Pirilänkosken Natura 2000 -alueen hoito- ja käyttösuunnitelma

Pirilänkosken Natura-alue (FI0200045) sijaitsee Satakunnassa Harjavallan kaupungin ja Nakkilan kunnan alueella Harjavallan keskustan välittömässä läheisyydessä. Se muodostuu Kokemäenjoessa sijaitsevan Harjavallan voimalaitoksen alapuolisesta suvannosta ja noin kuuden kilometrin jokiosuudesta sekä sen reunoilla olevista jyrkkään eroosiotörmään syntyneistä rantalehdoista. Alue kuuluu Euroopan yhteisön Natura 2000 – suojelualueverkostoon luontodirektiivin mukaisena SCI-alueena (Sites of Community Importance) Natura-alueen pinta-ala on 147 ha, josta noin 60 prosenttia on vettä. Alueen luontoarvot liittyvät jokiluonnon lisäksi maamme edustavimpiin kuuluviin lehtoihin, jotka ovat säilyneet melko luonnontilaisina. Luontoarvojen säilymisen uhkatekijöinä ovat mm lehtojen heinittyminen ja taimettuminen Jokiluonnon tilaan on aikanaan vaikuttanut Harjavallan voimalaitos ja muut Kokemäenjoen säännöstelyyn vaikuttaneet tekijät Alueella on tärkeä merkitys paikallisena virkistyskäyttö- ja opetuskohteena. Pirilänkosken rannalla kulkee noin viisi kilometriä pitkä Paratiisin-Pirilänkosken luontopolku Alueella harrastetaan aktiivisesti myös kalastusta. Osana Varsinais-Suomen elinkeino-, liikenne- ja ympäristökeskuksen (ELY) johtamaa ja EU:n LIFE -luontorahaston rahoittamaa Kokemäenjoki-LIFE -hanketta alueelle laadittiin hoito- ja käyttösuunnitelma, jonka tavoitteena on ohjata alueen hoitoa ja käyttöä luontoarvojen turvaamiseksi. Suunnitelma tehtiin Varsinais-Suomen ELYn ohjauksessa, ja suunnittelua varten perustettiin työryhmä, joka koottiin eri viranomaistahojen ja käyttäjäryhmien edustajista (alueella kalastavat ja retkeilevät) sekä maanomistajista. Työryhmän tavoitteena oli tunnistaa alueen suojeluun ja käyttöön liittyvät mahdolliset ongelmat ja ristiriidat, ratkaista ja sovittaa niitä. Tämän hoito- ja käyttösuunnitelman aikajänne on 15 vuotta. Suunnitelman tavoitteena on ohjata alueen hoitoa ja käyttöä niin, että alueen luontoarvot turvataan.

The pH-dependent phase distribution of wood pitch components in papermaking processes

Wood contains only a very small amount of lipophilic extractives, commonly known as wood pitch. The pitch is known to cause severe problems in papermaking processes. The amount of pitch in process waters can be decreased by seasoning of the raw material prior to pulping, pulp washing, removal of pitch by flotation, adsorption of pitch onto various mineral surfaces, and retention of pitch to the fibre material by cationic polymers. The aim of this study was to determine the influence of pH on some of the methods used for pitch control. Experiments were performed using laboratory-made wood pitch emulsions with varying pH, salt concentration, hemicellulose concentration and pitch composition. These emulsions were used to study the phase distribution of resin and fatty acids, the colloidal stability of pitch with and without steric stabilisation by galactoglucomannans, and the interactions between wood pitch and mineral particles. Purification of unbleached and peroxidebleached mill process water was performed by froth flotation in combination with a foaming agent. The distribution of resin and fatty acids (RFAs) between colloidal pitch droplets and the water phase was very dependent on pH. At pH 3, almost all of the RFAs were attached to the pitch droplets, while increasing the pH led to increasing concentration of dissolved RFAs in the water phase. The presence of salt shifted the release of RFAs towards higher pH, while lower ratio of neutral pitch in the emulsion resulted in release of RFAs at lower pH. It was also seen that the dissolution and adsorption of RFAs at sudden pHchanges takes place very quickly. Colloidal pitch was more stable against electrolyte-induced aggregation at higher pH, due to its higher anionic charge. The concentration of cationic polymers needed to aggregate colloidal pitch also increased with increasing pH. The surface characteristics of solid particles, such as amount of charged groups, were very important for understanding their interactions with colloidal wood pitch. Water-soluble galactoglucomannans stabilised the colloidal pitch sterically against aggregation, but could not completely prevent interactions between wood pitch and hydrophilic particles. Froth flotation of unbleached and peroxidebleached process water showed that the pitch could be removed more effectively and selectively at low pH, compared to at neutral pH. The pitch was removed more effectively, using lower concentrations of foaming agent, from peroxide-bleached water than from unbleached water. The results show that pH has a major impact on various pulping and papermaking processes. It determines the anionic charge of the colloidal pitch and the solubility of certain pitch components. Because of this, the pH influences the effectiveness of pitch retention and removal of pitch. The results indicate that pitch problems could be diminished by acknowledging the importance of pH in various papermaking processes.

