A minimal i-motif stabilized by minor groove G:T:G:T tetrads

The repetitive DNA sequences found at telomeres and centromeres play a crucial role in the structure and function of eukaryotic chromosomes. This role may be related to the tendency observed in many repetitive DNAs to adopt non-canonical structures. Although there is an increasing recognition of the importance of DNA quadruplexes in chromosome biology, the co-existence of different quadruplex-forming elements in the same DNA structure is still a matter of debate. Here we report the structural study of the oligonucleotide d(TCGTTTCGT) and its cyclic analog d. Both sequences form dimeric quadruplex structures consisting of a minimal i-motif capped, at both ends, by a slipped minor groove-aligned G:T:G:T tetrad. These mini i-motifs, which do not exhibit the characteristic CD spectra of other i-motif structures, can be observed at neutral pH, although they are more stable under acidic conditions. This finding is particularly relevant since these oligonucleotide sequences do not contain contiguous cytosines. Importantly, these structures resemble the loop moiety adopted by an 11-nucleotide fragment of the conserved centromeric protein B (CENP-B) box motif, which is the binding site for the CENP-B.

The complementary strand of the human T-cell leukemia virus type 1 RNA genome encodes a bZIP transcription factor that down-regulates viral transcription.

The RNA genome of the human T-cell leukemia virus type 1 (HTLV-1) codes for proteins involved in infectivity, replication, and transformation. We report in this study the characterization of a novel viral protein encoded by the complementary strand of the HTLV-1 RNA genome. This protein, designated HBZ (for HTLV-1 bZIP factor), contains a N-terminal transcriptional activation domain and a leucine zipper motif in its C terminus. We show here that HBZ is able to interact with the bZIP transcription factor CREB-2 (also called ATF-4), known to activate the HTLV-1 transcription by recruiting the viral trans-activator Tax on the Tax-responsive elements (TxREs). However, we demonstrate that the HBZ/CREB-2 heterodimers are no more able to bind to the TxRE and cyclic AMP response element sites. Taking these findings together, the functional inactivation of CREB-2 by HBZ is suggested to contribute to regulation of the HTLV-1 transcription. Moreover, the characterization of a minus-strand gene protein encoded by HTLV-1 has never been reported until now.

The histone-interacting domain of nuclear factor I activates simian virus 40 DNA replication in vivo.

Efficient initiation of SV40 DNA replication requires transcription factors that bind auxiliary sequences flanking the minimally required origin. To evaluate the possibility that transcription factors may activate SV40 replication by acting on the chromatin structure of the origin, we used an in vivo replication system in which we targeted GAL4 fusion proteins to the minimally required origin. We found that the proline-rich transcriptional activation domain of nuclear factor I (NF-I), which has been previously shown to interact with histone H3, specifically activates replication. Evaluation of a series of deletion and point mutants of NF-I indicates that the H3-binding domain and the replication activity coincide perfectly. Assays with other transcription factors, such as Sp1, confirmed the correlation between the interaction with H3 and the activation of replication. These findings imply that transcription factors such as NF-I can activate SV40 replication via direct interaction with chromatin components, thereby contributing to the relief of nucleosomal repression at the SV40 origin.

Biocontrol of seed pathogens and growth promotion of common bean seedlings by Trichoderma harzianum

The objective of this work was to evaluate isolates of Trichoderma harzianum regarding biocontrol of common bean seed-borne pathogens, plant growth promotion, and rhizosphere competence. Five isolates of T. harzianum were evaluated and compared with commercial isolate (Ecotrich), Carboxin+Thiram, and an absolute control. Bean seeds of the cultivar Jalo Precoce, contaminated with Aspergillus, Cladosporium, and Sclerotinia sclerotiorum, were microbiolized with antagonists, and seed health tests were carried out. Isolates were evaluated on autoclaved substrate and in field conditions. Ten days after sowing (DAS), plant length was measured. To test rhizosphere competence, isolates were applied in boxes containing autoclaved washed sand, and root colonization was evaluated at 10 DAS, using five plants per box. The most effective isolates in the seed health tests were: CEN287 and CEN289 to control Aspergillus; the commercial isolate to control Cladosporium; and CEN287 and CEN316 to control S. sclerotiorum. Isolates CEN289 and CEN290 promoted bean growth in greenhouse and field. Seed treatment with T. harzianum reduces the incidence of Aspergillus, Cladosporium, and S. sclerotiorum in 'Jalo Precoce' common bean seeds.

