The effects of density on the topological structure of the mitochondrial DNA from trypanosomes.

Trypanosomatida parasites, such as trypanosoma and lishmania, are the cause of deadly diseases in many third world countries. A distinctive feature of these organisms is the three dimensional organization of their mitochondrial DNA into maxi and minicircles. In some of these organisms minicircles are confined into a small disk volume and are topologically linked, forming a gigantic linked network. The origins of such a network as well as of its topological properties are mostly unknown. In this paper we quantify the effects of the confinement on the topology of such a minicircle network. We introduce a simple mathematical model in which a collection of randomly oriented minicircles are spread over a rectangular grid. We present analytical and computational results showing that a finite positive critical percolation density exists, that the probability of formation of a highly linked network increases exponentially fast when minicircles are confined, and that the mean minicircle valence (the number of minicircles that a particular minicircle is linked to) increases linearly with density. When these results are interpreted in the context of the mitochondrial DNA of the trypanosome they suggest that confinement plays a key role on the formation of the linked network. This hypothesis is supported by the agreement of our simulations with experimental results that show that the valence grows linearly with density. Our model predicts the existence of a percolation density and that the distribution of minicircle valences is more heterogeneous than initially thought.

The Early-Middle Pleistocene environmental and climatic change and the human expansion in Western Europe: A case study with small vertebrates (Gran Dolina, Atapuerca, Spain).

The dispersal of hominins may have been favored by the opening of the landscape during the Early-Middle Pleistocene transition (EMP) in Western Europe. The structure of the small-vertebrate assemblages of the archaeo-paleontological karstic site of Gran Dolina in Atapuerca (Burgos, Spain) shows important environmental and climatic changes in the faunal succession, across the Matuyama-Brunhes boundary at 780 ka. These changes are interpreted to indicate impoverishment of the forests, along with an increase in dry meadows, and open lands in general that entailed a tendency towards the loss of diversity in small-vertebrate communities above the EMP. We evaluate variation in diversity of the faunal succession of Gran Dolina using Shannon's Second Theorem as an index of ecosystem structure. The long cultural-stratigraphic sequence of Gran Dolina during the EMP is somewhat similar in its completeness and continuity to that in the locality of Gesher Benot Ya'aqov in the Upper Jordan Valley. We also evaluate related data including faunal and floral (pollen) succession. Both localities present cold, dry and humid, warm fluctuations at the transition between the Early and the Middle Pleistocene. Comparisons between these sites present opportunities to understand large-scale climatic changes.

Modeling of chromosome intermingling by partially overlapping uniform random polygons.

During the early phase of the cell cycle the eukaryotic genome is organized into chromosome territories. The geometry of the interface between any two chromosomes remains a matter of debate and may have important functional consequences. The Interchromosomal Network model (introduced by Branco and Pombo) proposes that territories intermingle along their periphery. In order to partially quantify this concept we here investigate the probability that two chromosomes form an unsplittable link. We use the uniform random polygon as a crude model for chromosome territories and we model the interchromosomal network as the common spatial region of two overlapping uniform random polygons. This simple model allows us to derive some rigorous mathematical results as well as to perform computer simulations easily. We find that the probability that one uniform random polygon of length n that partially overlaps a fixed polygon is bounded below by 1 − O(1/√n). We use numerical simulations to estimate the dependence of the linking probability of two uniform random polygons (of lengths n and m, respectively) on the amount of overlapping. The degree of overlapping is parametrized by a parameter [Formula: see text] such that [Formula: see text] indicates no overlapping and [Formula: see text] indicates total overlapping. We propose that this dependence relation may be modeled as f (ε, m, n) = [Formula: see text]. Numerical evidence shows that this model works well when [Formula: see text] is relatively large (ε ≥ 0.5). We then use these results to model the data published by Branco and Pombo and observe that for the amount of overlapping observed experimentally the URPs have a non-zero probability of forming an unsplittable link.

A hominid from the lower Pleistocene of Atapuerca, Spain: possible ancestor to Neandertals and modern humans.