Paimionlahden Natura 2000 -alueen hoito- ja käyttösuunnitelma

Paimionlahden Natura-alue (FI0200036) sijaitsee Paimion kaupungissa pitkän ja kapean lahden perukassa Paimionjoen suulla. Paimionlahti kuuluu Euroopan yhteisön Natura 2000 -verkostoon EU:n ns. lintudirektiivin perusteella eli linnustonsuojelualueena (SPA = Special Protection Area). Natura-alue kattaa lähes kokonaisuudessaan Paimionlahden perän lintuvesiensuojeluohjelmaan kuuluvan alan. Natura-alue on pinta-alaltaan 221 ha, josta maapinta-alaa on 115 ha. Paimionlahden tärkeimmät luonnonsuojelulliset arvot perustuvat pesivään ja levähtävään linnustoon sekä tiukasti suojeltavan meriuposkuoriaisen esiintymiseen. Alue kuuluu linnuston perusteella kansalliseen ja eurooppalaiseen suojelualueverkostoon. Alueen luontoarvojen säilymisen haasteena on Paimionjoesta tuleva ravinne- ja kiintoainekuormitus, vesistön rehevöityminen, vesistörakentaminen, ranta- ja vesialueiden umpeenkasvu ja vieraslajit. Alueella on myös tärkeä merkitys paikallisten ihmisten virkistyskäyttöalueena. Osana Varsinais-Suomen elinkeino-, liikenne- ja ympäristökeskuksen (ELY-keskus) vastuualueen johtamaa ja Euroopan maatalouden kehittämisen maatalousrahaston tukemaa vesien ja luonnonhoidon alueellinen ja paikallinen toteuttaminen Lounais-Suomen vesistö- alueilla -hanketta (VELHO) alueelle laadittiin hoito- ja käyttösuunnitelma, jonka tavoitteena on ohjata alueen hoitoa ja käyttöä luontoarvojen turvaamiseksi. Suunnitelma tehtiin Varsinais-Suomen ELY-keskuksen ohjauksessa. Suunnittelua varten perustettiin suunnitteluryhmä, joka koottiin eri viranomaistahojen ja käyttäjäryhmien edustajista sekä maanomistajista. Suunnitteluryhmän tavoitteena oli tunnistaa alueen suojeluun ja käyttöön liittyvät mahdolliset ongelmat ja ristiriidat, ratkaista ja sovittaa niitä. Tämän hoito- ja käyttösuunnitelman aikajänne on 15 vuotta. Suunnitelman tavoitteena on ohjata alueen hoitoa ja käyttöä niin, että alueen luontoarvot turvataan.

