Crystal structures of Salmonella typhimurium propionate kinase and its complex with Ap4A: evidence for a novel Ap4A synthetic activity

Propionate kinase catalyses the last step in the anaerobic breakdown of L-threonine to propionate in which propionyl phosphate and ADP are converted to propionate and ATR Here we report the structures of propionate kinase (TdcD) in the native form as well as in complex with diadenosine 5 ',5 '''-P-1,P-4-tetraphosphate (AP(4)A) by X-ray crystallography. Structure of TdcD obtained after cocrystallization with ATP showed Ap(4)A bound to the active site pocket suggesting the presence of Ap(4)A synthetic activity in TdcD. Binding of Ap(4)A to the enzyme was confirmed by the structure determination of a TdcD-Ap(4)A complex obtained after cocrystallization of TdcD with commercially available Ap(4)A. Mass spectroscopic studies provided further evidence for the formation of Ap(4)A by propionate kinase in the presence of ATP. In the TdcD-Ap(4)A complex structure, Ap(4)A is present in an extended conformation with one adenosine moiety present in the nucleotide binding site and other in the proposed propionate binding site. These observations tend to support direct in-line transfer of phosphoryl group during the kinase reaction.

Molekyylibiologisten menetelmien kehittäminen ihmisen suoliston sulfaattia pelkistävien bakteerien määrittämiseksi

Ihmisen ruuansulatuskanavan bakteeriston kehitys alkaa syntymästä, jolloin ensimmäiset bakteerit kansoittavat steriilin ruuansulatuskanavan. Bakteeristo kehittyy perimän, ympäristön ja varhaisen ruokavalion vaikutuksesta kohti monimuotoisempaa bakteeripopulaatiota. Aikuisen ruuansulatuskanavan normaalibakteeristo on varsin muuttumaton, mutta siihen vaikuttavat monet tekijät, kuten ikä, terveydentila, ruokavalio ja antibioottien käyttö. Bakteeriston koostumus vaihtelee ruuansulatuskanavan eri osissa ja bakteerimäärä kasvaa kohti paksusuolta, ollen paksusuolessa ja ulosteessa peräti 1010-1012 pmy/ml. Suurin osa ruuansulatuskanavan bakteereista on anaerobeja. Ruuansulatuskanavan bakteeristo vaikuttaa muun muassa suoliston kehittymiseen ja hiilihydraattien ja proteiinien hajotukseen sekä toimii osana immuunipuolustusta. Sulfaattia pelkistävät bakteerit (SRB) ovat monimuotoinen ryhmä pääosin anaerobisia bakteereita, jotka käyttävät aineenvaihdunnassaan elektronin vastaanottajana sulfaattia muuttaen sen lopulta sulfidiksi. SRB:t ovat sopeutuneet useisiin erilaisiin ympäristöihin. Niitä tavataan mm. vesistöjen sedimenteissä sekä ihmisen ruuansulatuskanavassa. Ihmisen ruuansulatuskanavassa on SRB:ta n. 105-108 pmy/g, ja niitä on löydetty erityisesti anaerobisista osista kuten suun ientaskuista ja paksusuolesta. SRB:t voivat olla haitaksi ruuansulatuskanavalle tuottamansa sulfidin vuoksi, joka esiintyy vesiliuoksessa vetysulfidina. Tämän on havaittu olevan toksista suoliston epiteelisoluille. Viimeaikoina on kiinnostuttu sulfaatinpelkistäjien yhteydestä suoliston sairaustiloihin, kuten tulehduksellisiin suolistosairauksiin (IBD). Pro gradu -tutkimukseni tavoitteena oli kehittää PCR-DGGE- ja qPCR-menetelmät ulosteen sulfaattia pelkistävien bakteerien määritykseen. Kohdegeeninä menetelmänkehityksessä käytettiin dsrAB-geeniä, joka koodaa dissimilatorista sulfiitinpelkistysentsyymiä. dsrAB-geeni on sulfaatinpelkistäjille ominainen konservoitunut geenialue, johon perustuvia tutkimuksia ei vielä ole paljon ihmispuolelta. qPCR-menetelmä saatiin optimoitua herkäksi ja spesifiseksi käyttäen dsrA-geenispesifisiä alukkeita, mutta PCR-DGGE-menetelmää ei saatu optimoitua käytössä olleilla alukkeilla, jotka monistivat PCR-DGGE:ssa myös negatiivikontrollikantoja. Tutkittaessa qPCR:lla IBD:tä (Crohn ja ulseratiivinen koliitti) sairastavien lasten ja terveiden kontrollihenkilöiden ulostenäytteistä eristettyä DNA:ta, merkittävää eroa SRB-määrissä ei havaittu eri ryhmien välillä. Crohnin tautia sairastavien aktiivisen vaiheen ja oireettoman vaiheen näytteiden välillä oli kuitenkin tilastollisesti merkitsevä ero (SRB-määrät; oireeton vaihe>oireellinen vaihe) (P <0,05).

