The distinctive signatures of promoter regions and operon junctions across prokaryotes

Here we show that regions upstream of first transcribed genes have oligonucleotide signatures that distinguish them from regions upstream of genes in the middle of operons. Databases of experimentally confirmed transcription units do not exist for most genomes. Thus, to expand the analyses into genomes with no experimentally confirmed data, we used genes conserved adjacent in evolutionarily distant genomes as representatives of genes inside operons. Likewise, we used divergently transcribed genes as representative examples of first transcribed genes. In model organisms, the trinucleotide signatures of regions upstream of these representative genes allow for operon predictions with accuracies close to those obtained with known operon data (0.8). Signature-based operon predictions have more similar phylogenetic profiles and higher proportions of genes in the same pathways than predicted transcription unit boundaries (TUBs). These results confirm that we are separating genes with related functions, as expected for operons, from genes not necessarily related, as expected for genes in different transcription units. We also test the quality of the predictions using microarray data in six genomes and show that the signature-predicted operons tend to have high correlations of expression. Oligonucleotide signatures should expand the number of tools available to identify operons even in poorly characterized genomes

Second record of Pseudimares aphrodite H. Asp?ck et U. Asp?ck, 2009 (Neuroptera, Myrmeleontidae)

Some adults of Pseudimares aphrodite H. Asp?ck et U. Asp?ck, 2009 were observed and photographed while attracted by light in Southern Morocco, in August 2009 and 2011. Only the typus of this species, a male, was known previously from South Morocco too. Moreover the genus Pseudimares Kimmins, 1933 is perhaps the most enigmatic taxon among Neuroptera Myrmeleontidae. Its second species Pseudimares iris Kimmins, 1933 from Southern Iran is known also only in the type series, a male and a female. What little information we know about Pseudimares is reporte

Teprotumumab for Thyroid-Associated Ophthalmopathy

BACKGROUND: Thyroid-associated ophthalmopathy, a condition commonly associated with Graves’ disease, remains inadequately treated. Current medical therapies, which primarily consist of glucocorticoids, have limited efficacy and present safety concerns. Inhibition of the insulin-like growth factor I receptor (IGF-IR) is a new therapeutic strategy to attenuate the underlying autoimmune pathogenesis of ophthalmopathy. / METHODS: We conducted a multicenter, double-masked, randomized, placebo-controlled trial to determine the efficacy and safety of teprotumumab, a human monoclonal antibody inhibitor of IGF-IR, in patients with active, moderate-to-severe ophthalmopathy. A total of 88 patients were randomly assigned to receive placebo or active drug administered intravenously once every 3 weeks for a total of eight infusions. The primary end point was the response in the study eye. This response was defined as a reduction of 2 points or more in the Clinical Activity Score (scores range from 0 to 7, with a score of ≥3 indicating active thyroid-associated ophthalmopathy) and a reduction of 2 mm or more in proptosis at week 24. Secondary end points, measured as continuous variables, included proptosis, the Clinical Activity Score, and results on the Graves’ ophthalmopathy–specific quality-of-life questionnaire. Adverse events were assessed. / RESULTS: In the intention-to-treat population, 29 of 42 patients who received teprotumumab (69%), as compared with 9 of 45 patients who received placebo (20%), had a response at week 24 (P<0.001). Therapeutic effects were rapid; at week 6, a total of 18 of 42 patients in the teprotumumab group (43%) and 2 of 45 patients in the placebo group (4%) had a response (P<0.001). Differences between the groups increased at subsequent time points. The only drug-related adverse event was hyperglycemia in patients with diabetes; this event was controlled by adjusting medication for diabetes. / CONCLUSIONS: In patients with active ophthalmopathy, teprotumumab was more effective than placebo in reducing proptosis and the Clinical Activity Score. (Funded by River Vision Development and others; ClinicalTrials.gov number, NCT01868997.

