ADRIPLAN Data Policy

This document sets the policy for accessing data and information gathered by ADRIPLAN and will ensure that data are handled in a consistent and transparent manner. The policy aims to strike a balance between the rights of investigators and the need for widespread access through the free and unrestricted sharing and exchange of ADRIPLAN data, meta-data and data products. In agreeing to share, data providers need to have assurance that their data are properly handled, disseminated and acknowledged following similar principles and rules across countries and stakeholders. This policy covers data, metadata and products on maritime uses, environmental conditions and planning documents which are acquired, processed and disseminated in the framework of ADRIPLAN. ADRIPLAN doesn't collect any new data so the information it uses depends on the contribution from partners, according to their role in the project and the provisions of the Grant Agreement and the Partnership Agreement, and on data acquired from external sources. Part of the source data are provided directly by ADRIPLAN partners and a large part of data are made available by other organizations. Independent data policies associated to datasets and databases merged in the framework of ADRIPLAN will be included and correct citations will be assured. From source data, added value data products are created as part of ADRIPLAN’s duties. The main goals of this data policy are: to allow ADRIPLAN's partners to discover, access, process and use as many data as possible to develop valuable MSP plans proposals, through the ADRIPLAN Data Portal to provide partners with pertinent, sound, updated, and accurate information to capitalize knowledge, efforts and investments from existing projects and national and international experiences to ensure acknowledgement to owners and producers of the data and information they will provide to ADRIPLAN to ensure that the conditions that are applied to the provided data will be documented and respected in the ADRIPLAN Data Portal to promote the widest possible dissemination and reuse of ADRIPLAN's products and outputs, not only to partners in the project but also to stakeholders, public administrations and citizens to adopt and promote the best and the most open international rules and licenses for sharing and reuse of dat

Characterization of C-S Lyase from C. diphtheriae

The emergence of antibiotic resistance in microbial pathogens requires the identification of new antibacterial drugs. The biosynthesis of methionine is an attractive target because of its central importance in cellular metabolism. Moreover, most of the steps in methionine biosynthesis pathway are absent in mammals, lowering the probability of unwanted side effects. Herein, detailed biochemical characterization of one enzyme required for methionine biosynthesis, a pyridoxal-5′-phosphate (PLP-) dependent C-S lyase from Corynebacterium diphtheriae, a pathogenic bacterium that causes diphtheria, has been performed. We overexpressed the protein in E. coli and analyzed substrate specificity, pH dependence of steady state kinetic parameters, and ligand-induced spectral transitions of the protein. Structural comparison of the enzyme with cystalysin from Treponema denticola indicates a similarity in overall folding. We used site-directed mutagenesis to highlight the importance of active site residues Tyr55, Tyr114, and Arg351, analyzing the effects of amino acid replacement on catalytic properties of enzyme. Better understanding of the active site of C. diphtheriae C-S lyase and the determinants of substrate and reaction specificity from this work will facilitate the design of novel inhibitors as antibacterial therapeutics

Editorial: Developmental model 2.0

Human pluripotent stem cells (PSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), have enabled the modeling of human development and helped to illuminate mechanisms of monogenic disease, complex disease, and cancer. Lately, the striking ability of PSCs to self-organize has engendered three-dimension (3D) models of human development. The 3D embryonic cell models partially reconstruct the complex architecture of mammalian early embryonic structures and therefore hold great potential for stem cell and developmental studies. In this Research Topic, Gordeeva et al. described a 3D embryoid body differentiation model and compared the spatiotemporal growth and patterning dynamics of embryoid bodies formed from different stem cell origins and culture conditions. Min et al. profiled the proteome and the protein phosphorylation of blastoids-blastocyst-like 3D structures derived from extended pluripotent stem cells (EPSC)

Residues in the Distal Heme Pocket of Arabidopsis Non-Symbiotic Hemoglobins: Implication for Nitrite Reductase Activity

