Ecosystem regimes and responses in a coupled ancient lake system from MIS 5b to present: the diatom record of lakes Ohrid and Prespa

We reconstruct the aquatic ecosystem interactions since the last interglacial period in the oldest, most diverse, hydrologically connected European lake system, by using palaeolimnological diatom and selected geochemistry data from Lake Ohrid “DEEP site” core and equivalent data from Lake Prespa core, Co1215. Driven by climate forcing, the lakes experienced two adaptive cycles during the last 92 ka: "interglacial and interstadial" and "glacial" cycle. The short-term ecosystems reorganizations, e.g. regime shifts within these cycles substantially differ between the lakes, as evident from the inferred amplitudes of variation. The deeper Lake Ohrid shifted between ultra oligo- and oligotrophic regimes in contrast to the much shallower Lake Prespa, which shifted from a deeper, (oligo-) mesotrophic to a shallower, eutrophic lake and vice versa. Due to the high level of ecosystem stability (e.g. trophic state, lake level), Lake Ohrid appears relatively resistant to external forcing, such as climate and environmental change. Recovering in a relatively short time from major climate change, Lake Prespa is a resilient ecosystem. At the DEEP site, the decoupling between the lakes' response to climate change is marked in the prolonged and gradual changes during the MIS 5/4 and 2/1 transitions. These response differences and the lakes' different physical and chemical properties may limit the influence of Lake Prespa on Lake Ohrid. Regime shifts of Lake Ohrid due to potential hydrological change in Lake Prespa are not evident in the data presented here. Moreover, a complete collapse of the ecosystems functionality and loss of their diatom communities did not happen in either lake for the period presented in the study.

Scientific drilling projects in ancient lakes: Integrating geological and biological histories

Sedimentary sequences in ancient or long-lived lakes can reach several thousands of meters in thickness and often provide an unrivalled perspective of the lake's regional climatic, environmental, and biological history. Over the last few years, deep-drilling projects in ancient lakes became increasingly multi- and interdisciplinary, as, among others, seismological, sedimentological, biogeochemical, climatic, environmental, paleontological, and evolutionary information can be obtained from sediment cores. However, these multi- and interdisciplinary projects pose several challenges. The scientists involved typically approach problems from different scientific perspectives and backgrounds, and setting up the program requires clear communication and the alignment of interests. One of the most challenging tasks, besides the actual drilling operation, is to link diverse datasets with varying resolution, data quality, and age uncertainties to answer interdisciplinary questions synthetically and coherently. These problems are especially relevant when secondary data, i.e., datasets obtained independently of the drilling operation, are incorporated in analyses. Nonetheless, the inclusion of secondary information, such as isotopic data from fossils found in outcrops or genetic data from extant species, may help to achieve synthetic answers. Recent technological and methodological advances in paleolimnology are likely to increase the possibilities of integrating secondary information. Some of the new approaches have started to revolutionize scientific drilling in ancient lakes, but at the same time, they also add a new layer of complexity to the generation and analysis of sediment-core data. The enhanced opportunities presented by new scientific approaches to study the paleolimnological history of these lakes, therefore, come at the expense of higher logistic, communication, and analytical efforts. Here we review types of data that can be obtained in ancient lake drilling projects and the analytical approaches that can be applied to empirically and statistically link diverse datasets to create an integrative perspective on geological and biological data. In doing so, we highlight strengths and potential weaknesses of new methods and analyses, and provide recommendations for future interdisciplinary deep-drilling projects.

Researching in ancient engineering physical and chemical analysis in hidraulic roman mortars

Around ten years ago investigation of technical and material construction in Ancient Roma has advanced in favour to obtain positive results. This process has been directed to obtaining some dates based in chemical composition, also action and reaction of materials against meteorological assaults or post depositional displacements. Plenty of these dates should be interpreted as a result of deterioration and damage in concrete material made in one landscape with some kind of meteorological characteristics. Concrete mixture like calcium and gypsum mortars should be analysed in laboratory test programs, and not only with descriptions based in reference books of Strabo, Pliny the Elder or Vitruvius. Roman manufacture was determined by weather condition, landscape, natural resources and of course, economic situation of the owner. In any case we must research the work in every facts of construction. On the one hand, thanks to chemical techniques like X-ray diffraction and Optical microscopy, we could know the granular disposition of mixture. On the other hand if we develop physical and mechanical techniques like compressive strength, capillary absorption on contact or water behaviour, we could know the reactions in binder and aggregates against weather effects. However we must be capable of interpret these results. Last year many analyses developed in archaeological sites in Spain has contributed to obtain different point of view, so has provide new dates to manage one method to continue the investigation of roman mortars. If we developed chemical and physical analysis in roman mortars at the same time, and we are capable to interpret the construction and the resources used, we achieve to understand the process of construction, the date and also the way of restoration in future.

