Alai! Alai! - a new species of the Gloydius halys (Pallas, 1776) complex (Viperidae, Crotalinae), including a brief review of the complex

During a scientific field expedition to the Alai-Pamir range five specimens of the genus Gloydius have been collected in the larger Alai. A morphological and genetical examination of the specimens has shown that they are part of the G. halys complex, but represent a new taxon which is characterized by the following unique character combination: It is a slender and moderately stout small snake, up to 479 mm total length. The head has nine symmetrical plates on the upper head, 7 supralabial and 8-9 infralabial scales. Body scales in 20-22 rows around midbody, 143-156 ventral and 35-45 usually paired subcaudal scales. The cloacal plate not divided. The general coloration consists of various different tones of olive, tan and brown, having a distinct head, but an indistinct body pattern with, excluding the tail, 26-29 transverse crossbands, which are not extending to the sides of the body. The haplotype network shows the new species within the G. halys complex and close related to both, G. h. halys and G. h. caraganus. So far the new described species is only known from the Alai range. However, various Gloydius specimens are found in Kyrgyzstan and because of the complicated taxonomy those specimens have to re-identified to clarify their status and the status of the new species.

Substâncias húmicas aquáticas: fracionamento molecular e caracterização de rearranjos internos após complexação com íons metálicos

The aquatic humic substances (AHS) investigated in this study were conventionally isolated from Rio Negro waters - Amazonas State/Brazil by means of the collector XAD 8. A special five-stage tangential-flow ultrafiltration device was used for analytical fractionation of AHS. The fractionation patterns (6 fractions each) showed that metal traces remaining in AHS after their XAD 8 isolation have different size distributions. For instance, the major percentage of traces of Ni, Cu, Zn, Cd and Pb (determined using ICP-AES) was preferably complexed by molecules with relatively high molecular size (30-100 kDa) and the following complexation order was characterized: F2 >> F1 = F4 = F5 > F3 > F6. Moreover, the species formed between AHS and metals prepared by spiking, showed distribution patterns changing as a function of the complexation time (ageing process), indicating a slow transformation process and an inner rearrangements in the binding sites within the AHS molecules.

Genotypic comparison of Pantoea agglomerans plant and clinical strains

Pantoea agglomerans strains are among the most promising biocontrol agents for avariety of bacterial and fungal plant diseases, particularly fire blight of apple and pear. However, commercial registration of P. agglomerans biocontrol products is hampered because this species is currently listed as a biosafety level 2 (BL2) organism due to clinical reports as an opportunistichuman pathogen. This study compares plant-origin and clinical strains in a search for discriminating genotypic/phenotypic markers using multi-locus phylogenetic analysis and fluorescent amplified fragment length polymorphisms (fAFLP) fingerprinting.Results: Majority of the clinical isolates from culture collections were found to be improperly designated as P. agglomerans after sequence analysis. The frequent taxonomic rearrangements underwent by the Enterobacter agglomerans/Erwinia herbicola complex may be a major problem in assessing clinical associations within P. agglomerans. In the P. agglomerans sensu stricto (in the stricter sense) group, there was no discrete clustering of clinical/biocontrol strains and no marker was identified that was uniquely associated to clinical strains. A putative biocontrol-specific fAFLP marker was identified only in biocontrol strains. The partial ORF located in this band corresponded to an ABC transporter that was found in all P. agglomerans strains. Conclusion: Taxonomic mischaracterization was identified as a major problem with P.agglomerans, and current techniques removed a majority of clinical strains from this species. Although clear discrimination between P. agglomerans plant and clinical strains was not obtained with phylogenetic analysis, a single marker characteristic of biocontrol strains was identified whichmay be of use in strain biosafety determinations. In addition, the lack of Koch's postulate fulfilment, rare retention of clinical strains for subsequent confirmation, and the polymicrobial nature of P. agglomerans clinical reports should be considered in biosafety assessment of beneficial strains in this species