Human fossil remains recovered from the TD6 level (Aurora stratum) of the lower Pleistocene cave site of Gran Dolina, Sierra de Atapuerca, Spain, exhibit a unique combination of cranial, mandibular, and dental traits and are suggested as a new species of Homo-H. antecessor sp. nov. The fully modern midfacial morphology of the fossils antedates other evidence of this feature by about 650, 000 years. The midfacial and subnasal morphology of modern humans may be a retention of a juvenile pattern that was not yet present in H. ergaster. Homo antecessor may represent the last common ancestor for Neandertals and modern humans.

Size variation in Middle Pleistocene humans.

It has been suggested that European Middle Pleistocene humans, Neandertals, and prehistoric modern humans had a greater sexual dimorphism than modern humans. Analysis of body size variation and cranial capacity variation in the large sample from the Sima de los Huesos site in Spain showed instead that the sexual dimorphism is comparable in Middle Pleistocene and modern populations.

Lower Pleistocene hominids and artifacts from Atapuerca-TD6 (Spain)

Human remains dating to more than 780,000 years ago are associated with a rich faunal and lithic assemblage in the Pleistocene cave site of Gran Dolina (TD), Sierra de Atapuerca, Burgos, Spain. The micromammal species represent the late Biharian (Mimomys savini zone), and the lithic objects represent pre-Acheulean technology (Mode 1) and comes from the TD6 level below the Matuyama-Brunhes boundary. The Gran Dolina hominid fossils cannot be comfortably accommodated in any of the defined Homo species. They could be considered a primitive form of Homo heidelbergensis, but a new species might be named in the future if the sample is enlarged. The new human fossil evidence demonstrates that Western Europe was settled at least since the late early Pleistocene.

Novel display of knotted DNA molecules by two-dimensional gel electrophoresis.

We describe a two-dimensional agarose gel electrophoresis procedure that improves the resolution of knotted DNA molecules. The first gel dimension is run at low voltage, and DNA knots migrate according to their compactness. The second gel dimension is run at high voltage, and DNA knots migrate according to other physical parameters such as shape and flexibility. In comparison with one-dimensional gel electrophoresis, this procedure segregates the knotted DNA molecules from other unknotted forms of DNA, and partially resolves populations of knots that have the same number of crossings. The two-dimensional display may allow quantitative and qualitative characterization of different types of DNA knots simply by gel velocity.

New interpretation of the Gran Dolina-TD6 bearing Homo antecessor deposits through sedimentological analysis.

Gran Dolina is a cavity infilled by at least 25 m of Pleistocene sediments. This sequence contains the TD6 stratigraphic unit, whose records include around 170 hominin bones that have allowed the definition of a new species, Homo antecessor. This fossil accumulation was studied as a single assemblage and interpreted as a succession of several human home bases. We propose a complete stratigraphic context and sedimentological interpretation for TD6, analyzing the relationships between the sedimentary facies, the clasts and archaeo-palaeontological remains. The TD6 unit has been divided into three sub-units and 13 layers. Nine sedimentary facies have been defined. Hominin remains appear related to three different sedimentary facies: debris flow facies, channel facies and floodplain facies. They show three kinds of distribution: first a group of scattered fossils, then a group with layers of fossils in fluvial facies, and third a group with a layer of fossils in mixed fluvial and gravity flow facies. The results of this work suggest that some of these hominin remains accumulated in the cave by geological processes, coming from the adjacent slope above the cave or the cave entry, as the palaeogeography and sedimentary characteristics of these allochthonous facies suggest.

Computer analysis of mFISH chromosome aberration data uncovers an excess of very complicated metaphases.