Air Formed Arch Culvert Construction: Crawford County, Construction Reports, HR-314, 1991

Iowa's secondary roads contain nearly 15,000 bridges which are less than 40 feet (12 m) in length. Many of these bridges were built several decades ago and need to be replaced. Box culvert construction has proven to be an adequate bridge replacement technique. Recently a new bridge replacement alternative, called the Air-0-Form method, has emerged which has several potential advantages over box culvert construction. This new technique uses inflated balloons as the interior form in the construction of an arch culvert. The objective of research project HR-314 was to construct an air formed arch culvert to determine the applicability of the Air-O-Form technique as a county bridge replacement alternative.

Liquid fructose down-regulates liver insulin receptor substrate 2 and gluconeogeneic enzymes by modifying nutrient sensing factors in rats

High consumption of fructose-sweetened beverages has been linked to a high prevalence of chronic metabolic diseases. We have previously shown that a short course of fructose supplementation as a liquid solution induces glucose intolerance in female rats. In the present work, we characterized the fructose-driven changes in the liver and the molecular pathways involved. To this end, female rats were supplemented or not with liquid fructose (10%, w/v) for 7 or 14 days. Glucose and pyruvate tolerance tests were performed, and the expression of genes related to insulin signaling, gluconeogenesis and nutrient sensing pathways was evaluated. Fructose-supplemented rats showed increased plasma glucose excursions in glucose and pyruvate tolerance tests and reduced hepatic expression of several genes related to insulin signaling, including insulin receptor substrate 2 (IRS-2). However, the expression of key gluconeogenic enzymes, glucose-6-phosphatase and phosphoenolpyruvate carboxykinase, was reduced. These effects were caused by an inactivation of hepatic forkhead box O1 (FoxO1) due to an increase in its acetylation state driven by a reduced expression and activity of sirtuin 1 (SIRT1). Further contributing to FoxO1 inactivation, fructose consumption elevated liver expression of the spliced form of X-box-binding-protein-1 as a consequence of an increase in the activity of the mammalian target of rapamycin 1 and protein 38-mitogen activated protein kinase (p38-MAPK). Liquid fructose affects both insulin signaling (IRS-2 and FoxO1) and nutrient sensing pathways (p38-MAPK, mTOR and SIRT1), thus disrupting hepatic insulin signaling without increasing the expression of key gluconeogenic enzymes.

Akt signalling through GSK-3beta, mTOR and Foxo1 is involved in human skeletal muscle hypertrophy and atrophy

Skeletal muscle size is tightly regulated by the synergy between anabolic and catabolic signalling pathways which, in humans, have not been well characterized. Akt has been suggested to play a pivotal role in the regulation of skeletal muscle hypertrophy and atrophy in rodents and cells. Here we measured the amount of phospho-Akt and several of its downstream anabolic targets (glycogen synthase kinase-3beta (GSK-3beta), mTOR, p70(s6k) and 4E-BP1) and catabolic targets (Foxo1, Foxo3, atrogin-1 and MuRF1). All measurements were performed in human quadriceps muscle biopsies taken after 8 weeks of both hypertrophy-stimulating resistance training and atrophy-stimulating de-training. Following resistance training a muscle hypertrophy ( approximately 10%) and an increase in phospho-Akt, phospho-GSK-3beta and phospho-mTOR protein content were observed. This was paralleled by a decrease in Foxo1 nuclear protein content. Following the de-training period a muscle atrophy (5%), relative to the post-training muscle size, a decrease in phospho-Akt and GSK-3beta and an increase in Foxo1 were observed. Atrogin-1 and MuRF1 increased after the hypertrophy and decreased after the atrophy phases. We demonstrate, for the first time in human skeletal muscle, that the regulation of Akt and its downstream signalling pathways GSK-3beta, mTOR and Foxo1 are associated with both the skeletal muscle hypertrophy and atrophy processes

