The curse of the uncultured fungus

The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as “uncultured fungus”. These sequences beget low-resolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length fungal ITS sequences to estimate what proportion of the 95,055 “uncultured fungus” sequences that represent truly unidentifiable fungal taxa – and what proportion of them that would have been straightforward to annotate to some more meaningful taxonomic level at the time of sequence deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers’ perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked

Diagnostico del Impacto del Palangre de Fondo en los Hábitats Bentónicos en los LICs de la RN20000

En prens

Profiles of Volatile Biomarkers Detect Tuberculosis from Skin

Tuberculosis (TB) is an infectious disease that threatens >10 million people annually. Despite advances in TB diagnostics, patients continue to receive an insufficient diagnosis as TB symptoms are not specific. Many existing biodiagnostic tests are slow, have low clinical performance, and can be unsuitable for resource-limited settings. According to the World Health Organization (WHO), a rapid, sputum-free, and cost-effective triage test for real-time detection of TB is urgently needed. This article reports on a new diagnostic pathway enabling a noninvasive, fast, and highly accurate way of detecting TB. The approach relies on TB-specific volatile organic compounds (VOCs) that are detected and quantified from the skin headspace. A specifically designed nanomaterial-based sensors array translates these findings into a point-of-care diagnosis by discriminating between active pulmonary TB patients and controls with sensitivity above 90%. This fulfills the WHO's triage test requirements and poses the potential to become a TB triage test

Seroprevalence of paramyxoviruses in synanthropic and semi-free-range birds

Avian paramyxoviruses (APMVs) are classified into nine different serotypes (APMV 1-9). Virulent strains of APMV-1 are already well characterized as the etiologic agent of Newcastle disease (ND), an important disease in poultry that is potentially capable of infecting all orders of avian species. However, very little is known about the other eight serotypes, the majority of which can cause disease in domestic birds. The role of synanthropic and semi-free-range birds as reservoirs of avian paramyxoviruses is not well understood and the main objective of this work was to evaluate the seroprevalence of APMV 1-9 in these kind of birds. A total of 296 sera, oropharyngeal swabs, and cloacal enemas were collected from semi-free-range birds belonging to four different species feral pigeons (Columba livia var. domestica), hybrid ducks (Anas sp.), domestic geese (Anser anser domesticus), and white storks (Ciconia ciconia). Antibodies against NDV were found in 56.3% of domestic geese, 42.9% of feral pigeons, and 30.4% of hybrid ducks. Antibodies for other APMVs (-3, -4, -6, -7, -8, -9) were also found. Seven positive individuals were positive to real-time RT-PCR detection, all of them feral pigeons captured in 2006 and 2007. The results obtained reinforce the idea that semi-free-range birds may be good sentinels for the detection of NDV and other avian paramyxoviruses. © American Association of Avian Pathologists

African swine fever virus (ASFV) protection mediated by NH/P68 and NH/P68 recombinant live-attenuated viruses

The risk of spread of African swine fever virus (ASFV) from Russia and Caucasian areas to several EU countries has recently emerged, making it imperative to improve our knowledge and defensive tools against this important pathogen. The ASFV genome encodes many genes which are not essential for virus replication but are known to control host immune evasion, such as NFκB and the NFAT regulator A238L, the apoptosis inhibitor A224L, the MHC-I antigen presenting modulator EP153R, and the A276R gene, involved in modulating type I IFN. These genes are hypothesized to be involved in virulence of the genotype I parental ASFV NH/P68. We here describe the generation of putative live attenuated vaccines (LAV) prototypes by constructing recombinant NH/P68 viruses lacking these specific genes and containing specific markers

Report mapping legal and policy instruments of the EU for human rights and democracy support, FRAME Deliverable 12.1

This report is devoted to the mapping of legal and policy instruments of the EU for human rights and democracy support. In particular, it highlights the EU´s human rights priorities in terms of themes and vulnerable groups in its external action based on a review of EU policy documents and literature. In order to do so the report first identifies the instruments that set up the frame of the human rights and democracy policy. The framework of the EU’s human rights and democracy policy is presided by the Strategic Framework on Human Rights and Democracy, which establishes the principles, objectives and priorities that must guide the EU’s action. Two general objectives, each with a different scope, can be identified in the Strategic Framework: the EU’s and its Member States’ commitment to promote the universality of human rights and the EU’s determination to promote human rights and democracy in its external action. In addition, the Strategic Framework highlights some areas of action which identify specific objectives and priority themes and groups. Although the Strategic Framework is on human rights and democracy, the emphasis throughout the document is on human rights, not on democracy. Democracy is ‘an aspiration’ that it is not defined. There are other relevant documents that set out the EU´s human rights and democracy policy. As well as general policy papers on mainstreaming human rights and promoting human rights and democracy in the EU external action, there are specific human rights guidelines on priority themes and vulnerable groups and human rights strategies towards particular third countries. In order to implement its human rights and democracy policy, the EU has developed a broad range of instruments. Some of them have been especially created in order to contribute to the specific objective of the promotion of human right and democracy worldwide; in particular, the EIDHR, the human rights clauses, the human rights focal points in EU Delegations, the EUSR for Human Rights, election support and the human rights dialogues and consultations. Moreover, the EU uses other traditional instruments of its CFSP to promote human rights and democracy in its relations with third countries. These instruments respond to the EU’s objective of mainstreaming human rights and democracy in all its policies and actions toward third countries. Among them, those that should be highlighted are the EU’s action in multilateral fora, bilateral political dialogues, démarches and declarations, , CFSP decisions, restrictive measures and, finally, thematic and geographic financial programmes. Regular assessment of the implementation of the EU’s human rights and democracy policy is one of the outcomes stated in the Action Plan. This evaluation of policy is mainly carried out through one specific instrument: the EU’s Annual Report on Human Rights and Democracy in the world. In addition, as a consequence of the EU’s approach to put human rights at the core of its external action, human rights and democracy promotion constitute also an important part of other EU’s Annual Reports relating to other external policies, such as CFSP and Development

A computer-based approach to the rational discovery of new trichomonacidal drugs by atom-type linear indices

Computational approaches are developed to design or rationally select, from structural databases, new lead trichomonacidal compounds. First, a data set of 111 compounds was split (design) into training and predicting series using hierarchical and partitional cluster analyses. Later, two discriminant functions were derived with the use of non-stochastic and stochastic atom-type linear indices. The obtained LDA (linear discrimination analysis)-based QSAR (quantitative structure-activity relationship) models, using non-stochastic and stochastic descriptors were able to classify correctly 95.56% (90.48%) and 91.11% (85.71%) of the compounds in training (test) sets, respectively. The result of predictions on the 10% full-out cross-validation test also evidenced the quality (robustness, stability and predictive power) of the obtained models. These models were orthogonalized using the Randić orthogonalization procedure. Afterwards, a simulation experiment of virtual screening was conducted to test the possibilities of the classification models developed here in detecting antitrichomonal chemicals of diverse chemical structures. In this sense, the 100.00% and 77.77% of the screened compounds were detected by the LDA-based QSAR models (Eq. 13 and Eq. 14, correspondingly) as trichomonacidal. Finally, new lead trichomonacidals were discovered by prediction of their antirichomonal activity with obtained models. The most of tested chemicals exhibit the predicted antitrichomonal effect in the performed ligand-based virtual screening, yielding an accuracy of the 90.48% (19/21). These results support a role for TOMOCOMD-CARDD descriptors in the biosilico discovery of new compounds. © 2005 Bentham Science Publishers Ltd.Peer Reviewe