Geological and mineralogical investigation of hydrothermal fluid discharge features at the sea bottom of Panarea, Italy

The thesis presents research on recent hydrothermal discharge features in a shallow marine hydrothermal system. It aims to clarify their occurrence, genesis, and preservation potential. A facies model is developed, being based on the processes involved in the formation and the prevailing lithofacies. It describes six major groups: channels, fractures, tubes, cones, bowls, and lineaments. Each of these groups subdivides into numerous facies types according to the cements or mineral precipitates prevailing. To clarify the rather complex formation processes of hydrothermal discharge features, genetic models for each facies are proposed. An integrated evolutionary model is developed considering the temporal evolution of the major types of hydrothermal discharge features in the Panarea system and their preservation potential. Confirming presumptions of former, preliminary data, the first documentation of secure paleo-evidences of such hydrothermal discharge features is presented.:1. Introduction ....11 1.1. Preamble .....11 1.2. Research questions, objectives, and hypotheses ......................................... 12 2. State of research - seafloor hydrothermal systems ................................ 15 2.1. Hydrothermal deposits in general ................................................................. 15 2.2. Deep-sea environments ............................................................................... 16 2.3. Shallow-water systems and their preservation potential ............................... 17 3. Panarea Island - the area of investigation ................................................ 20 3.1. The hydrothermal system of Panarea Island ................................................ 20 3.2. Fluid discharge features in Panarea ............................................................. 30 3.3. Study sites .................................................................................................... 34 4. Materials and methods ............................................................................... 40 4.1. Underwater research .................................................................................... 40 4.2. Field methods ............................................................................................... 41 4.3. Laboratory methods ..................................................................................... 44 5. Results ........................................................................................................ 47 5.1. Prevailing lithologies ..................................................................................... 47 5.1.1. Hardrocks ..................................................................................................... 47 5.1.2. Sedimentary rocks ........................................................................................ 51 5.1.3. Sediments .................................................................................................... 54 5.1.4. Cements ....................................................................................................... 58 5.2. Underwater investigation sites and findings ................................................. 66 HYDROTHERMAL FLUID DISCHARGE FEATURES IN PANAREA, ITALY PAGE 10 | 174 5.2.1. Area 26 ......................................................................................................... 66 5.2.2. Basiluzzo ...................................................................................................... 75 5.2.3. Black Point ................................................................................................... 77 5.2.4. Bottaro North ................................................................................................ 79 5.2.5. Bottaro West ................................................................................................. 81 5.2.6. Cave ............................................................................................................. 84 5.2.7. Fumarolic Field ............................................................................................. 87 5.2.8. Hot Lake ....................................................................................................... 89 5.2.9. La Calcara .................................................................................................... 92 5.2.10. Point 21 ........................................................................................................ 98 5.2.11. Subaerial locations ..................................................................................... 100 5.3. Summarizing tables .................................................................................... 104 6. Interpretation ............................................................................................ 106 6.1. Discharge features and secondary processes ............................................ 106 6.1.1. Complex genesis and development of discharge features and their occurrence throughout the system ............................................................. 119 6.1.1.1. Cones, bowls, and lineament structures ..................................................... 119 6.1.1.2. Tubes ......................................................................................................... 128 6.2. Preservation potential and paleo-record ..................................................... 138 7. Conclusion and Discussion .................................................................... 141 7.1. General context of the formation of hydrothermal discharge features in Panarea ...................................................................................................... 141 7.2. Evolution of hydrothermal discharge features in Panarea .......................... 142 7.3. Comprehensive summary ........................................................................... 14

p-BioSPRE-an information and communication technology framework for transnational biomaterial sharing and access

Biobanks represent key resources for clinico-genomic research and are needed to pave the way to personalised medicine. To achieve this goal, it is crucial that scientists can securely access and share high-quality biomaterial and related data. Therefore, there is a growing interest in integrating biobanks into larger biomedical information and communication technology (ICT) infrastructures. The European project p-medicine is currently building an innovative ICT infrastructure to meet this need. This platform provides tools and services for conducting research and clinical trials in personalised medicine. In this paper, we describe one of its main components, the biobank access framework p-BioSPRE (p-medicine Biospecimen Search and Project Request Engine). This generic framework enables and simplifies access to existing biobanks, but also to offer own biomaterial collections to research communities, and to manage biobank specimens and related clinical data over the ObTiMA Trial Biomaterial Manager. p-BioSPRE takes into consideration all relevant ethical and legal standards, e.g., safeguarding donors’ personal rights and enabling biobanks to keep control over the donated material and related data. The framework thus enables secure sharing of biomaterial within open and closed research communities, while flexibly integrating related clinical and omics data. Although the development of the framework is mainly driven by user scenarios from the cancer domain, in this case, acute lymphoblastic leukaemia and Wilms tumour, it can be extended to further disease entities.FP7/2007-2013/27008