Water circulations for effective bleaching of high-brightness mechanical pulps

The amount of water available is usually restricted, which leads to a situation where a complete understanding of the process, including water circulations and the influence of water components, is essential. The main aim of this thesis was to clarify the possibilities for the efficient use of residual peroxide by means of water circulation rearrangements. Rearranging water circulations and the reduction of water usage may cause new problems, such as metal induced peroxide decomposition that needs to be addressed. This thesis introduces theoretical methods of water circulations to combine two variables; effective utilization of residual peroxide and avoiding manganese in the alkaline peroxide bleaching stage. Results are mainly based on laboratory and mill site experiments concerning the utilization of residual peroxide. A simulation model (BALAS) was used to evaluate the manganese contents and residual peroxide doses. It was shown that with optimum recirculation of residual peroxide the brightness can be improved or chemical costs can be decreased. From the scientific perspective, it was also very important to discover that recycled peroxide was more effective pre-bleaching agent compared to fresh peroxide. This can be due to the organic acids i.e. per acetic acid in wash press filtrate that have been formed in alkaline bleaching stage. Even short retention time was adequate and the activation of residual peroxide using sodium hydroxide was not necessary. There are several possibilities for using residual peroxide in practice regarding bleaching. A typical modern mechanical pulping process line consist of defibering, screening, a disc filter, a bleach press, high consistency (HC) peroxide bleaching and a wash press. Furthermore there usually is not a particular medium consistency (MC) pre-bleaching stage that includes additional thickening equipment. The most advisable way to utilize residual peroxide in this kind of process is to recycle the wash press filtrate to the dilution of disc filter pulp (low MC pre-bleaching stage). An arrangement such as this would be beneficial in terms of the reduced convection of manganese to the alkaline bleaching stage. Manganese originates from wood material and will be removed to the water phase already in the early stages of the process. Recycling residual peroxide prior to the disc filter is not recommended because of low consistencies. Regarding water circulations, the novel point of view is that, it would be beneficial to divide water circulations into two sections and the critical location for the division is the disc filter. Both of these two sections have their own priority. Section one before the disc filter: manganese removal. Section two after the disc filter: brightening of pulp. This division can be carried out if the disc filter pulp is diluted only by wash press filtrate before the MC storage tower. The situation is even better if there is an additional press after the disc filter, which will improve the consistency of the pulp. This has a significant effect on the peroxide concentration in the MC pre-bleaching stage. In terms of manganese content, it is essential to avoid the use of disc filter filtrate in the bleach press and wash press showers. An additional cut-off press would also be beneficial for manganese removal. As a combination of higher initial brightness and lower manganese content, the typical brightness increase varies between approximately 0.5 and 1% ISO units after the alkaline peroxide bleaching stage. This improvement does not seem to be remarkable, but as it is generally known, the final brightness unit is the most expensive and difficult to achieve. The estimation of cost savings is not unambiguous. For example in GW/TMP mill case 0.6% ISO units higher final brightness gave 10% savings in the costs of bleaching chemicals. With an hypothetical 200 000 ton annual production, this means that the mill could save in the costs of bleaching chemicals more than 400 000 euros per year. In general, it can be said that there were no differences between the behavior of different types of processes (GW, PGW, TMP and BCTMP). The enhancement of recycling gave a similar response in all cases. However, we have to remember that the utilization of residual peroxide in older mills depends a great deal on the process equipment, the amount of water available and existing pipeline connections. In summary, it can be said that processes are individual and the same solutions cannot be applied to all cases.