PURPOSE: To analyse spectra of chromosome aberrations induced in vitro by low LET radiation, in order to characterize radiation damage mechanisms quantitatively. METHODS: Multiplex fluorescence in situ hybridization (mFISH) allows the simultaneous identification of each homologous chromosome pair by its own colour. mFISH data, specifying number distributions for colour junctions in metaphases of human peripheral blood lymphocytes 72 hours after exposure in vitro to a 3 Gy gamma-ray dose, were combined with similar, previously published results. Monte Carlo computer implementations of radiobiological models for chromosome aberration production guided quantitative analyses, which took into account distribution of cells among different metaphases and lethal effects or preferential elimination of some aberrations at cell division. RESULTS AND CONCLUSIONS: Standard models of DNA damage induction/repair/misrepair explain the main trends of the data as regards the fraction of metaphases having a particular number of colours involved in colour junctions. However, all standard models systematically under-predict the observed fraction of metaphases where a large number of different chromosomes participate in aberrations. An early appearance of chromosomal instability could explain most of the discrepancies.

Chromosome spatial clustering inferred from radiogenic aberrations.

PURPOSE: Analysing chromosome aberrations induced by low linear energy transfer (LET) radiation in order to characterize systematic spatial clustering among the 22 human autosomes in human lymphocytes and to compare their relative participation in interchanges. MATERIALS AND METHODS: A multicolour fluorescence in situ hybridization (mFISH) data set, specifying colour junctions in metaphases of human peripheral blood lymphocytes 72 h after in vitro exposure to low LET radiation, was analysed separately and in combination with previously published results. Monte Carlo computer simulations and mathematical modelling guided data analysis. RESULTS AND CONCLUSIONS: Statistical tests on aberration data confirmed two clusters of chromosomes, [1, 16, 17, 19, 22] and [13, 14, 15, 21, 22], as having their members being on average closer to each other than randomness would predict. The first set has been reported previously to be near the centre of the interphase nucleus and to be formed mainly by gene-rich chromosomes, while the second set comprises the nucleolus chromosomes. The results suggest a possible interplay between chromosome positioning and transcription. A number of other clusters suggested in the literature were not confirmed and considerable randomness of chromosome-chromosome juxtapositions was present. In addition, and consistent with previous results, it was found that chromosome participation in interchanges is approximately proportional to the two-thirds power of the DNA content.

Neandertal roots: Cranial and chronological evidence from Sima de los Huesos.

Seventeen Middle Pleistocene crania from the Sima de los Huesos site (Atapuerca, Spain) are analyzed, including seven new specimens. This sample makes it possible to thoroughly characterize a Middle Pleistocene hominin paleodeme and to address hypotheses about the origin and evolution of the Neandertals. Using a variety of techniques, the hominin-bearing layer could be reassigned to a period around 430,000 years ago. The sample shows a consistent morphological pattern with derived Neandertal features present in the face and anterior vault, many of which are related to the masticatory apparatus. This suggests that facial modification was the first step in the evolution of the Neandertal lineage, pointing to a mosaic pattern of evolution, with different anatomical and functional modules evolving at different rates.

Coupling membrane separation and photocatalytic oxidation processes for the degradation of pharmaceutical pollutants.

The coupling of membrane separation and photocatalytic oxidation has been studied for the removal of pharmaceutical pollutants. The retention properties of two different membranes (nanofiltration and reverse osmosis) were assessed. Comparable selectivity on the separation of pharmaceuticals were observed for both membranes, obtaining a permeate stream with concentrations of each pharmaceutical below 0.5 mg L(-)(1) and a rejected flux highly concentrated (in the range of 16-25 mg L(-)(1) and 18-32 mg L(-)(1) of each pharmaceutical for NF-90 and BW-30 membranes, respectively), when an initial stream of six pharmaceuticals was feeding to the membrane system (10 mg L(-)(1) of each pharmaceutical). The abatement of concentrated pharmaceuticals of the rejected stream was evaluated by means of heterogeneous photocatalytic oxidation using TiO2 and Fe2O3/SBA-15 in presence of hydrogen peroxide as photo-Fenton system. Both photocatalytic treatments showed remarkable removals of pharmaceutical compounds, achieving values between 80 and 100%. The nicotine was the most refractory pollutant of all the studied pharmaceuticals. Photo-Fenton treatment seems to be more effective than TiO2 photocatalysis, as high mineralization degree and increased nicotine removal were attested. This work can be considered an interesting approach of coupling membrane separation and heterogeneous photocatalytic technologies for the successful abatement of pharmaceutical compounds in effluents of wastewater treatment plants.

