A unified theory for upscaling aerobic granular sludge sequencing batch reactors

Aerobic granular sludge sequencing batch reactors (SBR) are a promising technology for treating wastewater. Increasing evidence suggests that aerobic granulation in SBRs is driven by selection pressures exerted on microorganisms. Three major selection pressures have been identified as follows: settling time, volume exchange ratio and discharge time. This review demonstrates that these three major selection pressures can all be unified to one, the minimal settling velocity of bio-particles, that determines aerobic granulation in SBRs. The unified selection pressure theory is a useful guide for manipulating and optimizing the formation and characteristics of aerobic granules in SBRs. Furthermore, the unified theory provides a single engineering basis for scale up of aerobic granular sludge SBRs.     

Sequence analysis of the hypervariable regions of the 56 kDa immunodominant protein genes of Orientia tsutsugamushi strains in Malaysia

The DNA sequences encompassing two hypervariable regions, VD II and III of the 56 kDa immunodominant protein gene of 21 Malaysian strains of Orientia tsutsugamushi were determined. Two strains demonstrated a 100% DNA homology with the Gilliam prototype strain, and one with TH1817 strain and TA678 strain respectively. High percentages of DNA similarity (95-99%) were observed with Karp (4 strains), Gilliam (2 strains), TH1817 (4 strains), TC586 (3 strains) and TA763 (1 strain). The remaining strains demonstrated the highest DNA similarity with TA763 (1 strain, 89%), TA678 (1 strain, 86%) and TA686 (1 strain, 87%). Our study provides additional evidence on the existence and the genetic heterogeneity of TA strains of the Southeast Asia and their closely related strains in Malaysia.     

The mycological and molecular study of <Emphasis Type="Italic">Hortaea werneckii</Emphasis> isolated from blood and splenic abscess

Hortaea werneckii is an environmental dematiaceous fungus found in the halophilic environment. It causes tinea nigra. We report the isolation of H. werneckii from blood and splenic abscess of two patients with acute myelomonocytic leukaemia. H. werneckii grew at room temperature but not at 37 °C, it was identified by biochemical tests, growth characteristics and the presence of conspicuous collarette intercalary on dividing yeast cells. The use of specific oligonucleotide primer Hor-F (5′-TGGACACCTTCA TAACTCTTG-3′) and Hor-R (5′-TCACAACGCTTAGAGACGG-3′) confirmed the two isolates were H. werneckii. The sequence for 281 nucleotide of HW299 and HW403 were 99% identical but differed only in one nucleotide. In vitro anti-fungal susceptibility testing showed that the isolates were resistant to amphotericin B and flucytosine.     

Induction of cytokine expression in rat post-ischemic sinoatrial node (SAN)

The aim of this study was to determine the spatial and temporal expression of various pro-inflammatory cytokines in the peri-sinoatrial nodal area after atrial infarction. Rats were subjected to permanent atrial infarction, in particular, sinoatrial node (SAN) infarction and sacrificed at various time points up to 7 days. Real-time polymerase chain reaction analysis demonstrated that mRNA levels of tumor necrosis factor alpha (TNF-alpha), interleukin-1beta, interleukin-6, and transforming growth factor beta 1 (TGF-beta(1)) were upregulated in the peri-sinoatrial nodal area after atrial infarction. Immunostaining for TNF-alpha and TGF-beta(1) proteins revealed that both cytokines were expressed persistently up to 7 days after atrial infarction around the peri-sinoatrial nodal area. Furthermore, the infiltrating inflammatory cells immunoreactive for both cytokines were predominant within the infarct SAN. In situ hybridization analysis showed that TNF-alpha gene expression was enhanced in the inflammatory cells and myocardium within the peri-sinoatrial nodal area in response to the infarction. These results provide evidence for the local expression of cytokines in the post-ischemic peri-sinoatrial nodal area, suggesting that the upregulation of the cytokines might be associated with the atrial arrhythmia observed after acute myocardial infarction.     

Bacillus naphthovorans sp. nov. from oil-contaminated tropical marine sediments and its role in naphthalene biodegradation

A Bacillus sp., designated as strain MN-003, was isolated as the dominant cultivatable naphthalene-degrading organism from oil-contaminated tropical marine sediments. Strain MN-003 is strictly aerobic, rod-shaped, Gram-positive, catalase positive, oxidase negative, and forms endospores. Strain MN-003 grew at salinities ranging from 0.28 to 7.00% and temperatures ranging from 15 to 41 degrees C. Phylogenetic analyses reveal that strain MN-003 is most similar to Bacillus sp. VAN14, with a 16S rRNA sequence identity of 97.9%. Based on taxonomic and 16S rRNA data, strain MN-003 was named Bacillus naphthovorans sp. nov. When grown with naphthalene as sole carbon source, strain MN-003 had a maximal specific growth rate (mu(max)) of 0.32 +/- 0.03 h(-1), and a half-saturation constant (K(S)) of 22.3 +/-4.2 microM. A batch study of the tropical marine sediments enriched with naphthalene showed that cells of the Bacillus genus grew to become dominant members of the microbial community. The bacilli comprised 39.5 +/- 6.5% of the microbial fraction after 20 days of enrichment.     