Factor XIII A-Subunit V34L Variant Affects Thrombus Cross-Linking in a Murine Model of Thrombosis

Objective-Factor XIII (FXIII) cross-links fibrin upon activation by thrombin. Activation involves cleavage at residue 37 by thrombin, releasing an activation peptide. A common polymorphism (valine to leucine variant at residue 34, V34L), located in the activation peptide, has been associated with increased activation rates and paradoxically a protective effect in cardiovascular disease. There is, currently, no data available on the effects of V34L from in vivo models of thrombosis. We examined the effect of FXIII V34L on clot formation and cross-linking in vivo. Approach and Results-We generated a panel of full-length recombinant human FXIII-A2 variants with amino acid substitutions in the activation peptide to investigate the effect of these variants on activation rate, and we used wild-type, V34L, and alanine to glycine variant at residue 33 variants to study the effects of varying FXIII activation rate on thrombus formation in a murine model of FeCl3 injury. FXIII activation assay showed that residues 29, 30, 33, and 34 play a critical role in thrombin interaction. Full-length recombinant human FXIII-A2 V34L has significant effects on clot formation, structure, and lysis in vitro, using turbidity assay. This variant influenced fibrin cross-linking but not size of the thrombus in vivo. Conclusions-Mutations in the activation peptide of full-length recombinant FXIII regulate activation rates by thrombin, and V34L influences in vivo thrombus formation by increased cross-linking of the clot

Structural and functional characterization of Pseudomonas aeruginosa CupB chaperones

Pseudomonas aeruginosa, an important human pathogen, is estimated to be responsible for,10% of nosocomial infections worldwide. The pathogenesis of P. aeruginosa starts from its colonization in the damaged tissue or medical devices (e. g. catheters, prothesis and implanted heart valve etc.) facilitated by several extracellular adhesive factors including fimbrial pili. Several clusters containing fimbrial genes have been previously identified on the P. aeruginosa chromosome and named cup [1]. The assembly of the CupB pili is thought to be coordinated by two chaperones, CupB2 and CupB4. However, due to the lack of structural and biochemical data, their chaperone activities remain speculative. In this study, we report the 2.5 A crystal structure of P. aeruginosa CupB2. Based on the structure, we further tested the binding specificity of CupB2 and CupB4 towards CupB1 (the presumed major pilus subunit) and CupB6 (the putative adhesin) using limited trypsin digestion and strep-tactin pull-down assay. The structural and biochemical data suggest that CupB2 and CupB4 might play different, but not redundant, roles in CupB secretion. CupB2 is likely to be the chaperone of CupB1, and CupB4 could be the chaperone of CupB4:CupB5:CupB6, in which the interaction of CupB4 and CupB6 might be mediated via CupB5

Production of monoclonal antibodies for detection of a secreted aspartyl proteinase from Candida spp. in biologic specimens

Secreted acid proteinases (SAP) constitute an important group of virulence factors in Candida albicans. In the present work, an acid proteinase from C. albicans was sequentially purified from the supernatant of a yeast culture by precipitation with ammonium sulfate, ion exchange chromatography, and molecular exclusion chromatography, yielding a specific enzymatic activity of 204.1 IU/mg on bovine serum albumin (BSA). The molecular mass of the purified proteinase was estimated at 43 kd after exclusion chromatography and at 41 kd by nondenaturating sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The purified proteinase was able to degrade BSA at pH 2.5, but was not active on collagen, and it was significantly inhibited by pepstatin A. The immunization of BALB/c mice with the purified proteinase and later fusion of their spleen cells with myeloma cells resulted in 19 monoclonal antibody secreting hybridomas (MAbs) capable of detecting SAP in enzyme-linked immunosorbent assay ( ELISA) assays. All MAbs obtained are isotype IgG1 kappa (kappa) immunoglobulins and develop a 41 kd protein band by Western blot (WB) in samples of SAP obtained from C. albicans (12-A) and C. dubliniensis ( strain 778) crude extracts. The anti-SAP MAbs were used in capture ELISA and two combinations of these antibodies proved suitable for SAP detection, that is, MAP1 (1B1B3) or MAP2 (2D2C10) as coat antibodies, and biotinylated MAP3 (2A6E8) as detect antibody. Capture ELISA using these sets of MAbs detected over 32 ng/mL protein in purified SAP samples as well as in crude C. albicans and C. dubliniensis extracts. The results herein obtained allow for the prediction of how this set of antibodies can be useful for SAP detection in biologic specimens.26420120

Human-like PB2 627K Influenza Virus Polymerase Activity Is Regulated by Importin-α1 and -α7

Influenza A viruses may cross species barriers and transmit to humans with the potential to cause pandemics. Interplay of human- (PB2 627K) and avian-like (PB2 627E) influenza polymerase complexes with unknown host factors have been postulated to play a key role in interspecies transmission. Here, we have identified human importin-α isoforms (α1 and α7) as positive regulators of human- but not avian-like polymerase activity. Human-like polymerase activity correlated with efficient recruitment of α1 and α7 to viral ribonucleoprotein complexes (vRNPs) without affecting subcellular localization. We also observed that human-like influenza virus growth was impaired in α1 and α7 downregulated human lung cells. Mice lacking α7 were less susceptible to human- but not avian-like influenza virus infection. Thus, α1 and α7 are positive regulators of human-like polymerase activity and pathogenicity beyond their role in nuclear transport

