was about +90° for the unprotonated form and an intermediate value of about +45° for the protonated form.     

Assigning stereodiversity of the 27-Me group of furostane-type steroidal saponins via NMR chemical shifts

Applicability of (13)C and (1)H NMR chemical shifts for the assignment of the 25R/25S configuration of the 27-methyl group in the case of furostane-type steroidal saponins has been investigated. A comparative study of (13)C NMR data suggest that chemical shift values for C-20, C-21, C-22, C-23, C-24, C-25, C-26 and C-27 resonances were not much influenced by R/S configuration of the 27-Me group, thus reflecting limited application of (13)C NMR chemical shifts for such stereochemical determinations. In contrast, (1)H NMR chemical shifts (delta(a), delta(b)) for geminal protons of glycosyloxy methylene (H(2)-26) exhibit pronounced dependence and the difference (Delta(ab)=delta(a)-delta(b)) among their chemical shifts [Delta(ab)= or <0.48 for 25R; Delta(ab)= or >0.57 for 25S] seems to be of general applicability for ascertaining 25R/25S orientation of the 27-methyl group of furostane-type steroidal saponins.     

Synthesis of a novel N[bond]O-interglycosidic disaccharide

The carbohydrate subunits carrying an N-O-interglycosidic bond play a very important role in the biological activity of the enediyne antibiotics. Condensation of O-(alpha- and beta-D-glucopyranosyl)hydroxylamine (5a and 5b) with the hex-3-ulopyranoside (6) furnished methyl 4,6-O-benzylidene-2,3-dideoxy-3-(2,3,4,6-tetra-O-benzyl-alpha-D-glucopyranosyloxy)imino-alpha- and beta-D-erythro-hexopyranoside (7a and 7b). Stereoselective reduction of the Cz.dbnd6;N bond of 7a and 7b with sodium cyanoborohydride resulted in the formation of the required protected N-O-interglycosidic disaccharides (8a and 8b). Finally, catalytic hydrogenation of 8a afforded methyl 2,3-dideoxy-3-(alpha-D-glucopyranosyloxy)amino-alpha-D-ribo-hexopyranoside (9a). Under similar conditions the beta anomer 8b underwent decomposition.     

Recruitment and mortality of early post-settlement stages of benthic algae

Four transitional life history stages are generally recognized for benthic marine algae. On the basis of differences in size, we propose two more: young germlings and young juveniles. Three of these (spores or zygotes, young germlings, and germlings) are considered early post-settlement (EPS) stages. Many of the available data on recruitment and mortality were not collected with EPS stages specifically in mind, and considerable extrapolation and inference are required to interpret effects on early phases. Data on EPS stages, and grazing in particular, are based on the disappearance of early stages (laboratory or field experiments, including outplantings), on indirect information on mortality from manipulations of grazers or juvenile stages, and combinations of observation and manipulation. We also provide original data on the effects of water motion and canopy sweeping on zygote mortality.

The most notable finding is the variability in, and multiplicity of, factors preventing successful recruitment of early life stages. Six intrinsic and about 17 extrinsic factors and/or processes were reported to affect recruitment and mortality. Grazing, canopy, and turf effects appear to be most important, but less well studied factors such as desiccation and water motion may be as important for early stages. Our review indicates that recruitment is highly variable, even episodic, and that mortality at this period is high. Combined, these elements suggest that chance events during EPS stages may play a large role in survival, and perhaps the evolution of benthic algae.     

Biophysical studies of a transmembrane peptide derived from the T cell antigen receptor

Summary Core peptide (CP) is a unique peptide derived from the transmembrane sequence of T cell antigen receptor (TCR)-alpha chain and is capable of inhibiting the immune response both invitro and in animal models of T cell mediated inflammation. The structure of CP, with sequence GLRILLLKV, is similar to the amphipathic region of many peptides. Unlike antimicrobial peptides, however, which damage cell membranes, electron microscopy and propidium iodide exclusion assays on cell membranes suggest that CP does not create pores and may act by interfering with signal transduction at the membrane level. To investigate this effect further we report the results of³¹P and²H solid-state NMR spectroscopy of CP on model membranes. As predicted, even at high concentrations of CP, the structure of model membranes was not significantly perturbed. Only at the very high peptide-to-lipid molar ratio of 1∶10 significant effects on the model membranes were observed. We conclude that CP does not destroy the integrity of the lipid bilayer.     

