Cycles of passive versus active diapirism recorded along an exposed salt wall

Acknowledgements GIA is grateful for funding from the Carnegie Trust for the Universities of Scotland that enabled fieldwork for this project. RW was supported by the Israel Science Foundation (ISF grant No. 1245/11). SM was supported by the Israel Science Foundation (ISF grant No. 1436/14). We would like to thank Chris Talbot and Yohann Poprawski for careful and constructive reviews. The authors appreciate the help of Nicolas Waldmann in precisely locating the positons of dated unconformities.

Mutant tau knock-in mice display frontotemporal dementia relevant behaviour and histopathology

Peer reviewed

Transposon mutagenesis in bifidobacterium breve: construction and characterization of a Tn5 transposon mutant library for bifidobacterium breve UCC2003

Bifidobacteria are claimed to contribute positively to human health through a range of beneficial or probiotic activities, including amelioration of gastrointestinal and metabolic disorders, and therefore this particular group of gastrointestinal commensals has enjoyed increasing industrial and scientific attention in recent years. However, the molecular mechanisms underlying these probiotic mechanisms are still largely unknown, mainly due to the fact that molecular tools for bifidobacteria are rather poorly developed, with many strains lacking genetic accessibility. In this work, we describe the generation of transposon insertion mutants in two bifidobacterial strains, B. breve UCC2003 and B. breve NCFB2258. We also report the creation of the first transposon mutant library in a bifidobacterial strain, employing B. breve UCC2003 and a Tn5-based transposome strategy. The library was found to be composed of clones containing single transposon insertions which appear to be randomly distributed along the genome. The usefulness of the library to perform phenotypic screenings was confirmed through identification and analysis of mutants defective in D-galactose, D-lactose or pullulan utilization abilities.

Aspects of Motives: Finite-dimensionality, Chow-Kunneth Decompositions and Intersections of Cycles

This thesis analyzes the Chow motives of 3 types of smooth projective varieties: the desingularized elliptic self fiber product, the Fano surface of lines on a cubic threefold and an ample hypersurface of an Abelian variety. For the desingularized elliptic self fiber product, we use an isotypic decomposition of the motive to deduce the Murre conjectures. We also prove a result about the intersection product. For the Fano surface of lines, we prove the finite-dimensionality of the Chow motive. Finally, we prove that an ample hypersurface on an Abelian variety possesses a Chow-Kunneth decomposition for which a motivic version of the Lefschetz hyperplane theorem holds.

Defining the Role of the Histone Methyltransferase, PR-Set7, in Maintaining the Genome Integrity of Drosophila Melanogaster

The complete and faithful duplication of the genome is essential to ensure normal cell division and organismal development. Eukaryotic DNA replication is initiated at multiple sites termed origins of replication that are activated at different time through S phase. The replication timing program is regulated by the S-phase checkpoint, which signals and repairs replicative stress. Eukaryotic DNA is packaged with histones into chromatin, thus DNA-templated processes including replication are modulated by the local chromatin environment such as post-translational modifications (PTMs) of histones.

One such epigenetic mark, methylation of lysine 20 on histone H4 (H4K20), has been linked to chromatin compaction, transcription, DNA repair and DNA replication. H4K20 can be mono-, di- and tri-methylated. Monomethylation of H4K20 (H4K20me1) is mediated by the cell cycle-regulated histone methyltransferase PR-Set7 and subsequent di-/tri- methylation is catalyzed by Suv4-20. Prior studies have shown that PR-Set7 depletion in mammalian cells results in defective S phase progression and the accumulation of DNA damage, which may be partially attributed to defects in origin selection and activation. Meanwhile, overexpression of mammalian PR-Set7 recruits components of pre-Replication Complex (pre-RC) onto chromatin and licenses replication origins for re-replication. However, these studies were limited to only a handful of mammalian origins, and it remains unclear how PR-Set7 impacts the replication program on a genomic scale. Finally, the methylation substrates of PR-Set7 include both histone (H4K20) and non-histone targets, therefore it is necessary to directly test the role of H4K20 methylation in PR-Set7 regulated phenotypes.

