Comparative analysis of genetic diversity in the mangrove species Avicennia marina (Forsk.) Vierh. (Avicenniaceae) detected by AFLPs and SSRs

Avicennia marina is an important mangrove species with a wide geographical and climatic distribution which suggests that large amounts of genetic diversity are available for conservation and breeding programs. In this study we compare the informativeness of AFLPs and SSRs for assessing genetic diversity within and among individuals, populations and subspecies of A. marina in Australia. Our comparison utilized three SSR loci and three AFLP primer sets that were known to be polymorphic, and could be run in a single analysis on a capillary electrophoresis system, using different-colored fluorescent dyes. A total of 120 individuals representing six populations and three subspecies were samplcd. At the locus level, SSRs were considerably more variable than AFLPs, with a total of 52 alleles and an average heterozygosity of 0.78. Average heterozygosity for AFLPs was 0.193, but all of the 918 bands scored were polymorphic. Thus, AFLPs were considerably more efficient at revealing polymorphic loci than SSRs despite lower average heterozygosities. SSRs detected more genetic differentiation between populations (19 vs 9%) and subspecies (35 vs 11%) than AFLPs. Principal co-ordinate analysis revealed congruent patterns of genetic relationships at the individual, population and subspecific levels for both data sets. Mantel testing confirmed congruence between AFLP and SSR genetic distances among, but not within, population comparisons, indicating that the markers were segregating inde- pendently but that evolutionary groups (populations and subspecies) were similar. Three genetic criteria of importance for defining priorities for ex situ collections or in situ conservation programs (number of alleles, number of locally common alleles and number of private alleles) were correlated between the AFLP and SSR data sets. The congruence between AFLP and SSR data sets suggest that either method, or a combination, is applicable to expanded genetic studies of mangroves. The codominant nature of SSRs makes them ideal for further population-based investigations, such as mating-system analyses, for which the dominant AFLP markers are less well suited. AFLPs may be particularly useful for monitoring propagation programs and identifying duplicates within collections, since a single PCR assay can reveal many loci at once.

Molecular archaeology

Advances in technologies such as mass spectrometry and capillary electrophoresis have encouraged the study of ancient lipids and other ancient biomolecules. Now, microarray technology looks set to revolutionise the study of ancient DNA, perhaps with as much impact as that of PCR.

Cloud-point extraction and preconcentration of cyanobacterial toxins (microcystins) from natural waters using a cationic surfactant

A new cloud-point extraction and preconcentration method, using a cationic, surfactant, Aliquat-336 (tricaprylyl-methy;ammonium chloride), his-been developed for the determination of cyanobacterial toxins, microcystins, in natural waters. Sodium sulfate was used to induce phase separation at 25 degreesC. The phase behavior of Aliquat-336 with respect to concentration of Na2SO4 was studied. The cloud-point system revealed a very high phase volume ratio compared to other established systems of nonionic, anionic, and cationic surfactants: At pH 6-7, it showed an outstanding selectivity in ahalyte extraction for anionic species. Only MC-LR and MC-YR, which are known to be predominantly anionic, were extracted (with averaged recoveries of 113.9 +/- 9% and 87.1 +/- 7%, respectively). MC-RR, which is likely to be amphoteric at the above pH range, was. not cle tectable in.the extract. Coupled to HPLC/UV separation and detection, the cloud-point extraction method (with 2.5 mM Aliquat-336 and 75 mM Na2SO4 at 25 degreesC) offered detection limits of 150 +/- 7 and 470 +/- 72 pg/mL for MC-LR and MC-YR, respectively, in 25 mL of deionized water. Repeatability of the method was 7.6% for MC-LR and 7.3% for MC-YR: The cloud-point extraction process can be. completed within 10-15 min with no cleanup steps required. Applicability of the new method to the determination of microcystins in real samples was demonstrated using natural surface waters, collected from a local river and a local duck pond spiked with realistic. concentrations of microcystins. Effects of salinity and organic matter (TOC) content in the water sample on the extraction efficiency were also studied.

