Identification of a BRCA1-mRNA splicing complex required for efficient DNA repair and maintenance of genomic stability

Mutations within BRCA1 predispose carriers to a high risk of breast and ovarian cancers. BRCA1 functions to maintain genomic stability through the assembly of multiple protein complexes involved in DNA repair, cell-cycle arrest, and transcriptional regulation. Here, we report the identification of a DNA damage-induced BRCA1 protein complex containing BCLAF1 and other key components of the mRNA-splicing machinery. In response to DNA damage, this complex regulates pre-mRNA splicing of a number of genes involved in DNA damage signaling and repair, thereby promoting the stability of these transcripts/proteins. Further, we show that abrogation of this complex results in sensitivity to DNA damage, defective DNA repair, and genomic instability. Interestingly, mutations in a number of proteins found within this complex have been identified in numerous cancer types. These data suggest that regulation of splicing by the BRCA1-mRNA splicing complex plays an important role in the cellular response to DNA damage.

Global, regional, and national disability-adjusted life years (DALYs) for 306 diseases and injuries and healthy life expectancy (HALE) for 188 countries, 1990–2013: Quantifying the epidemiological transition

Background The Global Burden of Disease Study 2013 (GBD 2013) aims to bring together all available epidemiological data using a coherent measurement framework, standardised estimation methods, and transparent data sources to enable comparisons of health loss over time and across causes, age–sex groups, and countries. The GBD can be used to generate summary measures such as disability-adjusted life-years (DALYs) and healthy life expectancy (HALE) that make possible comparative assessments of broad epidemiological patterns across countries and time. These summary measures can also be used to quantify the component of variation in epidemiology that is related to sociodemographic development. Methods We used the published GBD 2013 data for age-specific mortality, years of life lost due to premature mortality (YLLs), and years lived with disability (YLDs) to calculate DALYs and HALE for 1990, 1995, 2000, 2005, 2010, and 2013 for 188 countries. We calculated HALE using the Sullivan method; 95% uncertainty intervals (UIs) represent uncertainty in age-specific death rates and YLDs per person for each country, age, sex, and year. We estimated DALYs for 306 causes for each country as the sum of YLLs and YLDs; 95% UIs represent uncertainty in YLL and YLD rates. We quantified patterns of the epidemiological transition with a composite indicator of sociodemographic status, which we constructed from income per person, average years of schooling after age 15 years, and the total fertility rate and mean age of the population. We applied hierarchical regression to DALY rates by cause across countries to decompose variance related to the sociodemographic status variable, country, and time. Findings Worldwide, from 1990 to 2013, life expectancy at birth rose by 6·2 years (95% UI 5·6–6·6), from 65·3 years (65·0–65·6) in 1990 to 71·5 years (71·0–71·9) in 2013, HALE at birth rose by 5·4 years (4·9–5·8), from 56·9 years (54·5–59·1) to 62·3 years (59·7–64·8), total DALYs fell by 3·6% (0·3–7·4), and age-standardised DALY rates per 100 000 people fell by 26·7% (24·6–29·1). For communicable, maternal, neonatal, and nutritional disorders, global DALY numbers, crude rates, and age-standardised rates have all declined between 1990 and 2013, whereas for non–communicable diseases, global DALYs have been increasing, DALY rates have remained nearly constant, and age-standardised DALY rates declined during the same period. From 2005 to 2013, the number of DALYs increased for most specific non-communicable diseases, including cardiovascular diseases and neoplasms, in addition to dengue, food-borne trematodes, and leishmaniasis; DALYs decreased for nearly all other causes. By 2013, the five leading causes of DALYs were ischaemic heart disease, lower respiratory infections, cerebrovascular disease, low back and neck pain, and road injuries. Sociodemographic status explained more than 50% of the variance between countries and over time for diarrhoea, lower respiratory infections, and other common infectious diseases; maternal disorders; neonatal disorders; nutritional deficiencies; other communicable, maternal, neonatal, and nutritional diseases; musculoskeletal disorders; and other non-communicable diseases. However, sociodemographic status explained less than 10% of the variance in DALY rates for cardiovascular diseases; chronic respiratory diseases; cirrhosis; diabetes, urogenital, blood, and endocrine diseases; unintentional injuries; and self-harm and interpersonal violence. Predictably, increased sociodemographic status was associated with a shift in burden from YLLs to YLDs, driven by declines in YLLs and increases in YLDs from musculoskeletal disorders, neurological disorders, and mental and substance use disorders. In most country-specific estimates, the increase in life expectancy was greater than that in HALE. Leading causes of DALYs are highly variable across countries. Interpretation Global health is improving. Population growth and ageing have driven up numbers of DALYs, but crude rates have remained relatively constant, showing that progress in health does not mean fewer demands on health systems. The notion of an epidemiological transition—in which increasing sociodemographic status brings structured change in disease burden—is useful, but there is tremendous variation in burden of disease that is not associated with sociodemographic status. This further underscores the need for country-specific assessments of DALYs and HALE to appropriately inform health policy decisions and attendant actions.