Viurilanlahden Natura 2000 -alueen hoito- ja käyttösuunnitelma

Viurilanlahden Natura-alue (FI0200027) sijaitsee Salossa Halikonlahden pohjoisosassa, ja se muodostuu kolmesta toisistaan erillään olevasta osasta: Viurilanlahdesta, Jokiniemenlahdesta ja siihen liittyvästä Rauvolanselästä itärantoineen sekä Kaijanlammesta. Natura-alueeseen sisältyy ranta- ja vesialueiden lisäksi Salon Veden keskusjätevedenpuhdistamon alueita ja jonkin verran peltoja. Alue kuuluu Euroopan yhteisön Natura 2000 -verkostoon lintudirektiivin perusteella eli se on linnustonsuojelualue eli SPA-alue (Special Protection Area). Viurilanlahden Natura-alue on osittain päällekkäin Vaisakon Natura-alueen (FI0200125) kanssa, joka on luontodirektiivin mukainen SCI-alue (Sites of Community Importance). Natura-alueen pinta-ala on 628 ha, josta vesialaa on noin 400 ha. Viurilanlahden tärkeimmät luonnonsuojelulliset arvot perustuvat alueella pesivään ja levähtävään linnustoon. Luontoarvojen säilymisen haasteina ovat vesistökuormitus, rantojen ja vesialueen umpeenkasvu ja mataloituminen sekä vieraslajit. Viurilanlahdella on tärkeä merkitys myös virkistyskäyttöalueena. Osana Varsinais-Suomen elinkeino-, liikenne- ja ympäristökeskuksen (ELY-keskus) vastuualueen johtamaa ja Euroopan maatalouden kehittämisen maatalousrahaston tukemaa vesien ja luonnonhoidon alueellinen ja paikallinen toteuttaminen Lounais-Suomen vesistöalueilla -hanketta (VELHO) alueelle laadittiin hoito- ja käyttösuunnitelma, jonka tavoitteena on ohjata alueen hoitoa ja käyttöä luontoarvojen turvaamiseksi. Suunnitelma tehtiin Varsinais-Suomen ELY-keskuksen ohjauksessa. Suunnittelua varten perustettiin suunnitteluryhmä, joka koottiin eri viranomaistahojen ja käyttäjäryhmien edustajista sekä maanomistajista. Suunnitteluryhmän tavoitteena oli tunnistaa alueen suojeluun ja käyttöön liittyvät mahdolliset ongelmat ja ristiriidat, ratkaista ja sovittaa niitä. Tämän hoito- ja käyttösuunnitelman aikajänne on 15 vuotta. Suunnitelman tavoitteena on ohjata alueen hoitoa ja käyttöä niin, että alueen luontoarvot turvataan.

Artificial Ribonucleases: Oligonucleotides Conjugated with Metal Ion Chelates of Azacrowns

Ribonucleic acid (RNA) has many biological roles in cells: it takes part in coding, decoding, regulating and expressing of the genes as well as has the capacity to work as a catalyst in numerous biological reactions. These qualities make RNA an interesting object of various studies. Development of useful tools with which to investigate RNA is a prerequisite for more advanced research in the field. One of such tools may be the artificial ribonucleases, which are oligonucleotide conjugates that sequence-selectively cleave complementary RNA targets. This thesis is aimed at developing new efficient metal-ion-based artificial ribonucleases. On one hand, to solve the challenges related to solid-supported synthesis of metal-ion-binding conjugates of oligonucleotides, and on the other hand, to quantify their ability to cleave various oligoribonucleotide targets in a pre-designed sequence selective manner. In this study several artificial ribonucleases based on cleaving capability of metal ion chelated azacrown moiety were designed and synthesized successfully. The most efficient ribonucleases were the ones with two azacrowns close to the 3´- end of the oligonucleotide strand. Different transition metal ions were introduced into the azacrown moiety and among them, the Zn2+ ion was found to be better than Cu2+ and Ni2+ ions.

TP53 mutations and loss of heterozygosity of chromosome 17 in colorectal tumors

The incidence of TP53 point mutations and loss of heterozygosity (LOH) of chromosome 17 in colorectal tumors was determined in a group of Brazilian patients. We screened DNA samples from tumors and distal normal mucosa of 39 patients with colorectal cancer, for TP53 mutations by PCR-SSCP (single-strand conformation polymorphism) analysis. Chromosome 17 LOH was investigated using six PCR-based polymorphic markers and one VNTR probe. TP53 mutations were demonstrated in 15/39 of the cases. Mutations were distributed among all exons examined (five to eight), the majority of them being G/C to A/T transitions. LOH of chromosome 17p and 17q was detected in 70 and 46% of the tumors, respectively. There was a significant association between TP53 mutations and LOH in chromosome 17p (P = 0.0035) and 17q (P = 0.03). Although no correlation was observed between TP53 genetic alterations and clinical/ pathological characteristics, the association of TP53 mutations with loss of both chromosome 17 arms may indicate that TP53 inactivation provokes an unstable phenotype in tumor cells in colorectal tumors.