Heat-induced changes in UHT milks - Part 1

Raw milk was stored for 0, 2 and 4 days and processed in a UHT pilot plant by either direct or indirect heating. The unstored raw milk was also pasteurised. The thermally induced changes resulting from these treatments were investigated by examining a number of indices of heat damage. Lactulose, furosine, total and free hydroxymethylfurfural (HMF) and acid-soluble beta-lactoglobulin were analysed by high performance liquid chromatography (HPLC) while soluble tryptophan was examined by fluorescence spectroscopy. The directly heated UHT milk showed less heat damage than the indirectly heated milk, while the pasteurised milk displayed the least heat damage. During storage of the UHT milk for 12 weeks at similar to20degreesC, the levels of lactulose remained constant, while the furosine concentration increased. Both the total HMF and undenatured beta-lactoglobulin contents showed a general decrease during storage; however free HMF values initially rose but then decreased after four weeks' storage. As the age of the milk at the time of UHT processing increased, the levels of some of the indicators decreased. It is concluded that lactulose is the most reliable index of heat treatment, as it is virtually unaffected by refrigerated storage of the milk before or ambient storage after UHT processing. Reliance on other indicators may give misleading information on the heat load that UHT milk has received during processing.

Ionic liquids as catalysts of lignocellulosic biomass processing

The present work is devoted to study the pre-treatment of lignocellulosic biomass, especially wheat straw, by the application of the acidic ionic liquid (IL) such as 1-butyl-3-methylimidazolium hydrogen sulphate. The ability of this IL to hydrolysis and conversion of biomass was scrutinised. The pre-treatment with hydrogen sulphate-based IL allowed to obtain a liquor rich in hemicellulosic sugars, furans and organic acids, and a solid fraction mainly constituted by cellulose and lignin. Quantitative and qualitative analyses of the produced liquors were made by capillary electrophoresis and high-performance liquid chromatography. Pre-treatment conditions were set to produce xylose or furfural. Specific range of temperatures from 70 to 175 °C and residence times from 20.0 to 163.3 min were studied by fixing parameters such as biomass/IL ratio (10 % (w/w)) and water content (1.25 % (w/w)) in the pre-treatment process. Statistical modelling was applied to maximise the xylose and furfural concentrations. For the purpose of reaction condition comparison the severity factor for studied ionic liquid was proposed and applied in this work. Optimum conditions for xylose production were identified to be at 125 °C and 82.1 min, at which 16.7 % (w/w) xylose yield was attained. Furfural was preferably formed at higher pre-treatment temperatures and longer reaction time (161 °C and 104.5 min) reaching 30.7 % (w/w) maximum yield. The influence of water content on the optimum xylose formation was also studied. Pre-treatments with 5 and 10 % (w/w) water content were performed and an increase of 100 % and 140 % of xylose yield was observed, respectively, while the conversion into furfural maintained unchanged.

Aromatic amines sources, environmental impact and remediation

Aromatic amines are widely used industrial chemicals as their major sources in the environment include several chemical industry sectors such as oil refining, synthetic polymers, dyes, adhesives, rubbers, perfume, pharmaceuticals, pesticides and explosives. They result also from diesel exhaust, combustion of wood chips and rubber and tobacco smoke. Some types of aromatic amines are generated during cooking, special grilled meat and fish, as well. The intensive use and production of these compounds explains its occurrence in the environment such as in air, water and soil, thereby creating a potential for human exposure. Since aromatic amines are potential carcinogenic and toxic agents, they constitute an important class of environmental pollutants of enormous concern, which efficient removal is a crucial task for researchers, so several methods have been investigated and applied. In this chapter the types and general properties of aromatic amine compounds are reviewed. As aromatic amines are continuously entering the environment from various sources and have been designated as high priority pollutants, their presence in the environment must be monitored at concentration levels lower than 30 mg L1, compatible with the limits allowed by the regulations. Consequently, most relevant analytical methods to detect the aromatic amines composition in environmental matrices, and for monitoring their degradation, are essential and will be presented. Those include Spectroscopy, namely UV/visible and Fourier Transform Infrared Spectroscopy (FTIR); Chromatography, in particular Thin Layer (TLC), High Performance Liquid (HPLC) and Gas chromatography (GC); Capillary electrophoresis (CE); Mass spectrometry (MS) and combination of different methods including GC-MS, HPLC-MS and CE-MS. Choosing the best methods depend on their availability, costs, detection limit and sample concentration, which sometimes need to be concentrate or pretreated. However, combined methods may give more complete results based on the complementary information. The environmental impact, toxicity and carcinogenicity of many aromatic amines have been reported and are emphasized in this chapter too. Lately, the conventional aromatic amines degradation and the alternative biodegradation processes are highlighted. Parameters affecting biodegradation, role of different electron acceptors in aerobic and anaerobic biodegradation and kinetics are discussed. Conventional processes including extraction, adsorption onto activated carbon, chemical oxidation, advanced oxidation, electrochemical techniques and irradiation suffer from drawbacks including high costs, formation of hazardous by-products and low efficiency. Biological processes, taking advantage of the naturally processes occurring in environment, have been developed and tested, proved as an economic, energy efficient and environmentally feasible alternative. Aerobic biodegradation is one of the most promising techniques for aromatic amines remediation, but has the drawback of aromatic amines autooxidation once they are exposed to oxygen, instead of their degradation. Higher costs, especially due to power consumption for aeration, can also limit its application. Anaerobic degradation technology is the novel path for treatment of a wide variety of aromatic amines, including industrial wastewater, and will be discussed. However, some are difficult to degrade under anaerobic conditions and, thus, other electron acceptors such as nitrate, iron, sulphate, manganese and carbonate have, alternatively, been tested.

