High-resolution stratigraphy of Central and Southern Adriatic Quaternary deposits of sub-Milankovian climate change on Mediterranean circulation

This volume is a collection of the work done in a three years-lasting PhD, focused in the analysis of Central and Southern Adriatic marine sediments, deriving from the collection of a borehole and many cores, achieved thanks to the good seismic-stratigraphic knowledge of the study area. The work was made out within European projects EC-EURODELTA (coordinated by Fabio Trincardi, ISMAR-CNR), EC-EUROSTRATAFORM (coordinated by Phil P. E. Weaver, NOC, UK), and PROMESS1 (coordinated by Serge Bernè, IFREMER, France). The analysed sedimentary successions presented highly expanded stratigraphic intervals, particularly for the last 400 kyr, 60 kyr and 6 kyr BP. These three different time-intervals resulted in a tri-partition of the PhD thesis. The study consisted of the analysis of planktic and benthic foraminifers’ assemblages (more than 560 samples analysed), as well as in preparing the material for oxygen and carbon stable isotope analyses, and interpreting and discussing the obtained dataset. The chronologic framework of the last 400 kyr was achieved for borehole PRAD1-2 (within the work-package WP6 of PROMESS1 project), collected in 186.5 m water depth. The proposed chronology derives from a multi-disciplinary approach, consisting of the integration of numerous and independent proxies, some of which analysed by other specialists within the project. The final framework based on: micropaleontology (calcareous nannofossils and foraminifers’ bioevents), climatic cyclicity (foraminifers’ assemblages), geochemistry (oxygen stable isotope, made out on planktic and benthic records), paleomagnetism, radiometric ages (14C AMS), teprhochronology, identification of sapropel-equivalent levels (Se). It’s worth to note the good consistency between the oxygen stable isotope curve obtained for borehole PRAD1-2 and other deeper Mediterranean records. The studied proxies allowed the recognition of all the isotopic intervals from MIS10 to MIS1 in PRAD1-2 record, and the base of the borehole has been ascribed to the early MIS11. Glacial and interglacial intervals identified in the Central Adriatic record have been analysed in detail for the paleo-environmental reconstruction, as well. For instance, glacial stages MIS6, MIS8 and MIS10 present peculiar foraminifers’ assemblages, composed by benthic species typical of polar regions and no longer living in the Central Adriatic nowadays. Moreover, a deepening trend in the paleo-bathymetry during glacial intervals was observed, from MIS10 (inner-shelf environment) to MIS4 (mid-shelf environment).Ten sapropel-equivalent levels have been recognised in PRAD1-2 Central Adriatic record. They showed different planktic foraminifers’ assemblages, which allowed the first distinction of events occurred during warm-climate (Se5, Se7), cold-climate (Se4, Se6 and Se8) and temperate-intermediate-climate (Se1, Se3, Se9, Se’, Se10) conditions, consistently with literature. Cold-climate sapropel equivalents are characterised by the absence of an oligotrophic phase, whereas warm-temeprate-climate sapropel equivalents present both the oligotrophic and the eutrophic phases (except for Se1). Sea floor conditions vary, according to benthic foraminifers’ assemblages, from relatively well oxygenated (Se1, Se3), to dysoxic (Se9, Se’, Se10), to highly dysoxic (Se4, Se6, Se8) to events during which benthic foraminifers are absent (Se5, Se7). These two latter levels are also characterised by the lamination of the sediment, feature never observed in literature in such shallow records. The enhanced stratification of the water column during the events Se8, Se7, Se6, Se5, Se4, and the concurring strong dilution of shallow water, pointed out by the isotope record, lead to the hypothesis of a period of intense precipitation in the Central Adriatic region, possibly due to a northward shift of the African Monsoon. Finally, the expression of Central Adriatic PRAD1-2 Se5 equivalent was compared with the same event, as registered in other Eastern Mediterranean areas. The sequence of substantially the same planktic foraminifers’ bioevents has been consistently recognised, indicating a similar evolution of the water column all over the Eastern Mediterranean; yet, the synchronism of these events cannot be demonstrated. A high resolution analysis of late Holocene (last 6000 years BP) climate change was carried out for the Adriatic area, through the recognition of planktic and benthic foraminifers’ bioevents. In particular, peaks of planktic Globigerinoides sacculifer (four during the last 5500 years BP in the most expanded core) have been interpreted, based on the ecological requirements of this species, as warm-climate, arid intervals, correspondent to periods of relative climatic optimum, such as, for instance, the Medieval Warm Period, the Roman Age, the Late Bronze Age and the Copper Age. Consequently, the minima in the abundance of this biomarker could correspond to relatively cooler and more rainy periods. These conclusions are in good agreement with the isotopic and the pollen data. The Last Occurrence (LO) of G. sacculifer has been dated in this work at an average age of 550 years BP, and it is the best bioevent approximating the base of the Little Ice Age in the Adriatic. Recent literature reports the same bioevent in the Levantine Basin, showing a rather consistent age. Therefore, the LO of G. sacculifer has the potential to be extended to all the Eastern Mediterranean. Within the Little Ice Age, benthic foraminifer V. complanata shows two distinct peaks in the shallower Adriatic cores analysed, collected hundred kilometres apart, inside the mud belt environment. Based on the ecological requirements of this species, these two peaks have been interpreted as the more intense (cold and rainy) oscillations inside the LIA. The chronologic framework of the analysed cores is robust, being based on several range-finding 14C AMS ages, on estimates of the secular variation of the magnetic field, on geochemical estimates of the activity depth of 210Pb short-lived radionuclide (for the core-top ages), and is in good agreement with tephrochronologic, pollen and foraminiferal data. The intra-holocenic climate oscillations find out in the Adriatic have been compared with those pointed out in literature from other records of the Northern Hemisphere, and the chronologic constraint seems quite good. Finally, the sedimentary successions analysed allowed the review and the update of the foraminifers’ ecobiostratigraphy available from literature for the Adriatic region, thanks to the achievement of 16 ecobiozones for the last 60 kyr BP. Some bioevents are restricted to the Central Adriatic (for instance the LO of benthic Hyalinea balthica , approximating the MIS3/MIS2 boundary), others occur all over the Adriatic basin (for instance the LO of planktic Globorotalia inflata during MIS3, individuating Dansgaard-Oeschger cycle 8 (Denekamp)).

