Isolation and Maintenance.- Isolation and Differentiation of Medaka Embryonic Stem Cells.- Maintenance of Chicken Embryonic Stem Cells In Vitro.- Derivation and Culture of Mouse Trophoblast Stem Cells In Vitro.- Derivation, Maintenance, and Characterization of Rat Embryonic Stem Cells In Vitro.- Derivation, Maintenance, and Induction of the Differentiation In Vitro of Equine Embryonic Stem Cells.- Generation and Characterization of Monkey Embryonic Stem Cells.- Derivation and Propagation of Embryonic Stem Cells in Serum- and Feeder-Free Culture.- Signaling in Embryonic Stem Cell Differentiation.- Internal Standards in Differentiating Embryonic Stem Cells In Vitro.- Matrix Assembly, Cell Polarization, and Cell Survival.- Phosphoinositides, Inositol Phosphates, and Phospholipase C in Embryonic Stem Cells.- Cripto Signaling in Differentiating Embryonic Stem Cells.- The Use of Embryonic Stem Cells to Study Hedgehog Signaling.- Transfection and Promoter Analysis in Embryonic Stem Cells.- SAGE Analysis to Identify Embryonic Stem Cell-Predominant Transcripts.- Utilization of Digital Differential Display to Identify Novel Targets of Oct3/4.- Gene Silencing Using RNA Interference in Embryonic Stem Cells.- Genetic Manipulation of Embryonic Stem Cells.- Efficient Transfer of HSV-1 Amplicon Vectors Into Embryonic Stem Cells and Their Derivatives.- Lentiviral Vector-Mediated Gene Transfer in Embryonic Stem Cells.- Use of the Cytomegalovirus Promoter for Transient and Stable Transgene Expression in Mouse Embryonic Stem Cells.- Use of Simian Immunodeficiency Virus Vectors for Simian Embryonic Stem Cells.- Generation of Green Fluorescent Protein-Expressing Monkey Embryonic Stem Cells.- DNA Damage Response and Mutagenesis in Mouse Embryonic Stem Cells.- Ultraviolet-Induced Apoptosis in Embryonic Stem Cells In Vitro.- Use of Embryonic Stem Cells in Pharmacological and Toxicological Screens.- Use of Differentiating Embryonic Stem Cells in Pharmacological Studies.- Embryonic Stem Cells as a Source of Differentiated Neural Cells for Pharmacological Screens.- Use of Murine Embryonic Stem Cells in Embryotoxicity Assays.- Use of Chemical Mutagenesis in Mouse Embryonic Stem Cells.- Epigenetic Analysis of Embryonic Stem Cells.- Nuclear Reprogramming of Somatic Nucleus Hybridized With Embryonic Stem Cells by Electrofusion.- Methylation in Embryonic Stem Cells In Vitro.- Tumor-Like Properties.- Identification of Genes Involved in Tumor-Like Properties of Embryonic Stem Cells.- In Vivo Tumor Formation From Primate Embryonic Stem Cells.- Animal Models and Therapy.- Directed Differentiation and Characterization of Genetically Modified Embryonic Stem Cells for Therapy.- Use of Differentiating Embryonic Stem Cells in the Parkinsonian Mouse Model.

Isolation and characterization

Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.

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Cell biology and molecular basis of denitrification.

Phosphate solubilizing bacteria and their role in plant growth promotion

Dissimilatory Fe(III) and Mn(IV) reduction.

Removal of nutrients in various types of constructed wetlands.

Effects of growth conditions on mitochondrial morphology were studied in living Saccharomyces cerevisiae cells by vital staining with the fluorescent dye dimethyl-aminostyryl-methylpyridinium iodine (DASPMI), fluorescence microscopy, and confocal-scanning laser microscopy. Cells from respiratory, ethanol-grown batch cultures contained a large number of small mitochondria. Conversely, cells from glucose-grown batch cultures, in which metabolism was respiro-fermentative, contained small numbers of large, branched mitochondria. These changes did not significantly affect the fraction of the cellular volume occupied by the mitochondria. Similar differences in mitochondrial morphology were observed in glucose-limited chemostat cultures. In aerobic chemostat cultures, glucose metabolism was strictly respiratory and cells contained a large number of small mitochondria. Anaerobic, fermentative chemostat cultivation resulted in the large, branched mitochondrial structures also seen in glucose-grown batch cultures. Upon aeration of a previously anaerobic chemostat culture, the maximum respiratory capacity increased from 10 to 70 mumole.min-1.g dry weight-1 within 10 h. This transition resulted in drastic changes of mitochondrial number, morphology and, consequently, mitochondrial surface area. These changes continued for several hours after the respiratory capacity had reached its maximum. Cyanide-insensitive oxygen consumption contributed ca. 50% of the total respiratory capacity in anaerobic cultures, but was virtually absent in aerobic cultures. The response of aerobic cultures to oxygen deprivation was qualitatively the reverse of the response of anaerobic cultures to aeration. The results indicate that mitochondrial morphology in S. cerevisiae is closely linked to the metabolic activity of this yeast: conditions that result in repression of respiratory enzymes generally lead to the mitochondrial morphology observed in anaerobically grown, fermenting cells.