Seasonal variation in nitrification and nitrate-reduction pathways in coastal sediments in the Gulf of Finland, Baltic Sea

The Baltic Sea is one of the most eutrophic marine areas in the world. The role of nitrogen as a eutrophicating nutrient in the Baltic Sea has remained controversial, due to lack of understanding of nitrogen cycling in the area. We investigated the seasonal variation in sediment nitrification, denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA) at two coastal sites in the Gulf of Finland. In addition to the in situ rates, we assessed the potential for these processes in different seasons. The nitrification and nitrogen removal processes were maximal during the warm summer months, when the sediment organic content was highest. In colder seasons, the in situ rates of the nitrification and nitrate reduction processes decreased, but the potential for nitrification remained equal to or higher than that during the warm months. The denitrification and nitrification rates were usually higher in the accumulation basin, where the organic content of the sediment was higher, but the transportation area, despite lower denitrification rates and potential, typically had higher potential for nitrification than the accumulation basin. Anammox and DNRA were not significant nitrate sinks in any of the seasons sampled. The results also show that the denitrification rates in the coastal Gulf of Finland sediment have decreased, and that benthic denitrification might be a less important sink for fixed nitrogen than previously assumed.

Design and fabrication of an automated thermal desorption gas-solid reaction system: Oxidation of ammonia and methanol over YBa2Cu3O7−δ(123) oxide systems

A fully automated, versatile Temperature Programmed Desorption (TDP), Temperature Programmed Reaction (TPR) and Evolved Gas Analysis (EGA) system has been designed and fabricated. The system consists of a micro-reactor which can be evacuated to 10−6 torr and can be heated from 30 to 750°C at a rate of 5 to 30°C per minute. The gas evolved from the reactor is analysed by a quadrupole mass spectrometer (1–300 amu). Data on each of the mass scans and the temperature at a given time are acquired by a PC/AT system to generate thermograms. The functioning of the system is exemplified by the temperature programmed desorption (TPD) of oxygen from YBa2Cu3−xCoxO7 ± δ, catalytic ammonia oxidation to NO over YBa2Cu3O7−δ and anaerobic oxidation of methanol to CO2, CO and H2O over YBa2Cu3O7−δ (Y123) and PrBa2Cu3O7−δ (Pr123) systems.

Inhibitory effects of wood extracts on the spoilage flora of marinated poultry meat