It is well-established that plant hemoglobins (Hbs) are involved in nitric oxide (NO) metabolism via NO dioxygenase and/or nitrite reductase activity. The ferrous-deoxy Arabidopsis Hb1 and Hb2 (AHb1 and AHb2) have been shown to reduce nitrite to NO under hypoxia. Here, to test the hypothesis that a six- to five-coordinate heme iron transition might mediate the control of the nitrite reduction rate, we examined distal pocket mutants of AHb1 and AHb2 for nitrite reductase activity, NO production and spectroscopic features. Absorption spectra of AHbs distal histidine mutants showed that AHb1 mutant (H69L) is a stable pentacoordinate high-spin species in both ferrous and ferric states, whereas heme iron in AHb2 mutant (H66L) is hexacoordinated low-spin with Lys69 as the sixth ligand. The bimolecular rate constants for nitrite reduction to NO were 13.3 ± 0.40, 7.3 ± 0.5, 10.6 ± 0.8 and 171.90 ± 9.00 M(-1)·s(-1) for AHb1, AHb2, AHb1 H69L and AHb2 H66L, respectively, at pH 7.4 and 25 °C. Consistent with the reductase activity, the amount of NO detected by chemiluminescence was significantly higher in the AHb2 H66L mutant. Our data indicate that nitrite reductase activity is determined not only by heme coordination, but also by a unique distal heme pocket in each AHb

Residues in the Distal Heme Pocket of Arabidopsis Non-Symbiotic Hemoglobins: Implication for Nitrite Reductase Activity

It is well-established that plant hemoglobins (Hbs) are involved in nitric oxide (NO) metabolism via NO dioxygenase and/or nitrite reductase activity. The ferrous-deoxy Arabidopsis Hb1 and Hb2 (AHb1 and AHb2) have been shown to reduce nitrite to NO under hypoxia. Here, to test the hypothesis that a six- to five-coordinate heme iron transition might mediate the control of the nitrite reduction rate, we examined distal pocket mutants of AHb1 and AHb2 for nitrite reductase activity, NO production and spectroscopic features. Absorption spectra of AHbs distal histidine mutants showed that AHb1 mutant (H69L) is a stable pentacoordinate high-spin species in both ferrous and ferric states, whereas heme iron in AHb2 mutant (H66L) is hexacoordinated low-spin with Lys69 as the sixth ligand. The bimolecular rate constants for nitrite reduction to NO were 13.3 \ub1 0.40, 7.3 \ub1 0.5, 10.6 \ub1 0.8 and 171.90 \ub1 9.00 M(-1)\ub7s(-1) for AHb1, AHb2, AHb1 H69L and AHb2 H66L, respectively, at pH 7.4 and 25 \ub0C. Consistent with the reductase activity, the amount of NO detected by chemiluminescence was significantly higher in the AHb2 H66L mutant. Our data indicate that nitrite reductase activity is determined not only by heme coordination, but also by a unique distal heme pocket in each AHb

Generation of heterozygous SAMD9 CRISPR/Cas9-edited iPSC line (ESi086-A-3), carrying I1567M mutation

Germline SAMD9 mutations are one of the most common alterations that predispose to pediatric myelodysplastic syndrome (MDS), a clonal disorder characterized by ineffective hematopoiesis, increasing the risk of developing acute myeloid leukemia (AML). Up to date, a disease model to study the role of SAMD9 mutation in MDS is still lacking. Here, we have generated a human induced pluripotent stem cell (hiPSC) line carrying SAMD9mut (p.I1567M), taking advantage of CRISPR/Cas9 system. As a result, the genetic engineered hiPSC line represent a new in vitro disease model to understand the impact of SAMD9 mutation at molecular and cellular level during hematopoiesis

Using pluripotent stem cells to understand normal and leukemic hematopoietic development

Several decades have passed since the generation of the first embryonic stem cell (ESC) lines both in mice and in humans. Since then, stem cell biologists have tried to understand their potential biological and clinical uses for their implementation in regenerative medicine. The hematopoietic field was a pioneer in establishing the potential use for the development of blood cell products and clinical applications; however, early expectations have been truncated by the difficulty in generating bonafide hematopoietic stem cells (HSCs). Despite some progress in understanding the origin of HSCs during embryonic development, the reproduction of this process in vitro is still not possible, but the knowledge acquired in the embryo is slowly being implemented for mouse and human pluripotent stem cells (PSCs). In contrast, ESC-derived hematopoietic cells may recapitulate some leukemic transformation processes when exposed to oncogenic drivers. This would be especially useful to model prenatal leukemia development or other leukemia-predisposing syndromes, which are difficult to study. In this review, we will review the state of the art of the use of PSCs as a model for hematopoietic and leukemia development

A System for Managing Oceanographic Metadata Using XML and XQuery

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Generation of two transgene-free human iPSC lines from CD133+ cord blood cells

We have generated two human induced pluripotent stem cell (iPSC) lines from CD133+ cells isolated from umbilical cord blood (CB) of a female child using non-integrative Sendai virus. Here we describe the complete characterization of these iPSC lines: PRYDi-CB5 and PRYDi-CB40