MODELING SPORADIC TUMOR FORMATION DRIVEN BY TELOMERE DYSFUNCTION IN THE GASTROINTESTINAL TRACT

Colorectal cancer is a complex disease that is thought to arise when cells accumulate mutations that allow for uncontrolled growth. There are several recognized mechanisms for generating such mutations in sporadic colon cancer; one of which is chromosomal instability (CIN). One hypothesized driver of CIN in cancer is the improper repair of dysfunctional telomeres. Telomeres comprise the linear ends of chromosomes and play a dual role in cancer. Its length is maintained by the ribonucleoprotein, telomerase, which is not a normally expressed in somatic cells and as cells divide, telomeres continuously shorten. Critically shortened telomeres are considered dysfunctional as they are recognized as sites of DNA damage and cells respond by entering into replicative senescence or apoptosis, a process that is p53-dependent and the mechanism for telomere-induced tumor suppression. Loss of this checkpoint and improper repair of dysfunctional telomeres can initiate a cycle of fusion, bridge and breakage that can lead to chromosomal changes and genomic instability, a process that can lead to transformation of normal cells to cancer cells. Mouse models of telomere dysfunction are currently based on knocking out the telomerase protein or RNA component; however, the naturally long telomeres of mice require multiple generational crosses of telomerase null mice to achieve critically short telomeres. Shelterin is a complex of six core proteins that bind to telomeres specifically. Pot1a is a highly conserved member of this complex that specifically binds to the telomeric single-stranded 3’ G-rich overhang. Previous work in our lab has shown that Pot1a is essential for chromosomal end protection as deletion of Pot1a in murine embryonic fibroblasts (MEFs) leads to open telomere ends that initiate a DNA damage response mediated by ATR, resulting in p53-dependent cellular senescence. Loss of Pot1a in the background of p53 deficiency results in increased aberrant homologous recombination at telomeres and elevated genomic instability, which allows Pot1a-/-, p53-/- MEFs to form tumors when injected into SCID mice. These phenotypes are similar to those seen in cells with critically shortened telomeres. In this work, we created a mouse model of telomere ysfunction in the gastrointestinal tract through the conditional deletion of Pot1a that recapitulates the microscopic features seen in severe telomere attrition. Combined intestinal loss of Pot1a and p53 lead to formation of invasive adenocarcinomas in the small and large intestines. The tumors formed with long latency, low multiplicity and had complex genomes due to chromosomal instability, features similar to those seen in sporadic human colorectal cancers. Taken together, we have developed a novel mouse model of intestinal tumorigenesis based on genomic instability driven by telomere dysfunction.

AGROBACTERIUM VIRB10 CONTRIBUTIONS TO TYPE IV SUBSTRATE SECRETION, T-PILUS BIOGENESIS, AND OUTER MEMBRANE PORE FORMATION

The VirB/D4 type IV secretion system (T4SS) of Agrobacterium tumefaciens functions to transfer substrates to infected plant cells through assembly of a translocation channel and a surface structure termed a T-pilus. This thesis is focused on identifying contributions of VirB10 to substrate transfer and T-pilus formation through a mutational analysis. VirB10 is a bitopic protein with several domains, including a: (i) cytoplasmic N-terminus, (ii) single transmembrane (TM) α-helix, (iii) proline-rich region (PRR), and (iv) large C-terminal modified β-barrel. I introduced cysteine insertion and substitution mutations throughout the length of VirB10 in order to: (i) test a predicted transmembrane topology, (ii) identify residues/domains contributing to VirB10 stability, oligomerization, and function, and (iii) monitor structural changes accompanying energy activation or substrate translocation. These studies were aided by recent structural resolution of a periplasmic domain of a VirB10 homolog and a ‘core’ complex composed of homologs of VirB10 and two outer membrane associated subunits, VirB7 and VirB9. By use of the substituted cysteine accessibility method (SCAM), I confirmed the bitopic topology of VirB10. Through phenotypic studies of Ala-Cys insertion mutations, I identified “uncoupling” mutations in the TM and β-barrel domains that blocked T-pilus assembly but permitted substrate transfer. I showed that cysteine replacements in the C-terminal periplasmic domain yielded a variety of phenotypes in relation to protein accumulation, oligomerization, substrate transfer, and T-pilus formation. By SCAM, I also gained further evidence that VirB10 adopts different structural states during machine biogenesis. Finally, I showed that VirB10 supports substrate transfer even when its TM domain is extensively mutagenized or substituted with heterologous TM domains. By contrast, specific residues most probably involved in oligomerization of the TM domain are required for biogenesis of the T-pilus.

