Phylogenetic position of Fit insect toxin producing pseudomonads

Fit produced by Pseudomonas fluorescens CHA0 is a novel insect toxin in root colonizing pseudomonads, of which a homologue is described in Photorhabdus species.However, occurrence and abundance of insect pathogenicity in plant-associated pseudomonads is still unclear. An extensive screening outside the P. fluorescens complex identified strains of Pseudomonas chlororaphis as further Fit toxin producing candidates. Sequences of five different P. chlororaphis strains generated in this study were used to reconstruct the evolutionary history of the Fit toxin gene and to analyse its mode of evolution. We found that P. chlororaphis is closely associated with a small subgroup of 2,4-diacetylphloroglucinol and pyoluteorin- producing pseudomonads, both when analyzing four housekeeping genes and the nucleotide sequences for the Fit toxin gene. Additionally, we identified purifying selection to be the predominant mode of Fit toxin evolution.

Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells.

Recently, a handful of intergenic long noncoding RNAs (lncRNAs) have been shown to compete with mRNAs for binding to miRNAs and to contribute to development and disease. Beyond these reports, little is yet known of the extent and functional consequences of miRNA-mediated regulation of mRNA levels by lncRNAs. To gain further insight into lncRNA-mRNA miRNA-mediated crosstalk, we reanalyzed transcriptome-wide changes induced by the targeted knockdown of over 100 lncRNA transcripts in mouse embryonic stem cells (mESCs). We predicted that, on average, almost one-fifth of the transcript level changes induced by lncRNAs are dependent on miRNAs that are highly abundant in mESCs. We validated these findings experimentally by temporally profiling transcriptome-wide changes in gene expression following the loss of miRNA biogenesis in mESCs. Following the depletion of miRNAs, we found that >50% of lncRNAs and their miRNA-dependent mRNA targets were up-regulated coordinately, consistent with their interaction being miRNA-mediated. These lncRNAs are preferentially located in the cytoplasm, and the response elements for miRNAs they share with their targets have been preserved in mammals by purifying selection. Lastly, miRNA-dependent mRNA targets of each lncRNA tended to share common biological functions. Post-transcriptional miRNA-mediated crosstalk between lncRNAs and mRNA, in mESCs, is thus surprisingly prevalent, conserved in mammals, and likely to contribute to critical developmental processes.

Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse.

Protein-coding genes evolve at different rates, and the influence of different parameters, from gene size to expression level, has been extensively studied. While in yeast gene expression level is the major causal factor of gene evolutionary rate, the situation is more complex in animals. Here we investigate these relations further, especially taking in account gene expression in different organs as well as indirect correlations between parameters. We used RNA-seq data from two large datasets, covering 22 mouse tissues and 27 human tissues. Over all tissues, evolutionary rate only correlates weakly with levels and breadth of expression. The strongest explanatory factors of purifying selection are GC content, expression in many developmental stages, and expression in brain tissues. While the main component of evolutionary rate is purifying selection, we also find tissue-specific patterns for sites under neutral evolution and for positive selection. We observe fast evolution of genes expressed in testis, but also in other tissues, notably liver, which are explained by weak purifying selection rather than by positive selection.

Inference of Evolutionary Forces Acting on Human Biological Pathways.

Because natural selection is likely to act on multiple genes underlying a given phenotypic trait, we study here the potential effect of ongoing and past selection on the genetic diversity of human biological pathways. We first show that genes included in gene sets are generally under stronger selective constraints than other genes and that their evolutionary response is correlated. We then introduce a new procedure to detect selection at the pathway level based on a decomposition of the classical McDonald-Kreitman test extended to multiple genes. This new test, called 2DNS, detects outlier gene sets and takes into account past demographic effects and evolutionary constraints specific to gene sets. Selective forces acting on gene sets can be easily identified by a mere visual inspection of the position of the gene sets relative to their two-dimensional null distribution. We thus find several outlier gene sets that show signals of positive, balancing, or purifying selection but also others showing an ancient relaxation of selective constraints. The principle of the 2DNS test can also be applied to other genomic contrasts. For instance, the comparison of patterns of polymorphisms private to African and non-African populations reveals that most pathways show a higher proportion of nonsynonymous mutations in non-Africans than in Africans, potentially due to different demographic histories and selective pressures.