Mechanical properties of adobe bricks in ancient constructions

A study of the mechanical properties of adobe bricks collected from houses and land dividing walls in Aveiro district, Portugal, representative of existing traditional constructions, was conducted. Cylindrical adobe specimens were subjected to simple compression and splitting tests. From these tests it was possible to evaluate the strength capacity, stiffness and deformation evolution for increasing loading. Correlations between the evaluated properties were determined, and the results obtained for houses and land dividing walls were compared. This study contributes for the characterization of adobes traditionally used in Aveiro district, and provides reference values that can be considered in rehabilitation processes

Adobe's Mechanical Characterization in Ancient Constructions: The Case of Aveiro's Region

Adobe is commonly found in Aveiro's ancient constructions. Preservation and rehabilitation of those constructions, some of them with architectural and historical interest, has been forgotten for many years. As a result, in Aveiro region, the majority of existing constructions in adobe is structurally weak, and, in several cases, they are in the threshold of ruin. Rehabilitation and/or strengthening urge. Despite some efforts has been made, a great difficulty for technicians working on the rehabilitation of these constructions relies on the lack of knowledge on adobe's mechanical behaviour. In fact, in order to properly describe the structural behaviour of those constructions, there is a need to investigate the mechanical behaviour of adobe. Hence, this paper is based on a study intended to characterise the behaviour of adobe brick units. Specimens were prepared from selected representative constructions of the Aveiro region. The prepared specimens were tested in order to evaluate their mechanical behaviour in compression and tension

Outreach Testing of Ancient Astronomy

This work is an outreach approach to an ubiquitous recent problem in secondary-school education: how to face back the decreasing interest in natural sciences shown by students under ‘pressure’ of convenient resources in digital devices/applications. The approach rests on two features. First, empowering of teen-age students to understand regular natural events around, as very few educated people they meet could do. Secondly, an understanding that rests on personal capability to test and verify experimental results from the oldest science, astronomy, with simple instruments as used from antiquity down to the Renaissance (a capability restricted to just solar and lunar motions). Because lengths in astronomy and daily life are so disparate, astronomy basically involved observing and registering values of angles (along with times), measurements being of two types, of angles on the ground and of angles in space, from the ground. First, the gnomon, a simple vertical stick introduced in Babylonia and Egypt, and then in Greece, is used to understand solar motion. The gnomon shadow turns around during any given day, varying in length and thus angle between solar ray and vertical as it turns, going through a minimum (noon time, at a meridian direction) while sweeping some angular range from sunrise to sunset. Further, the shadow minimum length varies through the year, with times when shortest and sun closest to vertical, at summer solstice, and times when longest, at winter solstice six months later. The extreme directions at sunset and sunrise correspond to the solstices, swept angular range greatest at summer, over 180 degrees, and the opposite at winter, with less daytime hours; in between, spring and fall equinoxes occur, marked by collinear shadow directions at sunrise and sunset. The gnomon allows students to determine, in addition to latitude (about 40.4° North at Madrid, say), the inclination of earth equator to plane of its orbit around the sun (ecliptic), this fundamental quantity being given by half the difference between solar distances to vertical at winter and summer solstices, with value about 23.5°. Day and year periods greatly differing by about 2 ½ orders of magnitude, 1 day against 365 days, helps students to correctly visualize and interpret the experimental measurements. Since the gnomon serves to observe at night the moon shadow too, students can also determine the inclination of the lunar orbital plane, as about 5 degrees away from the ecliptic, thus explaining why eclipses are infrequent. Independently, earth taking longer between spring and fall equinoxes than from fall to spring (the solar anomaly), as again verified by the students, was explained in ancient Greek science, which posited orbits universally as circles or their combination, by introducing the eccentric circle, with earth placed some distance away from the orbital centre when considering the relative motion of the sun, which would be closer to the earth in winter. In a sense, this can be seen as hint and approximation of the elliptic orbit proposed by Kepler many centuries later.