A Cbfa1-dependent genetic pathway controls bone formation beyond embryonic development.

The molecular mechanisms controlling bone extracellular matrix (ECM) deposition by differentiated osteoblasts in postnatal life, called hereafter bone formation, are unknown. This contrasts with the growing knowledge about the genetic control of osteoblast differentiation during embryonic development. Cbfa1, a transcriptional activator of osteoblast differentiation during embryonic development, is also expressed in differentiated osteoblasts postnatally. The perinatal lethality occurring in Cbfa1-deficient mice has prevented so far the study of its function after birth. To determine if Cbfa1 plays a role during bone formation we generated transgenic mice overexpressing Cbfa1 DNA-binding domain (DeltaCbfa1) in differentiated osteoblasts only postnatally. DeltaCbfa1 has a higher affinity for DNA than Cbfa1 itself, has no transcriptional activity on its own, and can act in a dominant-negative manner in DNA cotransfection assays. DeltaCbfa1-expressing mice have a normal skeleton at birth but develop an osteopenic phenotype thereafter. Dynamic histomorphometric studies show that this phenotype is caused by a major decrease in the bone formation rate in the face of a normal number of osteoblasts thus indicating that once osteoblasts are differentiated Cbfa1 regulates their function. Molecular analyses reveal that the expression of the genes expressed in osteoblasts and encoding bone ECM proteins is nearly abolished in transgenic mice, and ex vivo assays demonstrated that DeltaCbfa1-expressing osteoblasts were less active than wild-type osteoblasts. We also show that Cbfa1 regulates positively the activity of its own promoter, which has the highest affinity Cbfa1-binding sites characterized. This study demonstrates that beyond its differentiation function Cbfa1 is the first transcriptional activator of bone formation identified to date and illustrates that developmentally important genes control physiological processes postnatally.

Inégalités de formation lors de l’accès à l’enseignement supérieur selon le sexe et le contexte migratoire: résultats de l’analyse des situations suisse, allemande et française

La présente contribution porte sur le passage dans le degré tertiaire en tenant compte de l’intrication des inégalités liées au sexe et au contexte migratoire. L’étude, qui repose sur des concepts de la théorie décisionnelle, s’articule principalement sur une comparaison entre la Suisse (TREE), l’Allemagne (élèves pouvant prétendre aux études supérieures 2002 HIS) et la France (Panel d'élèves du second degré 1995). Les résultats révèlent qu’en Suisse et en Allemagne, indépendamment de l’origine sociale, les jeunes hommes appartenant à certains groupes de migrants socialement défavorisés (2e génération) affichent un taux de passage dans le supérieur plus élevé que leurs camarades nationaux. Ils mettent par ailleurs en évidence que, ni en Suisse, ni en Allemagne, ni en France, les migrantes de deuxième génération issues de pays fortement marqués par le modèle patriarcal sont désavantagées.

The special Sm core structure of the U7 snRNP: far-reaching significance of a small nuclear ribonucleoprotein

The polypeptide composition of the U7 small nuclear ribonucleoprotein (snRNP) involved in histone messenger RNA (mRNA) 3' end formation has recently been elucidated. In contrast to spliceosomal snRNPs, which contain a ring-shaped assembly of seven so-called Sm proteins, in the U7 snRNP the Sm proteins D1 and D2 are replaced by U7-specific Sm-like proteins, Lsm10 and Lsm11. This polypeptide composition and the unusual structure of Lsm11, which plays a role in histone RNA processing, represent new themes in the biology of Sm/Lsm proteins. Moreover this structure has important consequences for snRNP assembly that is mediated by two complexes containing the PRMT5 methyltransferase and the SMN (survival of motor neurons) protein, respectively. Finally, the ability to alter this polypeptide composition by a small mutation in U7 snRNA forms the basis for using modified U7 snRNA derivatives to alter specific pre-mRNA splicing events, thereby opening up a new way for antisense gene therapy.

