An assessment of gene prediction accuracy in large DNA sequences

One of the first useful products from the human genome will be a set of predicted genes. Besides its intrinsic scientific interest, the accuracy and completeness of this data set is of considerable importance for human health and medicine. Though progress has been made on computational gene identification in terms of both methods and accuracy evaluation measures, most of the sequence sets in which the programs are tested are short genomic sequences, and there is concern that these accuracy measures may not extrapolate well to larger, more challenging data sets. Given the absence of experimentally verified large genomic data sets, we constructed a semiartificial test set comprising a number of short single-gene genomic sequences with randomly generated intergenic regions. This test set, which should still present an easier problem than real human genomic sequence, mimics the approximately 200kb long BACs being sequenced. In our experiments with these longer genomic sequences, the accuracy of GENSCAN, one of the most accurate ab initio gene prediction programs, dropped significantly, although its sensitivity remained high. Conversely, the accuracy of similarity-based programs, such as GENEWISE, PROCRUSTES, and BLASTX was not affected significantly by the presence of random intergenic sequence, but depended on the strength of the similarity to the protein homolog. As expected, the accuracy dropped if the models were built using more distant homologs, and we were able to quantitatively estimate this decline. However, the specificities of these techniques are still rather good even when the similarity is weak, which is a desirable characteristic for driving expensive follow-up experiments. Our experiments suggest that though gene prediction will improve with every new protein that is discovered and through improvements in the current set of tools, we still have a long way to go before we can decipher the precise exonic structure of every gene in the human genome using purely computational methodology.

A general definition and nomenclature for alternative splicing events

Understanding the molecular mechanisms responsible for the regulation of the transcriptome present in eukaryotic cells isone of the most challenging tasks in the postgenomic era. In this regard, alternative splicing (AS) is a key phenomenoncontributing to the production of different mature transcripts from the same primary RNA sequence. As a plethora ofdifferent transcript forms is available in databases, a first step to uncover the biology that drives AS is to identify thedifferent types of reflected splicing variation. In this work, we present a general definition of the AS event along with anotation system that involves the relative positions of the splice sites. This nomenclature univocally and dynamically assignsa specific ‘‘AS code’’ to every possible pattern of splicing variation. On the basis of this definition and the correspondingcodes, we have developed a computational tool (AStalavista) that automatically characterizes the complete landscape of ASevents in a given transcript annotation of a genome, thus providing a platform to investigate the transcriptome diversityacross genes, chromosomes, and species. Our analysis reveals that a substantial part—in human more than a quarter—ofthe observed splicing variations are ignored in common classification pipelines. We have used AStalavista to investigate andto compare the AS landscape of different reference annotation sets in human and in other metazoan species and found thatproportions of AS events change substantially depending on the annotation protocol, species-specific attributes, andcoding constraints acting on the transcripts. The AStalavista system therefore provides a general framework to conductspecific studies investigating the occurrence, impact, and regulation of AS.

Benefit of Cup Medialization in Total Hip Arthroplasty is Associated With Femoral Anatomy.