Polyphenolic compounds occurring naturally in knotwood of plants are known to have antimicrobial effects. The knots (i.e. the branch bases inside tree stems) and outer branches in pine trees contain a remarkably high concentration of phenolic stilbenes, while lignans are the major phenolic constituents of spruce knots. Large amount of these phenolic compounds can be extracted from wood knots at pulp and paper mills where their presence is undesirable. In Finland, marinating of broiler meat is done not only to increase or add value to the meat, but also to enhance the safety and shelf-life. These products are usually packed under a modified atmosphere for further protection against spoilage microorganisms. However, studies have revealed that addition of marinades to poultry products do not have an inhibitory effect on either some psychrotrophic anaerobic bacteria, such as Brochothrix thermosphacta or lactic acid bacteria associated with spoilage. Also, the activity of pathogenic Campylobacter jejuni is not affected by marinating. The objective of this study was to investigate the inhibitory and lethal activities of extracts from spruce (Picea spp.) and pine (Pinus spp.) knotwood and outer branches that are dissolved in ethanol against the spoilage microorganisms in modified atmosphere packaged marinated broiler products. Modified atmosphere packaged broiler products were separately inoculated with ‘normal’ marinades, marinades with 70% ethanol, marinades with a mixture of spruce and pine extracts dissolved in 70% ethanol or mixture of spruce and pine extracts in powder form. The bacterial colony forming units per gram obtained from each of the samples were analysed on de Man Rogosa and Sharpe agar at days 1, 6, 12 and 15. The results showed that there were significant differences in bacterial colony forming units per gram (P <0.05) between packages with ‘normal’ marinades and packages with extracts added to their marinades on the 12th and 15th day. It can be concluded that the addition of extracts from spruce and pine knotwood to marinades significantly retarded growth of spoilage microorganisms during the 15 day test period. However further research is warranted to characterise and establish the safety and suitability of the compound(s) in spruce and pine knotwood extracts that are responsible for inhibitory or lethal activity against the microbes that may be present in marinated poultry meat.

The roles of nitrification and nitrate reduction pathways in nitrogen cycling of Baltic Sea

The Baltic Sea is one of the largest brackish water bodies in the world. Primary production in the Baltic Sea is limited by nitrogen (N) availability with the exception of river outlets and the northernmost phosphorus limited basin. The excess human induced N load from the drainage basin has caused severe eutrophication of the sea. The excess N loads can be mitigated by microbe mediated natural N removal processes that are found in the oxic-anoxic interfaces in sediments and water column redoxclines. Such interfaces allow the close coupling between the oxic nitrification process, and anoxic denitrification and anaerobic ammonium oxidation (anammox) processes that lead to the formation of molecular nitrogen gas. These processes are governed by various environmental parameters. The effects of these parameters on N processes were investigated in the northern Baltic Sea sediments. During summer months when the sediment organic content is at its highest, nitrification and denitrification reach their maximum rates. However, nitrification had no excess potential, which was probably because of high competition for molecular oxygen (O2) between heterotrophic and nitrification microbes. Subsequently, the limited nitrate (NO3-) availability inhibited denitrification. In fall, winter and spring, nitrification was limited by ammonium availability and denitrification limited by the availability of organic carbon and occasionally by NO3-. Anaerobic ammonium oxidation (anammox) was not an important N removal process in the northern Baltic Sea. Modeling studies suggest that when hypoxia expands in the Baltic Sea, N removal intensifies. However, the results of this study suggest the opposite because bottom water hypoxia (O2< 2 ml l-1) decreased the denitrification rates in sediments. Moreover, N was recycled by the dissimilatory nitrate reduction to ammonium (DNRA) process instead of being removed from the water ecosystem. High N removal potentials were found in the anoxic water column in the deep basins of the Baltic Proper. However, the N removal in the water column appeared to be limited by low substrate availability, because the water at the depths at which the substrate producing nitrification process occurred, rarely mix with the water at the depths at which N removal processes were found. Overall, the natural N removal capacity of the northern Baltic Sea decreased compared to values measured in mid 1990s and early 2000. The reason for this appears to be increasing hypoxia.

Oral malodour – background and diagnostics

Bad breath or oral malodour can be related to gingival diseases, trimethylaminuria, various inflammation diseases of upper respiratory tract, foreign bodies in nasal cavity etc. Bad breath is usually, in 85 % to 95 % of cases, inflicted by gram negative anaerobic bacteria in tongue coating. These bacteria have a tendency of producing foul-smelling sulphur containing gases called volatile sulphur compounds or VSC. Main cause of bad breath is parodontitis or postnasal drip into posterior part of the tongue. Detecting bad breath is most efficiently done by organoleptic method. By skilled analyser the reason for oral malodour can be determined with great accuracy. For scientific study the most effective method is gas chromatography (GC) with flame photometric detector (FPD). With it almost every component of exhaled air can be detected both quantitative and qualitative. Effective chairside methods include portable sulphur monitors and saliva tests.

