STBCs with Reduced Sphere Decoding Complexity for Two-User MIMO-MAC

In this paper, Space-Time Block Codes (STBCs) with reduced Sphere Decoding Complexity (SDC) are constructed for two-user Multiple-Input Multiple-Output (MIMO) fading multiple access channels. In this set-up, both the users employ identical STBCs and the destination performs sphere decoding for the symbols of the two users. First, we identify the positions of the zeros in the R matrix arising out of the Q-R decomposition of the lattice generator such that (i) the worst case SDC (WSDC) and (ii) the average SDC (ASDC) are reduced. Then, a set of necessary and sufficient conditions on the lattice generator is provided such that the R matrix has zeros at the identified positions. Subsequently, explicit constructions of STBCs which results in the reduced ASDC are presented. The rate (in complex symbols per channel use) of the proposed designs is at most 2/N-t where N-t denotes the number of transmit antennas for each user. We also show that the class of STBCs from complex orthogonal designs (other than the Alamouti design) reduce the WSDC but not the ASDC.

Molecular background of three lethal fetal syndromes

This study identified the molecular defects underlying three lethal fetal syndromes. Lethal Congenital Contracture Syndrome 1 (LCCS1, MIM 253310) and Lethal Arthrogryposis with Anterior Horn Cell Disease (LAAHD, MIM 611890) are fetal motor neuron diseases. They affect the nerve cells that control voluntary muscle movement, and eventually result in severe atrophy of spinal cord motor neurons and fetal immobility. Both LCCS1 and LAAHD are caused by mutations in the GLE1 gene, which encodes for a multifunctional protein involved in posttranscriptional mRNA processing. LCCS2 and LCCS3, two syndromes that are clinically similar to LCCS1, are caused by defective proteins involved in the synthesis of inositol hexakisphosphate (IP6), an essential cofactor of GLE1. This suggests a common mechanism behind these fetal motor neuron diseases, and along with accumulating evidence from genetic studies of more late-onset motor neuron diseases such as Spinal muscular atrophy (SMA) and Amyotrophic lateral sclerosis (ALS), implicates mRNA processing as a common mechanism in motor neuron disease pathogenesis. We also studied gle1-/- zebrafish in order to investigate whether they would be a good model for studying the pathogenesis of LCCS1 and LAAHD. Mutant zebrafish exhibit cell death in their central nervous system at two days post fertilization, and the distribution of mRNA within the cells of mutant zebrafish differs from controls, encouraging further studies. The third lethal fetal syndrome is described in this study for the first time. Cocoon syndrome (MIM 613630) was discovered in a Finnish family with two affected individuals. Its hallmarks are the encasement of the limbs under the skin, and severe craniofacial abnormalities, including the lack of skull bones. We showed that Cocoon syndrome is caused by a mutation in the gene encoding the conserved helix-loop-helix ubiquitous kinase CHUK, also known as IκB kinase α (IKKα). The mutation results in the complete lack of CHUK protein expression. CHUK is a subunit of the IκB kinase enzyme that inhibits NF-κB transcription factors, but in addition, it has an essential, independent role in controlling keratinocyte differentiation, as well as informing morphogenetic events such as limb and skeletal patterning. CHUK also acts as a tumor suppressor, and is frequently inactivated in cancer. This study has brought significant new information about the molecular background of these three lethal fetal syndromes, as well as provided knowledge about the prerequisites of normal human development.

Pietismin kuva - ikkuna yksityiseen hengellisyyteen : Johann Arndtin opetukset pietistisen embleemin perustana