BACKGROUND: Medialization of the cup with a respective increase in femoral offset has been proposed in THA to increase abductor moment arms. Insofar as there are potential disadvantages to cup medialization, it is important to ascertain whether the purported biomechanical benefits of cup medialization are large enough to warrant the downsides; to date, studies regarding this question have disagreed. QUESTIONS/PURPOSES: The purpose of this study was to quantify the effect of cup medialization with a compensatory increase in femoral offset compared with anatomic reconstruction for patients undergoing THA. We tested the hypothesis that there is a (linear) correlation between preoperative anatomic parameters and muscle moment arm increase caused by cup medialization. METHODS: Fifteen patients undergoing THA were selected, covering a typical range of preoperative femoral offsets. For each patient, a finite element model was built based on a preoperative CT scan. The model included the pelvis, femur, gluteus minimus, medius, and maximus. Two reconstructions were compared: (1) anatomic position of the acetabular center of rotation, and (2) cup medialization compensated by an increase in the femoral offset. Passive abduction-adduction and flexion-extension were simulated in the range of normal gait. Muscle moment arms were evaluated and correlated to preoperative femoral offset, acetabular offset, height of the greater trochanter (relative to femoral center of rotation), and femoral antetorsion angle. RESULTS: The increase of muscle moment arms caused by cup medialization varied among patients. Muscle moment arms increase by 10% to 85% of the amount of cup medialization for abduction-adduction and from -35% (decrease) to 50% for flexion-extension. The change in moment arm was inversely correlated (R(2) = 0.588, p = 0.001) to femoral antetorsion (anteversion), such that patients with less femoral antetorsion gained more in terms of hip muscle moments. No linear correlation was observed between changes in moment arm and other preoperative parameters in this series. CONCLUSIONS: The benefit of cup medialization is variable and depends on the individual anatomy. CLINICAL RELEVANCE: Cup medialization with compensatory increase of the femoral offset may be particularly effective in patients with less femoral antetorsion. However, cup medialization must be balanced against its tradeoffs, including the additional loss of medial acetabular bone stock, and eventual proprioceptive implications of the nonanatomic center of rotation and perhaps joint reaction forces. Clinical studies should better determine the relevance of small changes of moment arms on function and joint reaction forces.

Phosphatidylethanolamine critically supports internalization of cell-penetrating protein C inhibitor.

Although their contribution remains unclear, lipids may facilitate noncanonical routes of protein internalization into cells such as those used by cell-penetrating proteins. We show that protein C inhibitor (PCI), a serine protease inhibitor (serpin), rapidly transverses the plasma membrane, which persists at low temperatures and enables its nuclear targeting in vitro and in vivo. Cell membrane translocation of PCI necessarily requires phosphatidylethanolamine (PE). In parallel, PCI acts as a lipid transferase for PE. The internalized serpin promotes phagocytosis of bacteria, thus suggesting a function in host defense. Membrane insertion of PCI depends on the conical shape of PE and is associated with the formation of restricted aqueous compartments within the membrane. Gain- and loss-of-function mutations indicate that the transmembrane passage of PCI requires a branched cavity between its helices H and D, which, according to docking studies, precisely accommodates PE. Our findings show that its specific shape enables cell surface PE to drive plasma membrane translocation of cell-penetrating PCI.

Impact of genetic SLC28 transporter and ITPA variants on ribavirin serum level, hemoglobin drop and therapeutic response in patients with HCV infection.

BACKGROUND & AIMS: In the last decade, pegylated interferon-α (PegIFN-α) plus ribavirin (RBV) was the standard treatment of chronic hepatitis C for genotype 1, and it remains the standard for genotypes 2 and 3. Recent studies reported associations between RBV-induced anemia and genetic polymorphisms of concentrative nucleoside transporters such as CNT3 (encoded by SLC28A3) and inosine triphosphatase (encoded by ITPA). We aimed at studying genetic determinants of RBV kinetics, efficacy and treatment-associated anemia. METHODS: We included 216 patients from two Swiss study cohorts (61% HCV genotype 1, 39% genotypes 2 or 3). Patients were analyzed for SLC28A2 single nucleotide polymorphism (SNP) rs11854484, SLC28A3 rs56350726, and SLC28A3 rs10868138 as well as ITPA SNPs rs1127354 and rs7270101, and followed for treatment-associated hemoglobin changes and sustained virological response (SVR). In 67 patients, RBV serum levels were additionally measured during treatment. RESULTS: Patients with SLC28A2 rs11854484 genotype TT had higher dosage- and body weight-adjusted RBV levels than those with genotypes TC or CC (p=0.02 and p=0.06 at weeks 4 and 8, respectively). ITPA SNP rs1127354 was associated with hemoglobin drop ≥3 g/dl during treatment, in genotype (relative risk (RR)=2.1, 95% CI 1.3-3.5) as well as allelic analyses (RR=2.0, 95%CI 1.2-3.4). SLC28A3 rs56350726 was associated with SVR in genotype (RR=2.2; 95% CI 1.1-4.3) as well as allelic analyses (RR=2.0, 95% CI 1.1-3.4). CONCLUSIONS: The newly identified association between RBV serum levels and SLC28A2 rs11854484 genotype, as well as the replicated association of ITPA and SLC28A3 genetic polymorphisms with RBV-induced anemia and treatment response, may support individualized treatment of chronic hepatitis C and warrant further investigation in larger studies.