Não normalidade multivariada e multicolinearidade na análise de trilha em milho

O objetivo deste trabalho foi avaliar a interferência da não normalidade multivariada e da multicolinearidade na análise de trilha, em milho. Foram utilizados os dados de 13 ensaios de competição de cultivares de milho. Foram mensuradas a variável principal (produtividade de grãos) e sete variáveis explicativas (número de dias até o florescimento, estatura de plantas, altura de inserção da espiga, posição relativa da espiga, número de plantas, número de espigas e prolificidade), em cada cultivar. Procedeu-se, então, à transformação dos dados e ao diagnóstico de normalidade univariada e multivariada. Antes e após a transformação de dados, foram calculados os coeficientes de correlação e realizado o diagnóstico de multicolinearidade. A análise de trilha foi realizada por três métodos: tradicional; sob condições de multicolinearidade (análise de trilha em crista); e tradicional com eliminação de variáveis. A transformação de dados reduz o grau de multicolinearidade e a variabilidade das estimativas dos efeitos diretos, na análise de trilha tradicional com alto grau de multicolinearidade. A multicolinearidade exerce maior impacto sobre a estimativa dos efeitos diretos nas análises de trilha do que a não normalidade multivariada. A análise de trilha tradicional com eliminação de variáveis é mais adequada do que a análise de trilha em crista.

Shelf life and sensory assessment of tilapia quenelle during frozen storage

The objective of this work was to evaluate the shelf life and sensory attributes of tilapia quenelle. Treatments consisted of two types of packages - polyethylene zipper (retort pouch) (QA) and polyethylene waxed paper box (QB) - stored at -18ºC for 120 days. Tilapia quenelle was stable for all parameters established by Brazilian legislation. Average values of the evaluated attributes in different packages, during storage, showed no significant difference, except for the "refrigeration" flavor. However, during the storage period, there were significant differences for sensory attributes, as "moist appearance", fish and product aroma, and off flavors of "mud" and "refrigeration". Preserving product quality as for its sensory attributes, during storage, shows that tilapia quenelle is a convenience product and contributes to the increase of fish consumption.

New pool of cortical interneuron precursors in the early postnatal dorsal white matter.

The migration of cortical γ-aminobutyric acidergic interneurons has been extensively studied in rodent embryos, whereas few studies have documented their postnatal migration. Combining in vivo analysis together with time-lapse imaging on cortical slices, we explored the origin and migration of cortical interneurons during the first weeks of postnatal life. Strikingly, we observed that a large pool of GAD65-GFP-positive cells accumulate in the dorsal white matter region during the first postnatal week. Part of these cells divides and expresses the transcription factor paired box 6 indicating the presence of local transient amplifying precursors. The vast majority of these cells are immature interneurons expressing the neuronal marker doublecortin and partly the calcium-binding protein calretinin. Time-lapse imaging reveals that GAD65-GFP-positive neurons migrate from the white matter pool into the overlying anterior cingulate cortex (aCC). Some interneurons in the postnatal aCC express the same immature neuronal markers suggesting ongoing migration of calretinin-positive interneurons. Finally, bromodeoxyuridine incorporation experiments confirm that a small fraction of interneurons located in the aCC are generated during the early postnatal period. These results altogether reveal that at postnatal ages, the dorsal white matter contains a pool of interneuron precursors that divide and migrate into the aCC.

Methods for the analysis of two dimensional measurement data of paper web

This work is devoted to the problem of reconstructing the basis weight structure at paper web with black{box techniques. The data that is analyzed comes from a real paper machine and is collected by an o®-line scanner. The principal mathematical tool used in this work is Autoregressive Moving Average (ARMA) modelling. When coupled with the Discrete Fourier Transform (DFT), it gives a very flexible and interesting tool for analyzing properties of the paper web. Both ARMA and DFT are independently used to represent the given signal in a simplified version of our algorithm, but the final goal is to combine the two together. Ljung-Box Q-statistic lack-of-fit test combined with the Root Mean Squared Error coefficient gives a tool to separate significant signals from noise.