El tiempo como sustancia de la forma : una aproximación al Museo de Arte Romano de Mérida desde los presupuestos del vitalismo

El modelo dominante durante la Era Moderna asume la presencia del hombre como sujeto dentro del gran engranaje mecánico del Cosmos. Asimismo, recoge una idea acerca del ser natural dentro de la tradición ontológica iniciada por el eleatismo presocrático que concibe a éste como lo inmutable y estático frente al cambio y al movimiento, los cuales se constituyen como meras apariencias. Durante el periodo anterior a la aparición de los grandes filósofos griegos se produce una transformación en donde, de la inicial cosmología vinculada a un tiempo primordial, se pasará a una visión del Universo como ente indestructible, atemporal, inmutable, perfecto, geométrico y espacial. Si en Demócrito se admite un universo sometido al azar y a la necesidad, en Platón el Universo sólo atiende a la necesidad. Este modelo ontológico se pone en entredicho cuando el hombre ya no es concebido como pieza de un sistema más amplio, sino como centro radical del pensamiento. La condición radical del hombre es entonces su propia vida, siendo éste el concepto troncal del denominado vitalismo cuyo más influyente representante en España es José Ortega y Gasset. El estatismo del ser –del hombre- pierde sentido; en palabras del propio Ortega, “no es un ser sino un estar siendo” lo que caracteriza a la vida humana. La razón cartesiana es ahora la razón vital y su objeto de estudio no es la naturaleza sino el propio devenir, es decir, el tiempo, la historia. Este planteamiento es fundamental para comprender el edificio que es objeto de este estudio, el Museo de Arte Romano de Mérida (1980-1985) de Rafael Moneo. Por ello el concepto de tiempo es utilizado como marco y estructura de la presente tesis, a sabiendas del notorio y muy significativo papel que este edificio desempeñó en la carrera de su autor y en el panorama nacional e internacional de la arquitectura y de la museología. Este proyecto nos permite acercarnos al pensamiento de su autor a través de un edificio que, aun habiendo sido ampliamente reconocido, no cuenta con un estudio suficientemente exhaustivo que recoja la amplitud y riqueza que encierra. Esta tesis no es un compendio de lo que ya se ha investigado sobre Mérida; es una aproximación global e interpretativa cuyo sentido sólo puede concebirse al vislumbrar la estructura completa de la misma en sintonía con el "lógos" vital, histórico y narrativo que el proyecto encierra. Se revisará la concepción histórica según la cual, la configuración espacial de la forma habría tenido primacía respecto a su configuración temporal, al remitir esta última a una condición espacializada y circunstancial. La componente vicaria de la circunstancia será elevada por Ortega a la categoría de esencial, visualizando así una paradoja cuya reformulación nos lleva a la concepción de un tiempo sustancial. El diccionario de la RAE, en su tercera acepción, define la sustancia como “aquello que permanece en algo que cambia”, lo cual nos remite al pensamiento antiguo. Se mostrará que lo que permanece no necesariamente implica una concepción estática y eleática de la forma, que la arquitectura esencial no es unívocamente la arquitectura atemporal del platonismo y que cabe concebir la "firmitas" desde la atención a la "durée" bergsoniana. Al asociar tradicionalmente la sustancia con el referido estatismo, se margina al tiempo y a la duración a lo no sustancial; por ello, se tratará de aproximar los términos de tiempo y sustancia para definir la forma. Ello conllevará al estudio de las notables patologías derivadas de la asunción de un tiempo cronológico en nuestra contemporaneidad frente a las cuales, las intuiciones contenidas en Mérida, se alinearán con la actual actitud revisionista en el ámbito del pensamiento filosófico y científico. En Mérida, la memoria recogerá los aspectos de la conciencia así como los aspectos vinculados a la experiencia íntima y colectiva como soporte para la consecución de un discurso. La dualidad entre intuición e inteligencia será recogida por Moneo con idea de trascender su incomunicabilidad, mediante una operación que consistirá en la reivindicación de una memoria irreductible, cuya morada estaría incardinada en el propio tiempo de la duración y de la vida y no en la espacialidad coextensiva del presente y de la acción funcional sobre la materia. Moneo asumirá el papel de la memoria como condición central de una forma que se encarnará al concebirse como un teatro. En la respuesta a la contradicción entre el hecho físico y el efecto psíquico de la experiencia humana residirá la pertinencia de un tiempo narrativo. Será entonces el lenguaje el encargado de aportar sentido a la obra mediante el recurso fundado en la dramatización de la experiencia, es decir, a través de una conexión entre la conciencia íntima y el carácter social y colectivo intrínseco en la arquitectura. ABSTRACT TIME AS A SUBSTANCE OF FORM. AN APPROACH TO THE ROMAN ART MUSEUM OF MÉRIDA FROM THE VIEWPOINT OF VITALISM. The dominant model during the Modern Era placed man as a subject inside the great mechanism of the cosmos. It is also based in an idea about natural being within the ontological tradition initiated by the pre-Socratic Eleatism that conceives it as something immutable and static in respect with change and movement, which are considered as mere appearances. Prior to the emergence of the great Greek philosophers occurred a transformation where concepts of cosmology linked to a primordial time, changed to a view of the universe as indestructible, timeless, unchanging, perfect, geometric and spatial. If Democritus accepted a universe subjected to randomness and necessity, Plato thought that the universe only worked by necessity. This ontological model is called into question when man is not conceived as a piece of a broader system, but as a radical center of thinking. The radical condition of man then is his own life. This is the core concept of so-called Vitalism, whose most influential representative in Spain was José Ortega y Gasset. The stillness of being – of man - loses its meaning; in the words of Ortega, “it is not being but being in progress” that characterizes human life. The Cartesian reason is now the vital reason and its subject of study is no longer nature but its own evolution, in other words, time and history. This approach is fundamental to understand the building which is the subject of this study, the Museum of Roman Art in Mérida (1980-1985) by Rafael Moneo. The concept of time is used as a framework and structure of this thesis, demonstrating the notorious and very significant role this building has implied in the career of its author and in the national and international panorama of architecture and museology. This project allow us to approach the thought of its author through a building that, even whilst widely recognized, does not yet have a sufficiently comprehensive study covering its breadth and richness. This thesis is not a compendium of what already has been researched on Merida; it is a global and interpretative approach whose meaning can only be conceived as a study of its complete structure in line with the vital, historical and narrative logos the project implies. We will review the historical idea where spatial configuration of the form would have had primacy with respect to temporary configuration, because the latter refers to a spatial and circumstantial condition. The vicarious nature of the circumstance will be elevated by Ortega to the category of essential, thus showing a paradox which reformulation leads us to the conception of a substantial time. The dictionary of the Spanish Royal Academy, in its third meaning, defines substance as "that which remains in something that changes". This is a reference to ancient thought. It will be shown that what remains does not necessarily imply a static and Eleatic conception of form. It will also be shown that the essential architecture is not uniquely the timeless architecture of Platonism and that it is possible to conceive the "firmitas" parallel to the "durée" of Henri Bergson. As a result of this traditional association between substance and stillness, it marginalizes the time and the duration to the non-substantial; for this reason, we will try to approach terms of time and substance to define the shape. This will involve studying significant pathologies resulting from an assumption of chronological time in our contemporary world against which, the insights contained in Merida, will be aligned with the current revisionist attitude in the fields of philosophical and scientific thought. In Merida, memory includes aspects of consciousness as well as aspects linked to the intimate and collective experience as a foundation for the achievement of discourse. The duality between intuition and intelligence is put forward by Moneo with the idea of transcending its lack of communication, by means of a resource consisting of the vindication of an irreducible memory, whose home would be embodied in the time of duration and life and not in the coextensive spatiality of the present and in the functional action on the matter. Moneo demonstrates the role of memory as a central condition of form as a theatre. In response to the contradiction between the physical fact and the psychological effect of human experience lies the relevance of narrative time. Language then assumes the responsibility of giving meaning to the work through the dramatization of experience, i.e., through a connection between the intimate consciousness and the intrinsic social and collective character of architecture.