The image of Pietism a window to personal spirituality. The teachings of Johann Arndt as the basis of Pietist emblems The Pietist effect on spiritual images has to be scrutinised as a continuum initiating from the teachings of Johann Arndt who created a protestant iconography that defended the status of pictures and images as the foundation of divine revelation. Pietist artworks reveal Arndtian part of secret, eternal world, and God. Even though modern scholars do not regarded him as a founding father of Pietism anymore, his works have been essential for the development of iconography, and the themes of the Pietist images are linked with his works. For Arndt, the starting point is in the affecting love for Christ who suffered for the humankind. The reading experience is personal and the words point directly at the reader and thus appear as evidence of the guilt of the reader as well as of the love of God. Arndt uses bounteous and descriptive language which has partially affected promoting and picturing of many themes. Like Arndt, Philipp Jakob Spener also emphasised the heart that believes. The Pietist movement was born to oppose detached faith and the lack of the Holy Ghost. Christians touched by the teachings of Arndt and Spener began to create images out of metaphors presented by Arndt. As those people were part of the intelligentsia, it was natural that the fashionable emblematics of the 17th century was moulded for the personal needs. For Arndt, the human heart is manifested as a symbol of soul, personal faith or unbelief as well as an allegory of the burning love for Jesus. Due to this fact, heart emblems were gradually widely used and linked with the love of Christ. In the Nordic countries, the introduction of emblems emanated from the gentry s connections to the Central Europe where emblems were exploited in order to decorate books, artefacts, interiors, and buildings as well as visual/literal trademarks of the intelligentsia. Emblematic paintings in the churches of the castles of Venngarn (1665) and Läckö (1668), owned by Magnus Gabriel De la Gardie, are one of the most central interior paintings preserved in the Nordic countries, and they emphasise personal righteous life. Nonetheless, it was the books by Arndt and the Poet s Society in Nurnberg that bound the Swedish gentry and the scholars of the Pietist movement together. The Finnish gentry had no castles or castle churches so they supported county churches, both in building and in maintenance. As the churches were not private, their iconography could not be private either. Instead, people used Pietist symbols such as Agnus Dei, Cor ardens, an open book, beams, king David, frankincense, wood themes and Virtues. In the Pietist images made for public spaces, the attention is focused on pedagogical, metaphorical, and meaningful presentation as well as concealed statements.

On BCH codes over arbitrary integer rings

Bose-C-Hocquenghem (BCH) atdes with symbols from an arbitrary fhite integer ring are derived in terms of their generator polynomials. The derivation is based on the factohation of x to the power (n) - 1 over the unit ring of an appropriate extension of the fiite integer ring. lke eomtruetion is thus shown to be similar to that for BCH codes over fink flelda.

Hantavirus glycoprotein GN in virion assembly and regulation of interferon response