Mathematical models of cognitive processes

The research activity carried out during the PhD course was focused on the development of mathematical models of some cognitive processes and their validation by means of data present in literature, with a double aim: i) to achieve a better interpretation and explanation of the great amount of data obtained on these processes from different methodologies (electrophysiological recordings on animals, neuropsychological, psychophysical and neuroimaging studies in humans), ii) to exploit model predictions and results to guide future research and experiments. In particular, the research activity has been focused on two different projects: 1) the first one concerns the development of neural oscillators networks, in order to investigate the mechanisms of synchronization of the neural oscillatory activity during cognitive processes, such as object recognition, memory, language, attention; 2) the second one concerns the mathematical modelling of multisensory integration processes (e.g. visual-acoustic), which occur in several cortical and subcortical regions (in particular in a subcortical structure named Superior Colliculus (SC)), and which are fundamental for orienting motor and attentive responses to external world stimuli. This activity has been realized in collaboration with the Center for Studies and Researches in Cognitive Neuroscience of the University of Bologna (in Cesena) and the Department of Neurobiology and Anatomy of the Wake Forest University School of Medicine (NC, USA). PART 1. Objects representation in a number of cognitive functions, like perception and recognition, foresees distribute processes in different cortical areas. One of the main neurophysiological question concerns how the correlation between these disparate areas is realized, in order to succeed in grouping together the characteristics of the same object (binding problem) and in maintaining segregated the properties belonging to different objects simultaneously present (segmentation problem). Different theories have been proposed to address these questions (Barlow, 1972). One of the most influential theory is the so called “assembly coding”, postulated by Singer (2003), according to which 1) an object is well described by a few fundamental properties, processing in different and distributed cortical areas; 2) the recognition of the object would be realized by means of the simultaneously activation of the cortical areas representing its different features; 3) groups of properties belonging to different objects would be kept separated in the time domain. In Chapter 1.1 and in Chapter 1.2 we present two neural network models for object recognition, based on the “assembly coding” hypothesis. These models are networks of Wilson-Cowan oscillators which exploit: i) two high-level “Gestalt Rules” (the similarity and previous knowledge rules), to realize the functional link between elements of different cortical areas representing properties of the same object (binding problem); 2) the synchronization of the neural oscillatory activity in the γ-band (30-100Hz), to segregate in time the representations of different objects simultaneously present (segmentation problem). These models are able to recognize and reconstruct multiple simultaneous external objects, even in difficult case (some wrong or lacking features, shared features, superimposed noise). In Chapter 1.3 the previous models are extended to realize a semantic memory, in which sensory-motor representations of objects are linked with words. To this aim, the network, previously developed, devoted to the representation of objects as a collection of sensory-motor features, is reciprocally linked with a second network devoted to the representation of words (lexical network) Synapses linking the two networks are trained via a time-dependent Hebbian rule, during a training period in which individual objects are presented together with the corresponding words. Simulation results demonstrate that, during the retrieval phase, the network can deal with the simultaneous presence of objects (from sensory-motor inputs) and words (from linguistic inputs), can correctly associate objects with words and segment objects even in