Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The collections of Lauraceae in the Herbarium of Henri Van Heurck (AWH)

Background and aims - The collections of Lauraceae in the Van Heurck Herbarium (AWH), which is currently on permanent loan to BR, have remained unknown by most of the specialists and by the general public up until the present. The taxonomic status of its one hundred and forty nine specimens of Lauraceae is here presented.Methods - Standard herbarium taxonomy practices were used in conjunction with the literature available. Specimens from fifty eight different herbaria were studied personally, or by checking their holdings available in the internet, or from digital images received from the curators.Key results - The specimens of Lauraceae from AWH are distributed in twenty four genera and seventy eight species with taxonomic status resolved, excepting for three specimens pertaining to species name of status uncertain (one), or to unresolved determination (two). From them, fifty three specimens are nomenclatural types of any sort, which corroborate the relevance of exsiccates acquired by Van Heurck, even for this relatively small set of specimens for the family. Fifteen lectotypifications and one neotypification of species names are proposed here.

Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns

Background: Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out. Results: Sixty complete LTR-RT elements were classified into 35 families within four Copia and three Gypsy lineages. Structurally, within lineages elements were similar, between lineages there were large size differences. FISH analysis resulted in the expected pattern of Gypsy/heterochromatin, Copia/euchromatin, but in two lineages there was localized clustering on some chromosomes. Analysis of related ESTs and RT-PCR showed transcriptional variation between tissues and families. Four distinct patterns were observed in sRNA mapping, the most unusual of which was that of Ale1, with very large numbers of 24nt sRNAs in the coding region. The results presented support the conclusion that distinct small RNA-regulated pathways in sugarcane target the lineages of LTR-RT elements. Conclusions: Individual LTR-RT sugarcane families have distinct structures, and transcriptional and regulatory signatures. Our results indicate that in sugarcane individual LTR-RT families have distinct behaviors and can potentially impact the genome in diverse ways. For instance, these transposable elements may affect nearby genes by generating a diverse set of small RNA's that trigger gene silencing mechanisms. There is also some evidence that ancestral genomes contribute significantly different element numbers from particular LTR-RT lineages to the modern sugarcane cultivar genome.

Work and Family: a complex interplay. An Italian application of the DISC Model on health care workers

The present thesis investigates the issue of work-family conflict and facilitation in a sanitarian contest, using the DISC Model (De Jonge and Dormann, 2003, 2006). The general aim has been declined in two empirical studies reported in this dissertation chapters. Chapter 1 reporting the psychometric properties of the Demand-Induced Strain Compensation Questionnaire. Although the empirical evidence on the DISC Model has received a fair amount of attention in literature both for the theoretical principles and for the instrument developed to display them (DISQ; De Jonge, Dormann, Van Vegchel, Von Nordheim, Dollard, Cotton and Van den Tooren, 2007) there are no studies based solely on psychometric investigation of the instrument. In addition, no previous studies have ever used the DISC as a model or measurement instrument in an Italian context. Thus the first chapter of the present dissertation was based on psychometric investigation of the DISQ. Chapter 2 reporting a longitudinal study contribution. The purpose was to examine, using the DISC model, the relationship between emotional job characteristics, work-family interface and emotional exhaustion among a health care population. We started testing the Triple Match Principle of the DISC Model using solely the emotional dimension of the strain-stress process (i.e. emotional demands, emotional resources and emotional exhaustion). Then we investigated the mediator role played by w-f conflict and w-f facilitation in relation to emotional job characteristics and emotional exhaustion. Finally we compared the mediator model across workers involved in chronic illness home demands and workers who are not involved. Finally, a general conclusion, integrated and discussed the main findings of the studies reported in this dissertation.