Ferrous-iron induces lipid peroxidation with little damage to energy transduction in mitochondria

Addition of ferrous sulfate, but not ferric chloride, in micromolar concentrations to rat liver mitochondria induced high rates of consumption of oxygen. The oxygen consumed was several times in excess of the reducing capacity of ferrous-iron (O: Fe ratios 5�8). This occurred in the absence of NADPH or any exogenous oxidizable substrate. The reaction terminated on oxidation of ferrous ions. Malondialdehyde (MDA), measured as thiobarbituric acid-reacting material, was produced indicating peroxidation of lipids. The ratio of O2: MDA was about 4: 1. Pretreatment of mitochondria with ferrous sulfate decreased the rate of oxidation (state 3) with glutamate (+malate) as the substrate by about 40% but caused little damage to energy tranduction process as represented by ratios of ADP: O and respiratory control, as well as calcium-stimulated oxygen uptake and energy-dependent uptake of [45Ca]-calcium. Addition of succinate or ubiquinone decreased ferrous iron-induced lipid peroxidation in intact mitochondria. In frozen-thawed mitochondria, addition of succinate enhanced lipid peroxidation whereas ubiquinone had little effect. These results suggest that ferrous-iron can cause peroxidation of mitochondrial lipids without affecting the energy transduction systems, and that succinate and ubiquinone can offer protection from damage due to such ferrous-iron released from the stores within the cells.

Jäätikön pinnanalaisten järvien hydrogeokemiallinen tutkimus läntisellä Kuningatar Maudin maalla, Etelämantereella

Tutkielma tarkastelee itäisellä Etelämantereella, läntisellä Kuningatar Maudin Maalla olevien jäätikön pinnanalaisten järvien (frozen lake) veden hydrogeokemiallisia ominaisuuksia. Keskeisin tutkimusalue on Vestfjellavuoristoketjun (73 74 °S, 13 16 °W) pohjoisimman vuoren, Basenin läheisyydessä sijaitseva jäätikön pinnanalainen järvi (Basen-järvi). Vertailevia tutkimuksia tehtiin lisäksi Plogenin ja Fossilryggenin nunatakkien läheisyydessä sekä Heimefrontfjellan vuoristoalueella. Tutkielma on Suomen Akatemian rahoittama grant # 54087 -hanke, ja siinä yhdistyvät Suomen tutkimusaseman, Aboan lähellä tehty geologinen, hydrogeologinen sekä glasiologinen tutkimus. Tutkimuksessa selvitetään Basenin jäätikön pinnanalaisen järven kemiallinen koostumus ja sen paikallinen ja ajallinen vaihtelu. Kemiallisen koostumuksen perusteella selvitetään myös ionien lähteet. Näytteenotto suoritettiin FINNARP 2003/04 Etelämanner-tutkimusretkellä. Basen -järveltä ja sen vieressä sijaitsevalta Basen -vuorelta kerättiin vesi-, suola-, kivi- ja moreeninäytteitä. Suola-, kivi- ja moreeninäytteillä selvitetään näytteissä silmillä havaittavan mineraalisaostuman koostumus. Kiinteän faasin kasvihuoneilmiö luo otolliset mahdollisuudet Basenin jäätikön pinnanalaisen järven synnylle ja kehitykselle. Basen -järven veden kemiallinen koostumus vaihtelee alueellisesti ja ajallisesti ja se on syntynyt kolmen komponentin yhteisvaikutuksesta: purovesien, nunatakilta sulavien lumien sekä sulaneen jään yhteisvaikutuksesta. Suurin vaikutus Basenin järven kemialliseen koostumukseen on kuitenkin Basenin rinteiltä virtaavilla purovesillä. Korkeimmat ionipitoisuudet havaittiin nunatakin reunan läheisyydessä. Basenin järven veden ionit ovat enimmäkseen ei-meriperäisiä. Runsain ioni on kalsium, jonka suurin lähde on jurakautisessa basaltissa esiintyvä mantelikarbonaatti. Basenin -järven vaiheista eteläisen talven aikana ei ole tietoa ja se, mitä talven aikana tapahtuu ja mikä saa veteen liuenneiden komponenttien pitoisuuden alenemaan, on vielä selvittämättä ja säilyy mahdollisena aiheena tulevaisuuden tutkimuksille.