The Caenorhabditis elegans histone hairpin-binding protein is required for core histone gene expression and is essential for embryonic and postembryonic cell division.

As in all metazoans, the replication-dependent histone genes of Caenorhabditis elegans lack introns and contain a short hairpin structure in the 3' untranslated region. This hairpin structure is a key element for post-transcriptional regulation of histone gene expression and determines mRNA 3' end formation, nuclear export, translation and mRNA decay. All these steps contribute to the S-phase-specific expression of the replication-dependent histone genes. The hairpin structure is the binding site for histone hairpin-binding protein that is required for hairpin-dependent regulation. Here, we demonstrate that the C. elegans histone hairpin-binding protein gene is transcribed in dividing cells during embryogenesis and postembryonic development. Depletion of histone hairpin-binding protein (HBP) function in early embryos using RNA-mediated interference leads to an embryonic-lethal phenotype brought about by defects in chromosome condensation. A similar phenotype was obtained by depleting histones H3 and H4 in early embryos, indicating that the defects in hairpin-binding protein-depleted embryos are caused by reduced histone biosynthesis. We have confirmed this by showing that HBP depletion reduces histone gene expression. Depletion of HBP during postembryonic development also results in defects in cell division during late larval development. In addition, we have observed defects in the specification of vulval cell fate in animals depleted for histone H3 and H4, which indicates that histone proteins are required for cell fate regulation during vulval development.

Local formation of varved sediments in a karstic collapse depression of Lake Banyoles (NE Spain)

Banyoles is the largest and deepest lake of karstic-tectonic origin in the Iberian Peninsula. The lake comprises several circular sub-basins characteri- zed by different oxygenation conditions at their hypolimnions. The multiproxy analysis of a > 5 m long sediment core combined with high resolution seis- mic stratigraphy (3.5 kHz pinger and multi-frequency Chirp surveys), allow a precise reconstruction of the evolution of a karstic depression (named B3) until present times. Local meromictic conditions in this sub-basin have been conducive to deposition and preservation of ca. 85 cm of varved sediments since the late 19th century. The onset of these conditions is likely related to lake waters eutrophication caused by increasing farming activities in the wa- tershed. Increasing clastic input and organic productivity during the second half of the 20th century have also been recorded within the laminated sedi- ments, revealing an intensification of human impact and warmer water tem- peratures.

Gas composition of the main volatile elements in protoplanetary discs and its implication for planet formation

Context. Direct observations of gaseous exoplanets reveal that their gas envelope has a higher C/O ratio than that of the host star (e.g., Wasp 12-b). This has been explained by considering that the gas phase of the disc could be inhomogeneous, exceeding the stellar C/O ratio in regions where these planets formed; but few studies have considered the drift of the gas and planet migration. Aims. We aim to derive the gas composition in planets through planet formation to evaluate if the formation of giant planets with an enriched C/O ratio is possible. The study focusses on the effects of different processes on the C/O ratio, such as the disc evolution, the drift of gas, and planet migration. Methods. We used our previous models for computing the chemical composition, together with a planet formation model, to which we added the composition and drift of the gas phase of the disc, which is composed of the main volatile species H2O, CO, CO2, NH3, N2, CH3OH, CH4, and H2S, H2 and He. The study focusses on the region where ice lines are present and influence the C/O ratio of the planets. Results. Modelling shows that the condensation of volatile species as a function of radial distance allows for C/O enrichment in specific parts of the protoplanetary disc of up to four times the solar value. This leads to the formation of planets that can be enriched in C/O in their envelope up to three times the solar value. Planet migration, gas phase evolution and disc irradiation enables the evolution of the initial C/O ratio that decreases in the outer part of the disc and increases in the inner part of the disc. The total C/O ratio of the planets is governed by the contribution of ices accreted, suggesting that high C/O ratios measured in planetary atmospheres are indicative of a lack of exchange of material between the core of a planet and its envelope or an observational bias. It also suggests that the observed C/O ratio is not representative of the total C/O ratio of the planet.