Chronostratigraphy of the 600,000 year old continental record of Lake Van

Lake Van sediment cores from the Ahlat Ridge and Northern Basin drill sites of the ICDP project PALEOVAN contain a wealth of information about past environmental processes. The sedimentary sequence was dated using climatostratigraphic alignment, varve chronology, tephrostratigraphy, argon-argon single-crystal dating, radiocarbon dating, magnetostratigraphy, and cosmogenic nuclides. Based on the lithostratigraphic framework, the different age constraints are compiled and a robust and precise chronology of the 600,000 year-old Lake Van record is constructed. Proxy records of total organic carbon content and sediment color, together with the calcium/potassium-ratios and arboreal pollen percentages of the 174-meter-long Ahlat Ridge record, mimic the Greenland isotope stratotype (NGRIP). Therefore, the proxy records are systematically aligned to the onsets of interstadials reflected in the NGRIP or synthesized Greenland ice-core stratigraphy. The chronology is constructed using 27 age control points derived from visual synchronization with the GICC05 timescale, an absolutely-dated speleothem record (e.g., Hulu, Sanbao, Linzhu cave) and the Epica Dome C timescale. In addition, the uppermost part of the sequence is complemented with four ages from Holocene varve chronology and two calibrated radiocarbon ages. Furthermore, nine argon-argon ages and a comparison of the relative paleointensity record of the magnetic field with reference curve PISO-1500 confirm the accuracy of the age model. Also the identification of the Laschamp event via measurements of 10Be in the sediment confirms the presented age model. The chronology of the Ahlat Ridge record is transferred to the 79-meter-long event-corrected composite record from the Northern Basin and supplemented by additional radiocarbon dating on organic marco-remains. The basal age of the Northern Basin record is estimated at ~90 ka. The variations of the time series of total organic carbon content, the Ca/K ratio, and the arboreal pollen percentages illustrate that the presented chronology and paleoclimate data are suited for reconstructions and modeling of the Quaternary and Pleistocene climate evolution in the Near East at millennial timescales. Furthermore, the chronology of the last 250 kyr can be used to test other dating techniques.

High-resolution multi-proxy record of the last glacial period from Lake Van, eastern Anatolian high plateau, Turkey

Detailed analyses of the Lake Van pollen, Ca/K ratio and stable oxygen isotope record allow the identification of millennial-scale vegetation and environmental changes in eastern Anatolia throughout the last glacial (~75-15 ka BP). The climate within the last glacial was cold and dry, with low arboreal pollen (AP) levels. The driest and coldest period corresponds to Marine Isotope Stage (MIS) 2 (~28-14.5 ka BP) dominated by the highest values of xerophytic steppe vegetation. Our high-resolution multi proxy record shows rapid expansions and contractions of tree populations that reflects variability in temperature and moisture availability. This rapid vegetation and environmental changes can be linked to the stadial-interstadial pattern of the Dansgaard-Oeschger (DO) events as recorded in the Greenland ice cores. Periods of reduced moisture availability were characterized by enhanced xerophytic species and high terrigenous input from the Lake Van catchment area. Furthermore, comparison with the marine realm reveals that the complex atmosphere-ocean interaction can be explained by the strength and position of the westerlies, which is responsible for the supply of humidity in eastern Anatolia. Influenced by diverse topography of the Lake Van catchment, larger DO interstadials (e.g. DO 19, 17-16, 14, 12 and 8) show the highest expansion of temperate species within the last glacial. However, Heinrich events (HE), characterized by highest concentrations of ice-rafted debris (IRD) in marine sediments, are identified in eastern Anatolia by AP values not lower and high steppe components not more abundant than during DO stadials. In addition, this work is a first attempt to establish a continuous microscopic charcoal record over the last glacial in the Near East, which documents an initial immediate response to millennial-scale climate and environmental variability and enables us to shed light on the history of fire activity during the last glacial.

High-resolution multi-proxy record of the last interglacial period from Lake Van, eastern Anatolian high plateau, Turkey

A high-resolution multi-proxy record from Lake Van, eastern Anatolia, derived from a lacustrine sequence cored at the 357 m deep Ahlat Ridge (AR), allows a comprehensive view of paleoclimate and environmental history in the continental Near East during the last interglacial (LI). We combined paleovegetation (pollen), stable oxygen isotope (d18Obulk) and XRF data from the same sedimentary sequence, showing distinct variations during the period from 135 to 110 ka ago leading into and out of full interglacial conditions. The last interglacial plateau, as defined by the presence of thermophilous steppe-forest communities, lasted ca. 13.5 ka, from ~129.1-115.6 ka BP. The detailed palynological sequence at Lake Van documents a vegetation succession with several climatic phases: (I) the Pistacia zone (ca. 131.2-129.1 ka BP) indicates summer dryness and mild winter conditions during the initial warming, (II) the Quercus-Ulmus zone (ca. 129.1-127.2 ka BP) occurred during warm and humid climate conditions with enhanced evaporation, (III) the Carpinus zone (ca. 127.2-124.1 ka BP) suggest increasingly cooler and wetter conditions, and (IV) the expansion of Pinus at ~124.1 ka BP marks the onset of a colder/drier environment that extended into the interval of global ice growth. Pollen data suggest migration of thermophilous trees from refugial areas at the beginning of the last interglacial. Analogous to the current interglacial, the migration documents a time lag between the onset of climatic amelioration and the establishment of an oak steppe-forest, spanning 2.1 ka. Hence, the major difference between the last interglacial compared to the current interglacial (Holocene) is the abundance of Pinus as well as the decrease of deciduous broad-leaved trees, indicating higher continentality during the last interglacial. Finally, our results demonstrate intra-interglacial variability in the low mid-latitudes and suggest a close connection with the high-frequency climate variability recorded in Greenland ice cores.