Hantaviruses have a tri-segmented negative-stranded RNA genome. The S segment encodes the nucleocapsid protein (N), M segment two glycoproteins, Gn and Gc, and the L segment the RNA polymerase. Gn and Gc are co-translationally cleaved from a precursor and targeted to the cis-Golgi compartment. The Gn glycoprotein consists of an external domain, a transmembrane domain and a C-terminal cytoplasmic domain. In addition, the S segment of some hantaviruses, including Tula and Puumala virus, have an open reading frame (ORF) encoding a nonstructural potein NSs that can function as a weak interferon antagonist. The mechanisms of hantavirus-induced pathogenesis are not fully understood but it is known that both hemorrhagic fever with renal syndrome (HFRS) and hantavirus (cardio) pulmonary syndrome (HCPS) share various features such as increased capillary permeability, thrombocytopenia and upregulation of TNF-. Several hantaviruses have been reported to induce programmed cell death (apoptosis), such as TULV-infected Vero E6 cells which is known to be defective in interferon signaling. Recently reports describing properties of the hantavirus Gn cytoplasmic tail (Gn-CT) have appeared. The Gn-CT of hantaviruses contains animmunoreceptor tyrosine-based activation motif (ITAM) which directs receptor signaling in immune and endothelial cells; and contain highly conserved classical zinc finger domains which may have a role in the interaction with N protein. More functions of Gn protein have been discovered, but much still remains unknown. Our aim was to study the functions of Gn protein from several aspects: synthesis, degradation and interaction with N protein. Gn protein was reported to inhibit interferon induction and amplication. For this reason, we also carried out projects studying the mechanisms of IFN induction and evasion by hantavirus. We first showed degradation and aggresome formation of the Gn-CT of the apathogenic TULV. It was reported earlier that the degradation of Gn-CT is related to the pathogenicity of hantavirus. We found that the Gn-CT of the apathogenic hantaviruses (TULV, Prospect Hill virus) was degraded through the ubiquitin-proteasome pathway, and TULV Gn-CT formed aggresomes upon treatment with proteasomal inhibitor. Thus the results suggest that degradation and aggregation of the Gn-CT may be a general property of most hantaviruses, unrelated to pathogenicity. Second, we investigated the interaction of TULV N protein and the TULV Gn-CT. The Gn protein is located on the Golgi membrane and its interaction with N protein has been thought to determine the cargo of the hantaviral ribonucleoprotein which is an important step in virus assembly, but direct evidence has not been reported. We found that TULV Gn-CT fused with GST tag expressed in bacteria can pull-down the N protein expressed in mammalian cells; a mutagenesis assay was carried out, in which we found that the zinc finger motif in Gn-CT and RNA-binding motif in N protein are indispensable for the interaction. For the study of mechanisms of IFN induction and evasion by Old World hantavirus, we found that Old World hantaviruses do not produce detectable amounts of dsRNA in infected cells and the 5 -termini of their genomic RNAs are monophosphorylated. DsRNA and tri-phosphorylated RNA are considered to be critical activators of innate immnity response by interacting with PRRs (pattern recognition receptors). We examined systematically the 5´-termini of hantavirus genomic RNAs and the dsRNA production by different species of hantaviruses. We found that no detectable dsRNA was produced in cells infected by the two groups of the old world hantaviruses: Seoul, Dobrava, Saaremaa, Puumala and Tula. We also found that the genomic RNAs of these Old World hantaviruses carry 5´-monophosphate and are unable to trigger interferon induction. The antiviral response is mainly mediated by alpha/beta interferon. Recently the glycoproteins of the pathogenic hantaviruses Sin Nombre and New York-1 viruses were reported to regulate cellular interferon. We found that Gn-CT can inhibit the induction of IFN activation through Toll-like receptor (TLR) and retinoic acid-inducible gene I-like RNA helicases (RLH) pathway and that the inhibition target lies at the level of TANK-binding kinase 1 (TBK-1)/ IKK epislon complex and myeloid differentiation primary response gene (88) (MyD88) / interferon regulatory factor 7 (IRF-7) complex.

Optimal Receive Antenna Selection in Time-Varying Fading Channels with Practical Training Constraints

Hardware constraints, which motivate receive antenna selection, also require that various antenna elements at the receiver be sounded sequentially to obtain estimates required for selecting the `best' antenna and for coherently demodulating data thereafter. Consequently, the channel state information at different antennas is outdated by different amounts and corrupted by noise. We show that, for this reason, simply selecting the antenna with the highest estimated channel gain is not optimum. Rather, a preferable strategy is to linearly weight the channel estimates of different antennas differently, depending on the training scheme. We derive closed-form expressions for the symbol error probability (SEP) of AS for MPSK and MQAM in time-varying Rayleigh fading channels for arbitrary selection weights, and validate them with simulations. We then characterize explicitly the optimal selection weights that minimize the SEP. We also consider packet reception, in which multiple symbols of a packet are received by the same antenna. New suboptimal, but computationally efficient weighted selection schemes are proposed for reducing the packet error rate. The benefits of weighted selection are also demonstrated using a practical channel code used in third generation cellular systems. Our results show that optimal weighted selection yields a significant performance gain over conventional unweighted selection.

Elämänmuutoksen, jännityksen ja asiantuntijuuden representointi Veikkaus Oy:n mainonnassa vuosina 1970— 2006