Global, regional, and national comparative risk assessment of 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks in 188 countries, 1990–2013: a systematic analysis for the Global Burden of Disease Study 2013

Background The Global Burden of Disease, Injuries, and Risk Factor study 2013 (GBD 2013) is the first of a series of annual updates of the GBD. Risk factor quantification, particularly of modifiable risk factors, can help to identify emerging threats to population health and opportunities for prevention. The GBD 2013 provides a timely opportunity to update the comparative risk assessment with new data for exposure, relative risks, and evidence on the appropriate counterfactual risk distribution. Methods Attributable deaths, years of life lost, years lived with disability, and disability-adjusted life-years (DALYs) have been estimated for 79 risks or clusters of risks using the GBD 2010 methods. Risk–outcome pairs meeting explicit evidence criteria were assessed for 188 countries for the period 1990–2013 by age and sex using three inputs: risk exposure, relative risks, and the theoretical minimum risk exposure level (TMREL). Risks are organised into a hierarchy with blocks of behavioural, environmental and occupational, and metabolic risks at the first level of the hierarchy. The next level in the hierarchy includes nine clusters of related risks and two individual risks, with more detail provided at levels 3 and 4 of the hierarchy. Compared with GBD 2010, six new risk factors have been added: handwashing practices, occupational exposure to trichloroethylene, childhood wasting, childhood stunting, unsafe sex, and low glomerular filtration rate. For most risks, data for exposure were synthesised with a Bayesian meta-regression method, DisMod-MR 2.0, or spatial-temporal Gaussian process regression. Relative risks were based on meta-regressions of published cohort and intervention studies. Attributable burden for clusters of risks and all risks combined took into account evidence on the mediation of some risks such as high body-mass index (BMI) through other risks such as high systolic blood pressure and high cholesterol. Findings All risks combined account for 57·2% (95% uncertainty interval [UI] 55·8–58·5) of deaths and 41·6% (40·1–43·0) of DALYs. Risks quantified account for 87·9% (86·5–89·3) of cardiovascular disease DALYs, ranging to a low of 0% for neonatal disorders and neglected tropical diseases and malaria. In terms of global DALYs in 2013, six risks or clusters of risks each caused more than 5% of DALYs: dietary risks accounting for 11·3 million deaths and 241·4 million DALYs, high systolic blood pressure for 10·4 million deaths and 208·1 million DALYs, child and maternal malnutrition for 1·7 million deaths and 176·9 million DALYs, tobacco smoke for 6·1 million deaths and 143·5 million DALYs, air pollution for 5·5 million deaths and 141·5 million DALYs, and high BMI for 4·4 million deaths and 134·0 million DALYs. Risk factor patterns vary across regions and countries and with time. In sub-Saharan Africa, the leading risk factors are child and maternal malnutrition, unsafe sex, and unsafe water, sanitation, and handwashing. In women, in nearly all countries in the Americas, north Africa, and the Middle East, and in many other high-income countries, high BMI is the leading risk factor, with high systolic blood pressure as the leading risk in most of Central and Eastern Europe and south and east Asia. For men, high systolic blood pressure or tobacco use are the leading risks in nearly all high-income countries, in north Africa and the Middle East, Europe, and Asia. For men and women, unsafe sex is the leading risk in a corridor from Kenya to South Africa. Interpretation Behavioural, environmental and occupational, and metabolic risks can explain half of global mortality and more than one-third of global DALYs providing many opportunities for prevention. Of the larger risks, the attributable burden of high BMI has increased in the past 23 years. In view of the prominence of behavioural risk factors, behavioural and social science research on interventions for these risks should be strengthened. Many prevention and primary care policy options are available now to act on key risks.