Retrieving the paleoclimatic signal from the deeper part of the EPICA Dome C ice core

An important share of paleoclimatic information is buried within the lowermost layers of deep ice cores. Because improving our records further back in time is one of the main challenges in the near future, it is essential to judge how deep these records remain unaltered, since the proximity of the bedrock is likely to interfere both with the recorded temporal sequence and the ice properties. In this paper, we present a multiparametric study (δD-δ18Oice, δ18Oatm, total air content, CO2, CH4, N2O, dust, high-resolution chemistry, ice texture) of the bottom 60 m of the EPICA (European Project for Ice Coring in Antarctica) Dome C ice core from central Antarctica. These bottom layers were subdivided into two distinct facies: the lower 12 m showing visible solid inclusions (basal dispersed ice facies) and the upper 48 m, which we will refer to as the "basal clean ice facies". Some of the data are consistent with a pristine paleoclimatic signal, others show clear anomalies. It is demonstrated that neither large-scale bottom refreezing of subglacial water, nor mixing (be it internal or with a local basal end term from a previous/initial ice sheet configuration) can explain the observed bottom-ice properties. We focus on the high-resolution chemical profiles and on the available remote sensing data on the subglacial topography of the site to propose a mechanism by which relative stretching of the bottom-ice sheet layers is made possible, due to the progressively confining effect of subglacial valley sides. This stress field change, combined with bottom-ice temperature close to the pressure melting point, induces accelerated migration recrystallization, which results in spatial chemical sorting of the impurities, depending on their state (dissolved vs. solid) and if they are involved or not in salt formation. This chemical sorting effect is responsible for the progressive build-up of the visible solid aggregates that therefore mainly originate "from within", and not from incorporation processes of debris from the ice sheet's substrate. We further discuss how the proposed mechanism is compatible with the other ice properties described. We conclude that the paleoclimatic signal is only marginally affected in terms of global ice properties at the bottom of EPICA Dome C, but that the timescale was considerably distorted by mechanical stretching of MIS20 due to the increasing influence of the subglacial topography, a process that might have started well above the bottom ice. A clear paleoclimatic signal can therefore not be inferred from the deeper part of the EPICA Dome C ice core. Our work suggests that the existence of a flat monotonic ice–bedrock interface, extending for several times the ice thickness, would be a crucial factor in choosing a future "oldest ice" drilling location in Antarctica.

Thrombus formation in the left ventricle after large myocardial infarction – assessment with cardiac magnetic resonance imaging

INTRODUCTION Left ventricular thrombus (LVT) formation may worsen the post-infarct outcome as a result of thromboembolic events. It also complicates the use of modern antiplatelet regimens, which are not compatible with long-term oral anticoagulation. The knowledge of the incidence of LVT may therefore be of importance to guide antiplatelet and antithrombotic therapy after acute myocardial infarction (AMI). METHODS In 177 patients with large, mainly anterior AMI, standard cardiac magnetic resonance imaging (CMR) including cine and late gadolinium enhancement (LGE) imaging was performed shortly after AMI as per protocol. CMR images were analysed at an independent core laboratory blinded to the clinical data. Transthoracic echocardiography (TTE) was not mandatory for the trial, but was performed in 64% of the cases following standard of care. In a logistic model, 3 out of 61 parameters were used in a multivariable model to predict LVT. RESULTS LVT was detected by use of CMR in 6.2% (95% confidence interval [CI] 3.1%-10.8%). LGE sequences were best to detect LVT, which may be missed in cine sequences. We identified body mass index (odds ratio 1.18; p = 0.01), baseline platelet count (odds ratio 1.01, p = 0.01) and infarct size as assessed by use of CMR (odds ratio 1.03, p = 0.02) as best predictors for LVT. The agreement between TTE and CMR for the detection of LVT is substantial (kappa = 0.70). DISCUSSION In the current analysis, the incidence of LVT shortly after AMI is relatively low, even in a patient population at high risk. An optimal modality for LVT detection is LGE-CMR but TTE has an acceptable accuracy when LGE-CMR is not available.

