Abnormal meiotic behavior in three species of Crotalaria

The objective of this work was to compare the meiotic behavior and pollen grain viability of three species of Crotalaria. Slides for meiotic analysis were prepared by the air-drying technique. Pollen grain viability was measured by three staining procedures (Alexander's solution, tetrazolium chloride and fluorescein diacetate) and in vitro germination in a sucrose solution. Eight bivalents were observed, confirming previous reports on populations from other regions of Brazil, as well as from other countries. All species showed abnormal meiotic behavior as follows: in Crotalaria micans, cytomixis and abnormal chromosome pairing in diakinesis; in C. spectabilis, abnormal chromosome pairing in diplotene; in C. zanzibarica, shrunk nuclei in leptotene and zygotene. Pollen grains of all three species show low viability, which may be associated with the irregularities of the meiotic behavior.

The human Rad52 protein exists as a heptameric ring.

The RAD52 epistasis group was identified in yeast as a group of genes required to repair DNA damaged by ionizing radiation [1]. Genetic evidence indicates that Rad52 functions in Rad51-dependent and Rad51-independent recombination pathways [2] [3] [4]. Consistent with this, purified yeast and human Rad52 proteins have been shown to promote single-strand DNA annealing [5] [6] [7] and to stimulate Rad51-mediated homologous pairing [8] [9] [10] [11]. Electron microscopic examinations of the yeast [12] and human [13] Rad52 proteins have revealed their assembly into ring-like structures in vitro. Using both conventional transmission electron microscopy and scanning transmission electron microscopy (STEM), we found that the human Rad52 protein forms heptameric rings. A three-dimensional (3D) reconstruction revealed that the heptamer has a large central channel. Like the hexameric helicases such as Escherichia coli DnaB [14] [15], bacteriophage T7 gp4b [16] [17], simian virus 40 (SV40) large T antigen [18] and papilloma virus E1 [19], the Rad52 rings show a distinctly chiral arrangement of subunits. Thus, the structures formed by the hexameric helicases may be a more general property of other proteins involved in DNA metabolism, including those, such as Rad52, that do not bind and hydrolyze ATP.

Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions

Single-stranded DNA (ssDNA) plays a major role in several biological processes. It is therefore of fundamental interest to understand how the elastic response and the formation of secondary structures are modulated by the interplay between base pairing and electrostatic interactions. Here we measure force-extension curves (FECs) of ssDNA molecules in optical tweezers set up over two orders of magnitude of monovalent and divalent salt conditions, and obtain its elastic parameters by fitting the FECs to semiflexible models of polymers. For both monovalent and divalent salts, we find that the electrostatic contribution to the persistence length is proportional to the Debye screening length, varying as the inverse of the square root of cation concentration. The intrinsic persistence length is equal to 0.7 nm for both types of salts, and the effectivity of divalent cations in screening electrostatic interactions appears to be 100-fold as compared with monovalent salt, in line with what has been recently reported for single-stranded RNA. Finally, we propose an analysis of the FECs using a model that accounts for the effective thickness of the filament at low salt condition and a simple phenomenological description that quantifies the formation of non-specific secondary structure at low forces.

Probing Rad51-DNA interactions by changing DNA twist.

In eukaryotes, Rad51 protein is responsible for the recombinational repair of double-strand DNA breaks. Rad51 monomers cooperatively assemble on exonuclease-processed broken ends forming helical nucleo-protein filaments that can pair with homologous regions of sister chromatids. Homologous pairing allows the broken ends to be reunited in a complex but error-free repair process. Rad51 protein has ATPase activity but its role is poorly understood, as homologous pairing is independent of adenosine triphosphate (ATP) hydrolysis. Here we use magnetic tweezers and electron microscopy to investigate how changes of DNA twist affect the structure of Rad51-DNA complexes and how ATP hydrolysis participates in this process. We show that Rad51 protein can bind to double-stranded DNA in two different modes depending on the enforced DNA twist. The stretching mode is observed when DNA is unwound towards a helical repeat of 18.6 bp/turn, whereas a non-stretching mode is observed when DNA molecules are not permitted to change their native helical repeat. We also show that the two forms of complexes are interconvertible and that by enforcing changes of DNA twist one can induce transitions between the two forms. Our observations permit a better understanding of the role of ATP hydrolysis in Rad51-mediated homologous pairing and strand exchange.

Mapping genetic variants associated with beta-adrenergic responses in inbred mice.