Structural features of pectic polysaccharides from the skin of Opuntia ficus-indica prickly pear fruits

After removal of the mucilage with water at room temperature, pectic polysaccharides were solubilized from Opuntia ficus-indica fruit skin, by sequential extraction with water at 60 degrees C (WSP) and EDTA solution at 60 degrees C (CSP). Polysaccharides with neutral sugar content of 0.48 and 0.36 mol/mol galacturonic acid residue were obtained, respectively, in the WSP and CSP extracts. These pectic polysaccharides were de-esterified and fractionated by anion-exchange chromatography, yielding for each extract five fractions, which were thereafter purified by size-exclusion chromatography. Two of these purified fractions were characterized by sugar analysis combined with methylation and reduction-methylation analysis. The study was then supported by (1)H and (13)C NMR spectroscopy. The results showed that the water-soluble fraction WSP3 and the EDTA soluble fraction CSP3, consisted of a disaccharide repeating unit -->2)-alpha-l-Rhap-(1-->4)-alpha-d-GalpA-(1--> backbone, with side chains attached to O-4 of the rhamnosyl residues. The side chains contained highly branched alpha-(1-->5)-linked arabinan and short linear beta-(1-->4)-linked galactan.     

Biophysical studies of a transmembrane peptide derived from the T cell antigen receptor

Core peptide (CP) is a unique peptide derived from thetransmembrane sequence of T cell antigen receptor (TCR)-alpha chain and is capable of inhibiting the immuneresponse both in vitro and in animal models of Tcell mediated inflammation. The structure of CP, withsequence GLRILLLKV, is similar to the amphipathic regionof many peptides. Unlike antimicrobial peptides,however, which damage cell membranes, electron microscopyand propidium iodide exclusion assays on cell membranessuggest that CP does not create pores and may act byinterfering with signal transduction at the membranelevel. To investigate this effect further we report theresults of ³¹P and ²H solid-state NMRspectroscopy of CP on model membranes. As predicted,even at high concentrations of CP, the structure of modelmembranes was not significantly perturbed. Only at thevery high peptide-to-lipid molar ratio of 1:10significant effects on the model membranes were observed. We conclude that CP does not destroy the integrity of thelipid bilayer.     

Quantitative analysis of sugars in wood hydrolyzates with H NMR during the autohydrolysis of hardwoods

The focus of this work was to determine the utility of ¹H NMR spectroscopy in the quantification of sugars resulting from the solubilization of hemicelluloses during the autohydrolysis of hardwoods and the use of this technique to evaluate the kinetics of this process over a range of temperatures and times. Yields of residual xylan, xylooligomers, xylose, glucose, and the degraded products of sugars, i.e., furfural and HMF (5-hydroxymethyl furfural), were determined. The monosaccharide and oligomer contents were quantified with a recently developed high resolution ¹H NMR spectroscopic analysis. This method provided precise measurement of the residual xylan and cellulose remaining in the extracted wood samples and xylose and glucose in the hydrolyzates. NMR was found to exhibit good repeatability and provided carbohydrate compositional results comparable to published methods for sugar maple and aspen woods.     

Exploring a DNA Sequence for the Three-Dimensional Structure Determination of a Silver(I)-Mediated C-C Base Pair in a DNA Duplex By 1H NMR Spectroscopy

Recently, we discovered novel silver(I)-mediated cytosine–cytosine base pair (C–Ag^I–C) in DNA duplexes. To understand the properties of these base pairs, we searched for a DNA sequence that can be used in NMR structure determination. After extensive sequence optimizations, a non-symmetric 15-base-paired DNA duplex with a single C–Ag^I–C base pair flanked by 14 A–T base pairs was selected. In spite of its challenging length for NMR measurements (30 independent residues) with small sequence variation, we could assign most non-exchangeable protons (254 out of 270) and imino protons for structure determination.     

Structural elucidation of the EPS of slime producing Brevundimonas vesicularis sp. isolated from a paper machine

The slime forming bacteria Brevundimonas vesicularis sp. was isolated from a paper mill and its EPS was produced on laboratory scale. After production, the exopolysaccharide (EPS) was purified and analysed for its purity and homogeneity, HPSEC revealed one distinct population with a molecular mass of more than 2,000 kDa. The protein content was around 9 w/w%. The sample was analysed to determine its chemical structure. The EPS was found to consist of rhamnose, glucose, galacturonic acid and glucuronic acid. Due to the presence of uronic acids the molar ratio between the four sugars found varies from 3:5:2:4 by sugar composition analyses after methanolysis to 1:1:1:1 found by NMR. A repeating unit with a molecular mass of 678 Da was confirmed by MALDI-TOF mass spectrometry after mild acid treatment. 13C and 1H hetero- and homonuclear 2D NMR spectroscopy of the native and partial hydrolysed EPS revealed a repeating unit, no non-sugar substituents were present.