Aim of this master's thesis paper for consumer economics, is to research gambling advertisements in Finland over a period of 35 years, from 1970 to 2006. Veikkaus Oy (later Veikkaus), was founded in 1940, as one of the three licensed gambling organizations in Finland. Material for the current research comprised 1494 advertisements published by Veikkaus in newspapers and magazines at that time. Veikkaus has the exclusive licence to organize lotto games, sport games, instant games and other draw games in Finland. The other two operators, The Finnish Slot Machine Association RAY and Fintoto (on-track horse betting), were not included in the current analysis. This study has been completed according to research contract and grand by the Finnish Foundation for Gaming Research (Pelitoiminnan tutkimussäätiö). In general, advertisements reflect surrounding culture and time, and their message is built on stratified meanings, symbols and codes. Advertising draws the viewer's attention, introduces the advertised subject, and finally, affects the individual's consumption habits. However, advertisements not only work on individual level, but also influence public perception of the advertised product. Firstly, in order to assess gambling as a phenomenon, this paper discusses gambling as consumer behaviour, and also reviews history of gambling in Finland. Winning is a major feature of gambling, and dreaming about positive change of life is a centre of most gambling ads. However, perceived excitement through risk of losing can also be featured in gambling ads. Secondly, this study utilizes Veikkaus’ large advertising archives, were advertising data is analyzed by content analysis and the semiotic analysis. Two methods have been employed to support analyzing outcome in a synergistic way. Content analysis helps to achieve accuracy and comprehensiveness. Semiotic analysis allows deeper and more sensitive analysis to emerged findings and occurrences. It is important to understand the advertised product, as advertising is bound to the culture and time. Hence, to analyze advertising, it is important to understand the environment where the ads appear. Content analysis of Veikkaus data discovered the main gambling and principal advertisement style for each.period. Interestingly, nearly half of Veikkaus’ advertisements promoted topic other than “just winning the bet”. Games of change, like Lotto, typically advertised indirectly represented dreams about winning. In the category of skill gambling, features were represented as investment, and the excitement of sporting expertise was emphasized. In addition, there were a number of gambling ads that emphasize social responsibility of Veikkaus as a government guided organization. Semiotic methods were employed to further elaborate on findings of content analysis. Dreaming in the advertisements was represented by the product of symbols, (e.g. cars and homes) that were found to have significance connection with each other. Thus, advertising represents change of life obtained by the winning. Interestingly, gambling ads promoting jackpots were often representing religious symbolisms. Ads promoting social responsibility were found to be the most common during economical depression of the 90’s. Deeper analysis showed that at that time, advertisements frequently represented depression-related meanings, such as unemployment and bank loans. Skill gaming ads were often represented by sports expertise – late 90’s, their number started sky rocketing, and continued increasing until 2006 (when this study ended). One may conclude that sport betting draws its meanings from the relevant consumer culture, and from the rules and features of the betted sport.

Diverse pathways for salicin utilization in Shigella sonnei and Escherichia coli carrying an impaired bgl operon

Utilization of the aryl-beta-glucosides salicin or arbutin in most wild-type strains of E. coli is achieved by a single-step mutational activation of the bgl operon. Shigella sonnei, a branch of the diverse E. coli strain tree, requires two sequential mutational steps for achieving salicin utilization as the bglB gene, encoding the phospho-beta-glucosidase B, harbors an inactivating insertion. We show that in a natural isolate of S. sonnei, transcriptional activation of the gene SSO1595, encoding a phospho-beta-glucosidase, enables salicin utilization with the permease function being provided by the activated bgl operon. SSO1595 is absent in most commensal strains of E. coli, but is present in extra-intestinal pathogens as bgcA, a component of the bgc operon that enables beta-glucoside utilization at low temperature. Salicin utilization in an E. coli bglB laboratory strain also requires a two-step activation process leading to expression of BglF, the PTS-associated permease encoded by the bgl operon and AscB, the phospho-beta-glucosidase B encoded by the silent asc operon. BglF function is needed since AscF is unable to transport beta-glucosides as it lacks the IIA domain involved in phopho-relay. Activation of the asc operon in the Sal(+) mutant is by a promoter-up mutation and the activated operon is subject to induction. The pathway to achieve salicin utilization is therefore diverse in these two evolutionarily related organisms; however, both show cooperation between two silent genetic systems to achieve a new metabolic capability under selection.