Vivienda y fondo edificatorio: análisis de las consecuencias del parámetro fondo en el edificio de vivienda colectiva

Este estudio ofrece una herramienta de aproximación al espacio morfológico-métrico en el que se formula la ciudad de alta densidad desde la vivienda colectiva. La vivienda colectiva es la célula básica de la ciudad. El estudio configurativo y dimensional del tejido urbano muestra la importancia del fondo edificatorio como parámetro clave a mitad de camino entre la vivienda y la ciudad. El fondo edificatorio traza el margen de la arquitectura en la ciudad y desde él se equipa y cuantifica el territorio urbano. Sus dinámicas van caracterizando los distintos entornos, mientras en su interior se formula el tipo en un ajuste de continua verificación y adaptación. La forma de la ciudad y sus distintas posibilidades configurativas —en cuanto masa construida y espacio público, pero sin perder de vista la relación entre ambos— depende en gran medida del fondo edificatorio. Se trata, por tanto, de un parámetro importante de relación entre las distintas configuraciones del espacio exterior e interior. Al proyectar, una vez establecido un fondo, algunas propiedades se adaptan con facilidad mientras que otras requieren un cierto grado de interpretación o deben ser descartadas. Dada una superficie, la especificación del fondo fuerza la dimensión del frente en las configuraciones posibles. Ambas dimensiones son vitales en el valor del factor de forma del continuo edificado y en su relación se produce el complejo rango de posibilidades. Partiendo de la ciudad, un gran fondo encierra y mezcla en su interior todo tipo de usos sin distinción, repercute un menor coste por unidad de superficie edificada y comparte su frente reduciendo los intercambios térmicos y lumínicos. Sin embargo la ciudad de fondo reducido ajusta la forma al uso y se desarrolla linealmente con repetitividad a lo largo de sus frentes exteriores. En ella, el fuerte intercambio energético se opone a las grandes posibilidades del espacio libre. En cambio desde la casa las distintas medidas del fondo se producen bajo determinados condicionantes: clima, compacidad, ocupación, hibridación, tamaño de casa, etc., mientras que el tipo se desarrolla en base a una métrica afín. Este trabajo parte de esta dialéctica. Estudia la relación de dependencia entre las condiciones del edificio de viviendas y su métrica. Jerarquiza edificios en base al parámetro “fondo” para constituir una herramienta que como un ábaco sea capaz de visibilizar las dinámicas relacionales entre configuración y métrica bajo la condición de alta densidad. Para ello en una primera fase se gestiona una extensa muestra de edificios representativos de vivienda colectiva principalmente europea, extraída de tres prestigiosos libros en forma de repertorio. Se ordenan y categorizan extrayendo datos conmensurables y temas principales que ligan la profundidad de la huella a la morfología y posteriormente, esta información se estudia en diagramas que ponen de manifiesto convergencias y divergencias, acumulaciones y vacíos, límites, intervalos característicos, márgenes y ejes, parámetros y atributos... cuya relación trata de factorizar el lugar morfológico y métrico de la casa como metavivienda y ciudad. La herramienta se establece así como un complejo marco relacional en el que posicionar casos concretos y trazar nexos transversales, tanto de tipo morfológico como cultural, climático o técnico, normativo o tecnológico. Cada nuevo caso o traza añadida produce consonancias y disonancias en el marco que requieren interpretación y verificación. De este modo este instrumento de análisis comparativo se tempera, se especializa, se completa y se perfecciona con su uso. La forma de la residencia en la ciudad densa se muestra así sobre un subsistema morfológico unitario y su entendimiento se hace más fácilmente alcanzable y acumulable tanto para investigaciones posteriores como para el aprendizaje o el ejercicio profesional. ABSTRACT This research study offers a tool to approach the morphometric space in which (multi-family) housing defines high-density cities. Multi-family housing is the basic cell of the city. The configuration and dimension studies of the urban fabric render the importance of building depth as a key parameter half way between the dwelling and the city. The building depth traces de limit of architecture in the city. It qualifies and quantifies the urban territory. Its dynamics characterize the different environments while in its essence, an adjustment process of continuous verification and adaption defines type. The shape of the city and its different configuration possibilities —in terms of built fabric and public space, always keeping an eye on the relationship between them— depend majorly on the building depth. Therefore, it is a relevant parameter that relates the diverse configurations between interior and exterior space. When designing, once the depth is established, some properties are easily adpated. However, others require a certain degree of interpretation or have to be left out of the study. Given a ceratin surface, the establishment of the depth forces the dimensions of the facade in the different configurations. Both depth and facade dimensions are crucial for the form factor of the built mass. Its relationship produces a complex range of possibilities. From an urban point of view, great depth means multiple uses (making no distinction whatsoever,) it presents a lower cost per unit of built area and shares its facade optimizing temperature and light exchange. On the contrary, the city of reduced depth adjusts its shape to the use, and develops linearly and repetitively along its facades. The strong energy exchange opposes to the great possibilities of free space. From the perspective of the dwelling, the different dimensions of depth are produced under certain determinants: climate, compactness, occupancy, hybridization, dwelling size, etc. Meanwhile, the type is developed based on a related meter (as in poetry). This work starts from the previous premise. It studies the dependency relation bewteen the conditions of the dwellings and their meter (dimensions). It organizes buildings hierarchically based on the parameter “depth” to create a tool that, as an abacus, is able to visibilise the relational dynamics between configuration and dimension in high density conditions. For this, in the first stage a large group of representative multi-family housing buildings is managed, mostly from Europe, picked from three prestigious books as a repertoir. They are categorized and ordered drawing commensurable data and key issues that link the depth of the fooprint to its morphology. Later, this information is studied deeply with diagrams that bring out connections and discrepancies, voids and accumulations, limits, charasteristic intervals, margins and axii, parameters, attributes, etc. These relationships try to create factors from a morphological and metrical point of view of the house as a metadwelling. This tool is established as a complex relation frame in which case studies are postitioned and cross-cutting nexii are traced. These can deal with morphology, climate, technique, law or technology. Each new case or nexus produces affinities and discrepancies that require interpretation and verification. Thus, this instrument of comparative analysis is fine-tuned, especialized and completed as its use is improved. The way housing is understood in high density cities is shown as a unitary metric subsystem and its understanding is easy to reach and accumulate for future researchers, students or practicing architects.