Do pornographic websites influence boys' sexual behavior?

Purpose: To compare the sexual behavior of adolescent males who do and do not watch pornographic websites. Methods: This study was presented as a school survey. Data were drawn from the 2002 Swiss Multicenter Adolescent Survey on Health (SMASH02) database, a survey including 7,548 adolescents age 16-20. The setting was post-mandatory schools in Switzerland. A total of 2,891 male students who connected to the internet in the last 30 days were enrolled and distributed into two groups: boys who deliberately watched pornographic websites in the last 30 days (n ¼ 942; 33%) and boys who did not (n ¼ 1,949; 67%). Socio-demographic characteristics; frequency of connection to the internet; sexual behavior parameters (having a girlfriend and if yes, for more or less than 6 months; having had sexual intercourse; age at first sexual intercourse; use of a condom at last sexual intercourse; number of sexual partners; having made a partner pregnant). Results: A logistic regression was performed using STATA 9.2. The only significant socio-demographic variable was having a low socioeconomic status (adjusted odds ratio [AOR] 1.66); no difference was found for age and academic track between the two groups. Boys who watch pornographic websites were also significantly more likely to connect frequently to the internet (one day a week: AOR 1.75; several days a week: AOR 2.36; every day: AOR 3.11), to have had sexual intercourse (AOR 2.06), and to have had their first sexual intercourse before age 15 (AOR 1.48). The stability of the relationship with their girlfriend did not appear to have any influence on the search for pornography on the internet. Conclusions: About one third of boys in our sample report having accessed pornographic websites in the last 30 days, a proportion similar to other studies. Watching such websites increases with the frequency of connection to the internet and seems to be correlated with an earlier sexual activity debut among adolescent males. However, having had first sexual intercourse before age 15 is the only sexual risk behavior that seems to be increased when watching pornographic websites among boys. Further studies should address the causality of this correlation and the factors influencing the search for pornography on the web among boys, in order to explore some new ways of prevention about sexual risk behaviors. Sources of Support: The SMASH02 survey was carried out with the financial support of the Swiss Federal Office of Public Health and the participating cantons.

Oxidative folding of synthetic polypeptides S-protected as tert-butylthio derivatives.

A new method for oxidative folding of synthetic polypeptides assembled by stepwise solid phase synthesis is introduced. Folding is obtained in excellent yields by reacting S-tert-butylthiolated polypeptides with a 100-fold molar excess of cysteine at 37 degrees C in a slightly alkaline buffer containing chaotropic salts, and in the presence of air-oxygen. This novel protocol has been applied to the folding of S-tert-butylthiolated human thymus and activation-regulated chemokine (hu-TARC) derivatives as well as to larger segments of Plasmodium falciparum and Plasmodium berghei circumsporozoite proteins. Folded P. falciparum polypeptides have been used as substrates of endoproteinase Glu-C (Glu-C) and endoproteinase Asp-N (Asp-N) in an attempt to identify their disulfide connectivities. Particular practical advantages of the present method are (i) easy purification and storage of the S-protected peptide derivatives, (ii) elimination of the risk of cysteine alkylation during the acidolytic cleavage deprotection and resin cleavage steps, (iii) possibility to precisely evaluate the extent of folding and disulfide bond formation by mass spectrometry, and (iv) facile recovery of the final folded product.

