Tertiary structure-function analysis reveals the pathogenic signaling potentiation mechanism of Helicobacter pylori oncogenic effector CagA

The Helicobacter pylori type IV secretion effector CagA is a major bacterial virulence determinant and critical for gastric carcinogenesis. Upon delivery into gastric epithelial cells, CagA localizes to the inner face of the plasma membrane, where it acts as a pathogenic scaffold/hub that promiscuously recruits host proteins to potentiate oncogenic signaling. We find that CagA comprises a structured N-terminal region and an intrinsically disordered C-terminal region that directs versatile protein interactions. X-ray crystallographic analysis of the N-terminal CagA fragment (residues 1-876) revealed that the region has a structure comprised of three discrete domains. Domain I constitutes a mobile CagA N terminus, while Domain II tethers CagA to the plasma membrane by interacting with membrane phosphatidylserine. Domain III interacts intramolecularly with the intrinsically disordered C-terminal region, and this interaction potentiates the pathogenic scaffold/hub function of CagA. The present work provides a tertiary-structural basis for the pathophysiological/oncogenic action of H. pylori CagA.     

Decreased Silica Land–sea Fluxes through Damming in the Baltic Sea Catchment – Significance of Particle Trapping and Hydrological Alterations

We tested the hypothesis that reservoirs with low water residence time and autochthonous production influence river biogeochemistry in eutrophied river systems draining cultivated watersheds. The effect of a single artificial water reservoir and consecutive reservoirs on silica (Si) river fluxes is exemplified by the moderately dammed Vistula River and the heavily regulated Daugava River that are compared with the practically undammed Oder River. The sum of the discharge weighted annual mean biogenic silica (BSi) and dissolved silicate (DSi) concentrations in the rivers Oder, Vistula and Daugava were about 160 μ M (40 + 120 μ M), 150 μ M (20 + 130 μ M) and 88 μ M (6 + 82 μ M), respectively. Assuming BSi and DSi concentrations as observed in the Oder River as typical for eutrophied but undammed rivers, complete trapping of this BSi could have lowered Si fluxes to the Baltic Sea from rivers with cultivated watersheds by 25%. The superimposed effect of hydrological alterations on reduced Si land–sea fluxes is demonstrated by studies in the boreal/subarctic and oligotrophic rivers Kalixälven and Lueälven. The DSi yield of the heavily dammed Luleälven (793 kg km^?2 yr^?1) constituted only 63% of that was found in the unregulated Kalixälven (1261 kg km^?2 yr^?1), despite the specific runoff of the Luleälven (672 mm m^?2 yr^?1) being 19% higher than that of theKalixälven (563 mm m^?2 yr^?1); runoff normalized DSi yield of the former, regulated watershed, was only half the DSi yield of the latter, unperturbed watershed. Based on these findings, it is hypothesized here that perturbed surface water–groundwater interactions are the major reasons for the reduced annual fluctuations in DSi concentrations as also seen in the heavily dammed and eutrophic river systems such as the Daugava and Danube.     

Cellulolytic activity of luminous bacteria

Summary The luminous bacteriaVibrio harveyi andV. fischeri degrade cellulose. Cellulase activity was high when carboxymethyl cellulose and cellobiose were used as substrates but low with cellulose powder. The role of these microbes in the digestion of food material in fish gut is also discussed.

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Resumen Las bacterias luminosasVibrio harveyi yV. fischeri degradan celulosa. La actividad celulásica fue alta cuando se utilizó Carboxy-metil-celulosa o celobiosa como sustrato y baja cuando se utilizó polvo de celulosa. Se discute el papel de estos microorganismos en la digestión intestinal de los alimentos en peces.

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Résumé Les bactéries lumineusesVibrio harveyi etV. fischeri dégradent la cellulose. L'activité cellulolytique était élevée lorsque la carboxméthylcellulose et la cellobiose servaient de substrats, mais elle était faible avec la poudre de cellulose. On discute également de rôle de ces microorganismes dans la digestion du matériau alimentaire.

     

The thermodynamic response of soft biological tissues to pulsed ultraviolet laser irradiation.