I employed genetic, cytological, and genomic approaches to better understand the role of H4K20 methylation in regulating DNA replication and genome stability in Drosophila melanogaster cells. Depletion of Drosophila PR-Set7 by RNAi in cultured Kc167 cells led to an ATR-dependent cell cycle arrest with near 4N DNA content and the accumulation of DNA damage, indicating a defect in completing S phase. The cells were arrested at the second S phase following PR-Set7 downregulation, suggesting that it was an epigenetic effect that coupled to the dilution of histone modification over multiple cell cycles. To directly test the role of H4K20 methylation in regulating genome integrity, I collaborated with the Duronio Lab and observed spontaneous DNA damage on the imaginal wing discs of third instar mutant larvae that had an alanine substitution on H4K20 (H4K20A) thus unable to be methylated, confirming that H4K20 is a bona fide target of PR-Set7 in maintaining genome integrity.

One possible source of DNA damage due to loss of PR-Set7 is reduced origin activity. I used BrdU-seq to profile the genome-wide origin activation pattern. However, I found that deregulation of H4K20 methylation states by manipulating the H4K20 methyltransferases PR-Set7 and Suv4-20 had no impact on origin activation throughout the genome. I then mapped the genomic distribution of DNA damage upon PR-Set7 depletion. Surprisingly, ChIP-seq of the DNA damage marker γ-H2A.v located the DNA damage to late replicating euchromatic regions of the Drosophila genome, and the strength of γ-H2A.v signal was uniformly distributed and spanned the entire late replication domain, implying stochastic replication fork collapse within late replicating regions. Together these data suggest that PR-Set7-mediated monomethylation of H4K20 is critical for maintaining the genomic integrity of late replicating domains, presumably via stabilization of late replicating forks.

In addition to investigating the function of H4K20me, I also used immunofluorescence to characterize the cell cycle regulated chromatin loading of Mcm2-7 complex, the DNA helicase that licenses replication origins, using H4K20me1 level as a proxy for cell cycle stages. In parallel with chromatin spindown data by Powell et al. (Powell et al. 2015), we showed a continuous loading of Mcm2-7 during G1 and a progressive removal from chromatin through S phase.

(Table S1) Diatom abundance according to ice cycles in ANDRILL AND1-1B drill core

The influence of Antarctica and the Southern Ocean on Late Pliocene global climate reconstructions has remained ambiguous due to a lack of well-dated Antarctic-proximal, paleoenvironmental records. Here we present ice sheet, sea-surface temperature, and sea ice reconstructions from the ANDRILL AND-1B sediment core recovered from beneath the Ross Ice Shelf. We provide evidence for a major expansion of an ice sheet in the Ross Sea that began at ~3.3 Ma, followed by a coastal sea surface temperature cooling of ~2.5°C, a stepwise expansion of sea ice, and polynya-style deep mixing in the Ross Sea between 3.3 and 2.5 Ma. The intensification of Antarctic cooling resulted in strengthened westerly winds and invigorated ocean circulation. The associated northward migration of Southern Ocean fronts has been linked with reduced Atlantic Meridional Overturning Circulation by restricting surface water connectivity between the ocean basins, with implications for heat transport to the high latitudes of the North Atlantic. While our results do not exclude low-latitude mechanisms as drivers for Pliocene cooling, they indicate an additional role played by southern high-latitude cooling during development of the bipolar world.

Diatom-bound N isotope records over the last two glacial cycles in sediment core PS75/072-4

In a sediment core from the Pacific sector of the Antarctic Zone (AZ) of the Southern Ocean, we report diatom-bound N isotope (d15Ndb) records for total recoverable diatoms and two distinct diatom assemblages (pennate and centric rich). These data indicate tight coupling between the degree of nitrate consumption and Antarctic climate across the last two glacial cycles, with d15Ndb (and thus the degree of nitrate consumption) increasing at each major Antarctic cooling event. Coupled with evidence from opal- and barium-based proxies for reduced export production during ice ages, the d15Ndb increases point to ice age reductions in the supply of deep ocean-sourced nitrate to the AZ surface. The two diatom assemblages and species abundance data indicate that the d15Ndb changes are not the result of changing species composition. The pennate and centric assemblage d15Ndb records indicate similar changes but with a significant decline in their difference during peak ice ages. A tentative seasonality-based interpretation of the centric-to-pennate d15Ndb difference suggests that late summer surface waters became nitrate free during the peak glacials.