Molecular determinants of vesicular storage and release of the gliotransmitter D-serine from cortical astrocytes

Neuron-astrocyte reciprocal communication at synapses has emerged as a novel signalling pathway in brain function. Astrocytes sense the level of synaptic activity and, in turn, influence its efficacy through the regulated release of 'gliotransmitters' such as glutamate, ATP or D-serine. A calcium-dependent exocytosis is proposed to drive the release of gliotransmitters but its existence is still debated. Over the last years, we have been studying the molecular determinants governing D-serine release from glia using different approaches. Using a novel bioassay for D-serine, we have been able to show that D-serine release occurs mainly through a calcium- and SNARE proteindependent mechanism just supporting the idea that this amino acid is released by exocytosis from glia. We next have pursued our exploration by confocal imaging and tracking of the exocytotic routes for Dserine- mediated gliotransmission and have shown that D-serine releasable pools are confined to synaptobrevin2/cellubrevin-bearing vesicles. To shed light onto the mechanisms controlling the storage and the release of gliotransmitters and namely D-serine, we have developed a new method for the immunoisolation of synaptobrevin 2- positive vesicles from rat cortical astrocytes in culture while preserving their content in gliotransmitters. The purified organelles are clear round shape vesicles of excellent purity with homogeneous size (40 nm) as judged by electron microscopy. Immunoblotting analysis revealed that isolated vesicles contain most of the major proteins already described for neuron-derived vesicles like synaptic vesicle protein 2 (SV2) and the proton pump H?-ATPase. In addition, we have analyzed the content for various amino acids of these vesicles by means of chiral capillary electrophoresis coupled to laser-induced fluorescence detection. The purified vesicles contain large amount of D-serine. We also detect peaks corresponding to unidentified compounds that may correspond to others amino acids. Postembedding immunogold labelling of the rat neocortex further revealed the expression of D-serine in astrocytes processes contacting excitatory synapses. Finally, we have examined the uptake properties for Dserine and glutamate inside the isolated glial vesicles. Our results provide significant support for the existence of an uptake system for D-serine in secretory glial vesicles and for the storage of chemical substances like D-serine and glutamate. 11th International Congress on Amino Acids, Peptides and Proteins 763 123

Adsorption of colloidal particles in the presence of external fields

We present a new class of sequential adsorption models in which the adsorbing particles reach the surface following an inclined direction (shadow models). Capillary electrophoresis, adsorption in the presence of a shear, and adsorption on an inclined substrate are physical manifestations of these models. Numerical simulations are carried out to show how the new adsorption mechanisms are responsible for the formation of more ordered adsorbed layers and have important implications in the kinetics, in particular, modifying the jamming limit.

ppGpp controlled by the Gac/Rsm regulatory pathway sustains biocontrol activity in Pseudomonas fluorescens CHA0.

In Pseudomonas fluorescens CHA0 and other fluorescent pseudomonads, the Gac/Rsm signal transduction pathway is instrumental for secondary metabolism and biocontrol of root pathogens via the expression of regulatory small RNAs (sRNAs). Furthermore, in strain CHA0, an imbalance in the Krebs cycle can affect the strain's ability to produce extracellular secondary metabolites, including biocontrol factors. Here, we report the metabolome of wild-type CHA0, a gacA-negative mutant, which has lost Gac/Rsm activities, and a retS-negative mutant, which shows strongly enhanced Gac/Rsm-dependent activities. Capillary electrophoresis-based metabolomic profiling revealed that the gacA and retS mutations had opposite effects on the intracellular levels of a number of central metabolites, suggesting that the Gac/Rsm pathway regulates not only secondary metabolism but also primary metabolism in strain CHA0. Among the regulated metabolites identified, the alarmone guanosine tetraphosphate (ppGpp) was characterized in detail by the construction of relA (for ppGpp synthase) and spoT (for ppGpp synthase/hydrolase) deletion mutants. In a relA spoT double mutant, ppGpp synthesis was completely abolished, the expression of Rsm sRNAs was attenuated, and physiological functions such as antibiotic production, root colonization, and plant protection were markedly diminished. Thus, ppGpp appears to be essential for sustaining epiphytic fitness and biocontrol activity of strain CHA0.