The use of textbooks in Capeverdean secondary schools: The Relationship between Use, Evaluation and Adaptation of Textbooks

This study examines the relationship between teacher’s use of English textbooks and the way teachers evaluate and adapt them, looking at a particular context, the Capeverdean secondary schools, specifically in Praia. The referred relationship was analyzed through teachers’ responses about how they use, evaluate and adapt their textbooks. The results of the study revealed that, on the one hand, the way teachers use their textbooks influences the way they evaluate the same textbooks; on the other hand, the use of textbooks doesn’t necessarily influence the way teachers adapt them. Moreover, the findings revealed that, in general, due to some particular constraints the Capeverdean English teachers are using their textbooks as resources, in which several textbooks are used in combination with one another. Additionally, although teachers assume that they are doing their best, they still need more confidence concerning the way they use, evaluate and adapt available textbooks. Teachers’ confidence in the way they are using their textbooks can be reinforced by establishing an intensive teacher training module on materials evaluation and adaptation, taking into account that a textbook is one of the most important tools in the process of teaching and learning. I hope that the elements presented may lead to further studies on this matter, specifically regarding textbook evaluation and adaptation.

Epiphytic lichens as surrogates for biodiversity and ecosystem resilience in native oakwoods of the Baixo Tamega region (Northern Portugal)

In the last 50 years, concern about the loss of lichen diversity associated with forest management and forest fragmentation has led to many studies designed to assess patterns and monitor trends of lichen biodiversity in forests worldwide. However there are surprisingly few studies focusing on the effect of natural disturbance for epiphytic lichens in forest ecosystems and, especially, on how these changes affect the relationships between epiphytic lichens and other organisms. The major goal of this thesis was to characterize and valuate the epiphytic lichens in the Baixo Tamega region (northern Portugal) and to assess its vulnerability to several drivers of change, particularly fire. The study area is located in Aboboreira and Castelo, a mountain area with 105 km2 and a top altitude of approximately 1000 m.a.s.l. In this region, fire is one of the worst natural catastrophes not only because of its high frequency and wide extension but also because of their enormous destructive effects. This thesis has included three case studies that proved the need to develop management and conservation actions for the area. In the first study we assessed the epiphytic lichen diversity in the oak woods of the Aboboreira and Castelo mountains. Results have revealed high diversity value and presence of a lichen community that has suffered general decline throughout Europe. The second study has addressed the impact of fire over epiphytic lichens and community recovering patterns. Results observed along the fire gradient showed that the most common and abundant lichen species establish themselves early in post-fire gradient while “old-growth” associated lichens tend to recover slowly along the same gradient. The third study intended to evaluate the potential use of selected lichen species or groups as biodiversity surrogates, in a scenario of fire-controlled ecological changes. Results showed that the use of epiphytic lichens as surrogates of bryophyte and vascular plant diversity should consider not only species richeness and composition, but also occurrence of disturbing factors, such fire. among the studied groups, lichen genera is the only group that can be used as surrogate of total epiphytic lichen diversity, independently of fire induced changes

Book production and the onset of modern economic growth

Endogenous growth theory suggests that human capital formation plays a significant role for the wealth and poverty of nations. In contrast to previous studies which denied the role of human capital as a crucial determinant of for really long-term growth, we confirm its importance. Indicators of human capital like literacy rates are lacking for the period of 1450-1913; hence, we use per capita book production as a proxy for advanced literacy skills. This study explains how, and to what extent, growth disparities are a function of human capital formation.

Mutation analysis in 54 propionic acidemia patients.