Hydraulic selection pressure-induced nitrifying granulation in sequencing batch reactors

The effect of hydraulic selection pressure on the development of nitrifying granules was investigated in four column-type sequencing batch reactors (SBR). The nature of SBR is cycle operation, thus SBR cycle time can serve as a main hydraulic selection pressure imposed on the microbial community in the system. No nitrifying granulation was observed in the SBR operated at the longest cycle time of 24 h, due to a very weak hydraulic selection pressure, while the washout of nitrifying sludge was found in the SBR run at the shortest cycle time of 3 h, and led to a failure of nitrifying granulation. Excellent nitrifying granules with a mean diameter of 0.25 mm and specific gravity of 1.014 were developed in a SBR operated at cycle times of 6 h and 12 h, respectively. The results further showed that a short cycle time would stimulate microbial activity, production of cell polysaccharides and also improve the cell hydrophobicity. These hydraulic selection pressure-induced microbial changes favour the formation of nitrifying granules. This work, probably for the first time, shows that nitrifying granules can be developed at a proper hydraulic selection pressure in terms of SBR cycle time. Nitrifying granulation is a novel biotechnology which has a great potential for wastewater nitrification.     

Optimization of slow-release fertilizer dosage for bioremediation of oil-contaminated beach sediment in a tropical environment

The optimization of fertilizer concentrations for stimulating bioremediation in contaminated marine substrates is desirable for minimizing both cost and environmental risks associated with eutrophication. In this study, the effect of various dosages of the slow-release fertilizer, Osmocote, in stimulating an indigenous microbial biomass in oil-contaminated beach sediments was investigated. The Osmocote used comprises water-soluble N–P–K at concentrations of 18, 4.8, and 8.3% w/w respectively, and dosages tested were in the range of 0–4.0% dry weight equivalent of sediment. The beach sediments were taken from a tropical foreshore environment and spiked with an Arabian light crude oil (ALCO) to achieve a petroleum hydrocarbon content of 4.4% w/w. The experiment was conducted in open microcosms irrigated with seawater over a 42-day period. It was found that all Osmocote-dosed sediments had a sustained nutrient release for at least 42 days. An addition of 0 8% Osmocote to the sediments was sufficient to maximize metabolic activity of the biomass, and the biodegradation of straight-chain alkanes (C₁₀–C₃₃). An Osmocote dosage of 1.5% resulted in optimal biodegradation of more recalcitrant branched-chain alkanes (i.e. pristane, and phytane).     

Size-effect on the physical characteristics of the aerobic granule in a SBR

Owing to a fast growth rate, aerobic granules display a wide range of sizes, approximately 0.3-5.0 mm in diameter. As the diameter increases, the aerobic granule undergoes serial morphological and physical changes that could cause problems to the reactor operation, a phenomenon which, however, has not been fully studied hitherto. In this study, aerobic granules from a sequencing batch reactor were mechanically separated into various size-categories in order to investigate their physical properties, including sludge volumetric index (SVI), settling velocity (sv), specific surface hydrophobicity, granule strength, total solids, percentage volatile solids and other structural properties. Also, the live and dead biomass distribution was examined under a confocal laser scanning microscope after treatment with nucleic acid viability stains. Regardless of size, the biomass (both live and dead) was densest in the outer layer of the granule, which was about 600+/-50 microm thick. The live cells appeared only in the peripheral zone, while dead biomass spread into the inner zone. The biomass distribution pattern justified the changing physical properties of the granules as they grew bigger. As size increased, the sv, granule total density and biomass density increased but not in parallel with the size increment, while the granule strength, specific surface hydrophobicity and SVI decreased. Nonetheless, beyond a threshold size (4.0 mm diameter), the granules presented peculiar values in those properties, deviating from the initial trends. This was due to both inner and outer structural changes. The physical properties associated significantly with the size factor, for which the correlation coefficients were above 0.67. In view of biological viability and physical properties, the operational size-range suggested for optimal performance and economically effective aerobic SBR granular sludge is a diameter of 1.0-3.0 mm.     

KDBI: Kinetic Data of Bio-molecular Interactions database

Understanding of cellular processes and underlying molecular events requires knowledge about different aspects of molecular interactions, networks of molecules and pathways in addition to the sequence, structure and function of individual molecules involved. Databases of interacting molecules, pathways and related chemical reaction equations have been developed. The kinetic data for these interactions, which is important for mechanistic investigation, quantitative study and simulation of cellular processes and events, is not provided in the existing databases. We introduce a new database of Kinetic Data of Bio-molecular Interactions (KDBI) aimed at providing experimentally determined kinetic data of protein-protein, protein-RNA, protein-DNA, protein-ligand, RNA-ligand, DNA-ligand binding or reaction events described in the literature. KDBI contains information about binding or reaction event, participating molecules (name, synonyms, molecular formula, classification, SWISS-PROT AC or CAS number), binding or reaction equation, kinetic data and related references. The kinetic data is in terms of one or a combination of the following quantities as given in the literature of a particular event: association/dissociation or on/off rate constant, first/second/third/. order rate constant, equilibrium rate constant, catalytic rate constant, equilibrium association/dissociation constant, inhibition constant and binding affinity constant. Each entry can be retrieved through protein or nucleic acid or ligand name, SWISS-PROT AC number, ligand CAS number and full-text search of a binding or reaction event. KDBI currently contains 8273 entries of biomolecular binding or reaction events involving 1380 proteins, 143 nucleic acids and 1395 small molecules. Hyperlinks are provided for accessing references in Medline and available 3D structures in PDB and NDB. This database can be accessed at http://xin.cz3.nus.edu.sg/group/kdbi/kdbi.asp.