Vapaussodan perintö : Valkoisuus paikallisyhteisössä sisältö, ylläpitäjät ja rapautuminen Iisalmessa 1918 1933

Legacy of the Finnish Civil War. White nationalism in a local community - content, supporters and disintegration in Iisalmi 1918 - 1933. Using one local community (Iisalmi) as an example, this study centres around the winners of the 1918 Finnish Civil War, exploring their collectivity its subsequent breakdown during 1918 - 1933. Referring to this collectivity by the methodological concept of white nationalism, the thesis first discusses its origin, content and forms. This is done by elucidating the discourses and symbols that came to constitute central ideological and ritualistic elements of white nationalism. Next, the thesis describes and analyzes fundamental actors of the Finnish civil society (such as White Guard and Lotta Svärd) that maintained white nationalism as a form of counter or parallel hegemony to the integration policy of the 1920s. Also highlighted is the significance of white nationalism as a power broker and an instrument of moral regulation in inter-war Finnish society. A third contribution of this thesis involves presenting a new interpretation of the legacy of the Civil War, i.e., the right-wing radicalism during the years 1919 - 1933. I shall describe attempts of the extreme right (Lapua Movement and IKL, Patriotic People s Movement) to use the white nationalism discourse as a vehicle for their political ambitions, as well as the strong counter-reaction these attempts induced among other middle-class groups. At the core of this research is the concept of white nationalism, whose key elements were the sacrifice of 1918, fatherland under threat and warrior citizenship. Winners of the civil war strove to blend these ideals into a homogenized culture, to which the working class and wavering members of the middle-class were coaxed and pressurized to subscribe. The thesis draws on Anglo-American symbol theories, theory of social identity groups, Antonio Gramsci s concept of cultural hegemony and Stuart Hall s approach to discourse and power.

Mammalian Mat1 subunit of Transcription Factor IIH in gene-specific and general transcription

All protein-encoding genes in eukaryotes are transcribed into messenger RNA (mRNA) by RNA Polymerase II (RNAP II), whose activity therefore needs to be tightly controlled. An important and only partially understood level of regulation is the multiple phosphorylations of RNAP II large subunit C-terminal domain (CTD). Sequential phosphorylations regulate transcription initiation and elongation, and recruit factors involved in co-transcriptional processing of mRNA. Based largely on studies in yeast models and in vitro, the kinase activity responsible for the phosphorylation of the serine-5 (Ser5) residues of RNAP II CTD has been attributed to the Mat1/Cdk7/CycH trimer as part of Transcription Factor IIH. However, due to the lack of good mammalian genetic models, the roles of both RNAP II Ser5 phosphorylation as well as TFIIH kinase in transcription have provided ambiguous results and the in vivo kinase of Ser5 has remained elusive. The primary objective of this study was to elucidate the role of mammalian TFIIH, and specifically the Mat1 subunit in CTD phosphorylation and general RNAP II-mediated transcription. The approach utilized the Cre-LoxP system to conditionally delete murine Mat1 in cardiomyocytes and hepatocytes in vivo and and in cell culture models. The results identify the TFIIH kinase as the major mammalian Ser5 kinase and demonstrate its requirement for general transcription, noted by the use of nascent mRNA labeling. Also a role for Mat1 in regulating general mRNA turnover was identified, providing a possible rationale for earlier negative findings. A secondary objective was to identify potential gene- and tissue-specific roles of Mat1 and the TFIIH kinase through the use of tissue-specific Mat1 deletion. Mat1 was found to be required for the transcriptional function of PGC-1 in cardiomyocytes. Transriptional activation of lipogenic SREBP1 target genes following Mat1 deletion in hepatocytes revealed a repressive role for Mat1apparently mediated via co-repressor DMAP1 and the DNA methyltransferase Dnmt1. Finally, Mat1 and Cdk7 were also identified as a negative regulators of adipocyte differentiation through the inhibitory phosphorylation of Peroxisome proliferator-activated receptor (PPAR) γ. Together, these results demonstrate gene- and tissue-specific roles for the Mat1 subunit of TFIIH and open up new therapeutic possibilities in the treatment of diseases such as type II diabetes, hepatosteatosis and obesity.