Disassembly of a Medial Transenvelope Structure by Antibiotics during Intracellular Division.

Chlamydiales possess a minimal but functional peptidoglycan precursor biosynthetic and remodeling pathway involved in the assembly of the division septum by an atypical cytokinetic machine and cryptic or modified peptidoglycan-like structure (PGLS). How this reduced cytokinetic machine collectively coordinates the invagination of the envelope has not yet been explored in Chlamydiales. In other Gram-negative bacteria, peptidoglycan provides anchor points that connect the outer membrane to the peptidoglycan during constriction using the Pal-Tol complex. Purifying PGLS and associated proteins from the chlamydial pathogen Waddlia chondrophila, we unearthed the Pal protein as a peptidoglycan-binding protein that localizes to the chlamydial division septum along with other components of the Pal-Tol complex. Together, our PGLS characterization and peptidoglycan-binding assays support the notion that diaminopimelic acid is an important determinant recruiting Pal to the division plane to coordinate the invagination of all envelope layers with the conserved Pal-Tol complex, even during osmotically protected intracellular growth.

Repeated Whole-Genome Duplication, Karyotype Reshuffling, and Biased Retention of Stress-Responding Genes in Buckler Mustard.

Whole-genome duplication (WGD) is usually followed by gene loss and karyotype repatterning. Despite evidence of new adaptive traits associated with WGD, the underpinnings and evolutionary significance of such genome fractionation remain elusive. Here, we use Buckler mustard (Biscutella laevigata) to infer processes that have driven the retention of duplicated genes after recurrent WGDs. In addition to the β- and α-WGD events shared by all Brassicaceae, cytogenetic and transcriptome analyses revealed two younger WGD events that occurred at times of environmental changes in the clade of Buckler mustard (Biscutelleae): a mesopolyploidy event from the late Miocene that was followed by considerable karyotype reshuffling and chromosome number reduction and a neopolyploidy event during the Pleistocene. Although a considerable number of the older duplicates presented signatures of retention under positive selection, the majority of retained duplicates arising from the younger mesopolyploidy WGD event matched predictions of the gene balance hypothesis and showed evidence of strong purifying selection as well as enrichment in gene categories responding to abiotic stressors. Retention of large stretches of chromosomes for both genomic copies supported the hypothesis that cycles of WGD and biased fractionation shaped the genome of this stress-tolerant polypolyloid, promoting the adaptive recruitment of stress-responding genes in the face of environmental challenges.

Recuperação de 241Am de para-raios e detectores de fumaça

A method is described for recovering and purifying 241Am from lightning-conductors and smoke detectors. The method is based on the precipitation of silver, as AgCl, the main impurity, and extraction of americium with TBP. Further purification with ion-exchange resin is also used. The results have shown that by this method the americium is obtained with high purity.

Recuperação de sílica-gel utilizando processos oxidativos avançados: uma alternativa simples e de baixo custo

Silica gel is widely used as adsorbent for isolating and purifying natural compounds. Intensive use and high cost make this process expensive and generate solid residues contaminated with many different organic compounds. In the present work a simple method for recycling silica was investigated, by using Advanced Oxidative Processes. Silica gel was treated with H2O2/solar light and compared with a sample treated by conventional methods (high temperature and oxidation with KMnO4). High temperature treatment changes the structure of the silica and, consequently, the separation efficiency. Oxidation by using KMnO4 requires multiple steps and produces residues, including manganese and oxalic acid. The method using H2O2/solar light to recuperate silica gel does not modify its separation efficiency and is less expensive than the traditional methods. Additionally, HPLC and GC-MS analysis indicate that H2O2/solar light eliminates all residues of the silica gel.