Excedente hídrico em diferentes solos e épocas de semeadura do girassol no Rio Grande do Sul

O objetivo deste trabalho foi identificar datas de semeadura com menor ocorrência média de dias com excedente hídrico para a cultura do girassol, e determinar a persistência de dias consecutivos com excedente hídrico ao se considerar a capacidade de armazenamento de água disponível de diferentes solos da região central do Rio Grande do Sul. O desenvolvimento da cultura e o aprofundamento do sistema radicular foram simulados de acordo com a soma térmica para 14 datas de semeadura, de agosto até meados de fevereiro, com dados de 1968 até 2011. A partir da capacidade de armazenamento de água disponível para as diferentes classes de solos da região, calculou-se o balanço hídrico sequencial diário para determinar os dias com excesso hídrico. Avaliou-se a ocorrência de dias com excesso hídrico em diferentes subperíodos de desenvolvimento da cultura, e procedeu-se à análise exploratória com gráficos box-plot para determinação da persistência de dias consecutivos com excesso hídrico durante todo o ciclo da cultura. O excedente hídrico limita o cultivo de girassol em determinadas áreas e períodos na região central do Rio Grande do Sul. A persistência de dias consecutivos com excedente hídrico e a duração do ciclo de desenvolvimento da cultura são influenciados pela data de semeadura.

Paperikoneen puristinosan siirtoimulaatikon suunnittelu

Märkäpuristus on paperin tuotannon toiminto, jossa vettä poistetaan paperiradasta puristamalla sitä mekaanisesti. Paperikoneen osaa, jossa tämä toiminto tuotetaan kutsutaan puristinosaksi. Puristinosassa paperiradan vettä poistava mekaaninen puristus toteutetaan puristamalla paperirataa kahden telan välissä, tai telan ja kengän välissä. Paperikoneen puristinosalla käytetään paperiradan kuljettamiseen huopia. On toiminnallisesti mahdotonta käyttää suurinopeuksisen paperikoneen puristinosalle vain yhtä huopakiertoa, täten täytyy paperirataa siirtää huovalta toiselle puristinosan sisällä. Tässä työssä kehiteltiin ja suunniteltiin yksityiskohtaisesti uusi paperiradan siirron huovalta toiselle toteuttava siirtoimulaatikko. Siirtoimulaatikko on koko paperikoneen levyinen komponentti, jonka sisäisen alipaineen tuottama voimavaikutus (ilman imeminen puristinhuovan läpi) toteuttaa paperiradan siirron. Siirtoimulaatikko suunniteltiin suurinopeuksisen paperikoneen puristinosalle, tarkoituksena alentaa puristinosan valmistuskustannuksia. Uuden siirtoimulaatikon tuotantolaitteesta luotiin parametrinen suunnittelumalli. Tämä tarkoittaa projektisuunnittelun apuna käytettävää tietokoneohjelmiston suunnittelutiedostoa, jonka ominaisuudet muuttuvat malliin ohjelmoitujen parametrien mukaisesti.

Paperikoneen vesi- ja energiatehokkuuden parantaminen

Työn tavoitteena oli laatia reaaliaikaiset vesi- ja energiatasenäytöt Stora Enso PublicationPaper Veitsiluodon tehtaalle, paperikone 5:lle. Tavoitteena oli myös simuloida kyseisen paperikonelinjan vesitase. Aluksi työssä piirrettiin lohkokaaviot taseita varten paperikoneen kaikista vettä tai energiaa sisältävistä jakeista. Näitä yksinkertaistettuja lohkokaavioita hyväksi käyttäen laadittiin taseidenlaskentakaavat, jotka testattiin tarkastuslaskelmien avulla. Vesi- ja energiataseista tehtiin myös suunnitelmat prosessinohjausjärjestelmän tasenäytöiksi. FlowMac-simulointiohjelmalla rakennetun paperikone 5 vesitaseen simulointimallin tulosten oikeellisuutta arvioitiin herkkyysanalyysin avulla. Tehdyn herkkyysanalyysin tuloksien perusteella voidaan olettaa, että simulointimalli toimii luotettavasti. Tämän vesitaseen simulointimallin avulla tarkasteltiin kiekkosuotimien uudistamisen vaikutuksia paperikonelinjan vesitaseeseen. Tarkastelussa huomattiin, että vaihtamalla kiekkosuotimien syöttöventtiilit kolmea jaetta tuottaviksi, voitaisiin flotaatioallas ja suihkuveden kaarisihti poistaa käytöstä. Tulevaisuudessa simulointimallia voidaan käyttää myös monilla muilla eri tavoin hyödyksi kyseisellä paperikoneella. Työssä laaditut vesi- ja energiataseet saatiin niin tarkoiksi kuin se nykyisiä mittauksia hyödyntäen on mahdollista. Jostaseita haluttaisiin tarkentaa, olisi paperikonelinjalle syytä lisätä joitakin mittauksia. Myös työssä tehty vesitaseen simulointi FlowMac:lla onnistui hyvin mutta kyseisessä ohjelmassa havaittiin silti joitakin kehittämistarpeita. Työn tuloksien perusteella vettä ja energiaa voitaisiin mahdollisesti säästää paperikone 5:llä esimerkiksi laimennussäätöisen perälaatikon avulla, kiekkosuotimien uusimisella sekä kenkäpuristimen käyttöönotolla. Jatkotutkimuskohteita voisivat olla esimerkiksi paperikone 5:n lämpötase, kemiallisesti puhdistetun veden tulolämpötilan nostaminen, hiomon suodosveden ylimääräisen lämmön hyödyntäminen paperikone 5 kirkassuodoksen lämmittämisen jälkeen, lämmön talteenotossa lämmitysvesikennon ja prosessivesikennon järjestyksen vaihtaminen sekä vastaavien vesi- ja energiataseiden laatiminen paperikone 1:lle ja hiomolle.