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Effects of growth conditions on mitochondrial morphology in Saccharomyces cerevisiae

SUMMARY: Methyl mercaptan (MM)-oxidase was purified tenfold to near homogeneity from Hyphomicrobium EG grown on dimethyl sulphoxide. The enzyme was a monomer with an Mr
value of about 40000-50000. It catalysed the formation of stoicheiometric amounts of formaldehyde, sulphide and H2O2 from MM and O2. It had a K
m of 5-10 μm for MM and was strongly inhibited by substrate concentrations above 14 μm, the K
i for this inhibition being 42 μm. Ethyl mercaptan and sulphide also served as substrates for the enzyme (K
m 18 and 60 μm respectively), whereas methanol was not oxidized. Upon oxidation of these compounds H2O2 was formed. Although sulphide was a substrate for the enzyme, it also acted as a non-competitive inhibitor of MM oxidation (K
i 90 μm). Alcohol oxidase (EC 1.1.3.13) purified from Hansenula polymorpha was also found to oxidize MM (K
m 110 μm) although at a low rate. The products formed were the same as for MM oxidation by the bacterial enzyme. In contrast to MM-oxidase however, alcohol oxidase was inactive with sulphide and was not inhibited by methyl mercaptan concentrations up to 500 μm.

/pdf/methyl-mercaptan-oxidase-a-key-enzyme-in-the-metabolism-of-4qh0w3k3qk.pdf

Methyl mercaptan oxidase, a key enzyme in the metabolism of methylated sulphur compounds by Hyphomicrobium EG

A stable mixed bacterial culture was obtained by chemostat enrichment using dimethyl-sulphoxide as a carbon and energy source. This culture could not only rapidly oxidize dimethyl-sulphoxide but also dimethyl-sulphide. Enzyme determinations indicated that an important part of it consisted of methylotrophs, which assimilated carbon via the serine pathway. Indeed plate counts revealed the majority of the community to be a Hyphomicrobium species. This organism, designated Hyphomicrobium EG, is an obligate methylotroph which can only grow aerobically on several different C1-compounds. Its performance on dimethyl-sulphoxide was compared with that of the community and of another recently isolated strain, Hyphomicrobium S. The mixed culture, Hyphomicrobium EG and Hyphomicrobium S had a μmax of 0.08, 0.08 and 0.014 h-1 respectively. The KS for dimethyl-sulphoxide was the same for all three cultures (3–6 μM), whereas that for dimethyl-sulphide of Hyphomicrobium EG after growth on dimethyl-sulphoxide was 3-fold higher than that of the other two cultures (48 and 16 μM respectively). After growth on dimethyl-sulphide it improved to 3 μM. Dimethyl-sulphide respiration was maximal at a concentration of 100 μM; higher concentrations were inhibitory. One of the accompanying organisms, a pink methylotroph, was able to derive energy from the oxidation of thiosulphate. Available cultures of Thiobacillus MS1 that were reported to be able to utilize dimethyl-sulphide could no longer metabolize this compound.

/pdf/chemostat-enrichment-and-isolation-of-hyphomicrobium-eg-a-259z3rp0kz.pdf

Chemostat enrichment and isolation of Hyphomicrobium EG. A dimethyl-sulphide oxidizing methylotroph and reevaluation of Thiobacillus MS1.

The activity of pyrrolo-quinoline quinone (PQQ)-dependent glucose dehydrogenase (GDH) was determined in Acinetobacter and Pseudomonas species, grown under different conditions. In Acinetobacter lwoffi which, in contrast to Acinetobacter calcoaceticus , is unable to oxidize glucose to gluconic acid, the absence of GDH activity was not due to the absence of GDH protein (apoenzyme) but to the absence of its prosthetic group, PQQ. GDH activity could be restored by addition of PQQ to cell suspensions. Taxonomic implication of these results are discussed. Pseudomonas aeruginosa , strain PAO1 is known to contain active GDH when grown aerobically on glucose, but to lack this activity when grown anaerobically with nitrate. Also in this organism the absence of active GDH was due to lack of PQQ synthesis under these conditions, since GDH activity could be reconstituted by addition of PQQ to cell-free extracts. Similar observations were made with cultures of Pseudomonas acidovorans and Rhodopseudomonas sphaeroides , indicating that control of GDH activity by PQQ synthesis maybe widespread among bacteria.

Non-coordinated synthesis of glucose dehydrogenase and its prosthetic group PQQ in Acinetobacter and Pseudomonas species

Cell-free extracts of Thiobacillus ferrooxidans grown with thiosulfate as energy source and prepared at high ammonium sulfate concentrations and at low pH are capable of polythionate hydrolysis. The enzyme responsible for the hydrolysis of tetrathionate (S4O2-
6) and pentathionate (S4O2-
6) was purified to homogeneity. Enzyme activity during the purification procedure was based on a continuous spectrophotometric method that detects soluble intermediates that absorb in the UV region. The end products of hydrolysis of both polythionates by the pure enzyme were thiosulfate, sulfur and sulfate. The purified enzyme has a pH optimum of around 4 and a temperature optimum of 65 °. The activity is strongly influenced by the presence of sulfate ions. The purified enzyme is a dimer with two identical subunits of molecular mass 52 kDa. During purification of tetrathionate hydrolase, fractions able to hydrolyse trithionate and tetrathionate were separated, indicating that the two substrates are hydrolysed by different enzymes.

/pdf/polythionate-degradation-by-tetrathionate-hydrolase-of-6p2nauygg7.pdf

J.G. Kuenen

Papers

Effects of growth conditions on mitochondrial morphology in Saccharomyces cerevisiae

Methyl mercaptan oxidase, a key enzyme in the metabolism of methylated sulphur compounds by Hyphomicrobium EG

Chemostat enrichment and isolation of Hyphomicrobium EG. A dimethyl-sulphide oxidizing methylotroph and reevaluation of Thiobacillus MS1.

Non-coordinated synthesis of glucose dehydrogenase and its prosthetic group PQQ in Acinetobacter and Pseudomonas species

Polythionate degradation by tetrathionate hydrolase of Thiobacillus ferrooxidans