Deficiency of propionyl CoA carboxylase (PCC), a dodecamer of alpha and beta subunits, causes inherited propionic acidemia. We have studied, at the molecular level, PCC in 54 patients from 48 families comprised of 96 independent alleles. These patients of various ethnic backgrounds came from research centers and hospitals in Germany, Austria and Switzerland. The thorough clinical characterization of these patients was described in the accompanying paper (Grünert et al. 2012). In all 54 patients, many of whom originated from consanguineous families, the entire PCCB gene was examined by genomic DNA sequencing and in 39 individuals the PCCA gene was also studied. In three patients we found mutations in both PCC genes. In addition, in many patients RT-PCR analysis of lymphoblast RNA, lymphoblast enzyme assays, and expression of new mutations in E.coli were carried out. Eight new and eight previously detected mutations were identified in the PCCA gene while 15 new and 13 previously detected mutations were found in the PCCB gene. One missense mutation, p.V288I in the PCCB gene, when expressed in E.coli, yielded 134% of control activity and was consequently classified as a polymorphism in the coding region. Numerous new intronic polymorphisms in both PCC genes were identified. This study adds a considerable amount of new molecular data to the studies of this disease.

Reconocimiento geofísico del deslizamiento de Rosiana (depresión de Tirajana, Gran Canaria)

The landslide of Rosiana is considered the largest slope movement amongst those known in historical times in Gran Canana, Canary Islands. It has been activated at least 4 times in the last century, and in the movement of 1956, when about 3.106 m3 of materials were involved, 250 people had to be evacuated and many buildings were destroyed. The present geological hazard has lead to specific studies of the phenomenon which, once characterised, can be used as a guide for the scientific and technical works that are to be made in this or similar areas. This paper wants to increase the knowledge about the unstable mass of Rosiana by using geophysical techniques based on the method of seismic by refraction. The geophysical measues have been interpreted with the aid of the available geomorphologic data, thus obtaining a first approximation to the geometry of the slope movements

Producción primaria en el ambiente marino en el Pacífico sudeste, Perú, 1960-2000

Los resultados de investigación sobre producción primaria dentro del alcance interdisciplinario del ambiente marino frente a la costa peruana incluyen estudios nacionales, extranjeros y de investigación conjunta a través de proyectos internacionales (1960-2000). La circulación en la costa peruana es dominada por una corriente hacia el ecuador en una capa de 20 a 50 m. La estructura de plumas del afloramiento se presenta en cada área y podría ser la clave para el desarrollo de cadenas cortas y productivas: fitoplancton peces clupeidos. La distribución de nutrientes sigue la pluma de temperatura, con altos valores en la costa y bajos lejos de la costa; la clorofila muestra mínimos valores cerca de la costa (10 mn) que se incrementa al alejarse. El crecimiento del fitoplancton en aguas peruanas, varía de 0,5 a 0,8 d/d. En aguas recién afloradas el crecimiento es limitado por falta de “condicionamiento biológico” y de compuestos orgánicos (15°S). Estos tipos de agua pueden estar relacionados con las “aguas azules” de altos nutrientes y pobre fitoplancton con células de pequeño tamaño (clorofila <2 μg/L) y con “aguas marrones” con denso fitoplancton, (clorofila >5 μg/L), mayor diversidad y con células de diámetro >5μ. La media de producción primaria fue 3 gC/m2/d (1960-1985), comparable a la mayoría de estudios en los cuales varía entre 3 y 4 gC/m2/d en la franja costera, el último valor es altamente variable en espacio, siendo más frecuente dentro de 10 km. Valores mayores de 12 gC/m2/d se encontraron en el afloramiento de Chimbote. El Niño, La Niña y fases del ENSO, afectan la producción primaria. Las temperaturas bajas originan cambios en la composición química del fitoplancton y reducen el índice de productividad mgC/mgclor-a/d que también es atribuido a limitaciones de luz.