A Novel, Balanced, and Energy-Efficient Training Method for Receive Antenna Selection

In receive antenna selection (AS), only signals from a subset of the antennas are processed at any time by the limited number of radio frequency (RF) chains available at the receiver. Hence, the transmitter needs to send pilots multiple times to enable the receiver to estimate the channel state of all the antennas and select the best subset. Conventionally, the sensitivity of coherent reception to channel estimation errors has been tackled by boosting the energy allocated to all pilots to ensure accurate channel estimates for all antennas. Energy for pilots received by unselected antennas is mostly wasted, especially since the selection process is robust to estimation errors. In this paper, we propose a novel training method uniquely tailored for AS that transmits one extra pilot symbol that generates accurate channel estimates for the antenna subset that actually receives data. Consequently, the transmitter can selectively boost the energy allocated to the extra pilot. We derive closed-form expressions for the proposed scheme's symbol error probability for MPSK and MQAM, and optimize the energy allocated to pilot and data symbols. Through an insightful asymptotic analysis, we show that the optimal solution achieves full diversity and is better than the conventional method.

Bear Shields of Plains Indians : Motifs and Meanings

The study is the outcome of two research projects on the North American Indian traditions: the role of the shields within the Plains Indians traditional culture and religion, and the bear ceremonialism of the Native North America, especially the significance of the bear among the Plains Indians. This article-based dissertation includes seven separately published scholar papers, forming Chapters 6 12. The introduction formulates the objectives and frame of reference of the study and the conclusions pulls together its results. The study reconsiders the role of the Plains Indian shields with bear motifs. Such shields are found in rock art, in the Plains Indian s paintings and drawings, and in various collections, the main source material being the shields in European and North American museums. The aim is not only to study shields with bear power motifs and the meanings of the bear, but also to discuss appropriate methods for studying these subjects. There are three major aims of the study: to consider methodical questions in studying Plains Indian shields, to examine the complexity of the Plains Indian shields with the bear power motifs, and to offer new interpretations for the basic meanings of the bear among the Plains Indians and the interrelationship between individualism and collectivism in the Plains Indians visionary art that show bear power motifs on the shields. The study constructs a view on the bear shields taking account of all sources of information available and analysing the shields both as physical artefacts and religious objects from different perspectives, studying them as a part of the ensemble of Plains culture and religious traditions. The bear motifs represented the superhuman power that medicine men and warriors could exploit through visions. For the Plains Indians, the bear was a wise animal from which medicine men could get power for healing but also a dangerous animal from which warriors could get power for warfare. The shields with bear motifs represented the bear powers of the owners of the shields. The bear shield was made to represent the vision, and the principal interpretation of the symbolism was based on the individual experience of spiritual world and its powers. The study argues that the bear shield as personal medicine object is based on wider tribal traditions, and the basic meaning is derived from the collective tradition. This means that the bear seen in vision represented particular affairs and it was represented on the shield surface using conventional ways of traditional artistry. In consequence of this, the bear shields reflect not only the individual experiences of bear power but whole field of tribal traditions that legitimated the experiences and offered acceptable interpretations and conventional modes for the bear symbols.

Triacylglycerol lipolysis is linked to sphingolipid and phospholipid metabolism of the yeast Saccharomyces cerevisiae

Previous work from our laboratory had demonstrated that deletion of TGL3 encoding the major yeast triacylglycerol (TAG) lipase resulted in decreased mobilization of TAG, a sporulation defect and a changed pattern of fatty acids, especially increased amounts of C22:0 and C26:0 very long chain fatty acids in the TAG fraction K. Athenstaedt and G. Daum, J. Biol. Chem. 278 (2003) 23317-23323]. To study a possible link between TAG lipolysis and membrane lipid biosynthesis, we carried out metabolic labeling experiments with wild type and deletion strains bearing defects in the three major yeast TAG lipases, Tgl3p, Tgl4p and Tgl5p. Using H-3]inositol. P-32]orthophosphate, 3H]palmitate and C-14]acetate as precursors for complex lipids we demonstrated that tgl mutants had a lower level of sphingolipids and glycerophospholipids than wild type. ESI-MS/MS analyses confirmed that TAG accumulation in these mutant cells resulted in reduced amounts of phospholipids and sphingolipids. In vitro and in vivo experiments revealed that TAG lipolysis markedly affected the metabolic flux of long chain fatty acids and very long chain fatty acids required for sphingolipid and glycerophospholipid synthesis. Activity and expression level of fatty acid elongases, Elo1p and Elo2p were enhanced as a consequence of reduced TAG lipolysis. Finally, the pattern of phosphatidylcholine, phosphatidylethanolamine and phosphatidylserine molecular species was altered in tgl deletion strain underlining the important role of TAG turnover in maintaining the pool size of these compounds and the remodeling of complex membrane lipids. (C) 2010 Elsevier B.V. All rights reserved.