Structure, function and intracellular dynamics of alphavirus replication complexes

Intracellular membrane alterations are hallmarks of positive-sense RNA (+RNA) virus replication. Strong evidence indicates that within these exotic compartments, viral replicase proteins engage in RNA genome replication and transcription. To date, fundamental questions such as the origin of altered membranes, mechanisms of membrane deformation and topological distribution and function of viral components, are still waiting for comprehensive answers. This study addressed some of the above mentioned questions for the membrane alterations induced during Semliki Forest virus (SFV) infection of mammalian cells. With the aid of electron and fluorescence microscopy coupled with radioactive labelling and immuno-cytochemistry techniques, our group and others showed that few hours after infection the four non structural proteins (nsP1-4) and newly synthesized RNAs of SFV colocalized in close proximity of small membrane invaginations, designated as spherules . These 50-70 nm structures were mainly detected in the perinuclear area, at the limiting membrane of modified endosomes and lysosomes, named CPV-I (cytopathic vacuoles type I). More rarely, spherules were also found at the plasma membrane (PM). In the first part of this study I present the first three-dimensional reconstruction of the CPV-I and the spherules, obtained by electron tomography after chemical or cryo-fixation. Different approaches for imaging these macromolecular assemblies to obtain better structure preservation and higher resolution are presented as unpublished data. This study provides insights into spherule organization and distribution of viral components. The results of this and other experiments presented in this thesis will challenge currently accepted models for virus replication complex formation and function. In a revisitation of our previous models, the second part of this work provides the first complete description of the biogenesis of the CPV-I. The results demonstrate that these virus-induced vacuoles, where hundreds of spherules accumulate at late stages during infection, represent the final phase of a journey initiated at the PM, which apparently serves as a platform for spherule formation. From the PM spherules were internalized by an endocytic event that required the activity of the class I PI3K, caveolin-1, cellular cholesterol and functional actin-myosin network. The resulting neutral endocytic carrier vesicle delivered the spherules to the membrane of pre-existing acidic endosomes via multiple fusion events. Microtubule based transport supported the vectorial transfer of these intermediates to the pericentriolar area where further fusions generated the CPV-I. A signal for spherule internalization was identified in one of the replicase proteins, nsP3. Infections of cells with viruses harbouring a deletion in a highly phosphorylated region of nsP3 did not result in the formation of CPV-Is. Instead, thousands of spherules remained at the PM throughout the infection cycle. Finally, the role of the replicase protein nsP2 during viral RNA replication and transcription was investigated. Three enzymatic activities, protease, NTPase and RNA-triphosphatase were studied with the aid of temperature sensitive mutants in vitro and, when possible, in vivo. The results highlighted the interplay of the different nsP2 functions during different steps of RNA replication and sub-genomic promoter regulation, and suggest that the protein could have different activities when participating in the replication complex or as a free enzyme.

Metabolomic and proteomic analysis of breast cancer patient samples suggests that glutamate and 12-HETE in combination with CA15-3 may be useful biomarkers reflecting tumour burden

Evaluation of protein and metabolite expression patterns in blood using mass spectrometry and high-throughput antibody-based screening platforms has potential for the discovery of new biomarkers for managing breast cancer patient treatment. Previously identified blood-based breast cancer biomarkers, including cancer antigen 15.3 (CA15-3) are useful in combination with imaging (computed tomography scans, magnetic resonance imaging, X-rays) and physical examination for monitoring tumour burden in advanced breast cancer patients. However, these biomarkers suffer from insufficient levels of accuracy and with new therapies available for the treatment of breast cancer, there is an urgent need for reliable, non-invasive biomarkers that measure tumour burden with high sensitivity and specificity so as to provide early warning of the need to switch to an alternative treatment. The aim of this study was to identify a biomarker signature of tumour burden using cancer and non-cancer (healthy controls/non-malignant breast disease) patient samples. Results demonstrate that combinations of three candidate biomarkers from Glutamate, 12-Hydroxyeicosatetraenoic acid, Beta-hydroxybutyrate, Factor V and Matrix metalloproteinase-1 with CA15-3, an established biomarker for breast cancer, were found to mirror tumour burden, with AUC values ranging from 0.71 to 0.98 when comparing non-malignant breast disease to the different stages of breast cancer. Further validation of these biomarker panels could potentially facilitate the management of breast cancer patients, especially to assess changes in tumour burden in combination with imaging and physical examination.