The physical mechanisms that enable short pulses of high-intensity ultraviolet laser radiation to remove tissue, in a process known as laser ablation, remain obscure. The thermodynamic response of biological tissue to pulsed laser irradiation was investigated by measuring and subsequently analyzing the stress transients generated by pulsed argon fluorine (ArF, lambda = 193 nm) and krypton fluorine (KrF, lambda = 248 nm) excimer laser irradiation of porcine dermis using thin-film piezoelectric transducers. For radiant exposures that do not cause material removal, the stress transients are consistent with rapid thermal expansion of the tissue. At the threshold radiant exposure for ablation, the peak stress amplitude generated by 248 nm irradiation is more than an order of magnitude larger than that produced by 193 nm irradiation. For radiant exposures where material removal is achieved, the temporal structure of the stress transient indicates that the onset of material removal occurs during irradiation. In this regime, the variation of the peak compressive stress with radiant exposure is consistent with laser-induced rapid surface vaporization. For 193 nm irradiation, ionization of the ablated material occurs at even greater radiant exposures and is accompanied by a change in the variation of peak stress with radiant exposure consistent with a plasma-mediated ablation process. These results suggest that absorption of ultraviolet laser radiation by the extracellular matrix of tissue leads to decomposition of tissue on the time scale of the laser pulse. The difference in volumetric energy density at ablation threshold between the two wavelengths indicates that the larger stresses generated by 248 nm irradiation may facilitate the onset of material removal. However, once material removal is achieved, the stress measurements demonstrate that energy not directly responsible for target decomposition contributes to increasing the specific energy of the plume (and plasma, when present), which drives the gas dynamic expansion of ablated material. This provides direct evidence that ultraviolet laser ablation of soft biological tissues is a surface-mediated process and not explosive in nature.     

Structural features of the human salivary mucin, MUC7

Human salivary mucin (MUC7) is characterized by a single polypeptide chain of 357 aa. Detailed analysis of the derived MUC7 peptide sequence reveals five distinct regions or domains: (1) an N-terminal basic, histatin-like domain which has a leucine-zipper segment, (2) a moderately glycosylated domain, (3) six heavily glycosylated tandem repeats each consisting of 23 aa, (4) another heavily glycosylated MUC1- and MUC2-like domain, and (5) a C-terminal leucine-zipper segment. Chemical analysis and semi-empirical prediction algorithms for O-glycosylation suggested that 86/105 (83%) Ser/Thr residues were O-glycosylated with the majority located in the tandem repeats. The high (～25%) proline content of MUC7 including 19 diproline segments suggested the presence of polyproline type structures. CD studies of natural and synthetic diproline-rich peptides and glycopeptides indicated that polyproline type structures do play a significant role in the conformational dynamics of MUC7. In addition, crystal structure analysis of a synthetic diproline segment (Boc-Ala-Pro-OBzl) revealed a polyproline type II extended structure. Collectively, the data indicate that the polyproline type II structure, dispersed throughout the tandem repeats, may impart a stiffening of the backbone and could act in consort with the glycosylated segments to keep MUC7 in a semi-rigid, rod shaped conformation resembling a ‘bottle-brush’ model.     

Long pepper (Piper longum) derived carbon dots as fluorescent sensing probe for sensitive detection of Sudan I

In this piece of work, microwave-assisted conversion of a natural precursor in to high-valued nano-scale material was carried out by a completely greener method. The fluorescent carbon dots prepared, designated as long pepper derived carbon dots (LPCDs), have been thoroughly characterized to explore the physical and chemical properties. The system exhibits excitation dependent emission behavior and from the optimal studies the excitation and emission wavelength of the system was found to be 330 nm and 455 nm respectively. On account of the superior fluorescent behavior of the LPCDs, it was successfully employed as a fluorescent sensing probe to detect Sudan I with good level of selectivity and sensitivity. This carcinogenic dye extensively used as food adulterant can impart several health issues. Food product safety is of high concern, therefore a simple facile and economical analytical method was proposed based on the fluorescence of LPCDs for this dye detection with satisfactory statistical parameters. A linear relationship was maintained in the range of 0 to 27.27 μM Sudan I with limit of detection of 0.92 μM. The quenching mechanism was studied and finally attributed to Förster resonance energy transfer (FRET) mechanism. In addition, the probe was effectively implemented for Sudan I detection in commercial chili powder samples with good level of recovery parameters.     

Architecture of a Nascent Sphingomonas sp. Biofilm under Varied Hydrodynamic Conditions

The architecture of a Sphingomonas biofilm was studied during early phases of its formation, using strain L138, a gfp-tagged derivative of Sphingomonas sp. strain LB126, as a model organism and flow cells and confocal laser scanning microscopy as experimental tools. Spatial and temporal distribution of cells and exopolymer secretions (EPS) within the biofilm, development of microcolonies under flow conditions representing varied Reynolds numbers, and changes in diffusion length with reference to EPS production were studied by sequential sacrificing of biofilms grown in multichannel flow cells and by time-lapse confocal imaging. The area of biofilm in terms of microscopic images required to ensure representative sampling varied by an order of magnitude when area of cell coverage (2 × 10⁵ μm²) or microcolony size (1 × 10⁶ μm²) was the biofilm parameter under investigation. Hence, it is necessary to establish the inherent variability of any biofilm metric one is attempting to quantify. Sphingomonas sp. strain L138 biofilm architecture consisted of microcolonies and extensive water channels. Biomass and EPS distribution were maximal at 8 to 9 μm above the substratum, with a high void fraction near the substratum. Time-lapse confocal imaging and digital image analysis showed that growth of the microcolonies was not uniform: adjacently located colonies registered significant growth or no growth at all. Microcolonies in the biofilm had the ability to move across the attachment surface as a unit, irrespective of fluid flow direction, indicating that movement of microcolonies is an inherent property of the biofilm. Width of water channels decreased as EPS production increased, resulting in increased diffusion distances in the biofilm. Changing hydrodynamic conditions (Reynolds numbers of 0.07, 52, and 87) had no discernible influence on the characteristics of microcolonies (size, shape, or orientation with respect to flow) during the first 24 h of biofilm development. Inherent factors appear to have overriding influence, vis-à-vis environmental factors, on early stages of microcolony development under these laminar flow conditions.     