The Structural Basis for inorganic Pyrophosphatase Catalysis and Regulation

Inorganic pyrophosphatases (PPases) are essential enzymes for every living cell. PPases provide the necessary thermodynamic pull for many biosynthetic reactions by hydrolyzing pyrophosphate. There are two types of PPases: integral membrane-bound and soluble enzymes. The latter type is divided into two non-homologous protein families, I and II. Family I PPases are present in all kingdoms of life, whereas family II PPases are only found in prokaryotes, including archae. Family I PPases, particularly that from Saccharomyces cerevisiae, are among the most extensively characterized phosphoryl transfer enzymes. In the present study, we have solved the structures of wild-type and seven active site variants of S. cerevisiae PPase bound to its natural metal cofactor, magnesium ion. These structures have facilitated derivation of the complete enzyme reaction scheme for PPase, fulfilling structures of all the reaction intermediates. The main focus in this study was on a novel subfamily of family II PPases (CBSPPase) containing a large insert formed by two CBS domains and a DRTGG domain within the catalytic domain. The CBS domain (named after cystathionine beta-synthase in which it was initially identified) usually occurs as tandem pairs with two or four copies in many proteins in all kingdoms of life. The structure formed by a pair of CBS domains is also known as a Bateman domain. CBS domains function as regulatory units, with adenylate ligands as the main effectors. The DRTGG domain (designated based on its most conserved residues) occurs less frequently and only in prokaryotes. Often, the domain co-exists with CBS domains, but its function remains unknown. The key objective of the current study was to explore the structural rearrangements in the CBS domains induced by regulatory adenylate ligands and their functional consequences. Two CBS-PPases were investigated, one from Clostridium perfringens (cpCBS-PPase) containing both CBS and DRTGG domains in its regulatory region and the other from Moorella thermoacetica (mt CBS-PPase) lacking the DRTGG domain. We additionally constructed a separate regulatory region of cpCBS-PPase (cpCBS). Both full-length enzymes and cpCBS formed homodimers. Two structures of the regulatory region of cpCBS-PPase complexed with the inhibitor, AMP, and activator, diadenosine tetraphosphate, were solved. The structures were significantly different, providing information on the structural pathway from bound adenylates to the interface between the regulatory and catalytic parts. To our knowledge, these are the first reported structures of a regulated CBS enzyme, which reveal large conformational changes upon regulator binding. The activator-bound structure was more open, consistent with the different thermostabilities of the activator- and inhibitor-bound forms of cpCBS-PPase. The results of the functional studies on wild-type and variant CBS-PPases provide support for inferences made on the basis of structural analyses. Moreover, these findings indicate that CBS-PPase activity is highly sensitive to adenine nucleotide distribution between AMP, ADP and ATP, and hence to the energy level of the cell. CBS-PPase activity is markedly inhibited at low energy levels, allowing PPi energy to be used for cell survival instead of being converted into heat.

The genetics of behaviour and other adaptive traits in nine-spined sticklebacks (Pungitius pungitius)

One of the main goals in current evolutionary biology research is to identify genes behind adaptive phenotypic variations. The advances in genomic technologies have made it possible to identify genetic loci behind these variations, also concerning non-model species. This thesis investigates the genetics of the behaviour and other adaptive traits of the nine-spined stickleback (Pungitius pungitius) through the application of different genetic approaches. Fennoscandian nine-spined stickleback populations express large phenotypical differences especially in behaviour, life –history traits and morphology. However the underlying genetic bases for these phenotypical differences have not been studied in detail. The results of the project will lay the foundation for further genetics studies and provide valuable information for our understanding of the genetics of the adaptive divergence of the nine-spined stickleback. A candidate gene approach was used to develop microsatellite markers situating close to candidate genes for behaviour in the nine-spined stickleback. Altogether 13 markers were developed and these markers were used in the subsequent studies with the anonymous random markers and physiologically important gene markers which are already currently available for nine-spined sticklebacks. It was shown that heterozygosity correlated with behaviour in one of the marine nine-spined stickleback populations but with contrasting effects: correlations with behaviour were negative when using physiological gene markers and positive with random markers. No correlation was found between behavioural markers and behaviour. From the physiological gene markers, a strong correlation was found between osmoregulation-related gene markers and behaviour. These results indicate that both local (physiological) and general (random) effects are important in the shaping of behaviour and that heterozygosity– behaviour correlations are population dependent. In this thesis a second linkage map for nine-spined sticklebacks was constructed. Compared to the earlier nine-spined stickleback linkage map, genomic rearrangements were observed between autosomal (LG7) and sex-determing (LG12) linkage groups. This newly constructed map was used in QTL mapping studies in order to locate genomic regions associated with pelvic structures, behaviour and body size/growth. One major QTL was found for pelvic structures and Pitx1 gene was related to these traits as was predicted from three-spined stickleback studies, but this was in contrast to earlier nine-spined stickleback study. The QTL studies also revealed that behaviour and body size/growth were genetically more complex by having more QTL than pelvic traits. However, in many cases, pelvic structure, body size/growth and behaviour were linked to similar map locations indicating possible pleiotropic effects of genes locating in these QTL regions. Many of the gene related markers resided in the QTL area. In the future, studying these possible candidate genes in depth might reveal the underlying mechanism behind the measured traits.