Cryptic splicing events in the iron transporter ABCB7 and other key target genes in SF3B1-mutant myelodysplastic syndromes

The splicing factor SF3B1 is the most frequently mutated gene in myelodysplastic syndromes (MDS), and is strongly associated with the presence of ring sideroblasts (RS). We have performed a systematic analysis of cryptic splicing abnormalities from RNA sequencing data on hematopoietic stem cells (HSCs) of SF3B1-mutant MDS cases with RS. Aberrant splicing events in many downstream target genes were identified and cryptic 3' splice site usage was a frequent event in SF3B1-mutant MDS. The iron transporter ABCB7 is a well-recognized candidate gene showing marked downregulation in MDS with RS. Our analysis unveiled aberrant ABCB7 splicing, due to usage of an alternative 3' splice site in MDS patient samples, giving rise to a premature termination codon in the ABCB7 mRNA. Treatment of cultured SF3B1-mutant MDS erythroblasts and a CRISPR/Cas9-generated SF3B1-mutant cell line with the nonsense-mediated decay (NMD) inhibitor cycloheximide showed that the aberrantly spliced ABCB7 transcript is targeted by NMD. We describe cryptic splicing events in the HSCs of SF3B1-mutant MDS, and our data support a model in which NMD-induced downregulation of the iron exporter ABCB7 mRNA transcript resulting from aberrant splicing caused by mutant SF3B1 underlies the increased mitochondrial iron accumulation found in MDS patients with RS.Leukemia advance online publication, 17 June 2016; doi:10.1038/leu.2016.149.

Synthetic Lethal Targeting of ARID1A-Mutant Ovarian Clear Cell Tumors with Dasatinib

New targeted approaches to ovarian clear cell carcinomas (OCCC) are needed, given the limited treatment options in this disease and the poor response to standard chemotherapy. Using a series of high-throughput cell-based drug screens in OCCC tumor cell models, we have identified a synthetic lethal (SL) interaction between the kinase inhibitor dasatinib and a key driver in OCCC, ARID1A mutation. Imposing ARID1A deficiency upon a variety of human or mouse cells induced dasatinib sensitivity, both in vitro and in vivo, suggesting that this is a robust synthetic lethal interaction. The sensitivity of ARID1A-deficient cells to dasatinib was associated with G₁ -S cell-cycle arrest and was dependent upon both p21 and Rb. Using focused siRNA screens and kinase profiling, we showed that ARID1A-mutant OCCC tumor cells are addicted to the dasatinib target YES1. This suggests that dasatinib merits investigation for the treatment of patients with ARID1Amutant OCCC. Mol Cancer Ther; 15(7); 1472-84. Ó2016 AACR.

Efficient Genotyping of KRAS Mutant Non-Small Cell Lung Cancer Using a Multiplexed Droplet Digital PCR Approach.

Droplet digital PCR (ddPCR) can be used to detect low frequency mutations in oncogene-driven lung cancer. The range of KRAS point mutations observed in NSCLC necessitates a multiplex approach to efficient mutation detection in circulating DNA. Here we report the design and optimisation of three discriminatory ddPCR multiplex assays investigating nine different KRAS mutations using PrimePCR™ ddPCR™ Mutation Assays and the Bio-Rad QX100 system. Together these mutations account for 95% of the nucleotide changes found in KRAS in human cancer. Multiplex reactions were optimised on genomic DNA extracted from KRAS mutant cell lines and tested on DNA extracted from fixed tumour tissue from a cohort of lung cancer patients without prior knowledge of the specific KRAS genotype. The multiplex ddPCR assays had a limit of detection of better than 1 mutant KRAS molecule in 2,000 wild-type KRAS molecules, which compared favourably with a limit of detection of 1 in 50 for next generation sequencing and 1 in 10 for Sanger sequencing. Multiplex ddPCR assays thus provide a highly efficient methodology to identify KRAS mutations in lung adenocarcinoma.

Transformation to "high grade" neuroendocrine carcinoma as an acquired drug resistance mechanism in EGFR-mutant lung adenocarcinoma.