Early stages of biofilm succession in a lentic freshwater environment

Initial events of biofilms development and succession were studied in a freshwater environment at Kalpakkam, East Coast of India. Biofilms were developed by suspending Perspex (Plexiglass) panels for 15 days at bimonthly intervals from January 1996 to January 1997. Changes in biofilm thickness, biomass, algal density, chlorophyll a concentration and species composition were monitored. The biofilm thickness, biomass, algal density and chlorophyll a concentration increased with biofilms age and colonization was greater during summer (March, May and July) than other months. The initial colonization was mainly composed of Chlorella vulgaris, Chlorococcum humicolo (green algae), Achnanthes minutissima, Cocconeis scutellum, C. placentula (diatoms) and Chroococcus minutus (cyanobacteria) followed by colonial green algae such as Pediastrum tetras, P. boryanumand Coleochaete scutata, cyanobacteria (Gloeocapsa nigrescens), low profile diatoms (Amphora coffeaeformis, Nitzschia amphibia, and Gomphonema parvulum) and long stalked diatoms (Gomphoneis olivaceumand Gomphonema lanceolatum). After the 10th day, the community consisted of filamentous green algae (Klebshormidium subtile, Oedogonium sp., Stigeoclonium tenue and Ulothrix zonata) and cyanobacteria (Calothrix elenkinii, Oscillatoria tenuis and Phormidium tenue). Based on the percentage composition of different groups in the biofilm, three phases of succession could be identified: the first phase was dominated by green algae, the second by diatoms and the third phase by cyanobacteria. Seasonal variation in species composition was observed but the sequence of colonization was similar throughout the study period.     

Laboratory studies on adhesion of microalgae to hard substrates

Adhesion of Chlorella vulgaris(chlorophyceae), Nitzschia amphibia(bacillariophceae) and Chroococcus minutus(cyanobacteria) to hydrophobic (perspex, titanium and stainless steel 316-L), hydrophilic (glass) and toxic (copper, aluminium brass and admiralty brass) substrata were studied in the laboratory. The influence of surface wettability, surface roughness, pH of the medium, culture age, culture density, cell viability and presence of organic and bacterial films on the adhesion of Nitzschia amphibia was also studied using titanium, stainless steel and glass surfaces. All three organisms attached more on titanium and stainless steel and less on copper and its alloys. The attachment varied significantly with respect to exposure time and different materials. The attachment was higher on rough surfaces when compared to smooth surfaces. Attachment was higher on pH 7 and above. The presence of organic film increased the attachment significantly when compared to control. The number of attached cells was found to be directly proportional to the culture density. Attachment by log phase cells was significantly higher when compared to stationary phase cells. Live cells attached more when compared to heat killed and formalin killed cells. Bacterial films of Pseudomonas putida increased the algal attachment significantly. %     

Biofilm formation by Pseudoalteromonas ruthenica and its removal by chlorine

The distribution of a recently described marine bacterium, SBT 033 GenBank Accession No. AY723742), Pseudoalteromonas ruthenica, at the seawater intake point, outfall and mixing point of an atomic power plant is described, and its ability to form biofilm was investigated. The effectiveness of the antifouling biocide chlorine in the inactivation of planktonic as well as biofilm cells of P. ruthenica was studied in the laboratory. The results show that the planktonic cells were more readily inactivated than the cells enclosed in a biofilm matrix. Viable counting showed that P. ruthenica cells in biofilms were up to 10 times more resistant to chlorine than those in liquid suspension. Using confocal laser scanning microscopy it was shown that significant detachment of P. ruthenica biofilm developed on a glass substratum could be accomplished by treatment with a dose of 1 mg l-1 chlorine. Chlorine-induced detachment led to a significant reduction in biofilm thickness (up to 69%) and substratum coverage (up to 61%), after 5-min contact time. The results show that P. ruthenica has a remarkable ability to form biofilms but chlorine, a common biocide, can be used to effectively kill and detach these biofilms.