DNA Knotting in Spooling Like Conformations in Bacteriophages

A number of idealized models have been proposed to explain the long range organization of the DNA in bacteriophages. However, none of these models can account for the distributions of complex knots found when examining DNA extracted from bacteriophage P4 capsids. Furthermore, these models do not consider possible chirality biases in the arrangement of the DNA molecule inside the capsid. In this paper, we address these two issues by proposing a randomized version of one of the most popular models: the coaxially spooled model. We present analytical and numerical results for the properties of the random polygons (knots) generated using this model. We show that such model can easily generate complex knotted conformations and although it accounts for some chirality of the organization of the DNA molecules inside bacteriophage capsids does not fully explain the experimental data

The Innominate Bone Sample from Krapina

The Croatian site of Krapina has yielded a large collection of human fossils attributed to the archaic Neandertals. The sample includes fourteen innominate bone specimens, minimum number of seven individuals (MNI=7). Among them, it is possible to distinguish two fully adults (one female, one male), two late adolescent or young adults (both males) and three children of unknown sex. Metric analysis reveals the Krapina hip bones to be characterized by relatively small vertical acetabular diameter compared to the classic Neandertals, and a long and remarkably slender pubis relative to living humans. Morphologically, the Krapina specimens are included within the Neandertal variation, showing a narrow, rounded and/or tilted bone surface between the coronal portion of the greater sciatic notch, and a distinctive morphology of the superior pubic ramus, the latter agreeingwith the metric data. On the other hand, they can be distinguished from the modern human innominate bone in aspect related with the anterior inferior iliac spine, the topography of the posterior wall of the acetabulum, the supraacetabular sulcus and some traits of the superior pubic ramus

Single-grain OSL dating of the Middle Palaeolithic site of Galería de las Estatuas, Atapuerca (Burgos, Spain)

This study presents single-grain optically stimulated luminescence (OSL) chronologies for the archaeological site of Galería de las Estatuas – the first systematically excavated Middle Palaeolithic site within the karst system of the Sierra de Atapuerca archaeological complex, northern Spain. The single-grain OSL ages are compared with paired single-grain thermally transferred OSL (TT-OSL) dating results for a selection of samples in order to better assess quartz signal bleaching characteristics of endokarstic deposits preserved at Atapuerca. In total, seven luminescence dating samples were collected from four lithostratigraphic units exposed in two excavation pits (GE-I and GE-II). The single-grain OSL equivalent dose (De) distributions are characterised by generally low overdispersion (20–30%), suggesting appropriate bleaching at deposition. The resultant single-grain OSL ages reveal that the sediment sequence and archaeological remains excavated in pit GE-I accumulated 80–112 ka, while the upper layers of excavation area GE-II were deposited 70–79 ka. The replicate single-grain TT-OSL ages are in agreement with the OSL chronologies at 2σ for three of the four samples investigated; although in all cases the TT-OSL ages were systematically older than their single-grain counterparts. Apparent TT-OSL residual doses (i.e., TT-OSL De values in excess of their corresponding OSL De values) of 9–65 Gy were observed for all samples. These excess TT-OSL De values are generally low in comparison to the natural dose ranges of TT-OSL dating applications undertaken elsewhere in the Atapuerca karst system. The single-grain TT-OSL and OSL dating comparisons build on daylight bleaching experiments and modern analogue studies performed on other Atapuerca exogeneous infill deposits and suggest reasonable potential for TT-OSL signal resetting down to relatively low levels for at least some sediments preserved in the Atapuerca karstic cavities. The quartz single-grain OSL chronologies obtained in this study place the Middle Palaeolithic sequence of Galería de las Estatuas within marine isotope stage (MIS) 5 and the beginning of MIS 4, and provide firm evidence for human occupation of the Sierra de Atapuerca during a previously unreported time period

Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract Background The chromosome of Escherichia coli is maintained in a negatively supercoiled state, and supercoiling levels are affected by growth phase and a variety of environmental stimuli. In turn, supercoiling influences local DNA structure and can affect gene expression. We used microarrays representing nearly the entire genome of Escherichia coli MG1655 to examine the dynamics of chromosome structure. Results We measured the transcriptional response to a loss of supercoiling caused either by genetic impairment of a topoisomerase or addition of specific topoisomerase inhibitors during log-phase growth and identified genes whose changes are statistically significant. Transcription of 7% of the genome (306 genes) was rapidly and reproducibly affected by changes in the level of supercoiling; the expression of 106 genes increased upon chromosome relaxation and the expression of 200 decreased. These changes are most likely to be direct effects, as the kinetics of their induction or repression closely follow the kinetics of DNA relaxation in the cells. Unexpectedly, the genes induced by relaxation have a significantly enriched AT content in both upstream and coding regions. Conclusions The 306 supercoiling-sensitive genes are functionally diverse and widely dispersed throughout the chromosome. We propose that supercoiling acts as a second messenger that transmits information about the environment to many regulatory networks in the cell.Published versio

Human activities, biostratigraphy and past environment revealed by small-mammal associations at the chalcolithic levels of El Portalón de Cueva Mayor (Atapuerca, Spain)