Mutations of androgen receptor gene in Brazilian patients with male pseudohermaphroditism

We describe the identification of point mutations in the androgen receptor gene in five Brazilian patients with female assignment and behavior. The eight exons of the gene were amplified by the polymerase chain reaction (PCR) and analyzed for single-strand conformation polymorphism (SSCP) to detect the mutations. Direct sequencing of the mutant PCR products demonstrated single transitions in three of these cases: G®A in case 1, within exon C, changing codon 615 from Arg to His; G®A in case 2, within exon E, changing codon 752 from Arg to Gln, and C®T in case 3, within exon B, but without amino acid change.

Photodynamic DNA damage induced by phycocyanin and its repair in Saccharomyces cerevisiae

In the present study, we analyzed DNA damage induced by phycocyanin (PHY) in the presence of visible light (VL) using a set of repair endonucleases purified from Escherichia coli. We demonstrated that the profile of DNA damage induced by PHY is clearly different from that induced by molecules that exert deleterious effects on DNA involving solely singlet oxygen as reactive species. Most of PHY-induced lesions are single strand breaks and, to a lesser extent, base oxidized sites, which are recognized by Nth, Nfo and Fpg enzymes. High pressure liquid chromatography coupled to electrochemical detection revealed that PHY photosensitization did not induce 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) at detectable levels. DNA repair after PHY photosensitization was also investigated. Plasmid DNA damaged by PHY photosensitization was used to transform a series of Saccharomyces cerevisiae DNA repair mutants. The results revealed that plasmid survival was greatly reduced in rad14 mutants, while the ogg1 mutation did not modify the plasmid survival when compared to that in the wild type. Furthermore, plasmid survival in the ogg1 rad14 double mutant was not different from that in the rad14 single mutant. The results reported here indicate that lethal lesions induced by PHY plus VL are repaired differently by prokaryotic and eukaryotic cells. Morever, nucleotide excision repair seems to play a major role in the recognition and repair of these lesions in Saccharomyces cerevisiae.

No evidence for mutations in exons 1, 8 and 18 of the patched gene in sporadic skin lesions of Brazilian patients

There is strong evidence that the patched (PTCH) gene is a gene for susceptibility to the nevoid basal cell carcinoma syndrome. PTCH has also been shown to mutate in both familial and sporadic basal cell carcinomas. However, mutations of the gene seem to be rare in squamous cell carcinomas. In order to characterize the role of the gene in the broader spectrum of sporadic skin malignant and pre-malignant lesions, we performed a polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) analysis of genomic DNA extracted from 105 adult patients (46 females and 59 males). There were 66 patients with basal cell carcinomas, 30 with squamous cell carcinomas, 2 with malignant melanomas and 7 patients with precancerous lesions. Two tissue samples were collected from each patient, one from the central portion of the tumor and another from normal skin. Using primers that encompass the entire exon 1, exon 8 and exon 18, where most of the mutations have been detected, we were unable to demonstrate any band shift. Three samples suspected to present aberrant migrating bands were excised from the gel and sequenced directly. In addition, we sequenced 12 other cases, including tumors and corresponding normal samples. A wild-type sequence was found in all 15 cases. Although our results do not exclude the presence of clonal alterations of the PTCH gene in skin cancers or mutations in other exons that were not screened, the present data do not support the presence of frequent mutations reported for non-melanoma skin cancer of other populations.

Normal expression of IFN-gammaR in four patients with uncommon mycobacterial infection phenotypes