Karyotype studies in Brazilian species of Lobelia L., subgenus Tupa (Campanulaceae)

Karyotypes of 14 populations including eight species of the genus Lobelia were studied using root tip mitotic metaphases. All populations were tetraploid with 2n = 28 chromosomes. The chromosome base number x = 7 was confirmed for the genus. Karyotype analysis showed that chromosome size varied from 1.05 µm to 2.02 µm with predominance of M and SM chromosome types. The karyotypes were similar among themselves with small intra- and interspecific variations on the size of haploid sets, symmetry indexes and centromere position of some chromosome pairs. These results showed that karyotypes of Brazilian lobelias of the subgenus Tupa were probably due to polyploidy associated with chromosomal rearrangements probably in small chromatin segments.

Chromosome studies in some Stevia. Cav. (Compositae) species from Southern Brazil

Karyotypes of six species of the genus Stevia from Southern Brazil were studied, utilizing root tip metaphases. All species were diploid with 2n = 22 chromosomes. It was possible to identify each species by chromosome morphology. The basic chromosome number for Brazilian species of Stevia is X = 11. This number is also found in almost all South American species. We suggest that in Stevia there is an evolutionary trend toward chromosomal rearrangement, caused mainly by pericentric inversions. It was found that, in addition to aneuploidy and polyploidy, chromosomal rearrangements are common in the tribe Eupatorieae.

Chromosome polymorphism in Ctenomys minutus (Rodentia-Octodontidae)

A sample of 101 specimens of Ctenomys minutus was collected along its geographic range. Eight karyotypes (2n = 42, 45, 46a, 46b, 47, 48, 49 and 50) were found. The chromosome polymorphisms were due to Robertsonian rearrangements and tandem fusions. The distribution of polymorphisms indicated three population blocks: northern (2n = 49 and 50), central (2n = 46a, 47, and 48) and southern (2n = 42, 45, and 46b). These findings suggest that this species is undergoing a speciation process due to geographic isolation.

21-Hydroxylase deficiency in Brazil

We determined the frequency of large rearrangements and point mutations in 130 Brazilian patients with 21-hydroxylase deficiency and correlated genotype with phenotype. The frequency of CYP21 deletions was lower (4.4%) than in most of the previous series described, whereas the frequency of large gene conversions was similar to the frequency reported in the literature (6.6%). The most frequent point mutations were I2 splice (41.8% in salt wasting - SW), I172N (32.6% in simple virilizing - SV) and V281L (40.2% in the late onset form - LO). The frequency of the nine most common point mutations was similar to that reported for other countries. The 93 fully genotyped patients were classified into 3 mutation groups based on the degree of enzymatic activity (A<2%, B @ 2%, C>20%). In group A, 62% of cases presented the SW form; in group B, 96% the SV form, and in group C, 88% the LO form. We diagnosed 80% of the affected alleles after screening for large rearrangements and 15 point mutations. To diagnose these remaining alleles we sequenced the CYP21 gene of one patient with the SV form and identified a heterozygous G->A transition in codon 424. This mutation leads to a substitution of glycine by serine in a conserved region and was also found in a compound heterozygous state in 4 other patients. The mutation G424S presented a linkage disequilibrium with CYP21P and C4A gene deletions and HLA DR17, suggesting a probable founder effect. Search for the G424S mutation in other populations will reveal if it is restricted to the Brazilian patients or if it has a wider ethnic distribution.