The Chalcolithic levels of El Portalón de Cueva Mayor (Atapuerca, Burgos, Spain) offer a good opportunity to test whether the small-mammal contents of different archaeo-stratigraphical units may be useful to characterize them as independent entities. With that purpose, we studied representative samples of small-mammal remains from the two main contexts identified: the Early Chalcolithic (EC) funerary context and the Late Chalcolithic (LC) habitat/stabling context, with the latter comprising three different archaeological units according to their origin, namely prepared floors, activity floors and stabling surfaces or fumiers. Following the distribution of taxa in their respective contexts, we performed several statistical tests to check for significant discrepancies between archaeological units. The exclusive presence of certain taxa, together with the statistical difference in relative taxonomic ratios, points to the integrity and unpolluted condition of the EC context. The interspersed arrangement of the different LC context’s units made them prone to inter-pollution as they are not statistically different. The unexpected presence of Pliomys lenki and Chionomys nivalis in the prepared floors evidences their Upper Pleistocene allochthonous origin. The EC levels of El Portalón contribute the first Holocene records of nine taxa in the Sierra de Atapuerca. An environment dominated by woodland, shrubland and wet meadows, with moderate presence of grassland, inland wetlands and rocky areas, is inferred from the small-mammal association of the EC levels

Binary metal oxides for composite ultrafiltration membranes

A new ultrafiltration membrane was developed by the incorporation of binary metal oxides inside polyethersulfone. Physico-chemical characterization of the binary metal oxides demonstrated that the presence of Ti in the TiO2?ZrO2 system results in an increase of the size of the oxides, and also their dispersity. The crystalline phases of the synthesized binary metal oxides were identified as srilankite and zirconium titanium oxide. The effect of the addition of ZrO2 can be expressed in terms of the inhibition of crystal growth of anocrystalline TiO2 during the synthesis process. For photocatalytic applications the band gap of the synthesized semiconductors was determined, confirming a gradual increase (blue shift) in the band gap as the amount of Zr loading increases. Distinct distributions of binary metal oxides were found along the permeation axis for the synthesized membranes. Particles with Ti are more uniformly dispersed throughout the membrane cross-section. The physico-chemical characterization of membranes showed a strong correlation between some key membrane properties and the spatial particle distribution in the membrane structure. The proximity of metal oxide fillers to the membrane surface determines the hydrophilicity and porosity of modified membranes. Membranes incorporating binary metal oxides were found to be promising candidates for wastewater treatment by ultrafiltration, considering the observed improvement influx and anti-fouling properties of doped membranes. Multi-run fouling tests of doped membranes confirmed the stability of permeation through membranes embedded with binary TiO2?ZrO2 particles

Numerical study of linear and circular model DNA chains confined in a slit: metric and topological properties

Advanced Monte Carlo simulations are used to study the effect of nano-slit confinement on metric and topological properties of model DNA chains. We consider both linear and circularised chains with contour lengths in the 1.2--4.8 $\mu$m range and slits widths spanning continuously the 50--1250nm range. The metric scaling predicted by de Gennes' blob model is shown to hold for both linear and circularised DNA up to the strongest levels of confinement. More notably, the topological properties of the circularised DNA molecules have two major differences compared to three-dimensional confinement. First, the overall knotting probability is non-monotonic for increasing confinement and can be largely enhanced or suppressed compared to the bulk case by simply varying the slit width. Secondly, the knot population consists of knots that are far simpler than for three-dimensional confinement. The results suggest that nano-slits could be used in nano-fluidic setups to produce DNA rings having simple topologies (including the unknot) or to separate heterogeneous ensembles of DNA rings by knot type.Comment: 12 pages, 10 figure

The Professional University Degree Of Actuary Through Bloom's Taxonomy

The aim of this paper is to determine the characteristics of the MScAFS in terms of how the Syllabus of the AAE sets out the subjects, organised into sub-areas, and the degree of development of the competences required to obtain the professional qualification of actuary in the EU. For this purpose, they are classified and quantified according to the type of conceptual development and the degree of in-depth study. This makes it possible to obtain the Master's degree graduate profile, which must coincide with the professional qualification agreed in the AAE. This profile is different from other master's degrees, whether complementary academic or with a research profile, and from other professions, which may or may not have one or more of the characteristics of the actuarial profession.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Essential ocean variables and high value biodiversity areas: Targets for the conservation of marine megafauna

Effective conservation and management measures are needed to face the unprecedented changes that marine ecosystems, and particularly marine megafauna, are suffering. These measures require the identification of highvalue biodiversity areas (HVBAs) which in turn require the identification of the essential ocean variables (EOVs) that shape the environmental envelope of communities (i.e. space defined by a set of environmental variables). The aim of this study was to delineate and characterise the HVBAs for the north and northwestern Spanish seabird and cetacean community taking advantage of the sightings collected during the annual PELACUS oceanographic survey (2007–2016). We used distance sampling methodology to analyse the species detectability based on environmental conditions. Then, we delimitated the HVBAs and identified the EOVs defining the environmental envelope of the community based on a spatio-temporal modelling approach using Generalized Additive Models. Overall, the main environmental variables driving species abundance were the sea surface temperature (SST), the distance to the shelf-break and the chlorophyll-a concentration (Chl-a). The SST and Chla were identified as dynamic EOVs due to their highest relative predictor importance, driving the environmental envelope and shaping areas of higher density. HVBAs were located mainly over the northwestern Spanish waters and decreased towards the inner Bay of Biscay remaining spatially stable over the study period. By identifying community-level HVBAs, we can understand the underlying ecological and oceanographic processes driving the spatio-temporal patterns of biological communities, such as those composed by seabirds and cetaceans. This information would identify conservation targets to assist the allocation of management resources. In addition, the location of HVBAs can help to fulfil the emergent need for sound spatial information to support the implementation of marine spatial planning.En prens