Definition of the halogen bond (IUPAC Recommendations 2013)

This recommendation proposes a definition for the term ``halogen bond'', which designates a specific subset of the inter- and intramolecular interactions involving a halogen atom in a molecular entity.

Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation

Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence.

Dielectric investigation of high-k yttrium copper titanate thin films

We report on the first dielectric investigation of high-k yttrium copper titanate thin films, which were demonstrated to be very promising for nanoelectronics applications. The dielectric constant of these films is found to vary from 100 down to 24 (at 100 kHz) as a function of deposition conditions, namely oxygen pressure and film thickness. The physical origin of such variation was investigated in the framework of universal dielectric response and Cole-Cole relations and by means of voltage dependence studies of the dielectric constant. Surface-related effects and charge hopping polarization processes, strictly dependent on the film microstructure, are suggested to be mainly responsible for the observed dielectric response. In particular, the bulky behaviour of thick films deposited at lower oxygen pressure evolves towards a more complex and electrically heterogeneous structure when either the thickness decreases down to 50 nm or the films are grown under high oxygen pressure.

Dielectric investigation of high-k yttrium copper titanate thin films

We report on the first dielectric investigation of high-k yttrium copper titanate thin films, which were demonstrated to be very promising for nanoelectronics applications. The dielectric constant of these films is found to vary from 100 down to 24 (at 100 kHz) as a function of deposition conditions, namely oxygen pressure and film thickness. The physical origin of such variation was investigated in the framework of universal dielectric response and Cole-Cole relations and by means of voltage dependence studies of the dielectric constant. Surface-related effects and charge hopping polarization processes, strictly dependent on the film microstructure, are suggested to be mainly responsible for the observed dielectric response. In particular, the bulky behaviour of thick films deposited at lower oxygen pressure evolves towards a more complex and electrically heterogeneous structure when either the thickness decreases down to 50 nm or the films are grown under high oxygen pressure.

Cesare e la retorica greca

Resumen: El presente trabajo se analizará un pasaje del Praeceptum deliberativae materiae, un texto retórico escrito por Emporius en el siglo V/VI, en el cual César reclama ser un Graecae exercitationis expers; tal extraña definición tiene sus raíces en la controversia de los populares contra la helenización de la nobilitas: desde una perspectiva popularis el vir romanus real tenía que preferir las habilidades militares a las retóricas, como C. Mario había hecho, y tenía que adquirir sus habilidades retóricas en Latín, no en griego, como el Rhetorica ad Herennium exhortaba. Luego ser Graecae exercitationis expers pasó a ser una cualidad requerida para un líder de los populares, tal como César quería ser reconocido, y podemos remontar sus orígenes en la propaganda literaria del partido cesariano, sobre todo en el Bellum Iugurthinum de Salustio y en el Anticato del propio César.

Letras, Nº 69-70, 2014

Contenido: Viel, así en el cieslo como en el canon : un lugar en el corpus de la poesía argentina / María Amelia Arancet Ruda -- Hacia un canon poético místico en clave estético teológica : vigencia de la figura del centro como expectación del Otro / Cecilia I. Avenatti de Palumbo -- La traducción como "instrumento poético" : Raúl Gustavo Aguirre, entre Rimbaud y Char / Magdalena Cámpora -- Giuseppe Ungaretti : un itinerario lírico / Daniel Alejandro Capano -- Teoría y práctica de la poesía cinética en Composición de lugar (1976) de Amanda Berenguer / María Lucía Puppo -- Poesía, subjetividad y memoria en la escritura de Alicia Genovese / Alicia Salomone -- "No nos legaron cartas, ni alianzas, ni retratos" : Olga Orozco o la autofiguración desde la muerte / Sebastián Urli -- Poesía lírica y teoría crítica del siglo XX : entrevista a Miguel Ángel Garrido Gallardo / Sofía M. Carrizo Rueda -- Reseñas bibliográficas

Paciano II: the report of a conversation on whaling and science, 1-3 March 2008 (Paciano, Umbria)