Detection of 400-year-old Yersinia pestis DNA in human dental pulp: An approach to the diagnosis of ancient septicemia

Ancient septicemic plague epidemics were reported to have killed millions of people for 2 millenniums. However, confident diagnosis of ancient septicemia solely on the basis of historical clinical observations is not possible. The lack of suitable infected material has prevented direct demonstration of ancient septicemia; thus, the history of most infections such as plague remains hypothetical. The durability of dental pulp, together with its natural sterility, makes it a suitable material on which to base such research. We hypothesized that it would be a lasting refuge for Yersinia pestis, the plague agent. DNA extracts were made from the dental pulp of 12 unerupted teeth extracted from skeletons excavated from 16th and 18th century French graves of persons thought to have died of plague (“plague teeth”) and from 7 ancient negative control teeth. PCRs incorporating ancient DNA extracts and primers specific for the human β-globin gene demonstrated the absence of inhibitors in these preparations. The incorporation of primers specific for Y. pestis rpoB (the RNA polymerase β-subunit-encoding gene) and the recognized virulence-associated pla (the plasminogen activator-encoding gene) repeatedly yielded products that had a nucleotide sequence indistinguishable from that of modern day isolates of the bacterium. The specific pla sequence was obtained from 6 of 12 plague skeleton teeth but 0 of 7 negative controls (P < 0.034, Fisher exact test). A nucleic acid-based confirmation of ancient plague was achieved for historically identified victims, and we have confirmed the presence of the disease at the end of 16th century in France. Dental pulp is an attractive target in the quest to determine the etiology of septicemic illnesses detected in ancient corpses. Molecular techniques could be applied to this material to resolve historical outbreaks.