Siltanosturin teräsrakenteen suunnittelun avuksi luodun ohjelman jatkokehitys

Diplomityössä tehdään jatkokehitystä KCI Konecranes yrityksen siltanosturin laskentaohjelmaan. Ohjelman tärkeimmät jatkokehityskohteet kartoitettiin käyttäjäkyselyn avulla ja niistä valittiin toivotuimmat, sekä diplomityön lujuusopilliseen aihepiiriin parhaiten soveltuvat. Työhön valitut kaksi aihetta ovat koteloprofiilin kaksiosaisen uuman lujuuslaskennan selvittäminen ja siltanosturin kahdeksanpyöräisenpäätykannattajan elementtimallin suunnittelu. Diplomityössä selvitetään jatkokehityskohteisiin liittyvä teoria, mutta varsinainen ohjelmointi jätetään työn ulkopuolelle. Kaksiosaisella uumalla varustetussa koteloprofiilissa nostovaunun kulkukiskon alla olevan uuman yläosa tehdään paksummaksi, jotta uuma kestäisi nostovaunun pyöräkuormasta aiheutuvan paikallisen jännityksen, eliniin sanotun rusennusjännityksen. Rusennusjännityksen määrittäminen uumalevyissä on kaksiosaisen uuman lujuuslaskennan tärkein tehtävä. Rusennuksen aiheuttamankalvojännityksen ja jännityskeskittymien määrittämiseen erilaisissa konstruktioissa etsittiin sopivimmat menetelmät kirjallisuudesta ja standardeista. Kalvojännitys voidaan määrittää luotettavasti käyttäen joko 45 asteen sääntöä tai standardin mukaista menetelmää ja jännityskonsentraatioiden suuruus saadaan kertomallakalvojännitys jännityskonsentraatiokertoimilla. Menetelmien toimivuus verifioitiin tekemällä kymmeniä uuman elementtimalleja erilaisin dimensioin ja reunaehdoin ja vertaamalla elementtimallien tuloksia käsin laskettuihin. Käsin lasketut jännitykset saatiin vastaamaan tarkasti elementtimallien tuloksia. Kaksiosaisen uuman lommahdus- ja väsymislaskentaa tutkittiin alustavasti. Kahdeksanpyöräisiä päätykannattajia käytetään suurissa siltanostureissa pienentämään pyöräkuormia ja radan rusennusjännityksiä. Kahdeksanpyöräiselle siltanosturin päätykannattajalle suunniteltiin elementtimallit molempiin rakenteesta käytettyihin konstruktioihin: nivelöityyn ja jäykkäkehäiseen malliin. Elementtimallien rakentamisessa hyödynnettiin jo olemassa olevia malleja, jolloin niiden lisääminen ohjelmakoodiin nopeutuu ja ne ovat varmasti yhteensopivia muiden laskentamoduuleiden kanssa. Elementtimallien värähtelyanalyysin reunaehtoja tarkasteltiin. Värähtelyanalyysin reunaehtoihin ei tutkimuksen perusteella tarvitse tehdä muutoksia, mutta staattisen analyysin reunaehdot kaipaavat vielä lisätutkimusta.