Direct structure analysis in protein electron crystallography: crystallographic phases for halorhodopsin to 6-A resolution.

The crystal structure of halorhodopsin was determined in (centrosymmetric) projection to 6-A resolution by direct methods that use only the amplitudes of the electron diffraction pattern. A multisolution technique was used to generate initial 15-A-resolution basis sets, and after selection of the best phase set (by the closest match of magnitude of Eobs and magnitude of Ecalc), annealing of individual reflections was used to improve its accuracy. The Sayre equation was then used to expand the phase terms to 10 A, followed again by phase annealing. A final expansion with the Sayre equation enlarged this corrected phase set to 6 A. When the condition of density flatness was used to locate the best phase solution after each extension, a final structure could be observed that was quite similar to the one found earlier by analysis of electron micrographs.

Periodicity of polar and nonpolar amino acids is the major determinant of secondary structure in self-assembling oligomeric peptides.

The tendency of a polypeptide chain to form alpha-helical or beta-strand secondary structure depends upon local and nonlocal effects. Local effects reflect the intrinsic propensities of the amino acid residues for particular secondary structures, while nonlocal effects reflect the positioning of the individual residues in the context of the entire amino acid sequence. In particular, the periodicity of polar and nonpolar residues specifies whether a given sequence is consistent with amphiphilic alpha-helices or beta-strands. The importance of intrinsic propensities was compared to that of polar/nonpolar periodicity by a direct competition. Synthetic peptides were designed using residues with intrinsic propensities that favored one or the other type of secondary structure. The polar/nonpolar periodicities of the peptides were designed either to be consistent with the secondary structure favored by the intrinsic propensities of the component residues or in other cases to oppose these intrinsic propensities. Characterization of the synthetic peptides demonstrated that in all cases the observed secondary structure correlates with the periodicity of the peptide sequence--even when this secondary structure differs from that predicted from the intrinsic propensities of the component amino acids. The observed secondary structures are concentration dependent, indicating that oligomerization of the amphiphilic peptides is responsible for the observed secondary structures. Thus, for self-assembling oligomeric peptides, the polar/nonpolar periodicity can overwhelm the intrinsic propensities of the amino acid residues and serves as the major determinant of peptide secondary structure.

A secondary-structure model for the self-cleaving region of Neurospora VS RNA.

Neurospora VS RNA performs an RNA-mediated self-cleavage reaction whose products contain 2',3'-cyclic phosphate and 5'-hydroxyl termini. This reaction is similar to those of hammerhead, hairpin, and hepatitis delta virus ribozymes; however, VS RNA is not similar in sequence to these other self-cleaving motifs. Here we propose a model for the secondary structure of the self-cleaving region of VS RNA, supported by site-directed mutagenesis and chemical modification structure probing data. The secondary structure of VS RNA is distinct from those of the other naturally occurring RNA self-cleaving domains. In addition to a unique secondary structure, several Mg-dependent interactions occur during the folding of VS RNA into its active tertiary conformation.

Identifying sequence regions undergoing conformational change via predicted continuum secondary structure

Motivation: Conformational flexibility is essential to the function of many proteins, e.g. catalytic activity. To assist efforts in determining and exploring the functional properties of a protein, it is desirable to automatically identify regions that are prone to undergo conformational changes. It was recently shown that a probabilistic predictor of continuum secondary structure is more accurate than categorical predictors for structurally ambivalent sequence regions, suggesting that such models are suited to characterize protein flexibility. Results: We develop a computational method for identifying regions that are prone to conformational change directly from the amino acid sequence. The method uses the entropy of the probabilistic output of an 8-class continuum secondary structure predictor. Results for 171 unique amino acid sequences with well-characterized variable structure (identified in the 'Macromolecular movements database') indicate that the method is highly sensitive at identifying flexible protein regions, but false positives remain a problem. The method can be used to explore conformational flexibility of proteins (including hypothetical or synthetic ones) whose structure is yet to be determined experimentally.

Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures

Background: The structure of proteins may change as a result of the inherent flexibility of some protein regions. We develop and explore probabilistic machine learning methods for predicting a continuum secondary structure, i.e. assigning probabilities to the conformational states of a residue. We train our methods using data derived from high-quality NMR models. Results: Several probabilistic models not only successfully estimate the continuum secondary structure, but also provide a categorical output on par with models directly trained on categorical data. Importantly, models trained on the continuum secondary structure are also better than their categorical counterparts at identifying the conformational state for structurally ambivalent residues. Conclusion: Cascaded probabilistic neural networks trained on the continuum secondary structure exhibit better accuracy in structurally ambivalent regions of proteins, while sustaining an overall classification accuracy on par with standard, categorical prediction methods.

