Mixing time and oxygen transfer characteristics of double draft tube airlift fermentor

Despite the increasing importance of airlift fermentors, very little published information is available on how the geometric configurations of the draft tubes and the air-sparging system affect the mixing and oxygen transfer characteristics of the fermentor. A 14-L air-lift fermentor was designed and build with a fixed liquid height to diameter ratio of 1.5 utilizing four equally spaced air jets at the bottom. Two jet orifice sizes were used, 1.27 and 3.81 mm i.d., and for each jet size the following four geometric configurations were used: Single inner concentric draft tube, single outer concentric draft tube, two concentric draft tubes, and no draft tubes where the fermentor was operated as a shallow bubble column. It was found that the presence of draft tubes stabilized liquid circulation patterns and gave systemically higher mixing times than those obtained in the absence of draft tubes. In addition, the double draft tube geometry resulted in higher mixing times than the single draft tubes. For the power unit volume range 20 to about 250 W/m³ the larger 3.81-mm orifices gave systemically higher k_L a values than the smaller 1.27-mm i.d. orifices. At 200 W/m³ the use of a single outer draft tube with the 3.81-mm orifices resulted in 94% increase in k_L a values over that obtained with no draft tubes. However, the effect of draft tube geometry on k_L a values when the 1.27-mm orifices were used was not significant. The air bubble formation characteristics at the jet orifices were found to be different, which reflected the differences observed in mass transfer and mixing characteristics. The power economy for oxygen transfer was found to be depend strongly on the orifice size and less on the geometric configuration of draft tubes.     

Draft versus finished sequence data for DNA and protein diagnostic signature development

Sequencing pathogen genomes is costly, demanding careful allocation of limited sequencing resources. We built a computational Sequencing Analysis Pipeline (SAP) to guide decisions regarding the amount of genomic sequencing necessary to develop high-quality diagnostic DNA and protein signatures. SAP uses simulations to estimate the number of target genomes and close phylogenetic relatives (near neighbors or NNs) to sequence. We use SAP to assess whether draft data are sufficient or finished sequencing is required using Marburg and variola virus sequences. Simulations indicate that intermediate to high-quality draft with error rates of 10⁻³–10⁻⁵ (~8× coverage) of target organisms is suitable for DNA signature prediction. Low-quality draft with error rates of ~1% (3× to 6× coverage) of target isolates is inadequate for DNA signature prediction, although low-quality draft of NNs is sufficient, as long as the target genomes are of high quality. For protein signature prediction, sequencing errors in target genomes substantially reduce the detection of amino acid sequence conservation, even if the draft is of high quality. In summary, high-quality draft of target and low-quality draft of NNs appears to be a cost-effective investment for DNA signature prediction, but may lead to underestimation of predicted protein signatures.     

A simple and low-cost airlift photobioreactor for microalgal mass culture

A simple, low-cost, and efficient airlift photobioreactor for microalgal mass culture was designed and developed. The reactor was made of Plexiglas, and composed of three major parts: outer tube, draft tube and air duct. The fluid-dynamic characteristics of the airlift reactor were studied. The system proved to be well suited to the mass cultivation of a marine microalga, Chlorella sp. In batch culture, the biomass volumetric output rate of 0.21 g l^–1 d^–1 was obtained at the superficial gas velocity of 4 mm s^–1 in the draft tube.     

Draft Genome Sequence of the Extremely Halophilic Archaeon Halogranum salarium B-1T

Halogranum salarium is an extremely halophilic archaeon isolated from evaporitic salt crystals and belongs to the family Halobacteriaceae. Here, we present the 4.5-Mb draft genome sequence of the type strain (B-1^T) of H. salarium. This is the first report of the draft genome sequence of a haloarchaeon in the genus Halogranum.     

Mass transfer and liquid mixing in an airlift reactor with a net draft tube

Mass transfer and liquid mixing in an airlift reactor with a net draft tube were experimentally investigated. Four different column diameters were considered. The mass transfer was measured using the volumetric gas-liquid mass transfer coefficient which was determined by the dynamic method. The mass transfer coefficients in the airlift reactors with different column diameters were not always higher than those in the bubble columns. The liquid mixing was measured using mixing time which was determined by a pulse technique. Under the same superficial gas velocity, the mixing times of the airlift reactors with a net draft tube were always less than those of the bubble columns.List of Symbols C mol·dm^–3 bulk concentration of dissolved oxygen - C ₀ mol·dm^–3 initial concentration of dissolved oxygen - C _e mol·dm^–3 saturated concentration of dissolved oxygen - ¯C dimensionless dissolved oxygen concentration - D _c cm diameter of column - D _N cm diameter of the nozzle hole - D _T cm diameter of the net draft tube - H _L cm static liquid height - H _T cm height of the net draft tube - k _L a hr^–1 volumetric mass transfer coefficient - L _T cm length of the net draft tube - t _M sec mixing time of the liquid phase - t ₀ sec mixing time of the liquid phase in a bubble column - V _L dm³ volume of the liquid phase - U _g cm/s superficial air velocity     