MAP3K7 is recurrently deleted in pediatric T-lymphoblastic leukemia and affects cell proliferation independently of NF-κB

Background: Deletions of 6q15–16.1 are recurrently found in pediatric T-cell acute lymphoblastic leukemia (T-ALL). This chromosomal region includes the mitogen-activated protein kinase kinase kinase 7 (MAP3K7) gene which has a crucial role in innate immune signaling and was observed to be functionally and prognostically relevant in different cancer entities. Therefore, we correlated the presence of MAP3K7 deletions with clinical parameters in a cohort of 327 pediatric T-ALL patients and investigated the function of MAP3K7 in the T-ALL cell lines CCRF-CEM, Jurkat and MOLT-4. Methods: MAP3K7 deletions were detected by multiplex ligation-dependent probe amplification (MLPA). T-ALL cell lines were transduced with adeno-associated virus (AAV) vectors expressing anti-MAP3K7 shRNA or a non-silencing shRNA together with a GFP reporter. Transduction efficiency was measured by flow cytometry and depletion efficiency by RT-PCR and Western blots. Induction of apoptosis was measured by flow cytometry after staining with PE-conjugated Annexin V. In order to assess the contribution of NF-κB signaling to the effects of MAP3K7 depletion, cells were treated with TNF-α and cell lysates analyzed for components of the NF-κB pathway by Western blotting and for expression of the NF-κB target genes BCL2, CMYC, FAS, PTEN and TNF-α by RT-PCR. Results: MAP3K7 is deleted in approximately 10% and point-mutated in approximately 1% of children with T-ALL. In 32 of 33 leukemias the deletion of MAP3K7 also included the adjacent CASP8AP2 gene. MAP3K7 deletions were associated with the occurrence of SIL-TAL1 fusions and a mature immunophenotype, but not with response to treatment and outcome. Depletion of MAP3K7 expression in T-ALL cell lines by shRNAs slowed down proliferation and induced apoptosis, but neither changed protein levels of components of NF-κB signaling nor NF-κB target gene expression after stimulation with TNF-α. Conclusions: This study revealed that the recurrent deletion of MAP3K7/CASP8AP2 is associated with SIL-TAL1 fusions and a mature immunophenotype, but not with response to treatment and risk of relapse. Homozygous deletions of MAP3K7 were not observed, and efficient depletion of MAP3K7 interfered with viability of T-ALL cells, indicating that a residual expression of MAP3K7 is indispensable for T-lymphoblasts

MAP3K7 is recurrently deleted in pediatric T-lymphoblastic leukemia and affects cell proliferation independently of NF-κB

Background: Deletions of 6q15–16.1 are recurrently found in pediatric T-cell acute lymphoblastic leukemia (T-ALL). This chromosomal region includes the mitogen-activated protein kinase kinase kinase 7 (MAP3K7) gene which has a crucial role in innate immune signaling and was observed to be functionally and prognostically relevant in different cancer entities. Therefore, we correlated the presence of MAP3K7 deletions with clinical parameters in a cohort of 327 pediatric T-ALL patients and investigated the function of MAP3K7 in the T-ALL cell lines CCRF-CEM, Jurkat and MOLT-4. Methods: MAP3K7 deletions were detected by multiplex ligation-dependent probe amplification (MLPA). T-ALL cell lines were transduced with adeno-associated virus (AAV) vectors expressing anti-MAP3K7 shRNA or a non-silencing shRNA together with a GFP reporter. Transduction efficiency was measured by flow cytometry and depletion efficiency by RT-PCR and Western blots. Induction of apoptosis was measured by flow cytometry after staining with PE-conjugated Annexin V. In order to assess the contribution of NF-κB signaling to the effects of MAP3K7 depletion, cells were treated with TNF-α and cell lysates analyzed for components of the NF-κB pathway by Western blotting and for expression of the NF-κB target genes BCL2, CMYC, FAS, PTEN and TNF-α by RT-PCR. Results: MAP3K7 is deleted in approximately 10% and point-mutated in approximately 1% of children with T-ALL. In 32 of 33 leukemias the deletion of MAP3K7 also included the adjacent CASP8AP2 gene. MAP3K7 deletions were associated with the occurrence of SIL-TAL1 fusions and a mature immunophenotype, but not with response to treatment and outcome. Depletion of MAP3K7 expression in T-ALL cell lines by shRNAs slowed down proliferation and induced apoptosis, but neither changed protein levels of components of NF-κB signaling nor NF-κB target gene expression after stimulation with TNF-α. Conclusions: This study revealed that the recurrent deletion of MAP3K7/CASP8AP2 is associated with SIL-TAL1 fusions and a mature immunophenotype, but not with response to treatment and risk of relapse. Homozygous deletions of MAP3K7 were not observed, and efficient depletion of MAP3K7 interfered with viability of T-ALL cells, indicating that a residual expression of MAP3K7 is indispensable for T-lymphoblasts