Land-cover detection and landscape structure analysis in the Pachitea Basin, Peruvian Amazon

Classification procedures, including atmospheric correction satellite images as well as classification performance utilizing calibration and validation at different levels, have been investigated in the context of a coarse land-cover classification scheme for the Pachitea Basin. Two different correction methods were tested against no correction in terms of reflectance correction towards a common response for pseudo-invariant features (PIF). The accuracy of classifications derived from each of the three methods was then assessed in a discriminant analysis using crossvalidation at pixel, polygon, region, and image levels. Results indicate that only regression adjusted images using PIFs show no significant difference between images in any of the bands. A comparison of classifications at different levels suggests though that at pixel, polygon, and region levels the accuracy of the classifications do not significantly differ between corrected and uncorrected images. Spatial patterns of land-cover were analyzed in terms of colonization history, infrastructure, suitability of the land, and landownership. The actual use of the land is driven mainly by the ability to access the land and markets as is obvious in the distribution of land cover as a function of distance to rivers and roads. When considering all rivers and roads a threshold distance at which disproportional agro-pastoral land cover switches from over represented to under represented is at about 1km. Best land use suggestions seem not to affect the choice of land use. Differences in abundance of land cover between watersheds are more prevailing than differences between colonist and indigenous groups.

Exploring associations between violent discipline and aggressive behavior in children ages 4-5 in The Republic of Nicaragua: A secondary data analysis of the 2011 Demographic and Health Survey

Thesis (Master's)--University of Washington, 2016-06

Does mode of follow-up influence contraceptive use after medical abortion in a low-resource setting? Secondary outcome analysis of a non-inferiority randomized controlled trial

BACKGROUND: Post-abortion contraceptive use in India is low and the use of modern methods of contraception is rare, especially in rural areas. This study primarily compares contraceptive use among women whose abortion outcome was assessed in-clinic with women who assessed their abortion outcome at home, in a low-resource, primary health care setting. Moreover, it investigates how background characteristics and abortion service provision influences contraceptive use post-abortion. METHODS: A randomized controlled, non-inferiority, trial (RCT) compared clinic follow-up with home-assessment of abortion outcome at 2 weeks post-abortion. Additionally, contraceptive-use at 3 months post-abortion was investigated through a cross-sectional follow-up interview with a largely urban sub-sample of women from the RCT. Women seeking abortion with a gestational age of up to 9 weeks and who agreed to a 2-week follow-up were included (n = 731). Women with known contraindications to medical abortions, Hb < 85 mg/l and aged below 18 were excluded. Data were collected between April 2013 and August 2014 in six primary health-care clinics in Rajasthan. A computerised random number generator created the randomisation sequence (1:1) in blocks of six. Contraceptive use was measured at 2 weeks among women successfully followed-up (n = 623) and 3 months in the sub-set of women who were included if they were recruited at one of the urban study sites, owned a phone and agreed to a 3-month follow-up (n = 114). RESULTS: There were no differences between contraceptive use and continuation between study groups at 3 months (76 % clinic follow-up, 77 % home-assessment), however women in the clinic follow-up group were most likely to adopt a contraceptive method at 2 weeks (62 ± 12 %), while women in the home-assessment group were most likely to adopt a method after next menstruation (60 ± 13 %). Fifty-two per cent of women who initiated a method at 2 weeks chose the 3-month injection or the copper intrauterine device. Only 4 % of women preferred sterilization. Caste, educational attainment, or type of residence did not influence contraceptive use. CONCLUSIONS: Simplified follow-up after early medical abortion will not change women's opportunities to access contraception in a low-resource setting, if contraceptive services are provided as intra-abortion services as early as on day one. Women's postabortion contraceptive use at 3 months is unlikely to be affected by mode of followup after medical abortion, also in a low-resource setting. Clinical guidelines need to encourage intra-abortion contraception, offering the full spectrum of evidence-based methods, especially long-acting reversible methods. TRIAL REGISTRATION: Clinicaltrials.gov NCT01827995.