<Emphasis Type="Italic">Amycolatopsis vastitatis</Emphasis> sp. nov., an isolate from a high altitude subsurface soil on Cerro Chajnantor,northern Chile

The taxonomic position of a novel Amycolatopsis strain isolated from a high altitude Atacama Desert subsurface soil was established using a polyphasic approach. The strain, isolate H5^T, was shown to have chemical properties typical of members of the genus Amycolatopsis such as meso-diaminopimelic acid as the diamino acid in the cell wall peptidoglycan, arabinose and galactose as diagnostic sugars and MK-9(H₄) as the predominant isoprenologue. It also has cultural and morphological properties consistent with its classification in the genus, notably the formation of branching substrate hyphae which fragment into rod-like elements. 16S rRNA gene sequence analyses showed that the strain is closely related to the type strain of Amycolatopsis mediterranei but could be distinguished from this and other related Amycolatopsis strains using a broad range of phenotypic properties. It was separated readily from the type strain of Amycolatopsis balhymycina, its near phylogenetic neighbour, based on multi-locus sequence data, by low average nucleotide identity (92.9%) and in silico DNA/DNA relatedness values (51.3%) calculated from draft genome assemblies. Consequently, the strain is considered to represent a novel species of Amycolatopsis for which the name Amycolatopsis vastitatis sp. nov. is proposed. The type strain is H5^T (= NCIMB 14970^T = NRRL B-65279^T).     

Draft Genome Sequence of Cecembia lonarensis Strain LW9T,Isolated from Lonar Lake,a Haloalkaline Lake in India

The draft genome sequence (4.84 Mb) of Cecembia lonarensis strain LW9^T, isolated from a water sample (4.5-m depth) from Lonar Lake, a meteorite-created haloalkaline lake in India, is reported. The enzymes produced by these microorganisms need to be stable under alkaline conditions prevailing in its habitat. Such enzymes would be of immense importance for enzymatic processes operating at high pH.     

Mixing performance of air-lift fermenters against working volume and draft tube dimensions

Mixing characteristics of a laboratory scale internal loop air-lift fermenter has been investigated. The effects of different draft tube dimensions and positions as well as varying levels of liquid height over the draft tube, on mixing time were determined. The results indicate the existance of an optimum liquid height and thus liquid volume with respect to mixing performance especially for the taller draft tubes.List of Symbols A mm distance between draft tube and reactor base - A _D mm² area of the downcomer region - A _R mm² area of the riser region - B mm width of annulus - D _d mm draft tube diameter - D _t mm fermenter diameter - H _d mm draft tube height - H _l mm liquid height in the fermenter - H _t mm fermenter height - V _d m³ draft tube volume - V _t m³ fermenter volume - D _d /D _l - _B H _d /H _l - _F H _l /D _t      

Genome Sequence of the Protease-Producing Bacterium Rheinheimera nanhaiensis E407-8T,Isolated from Deep-Sea Sediment of the South China Sea

The protease-producing bacterium E407-8^T was isolated from deep-sea sediment of the South China Sea and has been identified recently as representing a new species, Rheinheimera nanhaiensis. The draft genome of R. nanhaiensis E407-8^T consists of 3,987,205 bp and contains 3,730 predicated protein-coding genes, including 82 extracellular peptidase genes.     

Draft Genome Sequence of Oceaniovalibus guishaninsula JLT2003T

Oceaniovalibus guishaninsula, as a representative of a new genus within the family Rhodobacteraceae, was isolated from surface seawater that was sulfidic. Here, we present the draft genome sequence of the type strain, JLT2003^T.     

Genome Sequence of Bartonella rattimassiliensis,a Bacterium Isolated from European Rattus norvegicus

Bartonella rattimassiliensis is a facultative intracellular bacterium isolated from the blood of Rattus norvegicus in Marseille. The present study reports the draft genome of B. rattimassiliensis strain 15908 (CIP 107705^T).     