Several different acquired resistance mechanisms of EGFR mutant lung adenocarcinoma to EGFR-tyrosine kinase inhibitor (TKI) therapy have been described, most recently transformation to small cell lung carcinoma (SCLC). We describe the case of a 46-year-old female with relapsed EGFR exon 19 deletion lung adenocarcinoma treated with erlotinib, and on resistance, cisplatin-pemetrexed. Liver rebiopsy identified an afatinib-resistant combined SCLC and non-small cell carcinoma with neuroendocrine morphology, retaining the EGFR exon 19 deletion. This case highlights acquired EGFR-TKI resistance through transformation to the high-grade neuroendocrine carcinoma spectrum and that that such transformation may not be evident at time of progression on TKI therapy.

Analysis of testosterone pulsatility in women with ovulatory menstrual cycles

Objetivo: Avaliar o padrão pulsátil da secreção da testosterona em mulheres normais. Métodos: Oito mulheres saudáveis com ciclos ovulatórios foram selecionadas. Amostras sanguíneas foram coletadas a cada dez minutos durante seis horas, começando entre 7 e 8 h da manhã, após dez horas de jejum, nas três fases do ciclo menstrual: folicular média (Dia 7), folicular tardia (Dia 12) e lútea (Dia 21). Foram mensurados: testosterona, LH e, no basal, também SHBG. Resultados: A frequência dos pulsos de testosterona, média da amplitude do pulso, porcentagem do incremento da amplitude, duração e intervalos dos pulsos foram similares nas três fases (p > 0,05). A pulsatilidade do LH foi estatisticamente diferente entre as três fases (p < 0,001), caracterizando padrão característico do ciclo ovulatório normal. Conclusões: Esses dados aumentam o conhecimento sobre o padrão de secreção da testosterona no ciclo menstrual humano e representam uma contribuição para a investigação clínica, tanto no hiperandrogenismo como na síndrome de insuficiência androgênica __________________________________________________ ABSTRACT Objective: To evaluate the pattern of the pulsatile secretion of testosterone in normal menstrual cycle. Methods: Eight healthy women with ovulatory menstrual cycles were enrolled. Blood samples were collected at ten-minute intervals for six hours, starting between 7 and 8 am, after a ten-hour fasting, in three phases: mid-follicular (Day 7), late follicular (Day 12) and mid-luteal phase (Day 21). Samples were assayed for testosterone, LH and the baseline also for SHBG. Results: Testosterone pulse frequency, mean amplitude pulse, percentage of increment in pulse amplitude, mean duration of pulses and pulse interval were similar in the three phases. LH pulsatility was statistically different among the three phases (p < 0.001) representing normal ovulatory cycles. Conclusions: These data increase the knowledge about the testosterone secretion profile in the human menstrual cycle and can be used as a contribution to clinical investigation in both hyperandrogenism and androgen insufficiency syndrome

Étude communicationnelle des pratiques culturelles au Québec: analyses des enquêtes ministérielles (1979-2009). Facteurs et prédicteurs, générations et cycles de vie, et découpages territoriaux