Molecular Characterization of Viruses Causing the Cassava Brown Streak Disease Epidemic in Eastern Africa

Cassava brown streak disease (CBSD) was described for the first time in Tanganyika (now Tanzania) about seven decades ago. Tanganyika (now Tanzania) about seven decades ago. It was endemic in the lowland areas of East Africa and inland parts of Malawi and caused by Cassava brown streak virus (CBSV; genus Ipomovirus; Potyviridae). However, in 1990s CBSD was observed at high altitude areas in Uganda. The causes for spread to new locations were not known.The present work was thus initiated to generate information on genetic variability, clarify the taxonomy of the virus or viruses associated with CBSD in Eastern Africa as well as to understand the evolutionary forces acting on their genes. It also sought to develop a molecular based diagnostic tool for detection of CBSD-associated virus isolates. Comparison of the CP-encoding sequences of CBSD-associated virus isolates collected from Uganda and north-western Tanzania in 2007 and the partial sequences available in Genbank revealed occurrence of two genetically distinct groups of isolates. Two isolates were selected to represent the two groups. The complete genomes of isolates MLB3 (TZ:Mlb3:07) and Kor6 (TZ:Kor6:08) obtained from North-Western (Kagera) and North-Eastern (Tanga) Tanzania, respectively, were sequenced. The genomes were 9069 and 8995 nucleotides (nt), respectively. They translated into polyproteins that were predicted to yield ten mature proteins after cleavage. Nine proteins were typical in the family Potyviridae, namely P1, P3, 6K1, CI, 6K2, VPg, NIa-Pro, NIb and CP, but the viruses did not contain HC-Pro. Interestingly, genomes of both isolates contained a Maf/HAM1-like sequence (HAM1h; 678 nucleotides, 25 kDa) recombined between the NIb and CP domains in the 3’-proximal part of the genomes. HAM1h was also identified in Euphorbia ringspot virus (EuRSV) whose sequence was in GenBank. The HAM1 gene is widely spread in both prokaryotes and eukaryotes. In yeast (Saccharomyces cerevisiae) it is known to be a nucleoside triphosphate (NTP) pyrophosphatase. Novel information was obtained on the structural variation at the N-termini of polyproteins of viruses in the genus Ipomovirus. Cucumber vein yellowing virus (CVYV) and Squash vein yellowing virus (SqVYV) contain a duplicated P1 (P1a and P1b) but lack the HC-Pro. On the other hand, Sweet potato mild mottle virus (SPMMV), has a single but large P1 and has HC-Pro. Both virus isolates (TZ:Mlb3:07 & TZ:Kor6:08) characterized in this study contained a single P1 and lacked the HC-Pro which indicates unique evolution in the family Potyviridae. Comparison of 12 complete genomes of CBSD-associated viruses which included two genomes characterized in this study, revealed genetic identity of 69.0–70.3% (nt) and amino acid (aa) identities of 73.6–74.4% at polyprotein level. Comparison was also made among 68 complete CP sequences, which indicated 69.0-70.3 and 73.6-74.4 % identity at nt and aa levels, respectively. The genetic variation was large enough for dermacation of CBSD-associated virus isolates into two distinct species. The name CBSV was retained for isolates that were related to CBSV isolates available in database whereas the new virus described for the first time in this study was named Ugandan cassava brown streak virus (UCBSV) by the International Committee on Virus Taxonomy (ICTV). The isolates TZ:Mlb3:07 and TZ:Kor6:08 belong to UCBSV and CBSV, respectively. The isolates of CBSV and UCBSV were 79.3-95.5% and 86.3-99.3 % identitical at nt level, respectively, suggesting more variation amongst CBSV isolates. The main sources of variation in plant viruses are mutations and recombination. Signals for recombination events were detected in 50% of isolates of each virus. Recombination events were detected in coding and non-coding (3’-UTR) sequences except in the 5’UTR and P3. There was no evidence for recombination between isolates of CBSV and UCBSV. The non-synonomous (dN) to synonomous (dS) nucleotide substitution ratio (ω) for the HAM1h and CP domains of both viruses were ≤ 0.184 suggesting that most sites of these proteins were evolving under strong purifying selection. However, there were individual amino acid sites that were submitted to adaptive evolution. For instance, adaptive evolution was detected in the HAM1h of UCBSV (n=15) where 12 aa sites were under positive selection (P< 0.05) but not in CBSV (n=12). The CP of CBSV (n=23) contained 12 aa sites (p<0.01) while only 5 aa sites in the CP gene of UCBSV were predicted to be submitted to positive selection pressure (p<0.01). The advantages offered by the aa sites under positive selection could not be established but occurrence of such sites in the terminal ends of UCBSV-HAMIh, for example, was interpreted as a requirement for proteolysis during polyprotein processing. Two different primer pairs that simultaneously detect UCBSV and CBSV isolates were developed in this study. They were used successfully to study distribution of CBSV, UCBSV and their mixed infections in Tanzania and Uganda. It was established that the two viruses co-infect cassava and that incidences of co-infection could be as high as 50% around Lake Victoria on the Tanzanian side. Furthermore, it was revealed for the first time that both UCBSV and CBSV were widely distributed in Eastern Africa. The primer pair was also used to confirm infection in a close relative of cassava, Manihot glaziovii (Müller Arg.) with CBSV. DNA barcoding of M. glaziovii was done by sequencing the matK gene. Two out of seven M. glaziovii from the coastal areas of Korogwe and Kibaha in north eastern Tanzania were shown to be infected by CBSV but not UCBSV isolates. Detection in M. glaziovii has an implication in control and management of CBSD as it is likely to serve as virus reservoir. This study has contributed to the understanding of evolution of CBSV and UCBSV, which cause CBSD epidemic in Eastern Africa. The detection tools developed in this work will be useful in plant breeding, verification of the phytosanitary status of materials in regional and international movement of germplasm, and in all diagnostic activities related to management of CBSD. Whereas there are still many issues to be resolved such as the function and biological significance of HAM1h and its origin, this work has laid a foundation upon which the studies on these aspects can be based.