Several primary immunodeficiency diseases affecting the interleukin 12/interferon gamma (IFN-gamma) pathway have been identified, most of them characterized by recurrent and protracted infections produced by intracellular microorganisms, particularly by several species of mycobacteria. In the present study we analyzed the expression of IFN-gamma receptor (IFN-gammaR) and signal transducer and activator of transcription 1 (STAT-1) in 4 children with Mycobacterium tuberculosis infection of uncommon clinical presentation. These molecules were evaluated by flow cytometry and Western blotting in B cells transformed with Epstein-Barr virus and mutations were scanned by single-strand conformational polymorphisms and DNA sequencing. The expression of IFN-gammaR1 was normal in all 4 patients. The genetic analysis of IFN-gammaR1 and IFN-gammaR2 coding sequences did not reveal any mutation. The expression of the STAT-1 molecule was similar in patients and healthy controls; however, when the phosphorylation of this transcription factor in response to IFN-gamma activation was evaluated by Western blot, a significant lower signal was evident in one patient. These data indicate that there are no alterations in the expression or function of the IFN-gammaR chains in these patients. However, the low level of STAT-1 phosphorylation found in one of these patients might be explained by a defect in one of the molecules involved in the signal transduction pathway after IFN-gamma interacts with its receptor. In the other three patients the inability to eliminate the mycobacteria may be due to a defect in another effector mechanism of the mononuclear phagocytes.

Lack of evidence for mutations or deletions in the CDKN2A/p16 and CDKN2B/p15 genes of Brazilian neuroblastoma patients

Neuroblastoma, the most common extracranial tumor in childhood, has a wide spectrum of clinical and biological features. The loss of heterozygosity within the 9p21 region has been reported as a prognostic factor. Two tumor suppressor genes located in this region, the CDKN2B/p15 and CDKN2A/p16 (cyclin-dependent kinase inhibitors 2B and 2A, respectively) genes, play a critical role in cell cycle progression and are considered to be targets for tumor inactivation. We analyzed CDKN2B/p15 and CDKN2A/p16 gene alterations in 11 patients, who ranged in age from 4 months to 13 years (male/female ratio was 1.2:1). The most frequent stage of the tumor was stage IV (50%), followed by stages II and III (20%) and stage I (10%). The samples were submitted to the multiplex PCR technique for homozygous deletion analysis and to single-strand conformation polymorphism and nucleotide sequencing for mutation analysis. All exons of both genes were analyzed, but no deletion was detected. One sample exhibited shift mobility specific for exon 2 in the CDKN2B/p15 gene, not confirmed by DNA sequencing. Homozygous deletions and mutations are not involved in the inactivation mechanism of the CDKN2B/p15 and CDKN2A/p16 genes in neuroblastoma; however, these two abnormalities do not exclude other inactivation pathways. Recent evidence has shown that the expression of these genes is altered in this disease. Therefore, other mechanisms of inactivation, such as methylation of promoter region and unproperly function of proteins, may be considered in order to estimate the real contribution of these genes to neuroblastoma genesis or disease progression.

Mutations in SRY and WT1 genes required for gonadal development are not responsible for XY partial gonadal dysgenesis

The WT1 transcription factor regulates SRY expression during the initial steps of the sex determination process in humans, activating a gene cascade leading to testis differentiation. In addition to causing Wilms' tumor, mutations in WT1 are often responsible for urogenital defects in men, while SRY mutations are mainly related to 46,XY pure gonadal dysgenesis. In order to evaluate their role in abnormal testicular organogenesis, we screened for SRY and WT1 gene mutations in 10 children with XY partial gonadal dysgenesis, 2 of whom with a history of Wilms' tumor. The open reading frame and 360 bp of the 5' flanking sequence of the SRY gene, and the ten exons and intron boundaries of the WT1 gene were amplified by PCR of genomic DNA. Single-strand conformation polymorphism was initially used for WT1 mutation screening. Since shifts in fragment migration were only observed for intron/exon 4, the ten WT1 exons from all patients were sequenced manually. No mutations were detected in the SRY 5' untranslated region or within SRY open-reading frame sequences. WT1 sequencing revealed one missense mutation (D396N) in the ninth exon of a patient who also had Wilms' tumor. In addition, two silent point mutations were found in the first exon including one described here for the first time. Some non-coding sequence variations were detected, representing one new (IVS4+85A>G) and two already described (-7ATG T>G, IVS9-49 T>C) single nucleotide polymorphisms. Therefore, mutations in two major genes required for gonadal development, SRY and WT1, are not responsible for XY partial gonadal dysgenesis.