Cytosine arabinoside-metabolizing enzyme genes are underexpressed in children with MLL gene-rearranged acute lymphoblastic leukemia

Infant acute lymphoblastic leukemia (IALL) is characterized by mixed lineage leukemia (MLL) gene rearrangements, unique gene expression profiles, poor prognosis, and drug resistance. One exception is cytosine arabinoside (Ara-C) to which IALL cells seem to be more sensitive. We quantified mRNA expression of Ara-C key enzymes in leukemic lymphoblasts from 64 Brazilian ALL children, 15 of them presenting MLL gene rearrangement, and correlated it with clinical and biological features. The diagnosis was based on morphological criteria and immunophenotyping using monoclonal antibodies. MLL gene rearrangements were detected by conventional cytogenetic analysis, RT-PCR and/or fluorescence in situ hybridization. The DCK and HENT1 expression levels were determined by real-time quantitative PCR using SYBR Green I. Relative quantification was made by the standard curve method. The results were analyzed by Mann-Whitney and Fisher exact tests. A P value of £0.05 was considered to be statistically significant. DCK and HENT1 expression levels were significantly lower in children with MLL gene-rearranged ALL compared to children with MLL germ line ALL (P = 0.0003 and 0.03, respectively). Our results differ from previous ones concerning HENT1 mRNA expression that observed a higher expression level in MLL gene-rearranged leukemias. In conclusion, the expression of the genes related to Ara-C metabolism was lower in MLL-positive children in the sample studied, suggesting the presence of population differences in the expression profile of these genes especially for HENT1.

Acute leukemia in early childhood

Acute leukemia in early childhood is biologically and clinically distinct. The particular characteristics of this malignancy diagnosed during the first months of life have provided remarkable insights into the etiology of the disease. The pro-B, CD10 negative immunophenotype is typically found in infant acute leukemia, and the most common genetic alterations are the rearrangements of the MLL gene. In addition, the TEL/AML1 fusion gene is most frequently found in children older than 24 months. A molecular study on a Brazilian cohort (age range 0-23 months) has detected TEL/AML1+ve (N = 9), E2A/PBX1+ve (N = 4), PML/RARA+ve (N = 4), and AML1/ETO+ve (N = 2) cases. Undoubtedly, the great majority of genetic events occurring in these patients arise prenatally. The environmental exposure to damaging agents that give rise to genetic changes prenatally may be accurately determined in infants since the window of exposure is limited and known. Several studies have shown maternal exposures that may give rise to leukemogenic changes. The Brazilian Collaborative Study Group of Infant Acute Leukemia has found that mothers exposed to dipyrone, pesticides and hormones had an increased chance to give birth to babies with infant acute leukemia [OR = 1.48 (95%CI = 1.05-2.07), OR = 2.27 (95%CI = 1.56-3.31) and OR = 9.08 (95%CI = 2.95-27.96)], respectively. This review aims to summarize recent clues that have facilitated the elucidation of the biology of early childhood leukemias, with emphasis on infant acute leukemia in the Brazilian population.

Efficacy of HUMN criteria for scoring the micronucleus assay in human lymphocytes exposed to a low concentration of p,p'-DDT