β-blockers and β-agonists are primarily used to treat cardiovascular diseases. Inter-individual variability in response to both drug classes is well recognized, yet the identity and relative contribution of the genetic players involved are poorly understood. This work is the first genome-wide association study (GWAS) addressing the values and susceptibility of cardiovascular-related traits to a selective β(1)-blocker, Atenolol (ate), and a β-agonist, Isoproterenol (iso). The phenotypic dataset consisted of 27 highly heritable traits, each measured across 22 inbred mouse strains and four pharmacological conditions. The genotypic panel comprised 79922 informative SNPs of the mouse HapMap resource. Associations were mapped by Efficient Mixed Model Association (EMMA), a method that corrects for the population structure and genetic relatedness of the various strains. A total of 205 separate genome-wide scans were analyzed. The most significant hits include three candidate loci related to cardiac and body weight, three loci for electrocardiographic (ECG) values, two loci for the susceptibility of atrial weight index to iso, four loci for the susceptibility of systolic blood pressure (SBP) to perturbations of the β-adrenergic system, and one locus for the responsiveness of QTc (p<10(-8)). An additional 60 loci were suggestive for one or the other of the 27 traits, while 46 others were suggestive for one or the other drug effects (p<10(-6)). Most hits tagged unexpected regions, yet at least two loci for the susceptibility of SBP to β-adrenergic drugs pointed at members of the hypothalamic-pituitary-thyroid axis. Loci for cardiac-related traits were preferentially enriched in genes expressed in the heart, while 23% of the testable loci were replicated with datasets of the Mouse Phenome Database (MPD). Altogether these data and validation tests indicate that the mapped loci are relevant to the traits and responses studied.

Fructose Rich Diet-Induced High Plasminogen Activator Inhibitor-1 (PAI-1) Production in the Adult Female Rat: Protective Effect of Progesterone.

The effect of progesterone (P4) on fructose rich diet (FRD) intake-induced metabolic, endocrine and parametrial adipose tissue (PMAT) dysfunctions was studied in the adult female rat. Sixty day-old rats were i.m. treated with oil alone (control, CT) or containing P4 (12 mg/kg). Rats ate Purina chow-diet ad libitum throughout the entire experiment and, between 100 and 120 days of age drank ad libitum tap water alone (normal diet; CT-ND and P4-ND) or containing fructose (10% w/v; CT-FRD and P4-FRD). At age 120 days, animals were subjected to a glucose tolerance test or decapitated. Plasma concentrations of various biomarkers and PMAT gene abundance were monitored. P4-ND (vs. CT-ND) rats showed elevated circulating levels of lipids. CT-FRD rats displayed high (vs. CT-ND) plasma concentrations of lipids, leptin, adiponectin and plasminogen activator inhibitor-1 (PAI-1). Lipidemia and adiponectinemia were high (vs. P4-ND) in P4-FRD rats. Although P4 failed to prevent FRD-induced hyperleptinemia, it was fully protective on FRD-enhanced plasma PAI-1 levels. PMAT leptin and adiponectin mRNAs were high in CT-FRD and P4-FRD rats. While FRD enhanced PMAT PAI-1 mRNA abundance in CT rats, this effect was absent in P4 rats. Our study supports that a preceding P4-enriched milieu prevented the enhanced prothrombotic risk induced by FRD-elicited high PAI-1 production.

Paperin pinnan karakterisoinnin ja painettavuuden tutkimusmenetelmät

Työn tarkoituksena on ollut tutkia paperin pinnan karakterisoinnin menetelmiä ja tehdä katsauspaperin painettavuuden ennustamisen tutkimuksiin. Kaikkien kehitettyjen menetelmien tarkoituksena on tavalla tai toisella mitata paperin visuaalista vaikutelmaa loppukäyttäjän kannalta sekä ennustaa paperin painettavuutta. Menetelmiä on kehitetty aina 1940-luvulta lähtien ja tekniikan kehittyessä markkinoille tulee uusia menetelmiä, jotka ovat nopeampia ja tarkempia kuin edeltäjänsä. Työssä tarkasteltavat menetelmät on jaoteltu mekaanisiin, optisiin ja elektronisäteilyn läpäisyyn perustuviin menetelmiin. Lopuksi on tarkasteltu tutkimuksia, joiden pääasiallinen tarkoitus on ollut kehittää mittalaitteita ennustamaan paperin painotulosta todellisissa painatusolosuhteissa. Laboratoriolaitteita ja on-line-mittareita ei ole jaoteltu erikseen, koska menetelmän perusteella on helppo havaita, voiko laite mitata jotakin paperin ominaisuutta jopa yli 40 metriä sekunnissa liikkuvalla paperirainalla.