From niche to blockbuster: a greater role for allopurinol in maintenance treatment of acute lymphoblastic leukemia

Not available

The 9p21.3 risk of childhood acute lymphoblastic leukaemia is explained by a rare high-impact variant in CDKN2A

Genome-wide association studies (GWAS) have provided strong evidence for inherited predisposition to childhood acute lymphoblastic leukaemia (ALL) identifying a number of risk loci. We have previously shown common SNPs at 9p21.3 influence ALL risk. These SNP associations are generally not themselves candidates for causality, but simply act as markers for functional variants. By means of imputation of GWAS data and subsequent validation SNP genotyping totalling 2,177 ALL cases and 8,240 controls, we have shown that the 9p21.3 association can be ascribed to the rare highimpact CDKN2A p.Ala148Thr variant (rs3731249; Odds ratio=2.42, P=3.45×10−19). The association between rs3731249 genotype and risk was not specific to particular subtype of B-cell ALL. The rs3731249 variant is associated with predominant nuclear localisation of the CDKN2A transcript suggesting the functional effect of p.Ala148Thr on ALL risk may be through compromised ability to inhibit cyclin D within the cytoplasm

Tumor necrosis factor and lymphotoxin-alpha genetic polymorphisms and risk of relapse in childhood B-cell precursor acute lymphoblastic leukemia: a case-control study of patients treated with BFM therapy

BACKGROUND: Circulating levels of tumor necrosis factor (TNF) and lymphotoxin-α (LT-α) have been associated with outcome in solid and hematologic malignancies. Within the TNF gene and the LT-α gene, polymorphisms have been identified at nucleotide positions -308 and +252, respectively. The variant alleles for TNF are designated TNF1 and TNF2, the ones for LT-α LT-α (10.5 kb) and LT-α (5.5 kb). Of interest, TNF2 and LT-α (5.5 kb) were shown to be associated with higher TNF and LT-α plasma levels than their counterparts. In the present study, we investigated the associations of the above mentioned polymorphisms with risk of relapse in childhood acute lymphoblastic leukemia (ALL) treated according to Berlin-Frankfurt-Münster (BFM) protocols. METHODS: Matched case-control study of 64 relapsed and 64 successfully treated non-relapsed childhood B-cell precursor ALL patients of standard and intermediate risk for treatment failure. RESULTS: The odds ratio (OR) for the combined category of TNF1/TNF2 and TNF2/TNF2 genotypes in comparison to the TNF1/TNF1 genotype was 1.17 (95 % confidence interval (CI) = 0.53 - 2.56, P = 0.697). The ORs for the LT-α (10.5 kb/5.5 kb) and the LT-α (5.5 kb/5.5 kb) genotypes with reference to the LT-α (10.5 kb/10.5 kb) genotype were 2.17 (95 % CI = 0.84 - 5.58, P = 0.107) and 0.5 (95 % CI = 0.09 - 2.66, P = 0.418), respectively. CONCLUSIONS: Our results do not suggest a major role of the investigated genetic polymorphisms with regard to risk of relapse in standard- and intermediate-risk childhood B-cell precursor ALL treated according to BFM protocols

Frequent and sex-biased deletion of SLX4IP by illegitimate V(D)J-mediated recombination in childhood acute lymphoblastic leukemia