The quest for the solar g modes

Solar gravity modes (or g modes) -- oscillations of the solar interior for which buoyancy acts as the restoring force -- have the potential to provide unprecedented inference on the structure and dynamics of the solar core, inference that is not possible with the well observed acoustic modes (or p modes). The high amplitude of the g-mode eigenfunctions in the core and the evanesence of the modes in the convection zone make the modes particularly sensitive to the physical and dynamical conditions in the core. Owing to the existence of the convection zone, the g modes have very low amplitudes at photospheric levels, which makes the modes extremely hard to detect. In this paper, we review the current state of play regarding attempts to detect g modes. We review the theory of g modes, including theoretical estimation of the g-mode frequencies, amplitudes and damping rates. Then we go on to discuss the techniques that have been used to try to detect g modes. We review results in the literature, and finish by looking to the future, and the potential advances that can be made -- from both data and data-analysis perspectives -- to give unambiguous detections of individual g modes. The review ends by concluding that, at the time of writing, there is indeed a consensus amongst the authors that there is currently no undisputed detection of solar g modes.Comment: 71 pages, 18 figures, accepted by Astronomy and Astrophysics Revie

Efecto de diferentes regimenes de riego sobre la carga frutal, tama\uf1o de fruta y rendimiento del olivo cv. Sevillana

In order to determine the effects of different regulated deficit irrigation (RDC) strategies in olives ( Olea europea L.), four irrigation treatments were applied, for three seasons, in an eight-year-old orchard of cv. 'Sevillana' olives, growing in the locality of Tierras Blanca, San Felipe, V Region, Chile (32\ub047' S; 70\ub042' W; 800 m above sea level). Treatments were: T1, irrigated at 100% of crop evapotranspiration (ETc) for the entire season; T2, 100% ETc from beginning of shoot growth until the end of fruit growth stage II and 40% ETc during stage III; T3, 100% ETc from beginning of shoot growth until the end of fruit growth stage II and 25% ETc during stage III; and T4, 60% ETc throughout the entire season. Both stem water potential and stomatal conductance were affected by RDC, especially when 40 and 25% ETc were applied. During fruit stage III, water stress did not affect the fruit-bearing load, however during this stage severe water stress affected the final fruit weight. Water stress during the whole season (60% ETc), produced a strong reduction on the fruit-bearing load of the season of high production, which seems to have its origin in the previous season. According to the results, the best strategy for RDC in olives seems to be moderate stress (application of 40% Etc) in phase III of fruit growth.Con el objetivo de determinar el efecto de diferentes estrategias de riego deficitario controlado (RDC) en olivos ( Olea europea L.), se aplicaron cuatro tratamientos de riego, en tres temporadas, a un huerto de ocho a\uf1os de edad, del cv. Sevillana, ubicado en la localidad de Tierras Blancas, San Felipe, V Regi\uf3n (32\ub047' lat. Sur, 70\ub042' long. Oeste, 800 m.s.n.m). Los tratamientos fueron: T1, regado con el equivalente al 100% de la evapotranspiraci\uf3n del cultivo (ETc) durante toda la temporada; T2, 100% de la ETc desde brotaci\uf3n hasta el t\ue9rmino de la fase II de crecimiento del fruto y 40% durante la fase III; T3, 100% de la ETc desde brotaci\uf3n hasta el t\ue9rmino de la fase II de crecimiento del fruto y 25% durante la fase III; y T4, 60% de la ETc durante toda la temporada. Tanto el potencial h\ueddrico xilem\ue1tico como la conductancia estom\ue1tica se vieron afectados por la aplicaci\uf3n de riego restringido, especialmente cuando se aplicaron 40 y 25% de la ETc. D\ue9ficit h\ueddricos durante la fase III de crecimiento de frutos no afectaron la carga frutal, sin embargo restricciones h\ueddricas severas durante esta fase tuvieron incidencia en el peso final del fruto. D\ue9ficit h\ueddricos durante toda la temporada (60% ETc), produjeron una fuerte reducci\uf3n en la carga frutal de la temporada de alta producci\uf3n, la que parece tener su origen en el a\uf1o anterior. De acuerdo a los resultados, la mejor estrategia RDC en olivo parece ser un estr\ue9s moderado (aplicaci\uf3n del 40% de la ETc) en la fase III de crecimiento del fruto