Luotettavuuskeskeisen kunnossapidon soveltaminen vaneriteollisuuden koneille

Diplomityön tarkoituksena on tutkia luotettavuuskeskeisen kunnossapidon soveltamista Raute Oyj:n vanerikoneille. Työn tavoitteena on luoda suunnitelma luotettavuuskeskeisen kunnossapidon soveltamiseksi Raute Oyj:llä. Tavoitteena on myös kehittää malli ennakkohuoltosuunnitelmien sekä kriittisten huoltojen ja varaosien määrittelyyn päälinjoille. Kunnossapitoliiketoiminta on Rautella voimakkaasti kasvava liiketoiminta-alue. Voimakkaan kasvun seurauksena on yritykseen syntynyt kunnossapitotoimintojen kehitystarve. Luotettavuuskeskeistä kunnossapitoa hyödyntämällä on tarkoitus kehittää vanerikoneiden kunnossapitoa ja luoda Rautelle kunnossapitotuotteita. Työssä on tutkittu luotettavuuskeskeisen kunnossapidon soveltamista va-neriteollisuuden koneille laitevalmistajan näkökulmasta. Työssä on käsitelty kirjallisuuden pohjalta vanerin valmistusprosessia, vanerikoneita, kunnossapitoa sekä luotettavuuskeskeistä kunnossapitoa. Lisäksi on selvitetty vanerikoneiden kunnossapidon nykytilaa Raute Oyj:llä ja sen asiakkaiden vaneritehtaissa. Työn tuloksena syntyi toimintaehdotus luotettavuuskeskeisen kunnossapidon soveltamiseksi Rauten tuotteille. Ennakkohuoltosuunnitelmien luomiseen ja kehittämiseen työssä syntyi kunnossapitomalli, jonka pohjalta työssä luotiin xy-pöllinkeskittäjälle luotettavuuskeskeiseen kunnossapitoon perustuva ennakkohuoltosuunnitelma sekä määritettiin kriittiset varaosat.

Comparative analysis of the transcriptome across distant species.

The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters.

Linjasekoittimensekoituskyvyn määrittäminen

Työn tavoitteena oli kehittää sekoituskyvyn empiirinen monimuuttujafunktio eräälle dynaamiselle linjasekoittimelle. Monimuuttujafunktio oli tarkoitus kehittää sekoittimen kierrosnopeuden, virtaavien materiaalien ja tilavuusvirtausten perus-teella. Työn kirjallisuusosassa tarkasteltiin pääosin dynaamisia linjasekoittimia ja niiden toimintaperiaatteita sekä sekoituskyvyn määrittämiseen soveltuvia mittausmene-telmiä. Sekoitettavien aineiden epähomogeenisuus määritettiin mittaamalla termoelemen-teillä sekoittimen jälkeisen virran lämpötilavaihtelut. Sekoitettavina aineina käy-tettiin kolmea erilaista seosta: vesi-vesi-, kuitususpensio-vesi- ja karboksyylime-tyyliselluloosa-vesiseoksia. Muita muuttujia kokeissa olivat neljä eri sekoittimen kierrosnopeutta, neljä eri päävirran tilavuusvirtausta ja kolme päävirran sekäsii-hen lisättävän sivuvirran suhdetta. Monimuuttujafunktiokehitettiin vain kuitususpensio-vesiajojen pohjalta muilla seoksilla tehtyjen koeajojen osittaisen epäonnistumisen vuoksi. Hallitsevaksi pa-rametriksi monimuuttujafunktiossa osoittautui sekoittimen kierrosnopeus. Osittai-nen epäonnistuminen kokeissa johtui osaksi termoelementtien käytön sopimatto-muudesta sekoituskyvyn määrittämiseen ja osaksi sekoitettavien aineiden valin-nasta. Jatkotutkimuksiaajatellen muista sekoituskyvyn mittaamiseen käytettävissä olevista menetelmistäkäyttökelpoisimmaksi arvioitiin sähkötomografia.

Nota. Detección molecular de Heterobasidion annosum s.s. en claras de Pinus nigra en el Pirineo Aragonés

En diciembre de 2007, en la Sierra de Loarre (Huesca) observamos signos de Newrobasidion annosum sensu lato asociados a daños de defoliación y mortalidad en una repoblación de Pinus nigra. Se ha identificado la especie biológica de aislamientos recogidos de este patógeno mediante técnicas moleculares, y se ha corroborado mediante cruces con aislamientos homocariontes, que se trata de H. annosum sensu stricto. Esta especie biológica ataca al género Pinus y puede causar daños sobre Pinus nigra.

Single-trial multisensory memories affect later auditory and visual object discrimination.