Optimization of low-cost drying methods to minimize lipid peroxidation in <Emphasis Type="Italic">Spirulina platensis</Emphasis> grown in the Philippines

Three low-cost drying methods (sun, solar, and draft oven) were optimized to produce Spirulina powder of optimal quality. Optimization in the pre-dehydration stage included the use of two antioxidants, α-tocopherol and tertiary-butyl hydroquinone (TBHQ), and two blanching methods, microwave and water bath, to inactivate enzymes. The efficiency of the pre-dehydration treatments at minimizing lipid peroxidation were evaluated in terms of the product’s oxidative stability using the thiobarbituric acid (TBA) test. The sample with the lowest TBA reactive substance (TBARS) value was considered the most stable. TBHQ was found to be significantly better than α-tocopherol in minimizing lipid peroxidation in blanched samples while α-tocopherol was better than TBHQ in unblanched samples. Microwave blanching exerted a greater stabilizing effect than water bath blanching. The combined effect of TBHQ and microwave blanching was found to be the most effective pre-dehydration treatment for minimizing lipid peroxidation in drying Spirulina. Among the three low-cost optimized drying methods, sun-drying produced a dried product with the lowest TBARS value (0.472 mg malondialdehyde.kg⁻¹), which was closest to that of the spray-dried (control) sample (0.434 mg MDA.kg⁻¹). Draft oven and solar drying produced dried products with the same average TBARS value (0.56 mg MDA.kg⁻¹). Sun-drying, when optimized, produced a dried product that was almost as stable as the spray-dried product. Presented at the 6th Meeting of the Asian Pacific Society of Applied Phycology, Manila, Philippines     

Candidate Genes That May Be Responsible for the Unusual Resistances Exhibited by Bacillus pumilus SAFR-032 Spores

The spores of several Bacillus species, including Bacillus pumilus SAFR-032 and B. safensis FO-36b, which were isolated from the spacecraft assembly facility at NASA''s Jet Propulsion Laboratory, are unusually resistant to UV radiation and hydrogen peroxide. In order to identify candidate genes that might be associated with these resistances, the whole genome of B. pumilus SAFR-032, and the draft genome of B. safensis FO-36b were compared in detail with the very closely related type strain B. pumilus ATCC7061^T. 170 genes are considered characteristic of SAFR-032, because they are absent from both FO-36b and ATCC7061^T. Forty of these SAFR-032 characteristic genes are entirely unique open reading frames. In addition, four genes are unique to the genomes of the resistant SAFR-032 and FO-36b. Fifty three genes involved in spore coat formation, regulation and germination, DNA repair, and peroxide resistance, are missing from all three genomes. The vast majority of these are cleanly deleted from their usual genomic context without any obvious replacement. Several DNA repair and peroxide resistance genes earlier reported to be unique to SAFR-032 are in fact shared with ATCC7061^T and no longer considered to be promising candidates for association with the elevated resistances. Instead, several SAFR-032 characteristic genes were identified, which along with one or more of the unique SAFR-032 genes may be responsible for the elevated resistances. These new candidates include five genes associated with DNA repair, namely, BPUM_0608 a helicase, BPUM_0652 an ATP binding protein, BPUM_0653 an endonuclease, BPUM_0656 a DNA cytosine-5- methyltransferase, and BPUM_3674 a DNA helicase. Three of these candidate genes are in immediate proximity of two conserved hypothetical proteins, BPUM_0654 and BPUM_0655 that are also absent from both FO-36b and ATCC7061^T. This cluster of five genes is considered to be an especially promising target for future experimental work.     

Draft Genome Sequence of Lactobacillus gigeriorum CRBIP 24.85T,Isolated from a Chicken Crop

We report the draft genome of the strain Lactobacillus gigeriorum CRBIP 24.85^T, isolated from a chicken crop. The total length of the 60 scaffolds is about 1.9 Mb, with a GC content of 38% and 2,062 protein-coding sequences (CDS).     

Genome Sequence of Bartonella rattaustraliani,a Bacterium Isolated from an Australian Rat

Bartonella rattaustraliani is a facultative intracellular bacterium isolated from the blood of a Rattus sp. in Australia. The present study reports the draft genome of B. rattaustraliani strain AUST/NH4 (CSUR B609^T).     

A comparison of the fate and effects of prochloraz in artifical and natural sediments

The current draft EC regulatory guidance document for the authorisation of plant protection products, directive EEC 91/414, contains provision for testing the potential toxicity of pesticides to sediment dwelling organisms. Development of an appropriate method is currently in progress, by a German regulatory and industry working group. The compounds which are expected to trigger sediment toxicity data are likely to be those which are relatively persistent, with a high K _ow, with the potential for significant adsorption to sediments, and may have previously demonstrated toxicity to aquatic organisms. The current proposal from this working group involves an artificial sediment, prepared in accordance with OECD guideline 207, as used for earthworm toxicity tests. The implications of using this sediment on the distribution, fate and availability of the compound under test are considered. This paper presents toxicity data for Chironomus riparius generated using radiolabelled Prochloraz^® in systems using this artificial sediment and two natural sediments. The fate of prochloraz was also investigated in the same systems and compared with data generated from sediment/water studies carried out in accordance with regulatory guidelines. At the maximum Predicted Environmental Concentration (PEC) of 195 g^-1 nominal, prochloraz had no effects on the survival and development of Chironomus riparius. The fate of the compound in the systems used was enhanced possibly as a result of photodegradation.     