On the mean and variance of the writhe of random polygons.

We here address two problems concerning the writhe of random polygons. First, we study the behavior of the mean writhe as a function length. Second, we study the variance of the writhe. Suppose that we are dealing with a set of random polygons with the same length and knot type, which could be the model of some circular DNA with the same topological property. In general, a simple way of detecting chirality of this knot type is to compute the mean writhe of the polygons; if the mean writhe is non-zero then the knot is chiral. How accurate is this method? For example, if for a specific knot type K the mean writhe decreased to zero as the length of the polygons increased, then this method would be limited in the case of long polygons. Furthermore, we conjecture that the sign of the mean writhe is a topological invariant of chiral knots. This sign appears to be the same as that of an "ideal" conformation of the knot. We provide numerical evidence to support these claims, and we propose a new nomenclature of knots based on the sign of their expected writhes. This nomenclature can be of particular interest to applied scientists. The second part of our study focuses on the variance of the writhe, a problem that has not received much attention in the past. In this case, we focused on the equilateral random polygons. We give numerical as well as analytical evidence to show that the variance of the writhe of equilateral random polygons (of length n) behaves as a linear function of the length of the equilateral random polygon.

Human hyoid bones from the middle Pleistocene site of the Sima de los Huesos (Sierra de Atapuerca, Spain).

This study describes and compares two hyoid bones from the middle Pleistocene site of the Sima de los Huesos in the Sierra de Atapuerca (Spain). The Atapuerca SH hyoids are humanlike in both their morphology and dimensions, and they clearly differ from the hyoid bones of chimpanzees and Australopithecus afarensis. Their comparison with the Neandertal specimens Kebara 2 and SDR-034 makes it possible to begin to approach the question of temporal variation and sexual dimorphism in this bone in fossil humans. The results presented here show that the degree of metric and anatomical variation in the fossil sample was similar in magnitude and kind to living humans. Modern hyoid morphology was present by at least 530 kya and appears to represent a shared derived feature of the modern human and Neandertal evolutionary lineages inherited from their last common ancestor.

Luminescence chronology of cave sediments at the Atapuerca paleoanthropological site, Spain.

Ascertaining the timing of the peopling of Europe, after the first out-of-Africa demographic expansion at the end of the Pliocene, is of great interest to paleoanthropologists. One of the earliest direct evidences for fossil hominins in western Europe comes from an infilled karstic cave site called Gran Dolina at Atapuerca, in a stratum approximately 1.5m below the Brunhes-Matuyama (B-M) geomagnetic boundary (780ka) within lithostratigraphic unit TD6. However, most of the meters of fossil- and tool-bearing strata at Gran Dolina have been difficult to date. Therefore, we applied both thermoluminescence (TL) and infrared-stimulated-luminescence (IRSL) multi-aliquot dating methods to fine-silt fractions from sediment samples within Gran Dolina and the nearby Galería cave site. We also applied these methods to samples from the present-day surface soils on the surrounding limestone hill slopes to test the luminescence-clock-zeroing-by-daylight assumption. Within the uppermost 4m of the cave deposits at Gran Dolina, TL and paired TL and IRSL ages range stratigraphically from 198+/-19ka to 244+/-26ka. Throughout Gran Dolina, all luminescence results are stratigraphically self-consistent and, excepting results from two stratigraphic units, are consistent with prior ESR-U-series ages from progressively deeper strata. Thermoluminescence ages culminate at 960+/-120ka approximately 1m below the 780ka B-M boundary. At Galería, with one exception, TL and IRSL ages range stratigraphically downward from 185+/-26ka to 503+/-95ka at the base of the lowermost surface-inwash facies. These results indicate that TL and (sometimes) IRSL are useful dating tools for karstic inwash sediments older than ca. 100ka, and that a more accurate chronostratigraphic correlation is now possible among the main Atapuerca sites (Gran Dolina, Galería, Sima de los Huesos). Furthermore, the oldest TL age of ca. 960ka from Gran Dolina, consistent with biostratigraphic and paleomagnetic evidence, implies a probable numeric age of 900-950ka for the oldest hominin remains ( approximately 0.8m below the TL sample). This age window suggests a correspondence to Marine Isotope Stage (MIS) 25, a relatively warm and humid interglaciation.