Genomics: more than genes

The fundamentals of Real-time Polymerase Chain Reaction,Automated capillary electrophoresis -Sanger sequencing and Fragmentanalysis- and "Next-generation" sequencing are reviewed. An overview ofapplications is presented using our own examples carried out in our facility.

Molecular characterization of grapevine from Santa Catarina, Brazil, using microsatellite markers

The objective of this work was to characterize the grape germplasm in Santa Catarina, Brazil, using microsatellite DNA markers (simple sequence repeats - SSR). The DNA samples were collected from leaves and shoots of accessions of public and private collections from the counties Urussanga, Nova Trento, Rodeio, São Joaquim, Campos Novos, Videira, and Água Doce. Ten SSR loci (VVS2, VVMD5, VVMD7, VVMD27, VrZAG62, VrZAG79, VVMD25, VVMD28, VVMD31, and VVMD32) were analysed by capillary electrophoresis. Molecular profiling was conducted for 190 grapevines (European, American, and hybrids), and 67 genotypes were obtained. The data were compared with each other and with those from the literature and from online databases, in order to identify varieties and discover cases of synonymy and homonymy. Forty molecular profiles corresponded to known varieties, while 27 genotypes were described for the first time. The existence of typical germplasm composed mainly of American and hybrid varieties is an important finding for local viticulture. Applications of the results rely on quality control and certification at the nursery level. Increasing precision in the characterization of grapevine genotypes may help breeding programs.

Aminohappojen enantiomeerien kromatografinen erottaminen

Enantiomeerit ovat yhdisteitä, jotka ovat toistensa peilikuvamuotoja. Enantiomeerien erotusmenetelmiä ovat neste-nesteuutto, kalvotekniikka, kiteytys, kromatografia ja kapillaarielektroforeesi. Nestekromatografinen erotus perustuu joko suoraan erotukseen tai epäsuoraan erotukseen. Kiraaliset stationaarifaasit erottavat yhdisteet kolonnissa suoralla erotuksella. Derivoimattomia aminohappojen enantiomeerejä on erotettu käyttäen ligandinvaihto-, kruunueetteri-, antibiootti- ja polysakkaridistationaarifaaseja. Epäsuora erotus vaatii erotettavan enantiomeeriparin esikäsittelyn ennen kolonnia. Markkinoilta löytyy niukasti preparatiiviseen mittakaavaan soveltuvia enantiomeerien erotusmateriaaleja. Työn kokeellisessa osassa enantiomeerien erotuksia tehtiin sekä analyyttisessä mittakaavassa että preparatiivisessa mittakaavassa. Tutkittavina pääkomponentteina aminohapoista olivat metioniinin, proliinin ja seriinin enantiomeeriparit. Analyyttisessä mittakaavassa kuparimuotoisella ligandinvaihtokolonnilla tehty erotus onnistui erittäin hyvin. Piikkien resoluutioiden arvot vaihtelivat tyypillisesti välillä 2,0-35 ja erotustekijöiden arvot välillä 1,5-30. Parhaiten onnistuttiin erottamaan metioniinin enantiomeerit toisistaan. Prepatatiivisen mittakaavan erotusmateriaalin tutkimus keskittyi materiaalin kokeiluun ja kehitykseen aminohappojen enantiomeerien erotukseen soveltuvaksi. Erotusmateriaalilla onnistuttiin erottamaan aminohappoja toisistaan, mutta aminohappojen enantiomeerien erottumista ei onnistuttu selkeästi havaitsemaan. Erotusmateriaali toimi parhaiten muunnettuna alkaalisissa olosuhteissa kuparimuotoiseksi. Kuparin pysymättömyys erotusmateriaalissa aiheutti kuitenkin ongelmia kokeiden toistettavuuteen.