Test of Emotion Comprehension: Exploring the underlying structure through Confirmatory Factor Analysis and Similarity Structure Analysis

Some decades of research on emotional development have underlined the contribution of several domains to emotional understanding in childhood. Based on this research, Pons and colleagues (Pons & Harris, 2002; Pons, Harris & Rosnay, 2004) have proposed the Test of Emotion Comprehension (TEC) which assesses nine domains of emotional understanding, namely the recognition of emotions, based on facial expressions; the comprehension of external emotional causes; impact of desire on emotions; emotions based on beliefs; memory influence on emotions; possibility of emotional regulation; possibility of hiding an emotional state; having mixed emotions; contribution of morality to emotional experiences. This instrument was administered individually to 182 Portuguese children aged between 8 and 11 years, of 3rd and 4th grades, in public schools. Additionally, we used the Socially in Action-Peers (SAp) (Rocha, Candeias & Lopes da Silva, 2012) to assess TEC’s criterion-related validity. Mean differences results in TEC by gender and by socio-economic status (SES) were analyzed. The results of the TEC’s psychometric analysis were performed in terms of items’ sensitivity and reliability (stability, test-retest). Finally, in order to explore the theoretical structure underlying TEC a Confirmatory Factor Analysis and a Similarity Structure Analysis were computed. Implications of these findings for emotional understanding assessment and intervention in childhood are discussed.

The molecular characterization of RNA segment S9 of grass carp hemorrhage virus (GCHV), an aquareovirus

Although reovirus infection is one of the major virus diseases of grass carp in China, the available knowledge on the structure and function of genes and proteins of the virus is limited. The complete sequence of the S9 genome segment of grass carp hemorrhage virus (GCHV) was determined. The segment consists of 1130 nucleotides and has a large open reading frame (ORF) encoding a protein of 352 amino acids with predicted molecular mass of 37.7 kDa. Amino acid sequence comparison revealed that the deduced protein encoded by GCHV S9 is closely related to the sigma NS proteins of mammalian reovirus (MRV) and avian reovirus (ARV). Secondary structure analysis displayed that the form of alpha -helices (40.1%) and beta -sheets (49.4%) are the richest two contents in the protein encoded by S9, and this protein is predicted to be a nonstructural protein. (C) 2001 Elsevier Science B.V. All rights reserved.

Cloning and expression of tumor necrosis factor (TNF alpha) cDNA from red seabream Pagrus major

A fragment of TNFalpha cDNA sequence from red seabream was cloned by homology cloning approach with two degenerated primers which were designed based on the conserved regions of other animals' TNF sequences. The sequence was elongated by 3' and 5' RACE to get the full length CDS sequence. This sequence contained 1264 nucleotides that included a 5' UTR of 85 bp, a 3' UTR of 514 bp and an open reading frame (ORF) of 666 bp which could encode 222 amino acids propeptide. In 3' UTR, there were several mRNA instability motifs and three endotoxin-responsive sequences, but the sequence lacked the polyadenylation signal. The deduced peptide had a clear transmembrane domain, a TNFalpha family signature and a TNF2 family profile. The cell attachment sequence and the glycosaminoglycan attachment sites were also found in the sequence. The red seabream TNF sequence shared relatively high similarity with both mammalian TNFalpha and TNFbeta by multiple sequence alignments. Phylogenetic analysis showed that the piscine TNFalpha were located independently in a different branch compared with mammalian TNFalpha and TNFbeta. Based on the primary and secondary structure analysis and gene expression study, we could concluded that the red seabream TNF should be a TNFalpha, not TNFbeta. RT-PCR was used to study TNFa transcript expression. 24 h after the red seabream was challenged by Vibrio anguillarum, the RS TNFalpha transcript expression were detected in blood, brain, gill, heart, head kidney, kidney, Ever, muscle and spleen. Results showed that TNFalpha mRNA was constitutively expressed in parts of the tissues both in stimulated and unstimulated fish and the expression could be enhanced after the pathogen infection.

Purification, and Biochemical and Biophysical Characterization of Cellobiohydrolase I from Trichoderma harzianum IOC 3844

Because of its elevated cellulolytic activity, the filamentous fungus Trichoderma harzianum has a considerable potential in biomass hydrolysis applications. Trichoderma harzianum cellobiohydrolase I (ThCBHI), an exoglucanase, is an important enzyme in the process of cellulose degradation. Here, we report an easy single-step ion-exchange chromatographic method for purification of ThCBHI and its initial biophysical and biochemical characterization. The ThCBHI produced by induction with microcrystalline cellulose under submerged fermentation was purified on DEAE-Sephadex A-50 media and its identity was confirmed by mass spectrometry. The ThCBHI biochemical characterization showed that the protein has a molecular mass of 66 kDa and pi of 5.23. As confirmed by small-angle X-ray scattering (SAXS), both full-length ThCBHI and its catalytic core domain (CCD) obtained by digestion with papain are monomeric in solution. Secondary structure analysis of ThCBHI by circular dichroism revealed alpha-helices and beta-strands contents in the 28% and 38% range, respectively. The intrinsic fluorescence emission maximum of 337 nm was accounted for as different degrees of exposure of ThCBHI tryptophan residues to water. Moreover, ThCBHI displayed maximum activity at pH 5.0 and temperature of 50 degrees C with specific activities against Avicel and p-nitrophenyl-beta-D-cellobioside of 1.25 U/mg and 1.53 U/mg, respectively.