Counter-current Washing of Filter Cakes

The main objective of this thesis was to compare the efficiency of counter-current and co-current filter cake washing techniques. Filter cake washing is a common unit operation which is used in the chemical process industry for improving the recovery of the liquid phase or for purifying the solid phase of the filter cake. Counter-current displacement washing is more difficult to arrange and it requires additional process equipment but the advantage of counter-current method is that the consumption of wash water that is required for achieving certain filter cake purity may be considerably decreased when compared to the co-current washing method. This is true especially for materials that are difficult to wash. The literature part of this thesis consists of a review of filter cake washing in general, including the basic principles of co-current and counter-current techniques, and a description of the structure and operation of a horizontal vacuum belt filter, which is the equipment considered in the experimental part of this thesis. Also the most common cake washing models are introduced. The experiments were performed by washing wheat apatite filter cakes in a laboratory scale vacuum filter by using both co-current and counter-current washing methods. The main results of these tests were the washing curves that relate the purity of the filter cake to the amount of wash liquid used. Comparison between the obtained washing curves showed that both washing methods could be efficiently applied for achieving good washing results. The differences between the wash liquid consumptions in the co-current and counter-current washing methods were found to be surprisingly small but this is most probably explained by the relatively good washing characteristics of the apatite cakes. The washing models introduced in the literature part were compared with the results obtained from the experiments and it was found out that the studied cake washing processes could be described

Purificação e caracterização da beta-lapachona e estudo de estabilidade dos cristais em diferentes condições de armazenamento

The beta-lapachone is a product obtained from the Ipê Roxo tree [Tabebuia avellandae], which has proved its excellent antineoplasic potential acting through a particular mechanism of apoptosis against various cancer types. This study aims at determining the identity card of beta-lapachone by means of physico-chemical and pharmaco-technical characterization. A purifying process has been performed, as well as the isolation of a contaminant, its isomer alpha-lapachone. A stability study was also performed, determining the ideal storing conditions for beta-lapachone, essential for the ongoing pre-formulation studies for obtaining the different classic pharmaceutical forms and modified release systems.

Hydroksihappojen erotus mustalipeästä nanosuodatuksella

Hydroksihapoille on olemassa useita käyttömahdollisuuksia teollisuudessa, joten niiden hyödyntäminen sellunvalmistuksen sivuvirrasta eli mustalipeästä on suuren kiinnostuksen kohteena. Tässä työssä selvitettiin, onko hydroksihappojen erotus ja puhdistus mustalipeästä mahdollista nanosuodatuksella. Kokeellisessa osassa suodatettiin emäksisen mustalipeän lisäksi hapotettua ja jäähdytyskiteytettyä mustalipeää, johon oli lisätty liuotinta. Mustalipeäsuodatuksissa käytettiin viittä erilaista nanosuodatusmembraania (Microdyn Nadir® NP010 ja NP030, Dow Chemical Company NF-90, Woongjin Chemical NE-70 sekä Ge-Osmonics Desal 5 DK). Kirjallisuusosassa käsiteltiin puun sisältämien yhdisteiden kemiallista koostumusta, sellun valmistuksen pääperiaatteita, mustalipeän ja hydroksihappojen ominaisuuksia sekä hydroksihappojen käyttömahdollisuuksia. Lisäksi tarkasteltiin erilaisia hydroksihappojen erotusmenetelmiä, nanosuodatuksen teoriaa ja prosessiin sopivan membraanin valintakriteerejä. Työn kokeellisessa osassa tutkittiin emäksisen mustalipeän monivaiheisen nanosuodatuksen tehokkuutta hydroksihappojen erotuksessa. Hapotetun ja jäähdytyskiteytetyn mustalipeän suodatuskokeissa tutkittiin erityyppisten membraanien erotuskykyä sekä syötön liuotinlisäyksen vaikutusta hydroksihappojen erottumiseen. Lisäksi tarkasteltiin membraanien kestävyyttä ja foulaantumista suodatusolosuhteissa. Työn tulokset osoittivat, että hydroksihappoja voidaan fraktioida mustalipeästä nanosuodatuksella. Hydroksihappojen fraktiointiin vaikuttaa merkittävästi mustalipeässä käytetyn liuottimen läsnäolo sekä suodatuspaine. Lisäksi koetulosten perusteella havaittiin, että monivaiheisella nanosuodatuksella hydroksihapot läpäisevät membraanin ja permeaattiin saavutetaan puhtaampi happojae.