Measurement Problems and Problem-Solving in Kraft Pulping

Tämän työn tarkoituksena on koota yhteen selluprosessin mittausongelmat ja mahdolliset mittaustekniikat ongelmien ratkaisemiseksi. Pääpaino on online-mittaustekniikoissa. Työ koostuu kolmesta osasta. Ensimmäinen osa on kirjallisuustyö, jossa esitellään nykyaikaisen selluprosessin perusmittaukset ja säätötarpeet. Mukana on koko kuitulinja puunkäsittelystä valkaisuun ja kemikaalikierto: haihduttamo, soodakattila, kaustistamo ja meesauuni. Toisessa osassa mittausongelmat ja mahdolliset mittaustekniikat on koottu yhteen ”tiekartaksi”. Tiedot on koottu vierailemalla kolmella suomalaisella sellutehtaalla ja haastattelemalla laitetekniikka- ja mittaustekniikka-asiantuntijoita. Prosessikemian paremmalle ymmärtämiselle näyttää haastattelun perusteella olevan tarvetta, minkä vuoksi konsentraatiomittaukset on valittu jatkotutkimuskohteeksi. Viimeisessä osassa esitellään mahdollisia mittaustekniikoita konsentraatiomittausten ratkaisemiseksi. Valitut tekniikat ovat lähi-infrapunatekniikka (NIR), fourier-muunnosinfrapunatekniikka (FTIR), online-kapillaarielektroforeesi (CE) ja laserindusoitu plasmaemissiospektroskopia (LIPS). Kaikkia tekniikoita voi käyttää online-kytkettyinä prosessikehitystyökaluina. Kehityskustannukset on arvioitu säätöön kytketylle online-laitteelle. Kehityskustannukset vaihtelevat nollasta miestyövuodesta FTIR-tekniikalle viiteen miestyövuoteen CE-laitteelle; kehityskustannukset riippuvat tekniikan kehitysasteesta ja valmiusasteesta tietyn ongelman ratkaisuun. Työn viimeisessä osassa arvioidaan myös yhden mittausongelman – pesuhäviömittauksen – ratkaisemisen teknis-taloudellista kannattavuutta. Ligniinipitoisuus kuvaisi nykyisiä mittauksia paremmin todellista pesuhäviötä. Nykyään mitataan joko natrium- tai COD-pesuhäviötä. Ligniinipitoisuutta voidaan mitata UV-absorptiotekniikalla. Myös CE-laitetta voitaisiin käyttää pesuhäviön mittauksessa ainakin prosessikehitysvaiheessa. Taloudellinen tarkastelu pohjautuu moniin yksinkertaistuksiin ja se ei sovellu suoraan investointipäätösten tueksi. Parempi mittaus- ja säätöjärjestelmä voisi vakauttaa pesemön ajoa. Investointi ajoa vakauttavaan järjestelmään on kannattavaa, jos todellinen ajotilanne on tarpeeksi kaukana kustannusminimistä tai jos pesurin ajo heilahtelee eli pesuhäviön keskihajonta on suuri. 50 000 € maksavalle mittaus- ja säätöjärjestelmälle saadaan alle 0,5 vuoden takaisinmaksuaika epävakaassa ajossa, jos COD-pesuhäviön vaihteluväli on 5,2 – 11,6 kg/odt asetusarvon ollessa 8,4 kg/odt. Laimennuskerroin vaihtelee tällöin välillä 1,7 – 3,6 m3/odt asetusarvon ollessa 2,5 m3/odt.

Development of an enantioselective assay for simultaneous separation of venlafaxine and O-desmethylvenlafaxine by micellar electrokinetic chromatography-tandem mass spectrometry: Application to the analysis of drug-drug interaction.

To-date, there has been no effective chiral capillary electrophoresis-mass spectrometry (CE-MS) method reported for the simultaneous enantioseparation of the antidepressant drug, venlafaxine (VX) and its structurally-similar major metabolite, O-desmethylvenlafaxine (O-DVX). This is mainly due to the difficulty of identifying MS compatible chiral selector, which could provide both high enantioselectivity and sensitive MS detection. In this work, poly-sodium N-undecenoyl-L,L-leucylalaninate (poly-L,L-SULA) was employed as a chiral selector after screening several dipeptide polymeric chiral surfactants. Baseline separation of both O-DVX and VX enantiomers was achieved in 15min after optimizing the buffer pH, poly-L,L-SULA concentration, nebulizer pressure and separation voltage. Calibration curves in spiked plasma (recoveries higher than 80%) were linear over the concentration range 150-5000ng/mL for both VX and O-DVX. The limit of detection (LOD) was found to be as low as 30ng/mL and 21ng/mL for O-DVX and VX, respectively. This method was successfully applied to measure the plasma concentrations of human volunteers receiving VX or O-DVX orally when co-administered without and with indinivar therapy. The results suggest that micellar electrokinetic chromatography electrospray ionization-tandem mass spectrometry (MEKC-ESI-MS/MS) is an effective low cost alternative technique for the pharmacokinetics and pharmacodynamics studies of both O-DVX and VX enantiomers. The technique has potential to identify drug-drug interaction involving VX and O-DVX enantiomers while administering indinivar therapy.