the presence of incomplete information. Moreover, the network can realize some semantic links among words representing objects with some shared features. These results support the idea that semantic memory can be described as an integrated process, whose content is retrieved by the co-activation of different multimodal regions. In perspective, extended versions of this model may be used to test conceptual theories, and to provide a quantitative assessment of existing data (for instance concerning patients with neural deficits). PART 2. The ability of the brain to integrate information from different sensory channels is fundamental to perception of the external world (Stein et al, 1993). It is well documented that a number of extraprimary areas have neurons capable of such a task; one of the best known of these is the superior colliculus (SC). This midbrain structure receives auditory, visual and somatosensory inputs from different subcortical and cortical areas, and is involved in the control of orientation to external events (Wallace et al, 1993). SC neurons respond to each of these sensory inputs separately, but is also capable of integrating them (Stein et al, 1993) so that the response to the combined multisensory stimuli is greater than that to the individual component stimuli (enhancement). This enhancement is proportionately greater if the modality-specific paired stimuli are weaker (the principle of inverse effectiveness). Several studies have shown that the capability of SC neurons to engage in multisensory integration requires inputs from cortex; primarily the anterior ectosylvian sulcus (AES), but also the rostral lateral suprasylvian sulcus (rLS). If these cortical inputs are deactivated the response of SC neurons to cross-modal stimulation is no different from that evoked by the most effective of its individual component stimuli (Jiang et al 2001). This phenomenon can be better understood through mathematical models. The use of mathematical models and neural networks can place the mass of data that has been accumulated about this phenomenon and its underlying circuitry into a coherent theoretical structure. In Chapter 2.1 a simple neural network model of this structure is presented; this model is able to reproduce a large number of SC behaviours like multisensory enhancement, multisensory and unisensory depression, inverse effectiveness. In Chapter 2.2 this model was improved by incorporating more neurophysiological knowledge about the neural circuitry underlying SC multisensory integration, in order to suggest possible physiological mechanisms through which it is effected. This endeavour was realized in collaboration with Professor B.E. Stein and Doctor B. Rowland during the 6 months-period spent at the Department of Neurobiology and Anatomy of the Wake Forest University School of Medicine (NC, USA), within the Marco Polo Project. The model includes four distinct unisensory areas that are devoted to a topological representation of external stimuli. Two of them represent subregions of the AES (i.e., FAES, an auditory area, and AEV, a visual area) and send descending inputs to the ipsilateral SC; the other two represent subcortical areas (one auditory and one visual) projecting ascending inputs to the same SC. Different competitive mechanisms, realized by means of population of interneurons, are used in the model to reproduce the different behaviour of SC neurons in conditions of cortical activation and deactivation. The model, with a single set of parameters, is able to mimic the behaviour of SC multisensory neurons in response to very different stimulus conditions (multisensory enhancement, inverse effectiveness, within- and cross-modal suppression of spatially disparate stimuli), with cortex functional and cortex deactivated, and with a particular type of membrane receptors (NMDA receptors) active or inhibited. All these results agree with the data reported in Jiang et al. (2001) and in Binns and Salt (1996). The model suggests that non-linearities in neural responses and synaptic (excitatory and inhibitory) connections can explain the fundamental aspects of multisensory integration, and provides a biologically plausible hypothesis about the underlying circuitry.