Multisensory memory traces established via single-trial exposures can impact subsequent visual object recognition. This impact appears to depend on the meaningfulness of the initial multisensory pairing, implying that multisensory exposures establish distinct object representations that are accessible during later unisensory processing. Multisensory contexts may be particularly effective in influencing auditory discrimination, given the purportedly inferior recognition memory in this sensory modality. The possibility of this generalization and the equivalence of effects when memory discrimination was being performed in the visual vs. auditory modality were at the focus of this study. First, we demonstrate that visual object discrimination is affected by the context of prior multisensory encounters, replicating and extending previous findings by controlling for the probability of multisensory contexts during initial as well as repeated object presentations. Second, we provide the first evidence that single-trial multisensory memories impact subsequent auditory object discrimination. Auditory object discrimination was enhanced when initial presentations entailed semantically congruent multisensory pairs and was impaired after semantically incongruent multisensory encounters, compared to sounds that had been encountered only in a unisensory manner. Third, the impact of single-trial multisensory memories upon unisensory object discrimination was greater when the task was performed in the auditory vs. visual modality. Fourth, there was no evidence for correlation between effects of past multisensory experiences on visual and auditory processing, suggestive of largely independent object processing mechanisms between modalities. We discuss these findings in terms of the conceptual short term memory (CSTM) model and predictive coding. Our results suggest differential recruitment and modulation of conceptual memory networks according to the sensory task at hand.

Signalling value of maternal and paternal melanism in the barn owl : implication for the resolution of the lek paradox

Secondary sexual characters often signal qualities such as physiological processes associated with resistance to various sources of stress. When the expression of an ornament is not sex-limited, we can identify the costs and benefits of displaying a trait that is typical of its own sex or of the other sex. Indeed, the magnitude and sign of the covariation between physiology and the extent to which an ornament is expressed could differ between males and females if, for instance, the regulation of physiological processes is sensitive to sex hormones. Using data collected over 14 years in the nocturnal barn owl Tyto alba, we investigated how nestling body mass covaries with a heritable melanin-based sex-trait, females displaying on average larger black feather spots than males. Independently of nestling sex, year and time of the day large-spotted nestlings were heavier than small-spotted nestlings. In contrast, the magnitude and sign of the covariation between nestling body mass and the size of parental spots varied along the day in a way that depended on the year and parental gender. In poor years, offspring of smaller-spotted mothers were heavier throughout the resting period; in the morning, offspring sired by larger-spotted fathers were heavier than offspring of smaller-spotted fathers, while in the evening the opposite pattern was found. Thus, maternal and paternal coloration is differentially associated with behaviour or physiology, processes that are sensitive to time of the day and environmental factors. Interestingly, the covariation between offspring body mass and paternal coloration is more sensitive to these environmental factors than the covariation with maternal coloration. This indicates that the benefit of pairing with differently spotted males may depend on environmental conditions, which could help maintain genetic variation in the face of intense directional (sexual) selection.

Microscopic-macroscopic approach for binding energies with the Wigner-Kirkwood method

The semiclassical Wigner-Kirkwood ̄h expansion method is used to calculate shell corrections for spherical and deformed nuclei. The expansion is carried out up to fourth order in ̄h. A systematic study of Wigner-Kirkwood averaged energies is presented as a function of the deformation degrees of freedom. The shell corrections, along with the pairing energies obtained by using the Lipkin-Nogami scheme, are used in the microscopic-macroscopic approach to calculate binding energies. The macroscopic part is obtained from a liquid drop formula with six adjustable parameters. Considering a set of 367 spherical nuclei, the liquid drop parameters are adjusted to reproduce the experimental binding energies, which yields a root mean square (rms) deviation of 630 keV. It is shown that the proposed approach is indeed promising for the prediction of nuclear masses.

The structure of human tRNALys3 anticodon bound to HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs

Replication of human immunodeficiency virus (HIV) requires base pairing of the reverse transcriptase primer, human tRNA(Lys3), to the viral RNA. Although the major complementary base pairing occurs between the HIV primer binding sequence (PBS) and the tRNA's 3'-terminus, an important discriminatory, secondary contact occurs between the viral A-rich Loop I, 5'-adjacent to the PBS, and the modified, U-rich anticodon domain of tRNA(Lys3). The importance of individual and combined anticodon modifications to the tRNA/HIV-1 Loop I RNA's interaction was determined. The thermal stabilities of variously modified tRNA anticodon region sequences bound to the Loop I of viral sub(sero)types G and B were analyzed and the structure of one duplex containing two modified nucleosides was determined using NMR spectroscopy and restrained molecular dynamics. The modifications 2-thiouridine, s(2)U(34), and pseudouridine, Psi(39), appreciably stabilized the interaction of the anticodon region with the viral subtype G and B RNAs. The structure of the duplex results in two coaxially stacked A-form RNA stems separated by two mismatched base pairs, U(162)*Psi(39) and G(163)*A(38), that maintained a reasonable A-form helix diameter. The tRNA's s(2)U(34) stabilized the interaction between the A-rich HIV Loop I sequence and the U-rich anticodon, whereas the tRNA's Psi(39) stabilized the adjacent mismatched pairs.