Monitoreo y marcación de invertebrados marinos, Callao, Perú, 2014

En los alrededores de la isla San Lorenzo, en el 2014, bimensualmente se efectuaron muestreos en siete estaciones, monitoreando a los bivalvos Argopecten purpuratus, Glycymeris ovata y los crustáceos Romaleon polyodon, Cancer coronatus, Cancer porteri y Hepatus chilensis; también, se efectuaron experimentos de marcación y recaptura para determinar tasas de crecimiento en A. purpuratus, G. ovata, Semele spp., Gari solida y Protothaca thaca. A. purpuratus fue más abundante a finales del año, periodo en el que (como en el 2013) se registraron mayores valores de oxígeno a nivel de fondo del mar. R. polyodon presentó tendencia creciente de la talla media y biomasa. C. coronatus fue observado frecuentemente al norte de la isla San Lorenzo con densidades máximas de 10,67 ejemplares.10min. El cangrejo Platymera gaudichaudii fue observado solo en diciembre con densidades medias de 24 ejemplares.10 min de buceo. Se marcaron 7214 ejemplares y recapturaron 2730 ejemplares. G. ovata tuvo el 80% de recaptura y A. purpuratus 24%. Las tasas de crecimiento presentaron tendencias decrecientes a mayores tallas en todas las especies. En G. ovata la tasa de crecimiento fue mayor en ejemplares liberados en La Pampa diferente al comportamiento en Cabinzas; también se observaron diferencias entre las almejas Semele spp. y Gari solida. La abundancia de G. ovata en mayo y setiembre fue de hasta 190 ejemplares y 648,6 g por m². Las mayores densidades se registraron al noroeste de la isla San Lorenzo, mayor incidencia de esta especie estuvo en el substrato formado por conchuela molida. El rendimiento de G. ovata fue mayor en el área La Pampa respecto a Cabinzas, Palomino y Mal Nombre.

Ranibizumab versus Bevacizumab for Neovascular Age-related Macular Degeneration: Results from the GEFAL Noninferiority Randomized Trial.

OBJECTIVE: To evaluate the relative efficacy and safety profile of bevacizumab versus ranibizumab intravitreal injections for the treatment of neovascular age-related macular degeneration (AMD). DESIGN: Multicenter, prospective, noninferiority, double-masked, randomized clinical trial performed in 38 French ophthalmology centers. The noninferiority limit was 5 letters. PARTICIPANTS: Patients aged ≥50 years were eligible if they presented with subfoveal neovascular AMD, with best-corrected visual acuity (BVCA) in the study eye of between 20/32 and 20/320 measured on the Early Treatment of Diabetic Retinopathy Study chart and a lesion area of less than 12 optic disc areas (DA). METHODS: Patients were randomly assigned to intravitreal administration of bevacizumab (1.25 mg) or ranibizumab (0.50 mg). Hospital pharmacies were responsible for preparing, blinding, and dispensing treatments. Patients were followed for 1 year, with a loading dose of 3 monthly intravitreal injections, followed by an as-needed regimen (1 injection in case of active disease) for the remaining 9 months with monthly follow-up. MAIN OUTCOME MEASURES: Mean change in visual acuity at 1 year. RESULTS: Between June 2009 and November 2011, 501 patients were randomized. In the per protocol analysis, bevacizumab was noninferior to ranibizumab (bevacizumab minus ranibizumab +1.89 letters; 95% confidence interval [CI], -1.16 to +4.93, P < 0.0001). The intention-to-treat analysis was concordant. The mean number of injections was 6.8 in the bevacizumab group and 6.5 in the ranibizumab group (P = 0.39). Both drugs reduced the central subfield macular thickness, with a mean decrease of 95 μm for bevacizumab and 107 μm for ranibizumab (P = 0.27). There were no significant differences in the presence of subretinal or intraretinal fluid at final evaluation, dye leakage on angiogram, or change in choroidal neovascular area. The proportion of patients with serious adverse events was 12.6% in the bevacizumab group and 12.1% in the ranibizumab group (P = 0.88). The proportion of patients with serious systemic or ocular adverse events was similar in both groups. CONCLUSIONS: Bevacizumab was noninferior to ranibizumab for visual acuity at 1 year with similar safety profiles. Ranibizumab tended to have a better anatomic outcome. The results are similar to those of previous head-to-head studies. FINANCIAL DISCLOSURE(S): Proprietary or commercial disclosure may be found after the references.