Complexity of N-Myc transcriptional function in childhood neuroblastoma

Myc is a transcription factor that can activate transcription of several hundreds genes by direct binding to their promoters at specific DNA sequences (E-box). However, recent studies have also shown that it can exert its biological role by repressing transcription. Such studies collectively support a model in which c-Myc-mediated repression occurs through interactions with transcription factors bound to promoter DNA regions but not through direct recognition of typical E-box sequences. Here, we investigated whether N-Myc can also repress gene transcription, and how this is mechanistically achieved. We used human neuroblastoma cells as a model system in that N-MYC amplification/over-expression represents a key prognostic marker of this tumour. By means of transcription profile analyses we could identify at least 5 genes (TRKA, p75NTR, ABCC3, TG2, p21) that are specifically repressed by N-Myc. Through a dual-step-ChIP assay and genetic dissection of gene promoters, we found that N-Myc is physically associated with gene promoters in vivo, in proximity of the transcription start site. N-Myc association with promoters requires interaction with other proteins, such as Sp1 and Miz1 transcription factors. Furthermore, we found that N-Myc may repress gene expression by interfering directly with Sp1 and/or with Miz1 activity (i.e. TRKA, p75NTR, ABCC3, p21) or by recruiting Histone Deacetylase 1 (Hdac1) (i.e. TG2). In vitro analyses show that distinct N-Myc domains can interact with Sp1, Miz1 and Hdac1, supporting the idea that Myc may participate in distinct repression complexes by interacting specifically with diverse proteins. Finally, results show that N-Myc, through repressed genes, affects important cellular functions, such as apoptosis, growth, differentiation and motility. Overall, our results support a model in which N-Myc, like c-Myc, can repress gene transcription by direct interaction with Sp1 and/or Miz1, and provide further lines of evidence on the importance of transcriptional repression by Myc factors in tumour biology.

Molecular architecture of fur binding to iron-induced and - repressed genes in Helicobacter pylori

The ferric uptake regulator protein Fur regulates iron-dependent gene expression in bacteria. In the human pathogen Helicobacter pylori, Fur has been shown to regulate iron-induced and iron-repressed genes. Herein we investigate the molecular mechanisms that control this differential iron-responsive Fur regulation. Hydroxyl radical footprinting showed that Fur has different binding architectures, which characterize distinct operator typologies. On operators recognized with higher affinity by holo-Fur, the protein binds to a continuous AT-rich stretch of about 20 bp, displaying an extended protection pattern. This is indicative of protein wrapping around the DNA helix. DNA binding interference assays with the minor groove binding drug distamycin A, point out that the recognition of the holo-operators occurs through the minor groove of the DNA. By contrast, on the apo-operators, Fur binds primarily to thymine dimers within a newly identified TCATTn10TT consensus element, indicative of Fur binding to one side of the DNA, in the major groove of the double helix. Reconstitution of the TCATTn10TT motif within a holo-operator results in a feature binding swap from an holo-Fur- to an apo-Fur-recognized operator, affecting both affinity and binding architecture of Fur, and conferring apo-Fur repression features in vivo. Size exclusion chromatography indicated that Fur is a dimer in solution. However, in the presence of divalent metal ions the protein is able to multimerize. Accordingly, apo-Fur binds DNA as a dimer in gel shift assays, while in presence of iron, higher order complexes are formed. Stoichiometric Ferguson analysis indicates that these complexes correspond to one or two Fur tetramers, each bound to an operator element. Together these data suggest that the apo- and holo-Fur repression mechanisms apparently rely on two distinctive modes of operator-recognition, involving respectively the readout of a specific nucleotide consensus motif in the major groove for apo-operators, and the recognition of AT-rich stretches in the minor groove for holo-operators, whereas the iron-responsive binding affinity is controlled through metal-dependent shaping of the protein structure in order to match preferentially the major or the minor groove.