The eukaryotic Pso2/Snm1/Artemis proteins and their function as genomic and cellular caretakers

DNA double-strand breaks (DSBs) represent a major threat to the genomic stability of eukaryotic cells. DNA repair mechanisms such as non-homologous end joining (NHEJ) are responsible for the maintenance of eukaryotic genomes. Dysfunction of one or more of the many protein complexes that function in NHEJ can lead to sensitivity to DNA damaging agents, apoptosis, genomic instability, and severe combined immunodeficiency. One protein, Pso2p, was shown to participate in the repair of DSBs induced by DNA inter-strand cross-linking (ICL) agents such as cisplatin, nitrogen mustard or photo-activated bi-functional psoralens. The molecular function of Pso2p in DNA repair is unknown, but yeast and mammalian cell line mutants for PSO2 show the same cellular responses as strains with defects in NHEJ, e.g., sensitivity to ICLs and apoptosis. The Pso2p human homologue Artemis participates in V(D)J recombination. Mutations in Artemis induce a variety of immunological deficiencies, a predisposition to lymphomas, and an increase in chromosomal aberrations. In order to better understand the role of Pso2p in the repair of DSBs generated as repair intermediates of ICLs, an in silico approach was used to characterize the catalytic domain of Pso2p, which led to identification of novel Pso2p homologues in other organisms. Moreover, we found the catalytic core of Pso2p fused to different domains. In plants, a specific ATP-dependent DNA ligase I contains the catalytic core of Pso2p, constituting a new DNA ligase family, which was named LIG6. The possible functions of Pso2p/Artemis/Lig6p in NHEJ and V(D)J recombination and in other cellular metabolic reactions are discussed.

High frequencies of plexiform neurofibromas, mental retardation, learning difficulties, and scoliosis in Brazilian patients with neurofibromatosis type 1

A clinical study of Brazilian patients with neurofibromatosis type 1 (NF1) was performed in a multidisciplinary Neurofibromatosis Program called CEPAN (Center of Research and Service in Neurofibromatosis). Among 55 patients (60% females, 40% males) who met the NIH criteria for the diagnosis of NF1, 98% had more than six café-au-lait patches, 94.5% had axillary freckling, 45% had inguinal freckling, and 87.5% had Lisch nodules. Cutaneous neurofibromas were observed in 96%, and 40% presented plexiform neurofibromas. A positive family history of NF1 was found in 60%, and mental retardation occurred in 35%. Some degree of scoliosis was noted in 49%, 51% had macrocephaly, 40% had short stature, 76% had learning difficulties, and 2% had optic gliomas. Unexpectedly high frequencies of plexiform neurofibromas, mental retardation, learning difficulties, and scoliosis were observed, probably reflecting the detailed clinical analysis methods adopted by the Neurofibromatosis Program. These same patients were screened for mutations in the GAP-related domain/GRD (exons 20-27a) by single-strand conformation polymorphism. Four different mutations (Q1189X, 3525-3526delAA, E1356G, c.4111-1G>A) and four polymorphisms (c.3315-27G>A, V1146I, V1317A, c.4514+11C>G) were identified. These data were recently published.

The P48T germline mutation and polymorphism in the CDKN2A gene of patients with melanoma

CDKN2A has been implicated as a melanoma susceptibility gene in some kindreds with a family history of this disease. Mutations in CDKN2A may produce an imbalance between functional p16ink4a and cyclin D causing abnormal cell growth. We searched for germline mutations in this gene in 22 patients with clinical criteria of hereditary cancer (early onset, presence of multiple primary melanoma or 1 or more first- or second-degree relatives affected) by secondary structural content prediction, a mutation scanning method that relies on the propensity for single-strand DNA to take on a three-dimensional structure that is highly sequence dependent, and sequencing the samples with alterations in the electrophoretic mobility. The prevalence of CDKN2A mutation in our study was 4.5% (1/22) and there was a correlation between family history and probability of mutation detection. We found the P48T mutation in 1 patient with 2 melanoma-affected relatives. The patient descends from Italian families and this mutation has been reported previously only in Italian families in two independent studies. This leads us to suggest the presence of a mutational "hotspot" within this gene or a founder mutation. We also detected a high prevalence (59.1%) of polymorphisms, mainly alleles 500 C/G (7/31.8%) or 540 C/T (6/27.3%), in the 3' untranslated region of exon 3. This result reinforces the idea that these rare polymorphic alleles have been significantly associated with the risk of developing melanoma.