Environmental control on the occurrence of high-coercivity magnetic minerals and formation of iron sulfides in a 640 ka sediment sequence from Lake Ohrid (Balkans)

The bulk magnetic mineral record from Lake Ohrid, spanning the past 637 kyr, reflects large-scale shifts in hydrological conditions, and, superimposed, a strong signal of environmental conditions on glacial–interglacial and millennial timescales. A shift in the formation of early diagenetic ferrimagnetic iron sulfides to siderites is observed around 320 ka. This change is probably associated with variable availability of sulfide in the pore water. We propose that sulfate concentrations were significantly higher before  ∼  320 ka, due to either a higher sulfate flux or lower dilution of lake sulfate due to a smaller water volume. Diagenetic iron minerals appear more abundant during glacials, which are generally characterized by higher Fe / Ca ratios in the sediments. While in the lower part of the core the ferrimagnetic sulfide signal overprints the primary detrital magnetic signal, the upper part of the core is dominated by variable proportions of high- to low-coercivity iron oxides. Glacial sediments are characterized by high concentration of high-coercivity magnetic minerals (hematite, goethite), which relate to enhanced erosion of soils that had formed during preceding interglacials. Superimposed on the glacial–interglacial behavior are millennial-scale oscillations in the magnetic mineral composition that parallel variations in summer insolation. Like the processes on glacial–interglacial timescales, low summer insolation and a retreat in vegetation resulted in enhanced erosion of soil material. Our study highlights that rock-magnetic studies, in concert with geochemical and sedimentological investigations, provide a multi-level contribution to environmental reconstructions, since the magnetic properties can mirror both environmental conditions on land and intra-lake processes.

Global models of planet formation and evolution

Despite the strong increase in observational data on extrasolar planets, the processes that led to the formation of these planets are still not well understood. However, thanks to the high number of extrasolar planets that have been discovered, it is now possible to look at the planets as a population that puts statistical constraints on theoretical formation models. A method that uses these constraints is planetary population synthesis where synthetic planetary populations are generated and compared to the actual population. The key element of the population synthesis method is a global model of planet formation and evolution. These models directly predict observable planetary properties based on properties of the natal protoplanetary disc, linking two important classes of astrophysical objects. To do so, global models build on the simplified results of many specialized models that address one specific physical mechanism. We thoroughly review the physics of the sub-models included in global formation models. The sub-models can be classified as models describing the protoplanetary disc (of gas and solids), those that describe one (proto)planet (its solid core, gaseous envelope and atmosphere), and finally those that describe the interactions (orbital migration and N-body interaction). We compare the approaches taken in different global models, discuss the links between specialized and global models, and identify physical processes that require improved descriptions in future work. We then shortly address important results of planetary population synthesis like the planetary mass function or the mass-radius relationship. With these statistical results, the global effects of physical mechanisms occurring during planet formation and evolution become apparent, and specialized models describing them can be put to the observational test. Owing to their nature as meta models, global models depend on the results of specialized models, and therefore on the development of the field of planet formation theory as a whole. Because there are important uncertainties in this theory, it is likely that the global models will in future undergo significant modifications. Despite these limitations, global models can already now yield many testable predictions. With future global models addressing the geophysical characteristics of the synthetic planets, it should eventually become possible to make predictions about the habitability of planets based on their formation and evolution.