The cytokinesis-block micronucleus (CBMN) assay is one of the standard cytogenetic tools employed to assess chromosomal damage subsequent to exposure to genotoxic/cytotoxic agents, and is widely applicable to plant, animal and human cells. In the present study, the CBMN assay was used to assess the baseline damage in binuclear human peripheral blood lymphocytes exposed to 25 µg/L p,p'-DDT for 1, 2, 24, and 48 h by measuring the frequency of micronuclei, nucleoplasmic bridges and nuclear buds. These new scoring criteria facilitated the detection of different types of clastogenic and aneugenic effects induced by this type of pollutant. With these criteria, CBMN can also be used to measure nucleoplasmic bridges which are considered to be consequences of chromosome rearrangements and nuclear buds which are biomarkers of altered gene amplification and gene dosage. The total number of micronuclei observed in binuclear human peripheral blood lymphocytes of the exposed samples (ranging from 32 to 47) was significantly greater (P < 0.05) than that detected in the unexposed (0 time) control sample, where the total number of micronuclei was 7. The number of nucleoplasmic bridges and nuclear buds obtained after 24 and 48 h was also significantly (P < 0.05) greater in the samples treated with p,p'-DDT than in the unexposed control samples. Thus, our results confirmed the usefulness of the new criteria applicable for the CBMN assay employed in measuring the DNA damage and its role of a sensitive cytogenetic biomarker.

Low expression of APAF-1XL in acute myeloid leukemia may be associated with the failure of remission induction therapy

Apoptotic protease activating factor 1 (APAF-1) has a critical role in the regulation of apoptosis. In the present study, the mRNA expression analysis of different APAF-1 transcripts (APAF-1S, APAF-1LC, APAF-1LN, and APAF-1XL) was analyzed in bone marrow samples from 37 patients with acute myeloid leukemia (newly diagnosed, with no previous treatment). APAF-1XL and APAF-1LN transcripts (with and without an extra WD-40 repeat region, respectively) were detected in all samples, although the major form expressed was APAF-1XL in 65% of the samples (group 1), while 35% of the samples expressed primarily APAF-1LN (group 2). Only 46% of the patients presented complete remission in response to remission induction therapy (represented by less than 5% marrow blasts and hematological recovery), all but 2 cases being from group 1, 21.6% did not attain complete remission (only 1 case from group 1), and 32.4% of the patients died early. Lower expression of APAF-1XL (APAF-1XL/APAF-1LN ratio <1.2) was associated with a poor response to therapy (P = 0.0005, Fisher exact test). Both groups showed similar characteristics regarding white blood cell counts, cytogenetic data or presence of gene rearrangements associated with good prognosis as AML1-ETO, CBFB-MYH11 and PML/RARA. Since it has been shown that only the isoforms with the extra WD-40 repeat region activate procaspase-9, we suggest that low procaspase-9 activation may also be involved in the deregulation of apoptosis and chemotherapy resistance in acute myeloid leukemia.

Characterization of alpha thalassemic genotypes by multiplex ligation-dependent probe amplification in the Brazilian population

Alpha-thalassemia is the most common inherited disorder of hemoglobin synthesis. Genomic deletions involving the alpha-globin gene cluster on chromosome 16p13.3 are the most frequent molecular causes of the disease. Although common deletions can be detected by a single multiplex gap-PCR, the rare and novel deletions depend on more laborious techniques for their identification. The multiplex ligation-dependent probe amplification (MLPA) technique has recently been used for this purpose and was successfully used in the present study to detect the molecular alterations responsible for the alpha-thalassemic phenotypes in 8 unrelated individuals (3 males and 5 females; age, 4 months to 30 years) in whom the molecular basis of the disease could not be determined by conventional methods. A total of 44 probe pairs were used for MLPA, covering approximately 800 kb from the telomere to the MSLN gene in the 16p13.3 region. Eight deletions were detected. Four of these varied in size from 240 to 720 kb and affected a large region including the entire alpha-globin gene cluster and its upstream regulatory element (alpha-MRE), while the other four varied in size from 0.4 to 100 kb and were limited to a region containing this element. This study is the first in Brazil to use the MLPA method to determine the molecular basis of alpha-thalassemia. The variety of rearrangements identified highlights the need to investigate all cases presenting microcytosis and hypochromia, but without iron deficiency or elevated hemoglobin A2 levels and suggests that these rearrangements may be more frequent in our population than previously estimated.