Histone underacetylation is an ancient component of mammalian X chromosome inactivation

Underacetylation of histone H4 is thought to be involved in the molecular mechanism of mammalian X chromosome inactivation, which is an important model system for large-scale genetic control in eukaryotes. However, it has not been established whether histone underacetylation plays a critical role in the multistep inactivation pathway. Here we demonstrate differential histone H4 acetylation between the X chromosomes of a female marsupial, Macropus eugenii. Histone underacetylation is the only molecular aspect of X inactivation known to be shared by marsupial and eutherian mammals. Its strong evolutionary conservation implies that, unlike DNA methylation, histone underacetylation was a feature of dosage compensation in a common mammalian ancestor, and is therefore likely to play a central role in X chromosome inactivation in all mammals.

An ancient family of human endogenous retroviruses encodes a functional homolog of the HIV-1 Rev protein

The human endogenous retrovirus K (HERV-K) family of endogenous retroviruses consists of ≈50 proviral copies per haploid human genome. Herein, the HERV-Ks are shown to encode a sequence-specific nuclear RNA export factor, termed K-Rev, that is functionally analogous to the HIV-1 Rev protein. Like HIV-1 Rev, K-Rev binds to both the Crm1 nuclear export factor and to a cis-acting viral RNA target to activate nuclear export of unspliced RNAs. Surprisingly, this HERV-K RNA sequence, which is encoded within the HERV-K long terminal repeat, is also recognized by HIV-1 Rev. These data provide surprising evidence for an evolutionary link between HIV-1 and a group of endogenous retroviruses that first entered the human genome ≈30 million years ago.

Carbonic anhydrase is an ancient enzyme widespread in prokaryotes

Carbonic anhydrases catalyze the reversible hydration of CO2 and are ubiquitous in highly evolved eukaryotes. The recent identification of a third class of carbonic anhydrase (γ class) in a methanoarchaeon and our present finding that the β class also extends into thermophilic species from the Archaea domain led us to initiate a systematic search for these enzymes in metabolically and phylogenetically diverse prokaryotes. Here we show that carbonic anhydrase is widespread in the Archaea and Bacteria domains, and is an ancient enzyme. The occurrence in chemolithoautotrophic species occupying deep branches of the universal phylogenetic tree suggests a role for this enzyme in the proposed autotrophic origin of life. The presence of the β and γ classes in metabolically diverse species spanning the Archaea and Bacteria domains demonstrates that carbonic anhydrases have a far more extensive and fundamental role in prokaryotic biology than previously recognized.

Ancient mtDNA sequences in the human nuclear genome: A potential source of errors in identifying pathogenic mutations

Nuclear-localized mtDNA pseudogenes might explain a recent report describing a heteroplasmic mtDNA molecule containing five linked missense mutations dispersed over the contiguous mtDNA CO1 and CO2 genes in Alzheimer’s disease (AD) patients. To test this hypothesis, we have used the PCR primers utilized in the original report to amplify CO1 and CO2 sequences from two independent ρ° (mtDNA-less) cell lines. CO1 and CO2 sequences amplified from both of the ρ° cells, demonstrating that these sequences are also present in the human nuclear DNA. The nuclear pseudogene CO1 and CO2 sequences were then tested for each of the five “AD” missense mutations by restriction endonuclease site variant assays. All five mutations were found in the nuclear CO1 and CO2 PCR products from ρ° cells, but none were found in the PCR products obtained from cells with normal mtDNA. Moreover, when the overlapping nuclear CO1 and CO2 PCR products were cloned and sequenced, all five missense mutations were found, as well as a linked synonymous mutation. Unlike the findings in the original report, an additional 32 base substitutions were found, including two in adjacent tRNAs and a two base pair deletion in the CO2 gene. Phylogenetic analysis of the nuclear CO1 and CO2 sequences revealed that they diverged from modern human mtDNAs early in hominid evolution about 770,000 years before present. These data would be consistent with the interpretation that the missense mutations proposed to cause AD may be the product of ancient mtDNA variants preserved as nuclear pseudogenes.