Lannoitetehtaan prosessivesien käsittelyvaihtoehtojen soveltuvuuden arviointi

Phosphorus and nitrogen cause eutrophication of water bodies, causing severe damage to the ecosystem. Eutrophication of the waters causes oxygen depletion, which in turn increases fish mortality, releasing toxins in waters. The released toxins can cause damage to animals and humans, which is the reason in many countries to set emission limits for waste water. Nutrients exist naturally, but due to human activities there is high nutrient leaching to water bodies. Human activity is one of the main reasons to the eutrophication. The aim of this thesis was to estimate the suitability of different water treatment options for Yara Finland’s fertilizer plant’s process waters in Siilinjärvi. The fertilizer plant process waters are high concentrate and especially nitrogen concentrations are high, which bring challenge to the treatment. At the theoretical part was investigated conventional and as well advanced wastewater treatment methods like reverse osmosis, adsorption and ion exchange. Beside different treatment methods corporate environmental requirements, responsibility and strategies were researched. At the empirical part of the thesis the goal was to find out possibil-ities to intensify the efficiency of purification at lamella clarifier with chemical precipitation. In addition possibility to use already existing chemical purifying plant for process waters was estimated. As a result of the research Yara has a possibility to intensify lamella clarifier’s action by addi-tion of calcium hydroxide and thus to obtain the phosphorus and fluorine to precipitate out of the water. But in practice this would be too expensive. It is possible to eliminate nitrogen compounds by adsorption or ammonia stripping, both methods requires additional testing. It is possible to process waters in chemical purifying plant, if ammonium nitrogen has been reduced before. Reverse osmosis is possible to exploit for the phosphoric acid plant’s waters.

Platinaryhmän metallien talteenotto

Tässä työssä on selvitetty platinaryhmän metallien eli platinan, palladiumin, iridiumin, osmiumin, rhodiumin ja ruteniumin talteenottoa. Ensiksi on kerrottu jokaisen metallin kemiallisia ja fyysisiä ominaisuuksia, jonka jälkeen on perehdytty malmin jalostusprosessiin aina ensimmäisistä analyyseistä lopputuotteen, eli puhtaan metallin valmistamiseen. Sen jälkeen on pohdittu platinametallien kierrättämistä sekä fissiosta saatavien platinametallien kannattavuutta ja talteenottomahdollisuuksia.

Purification of bovine pancreatic glucagon as a by-product of insulin production

A process for purifying bovine pancreatic glucagon as a by-product of insulin production is described. The glucagon-containing supernatant from the alkaline crystallization of insulin was precipitated using ammonium sulfate and isoelectric precipitation. The isoelectric precipitate containing glucagon was then purified by ion-exchange chromatography on Q-Sepharose FF, gel filtration on Sephadex G-25 and ion-exchange chromatography on S-Sepharose FF. A pilot scale test was performed with a recovery of 87.6% and a purification factor of 8.78 for the first chromatographic step, a recovery of 75.1% and a purification factor of 3.90 for the second, and a recovery of 76.2% and a purification factor of 2.36 for the last one. The overall yield was 50%, a purification factor of 80.8 was obtained and the fraction containing active glucagon (suitable for pharmaceutical preparations) was 84% pure as analyzed by HPLC

Bone morphogenetic proteins: from structure to clinical use

Bone morphogenetic proteins (BMPs) are multi-functional growth factors belonging to the transforming growth factor ß superfamily. Family members are expressed during limb development, endochondral ossification, early fracture, and cartilage repair. The activity of BMPs was first identified in the 1960s but the proteins responsible for bone induction were unknown until the purification and cloning of human BMPs in the 1980s. To date, about 15 BMP family members have been identified and characterized. The signal triggered by BMPs is transduced through serine/threonine kinase receptors, type I and II subtypes. Three type I receptors have been shown to bind BMP ligands, namely: type IA and IB BMP receptors and type IA activin receptors. BMPs seem to be involved in the regulation of cell proliferation, survival, differentiation and apoptosis, but their hallmark is their ability to induce bone, cartilage, ligament, and tendon formation at both heterotopic and orthotopic sites. This suggests that, in the future, they may play a major role in the treatment of bone diseases. Several animal studies have illustrated the potential of BMPs to enhance spinal fusion, repair critical-size defects, accelerate union, and heal articular cartilage lesions. Difficulties in producing and purifying BMPs from bone tissue have prompted the attempts made by several laboratories, including ours, to express these proteins in the recombinant form in heterologous systems. This review focuses on BMP structure, molecular mechanisms of action and significance and potential applications in medical, dental and veterinary practice for the treatment of cartilage and bone-related diseases.