Acute lymphoblastic leukemia (ALL) accounts for ∼25% of pediatric malignancies. Of interest, the incidence of ALL is observed ∼20% higher in males relative to females. The mechanism behind the phenomenon of sex-specific differences is presently not understood. Employing genome-wide genetic aberration screening in 19 ALL samples, one of the most recurrent lesions identified was monoallelic deletion of the 5′ region of SLX4IP. We characterized this deletion by conventional molecular genetic techniques and analyzed its interrelationships with biological and clinical characteristics using specimens and data from 993 pediatric patients enrolled into trial AIEOP-BFM ALL 2000. Deletion of SLX4IP was detected in ∼30% of patients. Breakpoints within SLX4IP were defined to recurrent positions and revealed junctions with typical characteristics of illegitimate V(D)J-mediated recombination. In initial and validation analyses, SLX4IP deletions were significantly associated with male gender and ETV6/RUNX1-rearranged ALL (both overall P < 0.0001). For mechanistic validation, a second recurrent deletion affecting TAL1 and caused by the same molecular mechanism was analyzed in 1149 T-cell ALL patients. Validating a differential role by sex of illegitimate V(D)J-mediated recombination at the TAL1 locus, 128 out of 1149 T-cell ALL samples bore a deletion and males were significantly more often affected (P = 0.002). The repeatedly detected association of SLX4IP deletion with male sex and the extension of the sex bias to deletion of the TAL1 locus suggest that differential illegitimate V(D)J-mediated recombination events at specific loci may contribute to the consistent observation of higher incidence rates of childhood ALL in boys compared with girl

CortiLove: A pilot study on hair steroids in the context of being in love and separation

While romantic infatuation and separation influence psychological and physiological functioning, the hypothalamic-pituitary-adrenal axis with its biomarkers cortisol, dehydroepiandrosterone (DHEA), and progesterone central for coping and distress has been scarcely researched in this context. In particular, endocrine hair analyses assumed to be more valid than saliva or blood assessments for studying long-term processes have not yet been conducted in the context of romantic love. Thus, 101 female subjects in phases of infatuation (n = 16), separation (n = 14), long-term relationships (n = 40), and singlehood (n = 31) reported psychological distress and provided 1 cm hair samples for the assessment of long-term integrated cortisol, DHEA, and progesterone over the last month. Separated, infatuated, and single women exhibited higher cortisol levels than those in a long-term relationship (all ps ≤ .031), while self-reported distress was only evident in separated individuals. Further, no group differences for progesterone (p = .602), but higher DHEA levels in the separation (p = .009) and single group (p = .016) compared to the long-term relationship group were detected. This is the first study showing that compared to women in long-term relationships, infatuation, separation, and single groups exhibit higher levels of physiological, but not necessarily self-reported indicators of distress. These findings, albeit on a very small and preliminary sample, are discussed in the context of the stress-buffering effect of relationships, and provide important starting points for bigger, more balanced studies combining multimodal self-report and biological markers in psychological research of romantic love

Nomenclature for alleles of the thiopurine methyltransferase gene

The drug-metabolizing enzyme thiopurine methyltransferase (TPMT) has become one of the best examples of pharmacogenomics to be translated into routine clinical practice. TPMT metabolizes the thiopurines 6-mercaptopurine, 6-thioguanine, and azathioprine, drugs that are widely used for treatment of acute leukemias, inflammatory bowel diseases, and other disorders of immune regulation. Since the discovery of genetic polymorphisms in the TPMT gene, many sequence variants that cause a decreased enzyme activity have been identified and characterized. Increasingly, to optimize dose, pretreatment determination of TPMT status before commencing thiopurine therapy is now routine in many countries. Novel TPMT sequence variants are currently numbered sequentially using PubMed as a source of information; however, this has caused some problems as exemplified by two instances in which authors' articles appeared on PubMed at the same time, resulting in the same allele numbers given to different polymorphisms. Hence, there is an urgent need to establish an order and consensus to the numbering of known and novel TPMT sequence variants. To address this problem, a TPMT nomenclature committee was formed in 2010, to define the nomenclature and numbering of novel variants for the TPMT gene. A website (http://www.imh.liu.se/tpmtalleles) serves as a platform for this work. Researchers are encouraged to submit novel TPMT alleles to the committee for designation and reservation of unique allele numbers. The committee has decided to renumber two alleles: nucleotide position 106 (G>A) from TPMT*24 to TPMT*30 and position 611 (T>C, rs79901429) from TPMT*28 to TPMT*31. Nomenclature for all other known alleles remains unchanged