Characterization of breast cancer by array comparative genomic hybridization.

Cancer progression is due to the accumulation of recurrent genomic alterations that induce growth advantage and clonal expansion. Most of these genomic changes can be detected using the array comparative genomic hybridization (CGH) technique. The accurate classification of these genomic alterations is expected to have an important impact on translational and basic research. Here we review recent advances in CGH technology used in the characterization of different features of breast cancer. First, we present bioinformatics methods that have been developed for the analysis of CGH arrays; next, we discuss the use of array CGH technology to classify tumor stages and to identify and stratify subgroups of patients with different prognoses and clinical behaviors. We finish our review with a discussion of how CGH arrays are being used to identify oncogenes, tumor suppressor genes, and breast cancer susceptibility genes.

New Neandertal remains from Cova Negra (Valencia, Spain).

New Neandertal fossils from the Mousterian site of Cova Negra in the Valencia region of Spain are described, and a comprehensive study of the entire human fossil sample is provided. The new specimens significantly augment the sample of human remains from this site and make Cova Negra one of the richest human paleontological sites on the Iberian Peninsula. The new specimens include cranial and postcranial elements from immature individuals and provide an opportunity to study the ontogenetic appearance of adult Neandertal characteristics in this Pleistocene population. Children younger than 10 years of age constitute four of the seven minimum number of individuals in the sample, and this relative abundance of children at Cova Negra is similar that in to other Neandertal sites in Europe and southwest Asia. The recognition of diagnostic Neandertal features in several of the specimens, as well as their western European context and late Pleistocene age, suggests that all the human remains from Cova Negra represent Neandertals. The archaeological evidence from Cova Negra indicates sporadic, short-term occupations of the site, suggesting a high degree of mobility among Neandertals.

Dental evidence on the hominin dispersals during the Pleistocene.

A common assumption in the evolutionary scenario of the first Eurasian hominin populations is that they all had an African origin. This assumption also seems to apply for the Early and Middle Pleistocene populations, whose presence in Europe has been largely explained by a discontinuous flow of African emigrant waves. Only recently, some voices have speculated about the possibility of Asia being a center of speciation. However, no hard evidence has been presented to support this hypothesis. We present evidence from the most complete and up-to-date analysis of the hominin permanent dentition from Africa and Eurasia. The results show important morphological differences between the hominins found in both continents during the Pleistocene, suggesting that their evolutionary courses were relatively independent. We propose that the genetic impact of Asia in the colonization of Europe during the Early and Middle Pleistocene was stronger than that of Africa.

A geometric morphometric analysis of hominin upper first molar shape.

Recent studies have revealed interesting differences in upper first molar morphology across the hominin fossil record, particularly significant between H. sapiens and H. neanderthalensis. Usually these analyses have been performed by means of classic morphometric methods, including the measurement of relative cusp areas or the angles defined between cusps. Although these studies have provided valuable information for the morphological characterization of some hominin species, we believe that the analysis of this particular tooth could be more conclusive for taxonomic assignment. In this study, we have applied geometric morphometric methods to explore the morphological variability of the upper first molar (M(1)) across the human fossil record. Our emphasis focuses on the study of the phenetic relationships among the European middle Pleistocene populations (designated as H. heidelbergensis) with H. neanderthalensis and H. sapiens, but the inclusion of Australopithecus and early Homo specimens has helped us to assess the polarity of the observed traits. H. neanderthalensis presents a unique morphology characterized by a relatively distal displacement of the lingual cusps and protrusion in the external outline of a large and bulging hypocone. This morphology can be found in a less pronounced degree in the European early and middle Pleistocene populations, and reaches its maximum expression with the H. neanderthalensis lineage. In contrast, modern humans retain the primitive morphology with a square occlusal polygon associated with a round external outline.