Cette thèse porte sur les pratiques culturelles des Québécois et des Québécoises et, plus spécifiquement dans un premier temps, sur les facteurs qui les influencent. Elle traite ensuite des comparaisons entre les individus selon les générations et les cycles de vie. Finalement, elle porte sur les découpages territoriaux régionaux sur le plan des pratiques culturelles et sur les questions liées au territoire. Tous les résultats sont tirés des enquêtes sur les pratiques culturelles au Québec menées à tous les cinq ans depuis 1979 par les ministères en charge de la culture. Les deux principaux référents théoriques sont la théorie de la légitimité de Bourdieu et la figure de l’omnivore de Peterson. Dans la première partie, cette thèse a cherché à savoir si les usages d’Internet sont associés à une ouverture culturelle ou à un confinement. Les résultats montrent que l’âge, la scolarité et les usages culturels que l’on fait d’Internet sont des prédicteurs importants des visites des lieux culturels et des sorties au spectacle. Les modèles qui incluent les usages d’Internet et des variables sociodémographiques sont plus performants que ceux ne considérant que ces dernières. Dans la deuxième partie, les quasi-cohortes à l’étude ont été comparées afin de voir si leurs comportements culturels diffèrent selon les cycles de vie et si leur parcours culturel a varié dans le temps. Finalement, la diversification des pratiques des quasi-cohortes a été étudiée afin d’estimer si elles deviennent plus omnivores avec le temps et d’une quasi-cohorte à l’autre. Le modèle explicatif créé affiche des différences dans le parcours culturel selon les cycles de vie, de même qu’au fil du temps. Il met également en lumière des différences d’une génération à l’autre, de même que des différences entre les générations lorsqu’elles traversent un même cycle de vie. À la différence de ceux de Peterson (2004), les résultats ne permettent pas de conclure que les quasi-cohortes plus âgées sont plus omnivores qu’avant ni que les jeunes sont plus omnivores que leurs aînés. La troisième partie de ce travail avait un objectif comparatif : il s’agissait de voir si les régions administratives du Québec, lorsqu’elles sont étudiées sous l’angle des pratiques culturelles, se regroupent conformément à la typologie des espaces culturels régionaux développée par Harvey et Fortin (1995) sur la base de l’offre culturelle. Les résultats montrent que les regroupements ne sont pas toujours conformes à la typologie et que les pratiques sont très hétérogènes, ce qui permet difficilement d’établir une constance dans les regroupements. Aussi semble-t-il indiqué de fonder la comparaison des territoires sur la prise en compte de l’objet (p. ex. offre ou pratique culturelle), de l’échelle territoriale (p. ex. bibliothèque municipale ou musée national) et de la nature du produit ou de la pratique (p. ex. mobile ou immobile). En conclusion, la pertinence d’élargir l’horizon des pratiques culturelles mesurées dans les enquêtes et d’y inclure des phénomènes transcendants, comme les valeurs, les contraintes et la motivation a été remise en question. À titre d’exemple, l’étude de la motivation pourrait permettre de préciser la figure de l’omnivore au Québec. Il est également apparu pertinent de poursuivre la réflexion en étudiant la manière dont les pratiques culturelles sont consommées afin de voir si, et comment, le cas échéant, s’opère la distinction.

Analysis of testosterone pulsatility in women with ovulatory menstrual cycles

Objetivo: Avaliar o padrão pulsátil da secreção da testosterona em mulheres normais. Métodos: Oito mulheres saudáveis com ciclos ovulatórios foram selecionadas. Amostras sanguíneas foram coletadas a cada dez minutos durante seis horas, começando entre 7 e 8 h da manhã, após dez horas de jejum, nas três fases do ciclo menstrual: folicular média (Dia 7), folicular tardia (Dia 12) e lútea (Dia 21). Foram mensurados: testosterona, LH e, no basal, também SHBG. Resultados: A frequência dos pulsos de testosterona, média da amplitude do pulso, porcentagem do incremento da amplitude, duração e intervalos dos pulsos foram similares nas três fases (p > 0,05). A pulsatilidade do LH foi estatisticamente diferente entre as três fases (p < 0,001), caracterizando padrão característico do ciclo ovulatório normal. Conclusões: Esses dados aumentam o conhecimento sobre o padrão de secreção da testosterona no ciclo menstrual humano e representam uma contribuição para a investigação clínica, tanto no hiperandrogenismo como na síndrome de insuficiência androgênica __________________________________________________ ABSTRACT Objective: To evaluate the pattern of the pulsatile secretion of testosterone in normal menstrual cycle. Methods: Eight healthy women with ovulatory menstrual cycles were enrolled. Blood samples were collected at ten-minute intervals for six hours, starting between 7 and 8 am, after a ten-hour fasting, in three phases: mid-follicular (Day 7), late follicular (Day 12) and mid-luteal phase (Day 21). Samples were assayed for testosterone, LH and the baseline also for SHBG. Results: Testosterone pulse frequency, mean amplitude pulse, percentage of increment in pulse amplitude, mean duration of pulses and pulse interval were similar in the three phases. LH pulsatility was statistically different among the three phases (p < 0.001) representing normal ovulatory cycles. Conclusions: These data increase the knowledge about the testosterone secretion profile in the human menstrual cycle and can be used as a contribution to clinical investigation in both hyperandrogenism and androgen insufficiency syndrome