Aktivierung von Hämocyanin zur Tyrosinase

Ziel der Arbeit war die enzymatische Aktivierung von Cheliceraten-Hämocyanin zur Erforschung ihrer Phenoloxidase-Aktivität. Hierzu wurden zwei Hämocyanine in vergleichenden Untersuchungen herangezogen: Das bekannte 24-mer aus der Spinne Eurypelma californicum und das ebenfalls 24-mere Hämocyanin des Skorpions Pandinus imperator, dessen Struktur hier aufgeklärt wurde. Elektronenmikroskopisch und in der dynamischer Lichtstreuung sind sich beide Hämocyanine sehr ähnlich und sedimentieren bei analytischer Ultrazentrifugation ebenfalls in gleicher Weise (Sedimentationskoeffizient von 37 S (S20, W)). Durch Dissoziation im alkalischen Milieu gewinnt man bis zu zwölf Untereinheiten, von denen sich neun immunologisch unterscheiden lassen. Das absorptionsspektroskopische Verhalten von P. imperator- und E. californicum-Hämocyanin sowie Sekundärstrukturanalyse mittels CD-Spektroskopie ist nahezu identisch. Die Stabilität des Hämocyanins gegenüber Temperatur und Denaturierungsmitteln wurde mit Circulardichroismus- und Fluoreszenzspektroskopie sowie durch die enzymatische Aktivität untersucht. Erstmals konnten die Hämocyanine von P. imperator und E. californicum nicht nur zu einer stabilen Diphenoloxidase umgewandelt werden, sondern auch eine Monophenolhydroxylase-Aktivität induziert und reguliert werden. Für letztere Aktivität ist dabei die Präsenz von Tris- oder Hepes-Puffer wesentlich. Während sich die Monophenolhydroxylase-Aktivität nur auf Ebene der oligomeren Zustände beobachten lässt, erkennt man bei den isolierten Untereinheiten-Typen lediglich eine Diphenoloxidase-Aktivität. Bei dem Spinnen-Hämocyanin zeigen die Untereinheiten bc die stärkste katalytische Aktivität auf, bei P. imperator-Hämocyanin findet man drei bis vier Untereinheiten, die enzymatisch aktiv sind. Die Aktivierung mit SDS liefert den Hinweis, dass die Quartärstruktur in eine andere Konformation gebracht und nicht durch SDS denaturiert wird. Zugabe von Mg2+ reguliert die Phenoloxidase-Aktivität und verschiebt bei P. imperator-Hämocyanin die enzymatische Aktivität zugunsten der Diphenoloxidase. Mit keiner der zur Verfügung stehenden Methoden konnte jedoch ein Konformationsübergang eindeutig nachgewiesen werden. Die Stabilität scheint durch die niedrigen SDS-Konzentrationen nicht beeinträchtigt zu werden. Die sehr lange “Verzögerungsphase“ bei der Monophenolhydroxylase-Aktivität konnte durch Zugabe von katalytischem Diphenol drastisch verkürzt werden, was ein Hinweis auf die echte Tyrosinase-Aktivität des aktivierten Hämocyanins ist. Ein in vivo-Aktivator konnte bis jetzt noch nicht gefunden werden. Trotzdem scheinen die Hämocyanine in der Immunologie von Cheliceraten eine bedeutende Rolle zu spielen, indem sie die Rolle der Tyrosinasen / Phenoloxidasen beziehungsweise Catecholoxidasen übernehmen, die bei Cheliceraten nicht vorkommen. Weitere Möglichkeiten des Cheliceraten-Immunsystems, eindringende Fremdorganismen abzuwehren, wurden untersucht. Das Fehlen einer ´echten` Phenoloxidase-Aktivität bei den Cheliceraten, mit der Fähigkeit, sowohl mono- als auch diphenolische Substrate umzusetzen, stützt die Hypothese, dass aktiviertes Hämocyanin in vivo an die Stelle der Phenoloxidase tritt.