Molecular Characterization of Three Canine Models of Human Rare Bone Diseases: Caffey, van den Ende-Gupta, and Raine Syndromes.

One to two percent of all children are born with a developmental disorder requiring pediatric hospital admissions. For many such syndromes, the molecular pathogenesis remains poorly characterized. Parallel developmental disorders in other species could provide complementary models for human rare diseases by uncovering new candidate genes, improving the understanding of the molecular mechanisms and opening possibilities for therapeutic trials. We performed various experiments, e.g. combined genome-wide association and next generation sequencing, to investigate the clinico-pathological features and genetic causes of three developmental syndromes in dogs, including craniomandibular osteopathy (CMO), a previously undescribed skeletal syndrome, and dental hypomineralization, for which we identified pathogenic variants in the canine SLC37A2 (truncating splicing enhancer variant), SCARF2 (truncating 2-bp deletion) and FAM20C (missense variant) genes, respectively. CMO is a clinical equivalent to an infantile cortical hyperostosis (Caffey disease), for which SLC37A2 is a new candidate gene. SLC37A2 is a poorly characterized member of a glucose-phosphate transporter family without previous disease associations. It is expressed in many tissues, including cells of the macrophage lineage, e.g. osteoclasts, and suggests a disease mechanism, in which an impaired glucose homeostasis in osteoclasts compromises their function in the developing bone, leading to hyperostosis. Mutations in SCARF2 and FAM20C have been associated with the human van den Ende-Gupta and Raine syndromes that include numerous features similar to the affected dogs. Given the growing interest in the molecular characterization and treatment of human rare diseases, our study presents three novel physiologically relevant models for further research and therapy approaches, while providing the molecular identity for the canine conditions.

The ancestors of two sisters; records of the ancestors of Helen Robina Cortelyou and Carol Van Zandt Cortelyou.

Mode of access: Internet.