Investigation of Quaternary diatoms in sediment core CRP-1 from the Ross Sea, Antarctica

In the first season of drilling, the Cape Roberts Project (CRP) recovered one drillcore (CRP-l) from Roberts Ridge in western McMurdo Sound, Ross Sea, Antarctica Diatom biostratigraphy places the upper six lithostratigraphic units (Units 1.1, 2.1, 2.2, 2.3, 3.1, and 4.1) of CRP-l (0.0 to 43.15 mbsf) within the Quaternary. Both non-marine and marine Quaternary diatoms occur in variable abundance in the Quaternary interval of CRP- 1 Biostratigraphic data resolve two Quaternary time slices or events within CRP-1. Marine diatom assemblages in Units 4.1 and 3.1 represent sedimentation within the diatom Actinocyclus ingens Zone (1.35 to 0.66 Ma). Further refinement of the age of Unit 3.l places deposition in the interval 1.15 to 0.75 Ma based on the common occurrence of Thalassiosira elliptipora and correlation to the Southern Ocean acme of this taxon The absence of ActiActinocyclus ingens and the presence ot Thalassiosira antarctica in Unit 2.2 require a younger zonal assignment for this interval, within the diatom Thalassiosira lentiginosa Zone (0.66 to 0.0 Ma). A new diatom species. Rouxia leventerae, is described from marine assemblages of Units 2.2, 2.3, 3.1, and 4.l. Lithostratigraphic Unit 3.1 (33.82 to 31.89 mbsf) is a bryozoan-dominated skeletal-carbonate facies. Low abundance of Fragilariopsis curta and Fragilariopsis cylindrus within this unit combined with the relatively high abundance of species associated with open water indicates deposition in waters that remained ice free for much or all of the year Diatom assemblages suggest carbonate deposition in Unit 3.1 is linked to a significant early Pleistocene event in McMurdo Sound, when elevated surface-water temperatures inhibited the formation of sea ice.

Investigation of diagenesis in sediment core CRP-1 from the Ross Sea, Antarctica

A diagenetic study was carried out on the cored Miocene section in CRP-1 by thin-section, X-ray diffraction, scanning electron microscope, electron microprobe and stable isotopic analysis. Carbonate (calcite, siderite) microconcretions occur locally within intergranular pores and open fractures, and some sands are cemented by microcrystalline calcite. Calcite cement at 115.12 mbsf (metres below sea floor) and possibly microconcretionary calcite at 44.62 mbsf record infiltration of meteoric waters into the section, consistent with sequence stratigraphic evidence for multiple glacial advances over the CRP-1 drillsite. Diagenetic carbonates incorporated carbon derived from both organic matter and marine carbonate. Carbon isotope data are consistent with microconcretion formation at shallow depths. Sandstones are poorly compacted and, despite containing a large component of chemically unstable grains, are virtually unaltered. Preservation of the chemically unstable grain component reflects the cold climate depositional setting and shallow maximum burial depths.

Facies analysis on sediment core CRP-3 from the Ross Sea, Antarctica

Cape Roberts Project drill core 3 (CRP-3) was obtained from Roberts ridge, a sea-floor high located at 77°S, 12 km offshore from Cape Roberts in western McMurdo Sound, Antarctica. The recovered core is about 939 m long and comprises strata dated as being early Oligocene (possibly latest Eocene) in age, resting unconformably on ~116 m of basement rocks consisting of Palaeozoic Beacon Supergroup sediments. The core includes ten facies commonly occurring in five major associations that are repeated in particular sequences throughout the core and which are interpreted as representing different depositional environments through time. Depositional systems inferred to be represented in the succession include: outer shelf, inner shelf, nearshore to shoreface each under iceberg influence, deltaic and/or grounding-line fan, and ice proximal-ice marginal-subglacial (mass flow/rainout diamictite/subglacial till) singly or in combination. The record is taken to represent the initial talus/alluvial fan setting of a glaciated rift margin adjacent to the block-uplifted Transantarctic Mountains. Development of a deltaic succession upcore was probably associated with the formation of palaeo-Mackay valley with temperate glaciers in its headwaters. At that stage glaciation was intense enough to support glaciers ending in the sea elsewhere along the coast, but a local glacier was fluctuating down to the sea by the time the youngest part of CRP-3 was being deposited. Changes in palaeoenvironmental interpretations in this youngest part of the core are used to estimate relative glacial proximity to the drillsite through time. These inferred glacial fluctuations are compared with the global d180 and Mg/Ca curves to evaluate the potential of glacial fluctuations on Antarctica for influencing these records of global change. Although the comparisons are tentative at present, the records do have similarities, but there are also some differences that require further evaluation.