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Populations of RNA and ssDNA viruses within their hosts contain a heterogeneous collection of variant genomes known as quasispecies. Large variability in mitochondrial DNA has also been found within the same organism, drawing an interesting parallel between the two situations. The advent of next-generation sequencing technologies facilitated studying genetic variation, but many open-source bioinformatic tools have to be combined in a non-trivial approach. Here it is presented QuasiFlow, a workflow based on well-stablished software that extracts reliable mutations and recombinations, even at low frequencies (~10-4), provided that at least 250 million nucleotides are analysed. Accurate prediction of mutations and recombinations has been demonstrated with synthetic reads and with in vitro rolling-circle amplification of a plant geminivirus. An in-depth analysis of viral quasispecies was performed and QuasiFlow revealed the coexistence in the plant of three virus genomes and distinct recombinations between some of them. Human mitochondrial variants were also investigated and high level of heteroplasmy (75%) was confirmed, and the relation between low-frequency heteroplasmy (0.1- 0.2%) and some human diseases, regardless of sex, was established. Hence, we propose that QuasiFlow may find use with known and emerging viruses to reveal evolutionary jumps and co-infections, with mitochondrial DNA to detect relevant heteroplasmy would otherwise be elusive, or even in other population studies such as those considering single cell sequencing.

Background Investigations of evolution knowledge and acceptance and their relation are central to evolution education research. Ambiguous results in this field of study demonstrate a variety of measuring issues, for instance differently theorized constructs, or a lack of standardized methods, especially for cross-country comparisons. In particular, meaningful comparisons across European countries, with their varying cultural backgrounds and education systems, are rare, often include only few countries, and lack standardization. To address these deficits, we conducted a standardized European survey, on 9200 first-year university students in 26 European countries utilizing a validated, comprehensive questionnaire, the “Evolution Education Questionnaire”, to assess evolution acceptance and knowledge, as well as influencing factors on evolution acceptance. Results We found that, despite European countries’ different cultural backgrounds and education systems, European first-year university students generally accept evolution. At the same time, they lack substantial knowledge about it, even if they are enrolled in a biology-related study program. Additionally, we developed a multilevel-model that determines religious faith as the main influencing factor in accepting evolution. According to our model, knowledge about evolution and interest in biological topics also increase acceptance of evolution, but to a much lesser extent than religious faith. The effect of age and sex, as well as the country’s affiliation, students’ denomination, and whether or not a student is enrolled in a biology-related university program, is negligible. Conclusions Our findings indicate that, despite all their differences, most of the European education systems for upper secondary education lead to acceptance of evolution at least in university students. It appears that, at least in this sample, the differences in knowledge between countries reflect neither the extent to which school curricula c

“Encuentros con la Ciencia” is a multidisciplinary collaborative project with the main objective of making science accessible to society. University and secondary school professors join forces with different agents (institutional and private) and organizations to inform the public about the importance of science in our daily lives. This is possible by involving the scientific community itself to disseminate the scientific knowledge that is currently developed in Spanish research centers. It is achieved through a variety of dissemination activities and scientific practice in two contexts: a general one, with activities opened tom the public, aimed at a heterogeneous audience with different interests in science; and in an educational framework, targeted at students and their teaching staff. The project is based on the structure of the scientific dissemination cycle “Encuentros con la Ciencia”, currently in its fifteenth edition. It is a consolidated structure with headquarters, public, and own resources. The project brings together up to 8 actions: scientific conferences, scientific exhibitions, open workshops on science, Scientific cinema, scientific workshops focused of gifted students (GuíaMe-AC-UMA and “When I grow up I want to be ...”), scientific updates focused on secondary level teachers and Experimenta. We emphasize the media repercussion of this activity that has opened frequent communication channels with the main media of the city (SUR, Cadena SER, Canal SURTV, La Opinión, Malaga Hoy, etc), so that speakers and organizers of "Encuentros con la Ciencia" have in fact, become common sources of scientific information, often even outside the context of the conference. In fact, the media have incorporated "Encuentros con la Ciencia" as a habitual suggestion of the proposals, “Encuentros con la Ciencia” es un proyecto colaborativo multidisciplinar que nace con el objetivo principal de hacer accesible el avance de la ciencia a la sociedad. Profesores universitarios y educadores de secundaria unen esfuerzos con diferentes agentes (institucionales y privados) y organizaciones para informar al público sobre la importancia de la ciencia en nuestra vida cotidiana. Esto se hace posible involucrando a la propia comunidad científica para difundir el conocimiento científico que se desarrolla actualmente en los Centros de investigación españoles. Se logra por medio de una variedad de actividades de difusión y práctica científica en dos contextos: uno general, con actividades abiertas a un público heterogéneo con diferentes intereses por la ciencia; y en el marco educativo, dirigido a los estudiantes y al personal docente principalmente. El proyecto se basa en la estructura del ciclo de divulgación científica “Encuentros con la Ciencia”, actualmente en su decimoquinta edición. Es una estructura consolidada con sede, público y recursos propios. El proyecto reúne 8 acciones: Conferencias científicas, Exposiciones científicas, Talleres abiertos sobre ciencia, Ciencia de cine, Talleres científicos como los GuíaMe-AC-UMA o “Yo de mayor quiero ser...”, actividades de actualización científica y formación del profesorado y Experimenta. Destacamos la repercusión mediática de esta actividad que ha abierto canales de comunicación con los principales medios de comunicación de la ciudad (Cadena Ser, Canal Sur, La Opinión, Málaga Hoy, etc), de manera que ponentes y organizadores de Encuentros con la Ciencia se han convertido, de hecho, en fuentes expertas habituales de información científica, a menudo incluso fuera del contexto de las jornadas. Por todo ello, se ha conseguido que los medios de comunicación hayan incorporado a "Encuentros con la Ciencia" como una referencia en divulgación de la ciencia