Biochemical and structural characterization of recombinant hyoscyamine 6 beta-hydroxylase from Datura metel L.

Hyoscyamine 6 beta-hydroxylase (H6H; EC 1.14.11.11), an important enzyme in the biosynthesis of tropane alkaloids, catalyzes the hydroxylation of hyoscyamine to give 6 beta-hydroxyhyoscyamine and its epoxidation in the biosynthetic pathway leading to scopolamine. Datura metel produces scopolamine as the predominant tropane alkaloid. The cDNA encoding H6H from D. mete! (DmH6H) was cloned, heterologously expressed and biochemically characterized. The purified recombinant His-tagged H6H from D. mete! (DmrH6H) was capable of converting hyoscyamine to scopolamine. The functionally expressed DmrH6H was confirmed by HPLC and ESI-MS verification of the products, 6 beta-hydroxyhyoscyamine and its derivative, scopolamine; the DmrH6H epoxidase activity was low compared to the hydroxylase activity. The K-m values for both the substrates, hyoscyamine and 2-oxoglutarate, were 50 mu M each. The CD (circular dichroism) spectrum of the DmrH6H indicated a preponderance of alpha-helicity in the secondary structure. From the fluorescence studies, Stern-Volmer constants for hyoscyamine and 2-oxoglutarate were found to be 0.14 M-1 and 0.56 M-1, respectively. These data suggested that the binding of the substrates, hyoscyamine and 2-oxoglutarate, to the enzyme induced significant conformational changes. (C) 2010 Elsevier Masson SAS. All rights reserved.