In 2006 the UK-based charity, Global Ocean, with local support from the Third Millennium Foundation, convened a Conversation among specialists about the problems facing the conservation of whales. Called "A consultation on whaling", this gathering was held in the ancient village of Paciano, in Umbria near the border with Tuscany, 15 – 17 October 2006. There were 15 participants from 11 countries. Dr Kees Lankester served as moderator. The outcome was an Aide Memoire which served to guide the participants in the run-up to the 2007 meeting of the International Whaling Commission (IWC), held in Anchorage, Alaska, in June. One point of agreement was that a second consultation should be held in the months following the Anchorage meeting, involving some but not necessarily all of the participants in the first, but concentrating this time on scientific issues – especially those encountered in the Scientific Committee of the IWC –with particular attention to informing a wider public about those scientific activities in relation to the problems confronting the IWC and the views of scientists about them. This document is the report of that Conversation, referred to as Paciano II. The moderator was Dr Giuseppe Notarbartolo di Sciara and the Report was written by Kieran Mulvaney in consultation with all participants, and with reference to an Aide Memoire prepared by the Rapporteur, Dr Russell Leaper. The sponsor and organisers have agreed with the general sentiment expressed by participants in Paciano II that further such conversations should be held at roughly yearly intervals and they will try to satisfy that desire. Although these future gatherings would be concerned with the living ocean they would not necessarily be restricted in future to consideration of whales and whaling. Discussions are on-going for selection of a theme which is of both scientific interest and practical concern for conservation of marine life and management of the uses of ocean space. (Document has 18 pages)

Paciano II: a report of a conversation on whaling and science, 1-3 March 2008

In 2006 the UK-based charity, Global Ocean, with local support from the Third Millennium Foundation, convened a Conversation among specialists about the problems facing the conservation of whales. Called "A consultation on whaling", this gathering was held in the ancient village of Paciano, in Umbria near the border with Tuscany, 15 – 17 October 2006. There were 15 participants from 11 countries. Dr Kees Lankester served as moderator. The outcome was an Aide Memoire which served to guide the participants in the run-up to the 2007 meeting of the International Whaling Commission (IWC), held in Anchorage, Alaska, in June. One point of agreement was that a second consultation should be held in the months following the Anchorage meeting, involving some but not necessarily all of the participants in the first, but concentrating this time on scientific issues – especially those encountered in the Scientific Committee of the IWC –with particular attention to informing a wider public about those scientific activities in relation to the problems confronting the IWC and the views of scientists about them. This document is the report of that Conversation, referred to as Paciano II. The moderator was Dr Giuseppe Notarbartolo di Sciara and the Report was written by Kieran Mulvaney in consultation with all participants, and with reference to an Aide Memoire prepared by the Rapporteur, Dr Russell Leaper. The sponsor and organisers have agreed with the general sentiment expressed by participants in Paciano II that further such conversations should be held at roughly yearly intervals and they will try to satisfy that desire. Although these future gatherings would be concerned with the living ocean they would not necessarily be restricted in future to consideration of whales and whaling. Discussions are on-going for selection of a theme which is of both scientific interest and practical concern for conservation of marine life and management of the uses of ocean space. (19 page document)

Celiac disease in the Mediterranean area

Background: The World Gastroenterology Organization recommends developing national guidelines for the diagnosis of Celiac Disease (CD): hence a profile of the diagnosis of CD in each country is required. We aim to describe a cross-sectional picture of the clinical features and diagnostic facilities in 16 countries of the Mediterranean basin. Since a new ESPGHAN diagnostic protocol was recently published, our secondary aim is to estimate how many cases in the same area could be identified without a small intestinal biopsy. Methods: By a stratified cross-sectional retrospective study design, we examined clinical, histological and laboratory data from 749 consecutive unselected CD children diagnosed by national referral centers. Results: The vast majority of cases were diagnosed before the age of 10 (median: 5 years), affected by diarrhea, weight loss and food refusal, as expected. Only 59 cases (7.8%) did not suffer of major complaints. Tissue transglutaminase (tTG) assay was available, but one-third of centers reported financial constraints in the regular purchase of the assay kits. 252 cases (33.6%) showed tTG values over 10 times the local normal limit. Endomysial antibodies and HLA typing were routinely available in only half of the centers. CD was mainly diagnosed from small intestinal biopsy, available in all centers. Based on these data, only 154/749 cases (20.5%) would have qualified for a diagnosis of CD without a small intestinal biopsy, according to the new ESPGHAN protocol. Conclusions: This cross-sectional study of CD in the Mediterranean referral centers offers a puzzling picture of the capacities to deal with the emerging epidemic of CD in the area, giving a substantive support to the World Gastroenterology Organization guidelines.