We present a computer model to predict the patterns expected for the replication intermediates (RIs) of DNA fragments analyzed by neutral/neutral two-dimensional (2D) agarose gel electrophoresis. The model relies on the mode of replication (uni- or bi-directional), the electrophoretic mobility of linear DNA fragments and the retardation caused by the three-dimensional shape of non-linear molecules. The utility of this model is demonstrated with two examples: replication analysis of the plasmids pBR322 and pHH5.8 in Escherichia coli after digestions with EcoRI and HindIII, respectively.

Co-orientation of replication origins is the most common organization found in nature for multimeric plasmids. Streptococcus pyogenes broad-host-range plasmid pSM19035 and Escherichia coli pPI21 are among the exceptions. pPI21, which is a derivative of pSM19035 and pBR322, has two long inverted repeats, each one containing a potentially active ColE1 unidirectional origin. Analysis of pPI21 replication intermediates (RIs) by two-dimensional agarose gel electrophoresis and electron microscopy revealed the accumulation of a specific RI containing a single internal bubble. The data obtained demonstrated that initiation of DNA replication occurred at a single origin in pPI21. Progression of the replicating fork initiated at either of the two potential origins was transiently stalled at the other inversely oriented silent ColE1 origin of the plasmid. The accumulated RIs, containing an internal bubble, occurred as a series of stereoisomers with different numbers of knots in their replicated portion. These observations provide one of the first functional explanations for the disadvantage of head-to-head plasmid multimers with respect to head-to-tail ones.

Replication slippage or slipped-strand mispairing involves the misalignment of DNA strands during the replication of repeated DNA sequences, and can lead to genetic rearrangements such as microsatellite instability. Here, we show that PolB and PolD replicative DNA polymerases from the archaeal model Pyrococcus abyssi (Pab) slip in vitro during replication of a single-stranded DNA template carrying a hairpin structure and short direct repeats. We find that this occurs in both their wild-type (exo+) and exonuclease deficient (exo-) forms. The slippage behavior of PabPolB and PabPolD, probably due to limited strand displacement activity, resembles that observed for the high fidelity P furiosus (Pfu) DNA polymerase. The presence of PabPCNA inhibited PabPolB and PabPolD slippage. We propose a model whereby PabPCNA stimulates strand displacement activity and polymerase progression through the hairpin, thus permitting the error-free replication of repetitive sequences.

Automatic sequence annotation is an essential component of modern 'omics' studies, which aim to extract information from large collections of sequence data. Most existing tools use sequence homology to establish evolutionary relationships and assign putative functions to sequences. However, it can be difficult to define a similarity threshold that achieves sufficient coverage without sacrificing annotation quality. Defining the correct configuration is critical and can be challenging for non-specialist users. Thus, the development of robust automatic annotation techniques that generate high-quality annotations without needing expert knowledge would be very valuable for the research community. We present Sma3s, a tool for automatically annotating very large collections of biological sequences from any kind of gene library or genome. Sma3s is composed of three modules that progressively annotate query sequences using either: (i) very similar homologues, (ii) orthologous sequences or (iii) terms enriched in groups of homologous sequences. We trained the system using several random sets of known sequences, demonstrating average sensitivity and specificity values of ∼85%. In conclusion, Sma3s is a versatile tool for high-throughput annotation of a wide variety of sequence datasets that outperforms the accuracy of other well-established annotation algorithms, and it can enrich existing database annotations and uncover previously hidden features. Importantly, Sma3s has already been used in the functional annotation of two published transcriptomes.