Nutritional evaluation of silage made from the toxic weed parthenium hysterophorus in animals

After ensilation, the toxic Compositae weed Parthenium hysterophorus was devoid of the toxic principle parthenin. Laboratory-scale ensilation indicated that no parthenin was detectable after 5 wk of anaerobic fermentation. For animal feeding studies, silage was made on a large scale from Parthenium mixed with maize or from Parthenium alone. Crossbred bull and buffalo bull calves were fed diets containing the silages, or control diet without silage, for 12 wk. The animals consumed both silages with relish, and body weight gains of silage-fed calves did not differ from those of the controls. The digestibilities of dry matter, fibre and nitrogen-free extract were greater with the control diet, but the biological value of proteins tended to be greater with the silage-containing diets. Haematological studies indicated no significant differences between experimental and control groups in selected parameters, except for a reduction in blood urea nitrogen in the animals fed silage. The possible causes for these biochemical alterations are discussed. Since the nutritive value of Parthenium silage compares favourably with the standard diet, and Parthenium seeds collected from the silage did not germinate, we suggest that ensilation can be used as an additional method in the containment and eradication of these plants, which grow wild in India.

Purification of 3,5-Dichlorocatechol 1,2-Dioxygenase, a Nonheme Iron Dioxygenase and a Key Enzyme in the Biodegradation of a Herbicide, 2,4-Dichlorophenoxyacetic acid (2,4-D), from Pseudomonas cepacia CSV90

An enzyme which cleaves the benzene ring of 3,5-dichiorocatechol has been purified to homogeneity from Pseudomonas cepacia CSV90, grown with 2,4-dichlorophenoxyacetic acid (2,4-D) as the sole carbon source. The enzyme was a nonheme ferric dioxygenase and catalyzed the intradiol cleavage of all the examined catechol derivatives, 3,5-dichlorocatechol having the highest specificity constant of 7.3 μM−1 s−1 in an air-saturated buffer. No extradiol-cleaving activity was observed. Thus, the enzyme was designated as 3,5-dichlorocatechol 1,2-dioxygenase. The molecular weight of the native enzyme was ascertained to be 56,000 by light scattering method, while the Mr value of the enzyme denatured with 6 M guanidine-HCl or sodium dodecyl sulfate was 29,000 or 31,600, respectively, suggesting that the enzyme was a homodimer. The iron content was estimated to be 0.89 mol per mole of enzyme. The enzyme was deep red and exhibited a broad absorption spectrum with a maximum at around 425 nm, which was bleached by sodium dithionite, and shifted to 515 nm upon anaerobic 3,5-dichlorocatechol binding. The catalytic constant and the Km values for 3,5-dichlorocatechol and oxygen were 34.7 s−1 and 4.4 and 652 μM, respectively, at pH 8 and 25°C. Some heavy metal ions, chelating agents and sulfhydryl reagents inhibited the activity. The NH2-terminal sequence was determined up to 44 amino acid residues and compared with those of the other catechol dioxygenases previously reported.

Seasonal and short-term variation in denitrification and anammox at a coastal station on the Gulf of Finland, Baltic Sea

Benthic processes were measured at a coastal deposition area in the northern Baltic Sea, covering all seasons. The N-2 production rates, 90-400 mu mol N m(-2) d(-1), were highest in autumn-early winter and lowest in spring. Heterotrophic bacterial production peaked unexpectedly late in the year, indicating that in addition to the temperature, the availability of carbon compounds suitable for the heterotrophic bacteria also plays a major role in regulating the denitrification rate. Anaerobic ammonium oxidation (anammox) was measured in spring and autumn and contributed 10% and 15%, respectively, to the total N-2 production. The low percentage did, however, result in a significant error in the total N-2 production rate estimate, calculated using the isotope pairing technique. Anammox must be taken into account in the Gulf of Finland in future sediment nitrogen cycling research.