Whole-genome sequencing of eukaryotes: From sequencing of DNA fragments to a genome assembly

Rapid advances in sequencing technologies of second- and even third-generation made the whole genome sequencing a routine procedure. However, the methods for assembling of the obtained sequences and its results require special consideration. Modern assemblers are based on heuristic algorithms, which lead to fragmented genome assembly composed of scaffolds and contigs of different lengths, the order of which along the chromosome and belonging to a particular chromosome often remain unknown. In this regard, the resulting genome sequence can only be considered as a draft assembly. The principal improvement in the quality and reliability of a draft assembly can be achieved by targeted sequencing of the genome elements of different size, e.g., chromosomes, chromosomal regions, and DNA fragments cloned in different vectors, as well as using reference genome, optical mapping, and Hi-C technology. This approach, in addition to simplifying the assembly of the genome draft, will more accurately identify numerical and structural chromosomal variations and abnormalities of the genomes of the studied species. In this review, we discuss the key technologies for the genome sequencing and the de novo assembly, as well as different approaches to improve the quality of existing drafts of genome sequences.     

Draft Genome Sequence of Halomonas smyrnensis AAD6T

Halomonas smyrnensis AAD6^T is a Gram-negative, aerobic, exopolysaccharide-producing, and moderately halophilic bacterium that produces levan, a fructose homopolymer with many potential uses in various industries. We report the draft genome sequence of H. smyrnensis AAD6^T, which will accelerate research on the rational design and optimization of microbial levan production.     

Spongiibacter pelagi sp. nov., a marine gammaproteobacterium isolated from coastal seawater

A novel gammaproteobacterium, designated as KMU-158^T, was isolated from seawater collected on the coastline of Dadaepo in the Republic of Korea, and characterized using a polyphasic taxonomic approach. Strain KMU-158^T was Gram-staining-negative, pale beige-colored, strictly aerobic, rod-shaped, motile, and chemoorganoheterotrophic. The novel isolate was able to grow at 0–3% NaCl concentrations (w/v), pH 6.5–9.5, and 15–40 °C. The analysis based on 16S rRNA gene sequences indicated that strain KMU-158^T belongs to the family Spongiibacteraceae and shared the highest similarity with Spongiibacter tropicus CL-CB221^T (96.1%). The major cellular fatty acids were summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c) and C_17:1 ω8c. The only respiratory quinone was identified as ubiquinone-8. The polar lipids of strain KMU-158^T contained phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and two unidentified lipids. The assembled draft genome size of strain KMU-158^T was 3.29 Mbp with a DNA G?+?C content of 51.3%. The average nucleotide identity, digital DNA–DNA hybridization, and average amino acid identity values of KMU-158^T and the representatives of the genus Spongiibacter were found to be 78.5–79.1%, 13.8–14.1%, and 66.6–66.8%, respectively. From the distinct phenotypic, phylogenetic, genomic, and chemotaxonomic properties, the strain KMU-158^T is considered to represent a novel species of the genus Spongiibacter, for which the name Spongiibacter pelagi sp. nov. is proposed. The type strain of the species S. pelagi sp. nov. is KMU-158^T (=?KCCM 90448^T?=?NBRC 114307^T).

     

Overall volumetric mass transfer coefficient in a modified reversed flow jet loop bioreactor with low density particles

Experiments were conducted using glass beads and low-density particles such as polyurethane and polystyrene which are comparable to bioparticles found in biological applications to evaluate the overall volumetric mass transfer coefficient (K _L a) in a modified reversed flow jet loop bioreactor having the liquid outlet at the top section of the reactor. The influence of the gas and liquid flow rates, draft tube to reactor diameter ratio, solids loading and physical properties of solids onK _L a were studied. TheK _L a was found to increase with the increased gas and liquid flow rates. TheK _L a values were found to be higher in the bubbly flow region i.e., at the lower range of energy dissipation rates. The optimum draft tube to reactor diameter ratio and solids loading with respect to maximumK _L a were found to be 0.4 and 0.9×10^?3 m³ (? _s =0.025) respectively. Dimensionless correlations were presented to predict the experimental values in terms of operational and geometrical variables.