Thermophilic fungi: An assessment of their potential for growth in soil

An attempt has been made to forecast the potential of thermophilic fungi to grow in soil in the laboratory and in the field in the presence of a predominantly mesophilic fungal flora at usual temperature. The respiratory rate of thermophilic fungi was markedly responsive to changes in temperature, but that of mesophilic fungi was relatively independent of such changes. This suggested that in a thermally fluctuating environment, thermophilic fungi may be at a physiological disadvantage compared to mesophilic fungi. In mixed cultures in soil plates, thermophilic fungi outgrew mesophilic fungi under a fluctuating temperature regime only when the amplitude of the fluctuating temperatures was small and approached their temperature optima for growth. An antibody probe was used to detect the activity of native or an introduced strain of a thermophilic fungus, Thermomyces lanuginosus, under field conditions. The results suggest that although widespread, thermophilic fungi are ordinarily not an active component of soil microflora. Their presence in soil most likely may be the result of the aerial dissemination of propagules from composting plant material.

Copper( 11) Complexes of Novel Tripodal Ligands containing Phenolate and Benzimidazole/Pyridine Pendants: Synthesis, Structure, Spectra and Electrochemical Behaviour

Mononuclear copper(II) complexes of tri- and tetra-dentate tripodal ligands containing phenolic hydroxyl and benzimidazole or pyridine groups have been isolated. They are of the type (CuL(X)].nH2O, [CuL(H2O)]X.nH2O or [CuL].nH2O where X = Cl-, ClO4-, N3- or NCS- and n = 0-4. The electronic spectra of all the complexes exhibit a broad absorption band around 14000 cm-1 and the polycrystalline as well as the frozen-solution EPR spectra are axial, indicating square-based geometries. The crystal structure of [CuL(Cl)] [HL = (2-hydroxy-5-nitrobenzyl)bis(2-pyridyl-methyl)amine] revealed a square-pyramidal geometry around Cu(II). The mononuclear complex crystallises in the triclinic space group P1BAR with a = 6.938(1), b = 11.782(6), c = 12.678(3) angstrom and alpha = 114.56(3), beta = 92.70(2), gamma = 95.36(2)-degrees. The co-ordination plane is comprised of one tertiary amine and two pyridine nitrogens and a chloride ion. The phenolate ion unusually occupies the axial site, possibly due to the electron-withdrawing p-nitro group. The enhanced pi delocalisation involving the p-nitrophenolate donor elevates the E1/2 values. The spectral and electrochemical results suggest the order of donor strength as nitrophenolate < pyridine < benzimidazole in the tridentate and nitrophenolate < benzimidazole < pyridine in the tetradentate ligand complexes.

Preparation of a soluble 58kDa-3-hydroxy-3-methylglutaryl CoA reductase from liver microsomes and its inhibition by ethoxysilatrane, a hypocholesterolemic compound

On repeated thawing at room temperature of frozen preparations of heavy microsomes from rat livers, HMGCoA reductase activity was solubilized due to limited proteolysis. This soluble enzyme was partially purified by fractionation with ammonium sulfate and filtration on Sephacryl S-200 column. The active enzyme was coeluted with a major 92 kDa-protein and was identified as a 58kDa-protein after separation by SDS-PAGE and immunoblotting. Ethoxysilatrane, a hypocholesterolemic compound, which decreased the liver-microsomal activity of HMGCoA reductase on intra-peritonial treatment of animals, showed little effect on the enzyme activity with isolated microsomes or the 50kDa-soluble enzyme when added in the assay. But it was able to inhibit the activity of the soluble 58kDa-enzyme in a concentration-dependent, reversible manner. Cholesterol and an oxycholesterol were without effect whereas chlorophenoxyisobutyrate and ubiquinone showed small inhibition under these conditions. The extra region that links the active site domain (50kDa protein) to the membrane, present in the 58kDa-protein appears to be involved in mediating the inhibition by silatrane.