Iron Utilization in Marine Cyanobacteria and Eukaryotic Algae

Iron is essential for aerobic organisms. Additionally, photosynthetic organisms must maintain the iron-rich photosynthetic electron transport chain, which likely evolved in the iron-replete Proterozoic ocean. The subsequent rise in oxygen since those times has drastically decreased the levels of bioavailable iron, indicating that adaptations have been made to maintain sufficient cellular iron levels in the midst of scarcity. In combination with physiological studies, the recent sequencing of marine microorganism genomes and transcriptomes has begun to reveal the mechanisms of iron acquisition and utilization that allow marine microalgae to persist in iron limited environments

Functional characterization of the diatom cyclin-dependent kinase A2 as a mitotic regulator reveals plant-like properties in a non-green lineage

Background: Cyclin-dependent kinases (CDKs) are crucial regulators of cell cycle progression in eukaryotes. The diatom CDKA2 was originally assigned to the classical A-type CDKs, but its cell cycle phase-specific transcription at the G2-to-M phase transition is typical for plant-specific B-type CDKs. Results: Here, we report the functional characterization of CDKA2 from the diatom Phaeodactylum tricornutum. Through a yeast two-hybrid library screen, CDKA2 was found to interact with the G2/M-specific CDK scaffolding factor CKS1. Localization of CDKA2 was found to be nuclear in interphase cells, while in cells undergoing cytokinesis, the signal extended to the cell division plane. In addition, overexpression of CDKA2 induced an overall reduction in the cell growth rate. Expression analysis of cell cycle marker genes in the overexpression lines indicates that this growth reduction is primarily due to a prolongation of the mitotic phase. Conclusions: Our study indicates a role for CDKA2 during cell division in diatoms. The functional characterization of a CDK with clear CDKB properties in a non-green organism questions whether the current definition of B-type CDKs being plant-specific might need revision

Money: Who Has a Stake in the Most Value-Centric Common Design Material?

Money is more than just a numeric value. It embodies trust and moral gravity, and it offers flexible ways to transact. However, the emergence of Central Bank Digital Currency (CBDC) is set to bring about a drastic change in the future of money. This paper invites designers to reflect on their role in shaping material and immaterial monetary change. In this rapidly changing landscape, design could be instrumental in uncovering and showcasing the diverse values that money holds for different stakeholders. Understanding these diversities could promote a more equitable and inclusive financial, social, and global landscape within emergent forms of cash-like digital currency. Without such consideration, certain forms of money we have come to know could disappear, along with the values people hold upon them. We report on semi-structured interviews with stakeholders who have current knowledge or involvement in the emerging field of Central Bank Digital Currency (CBDC). Our research indicates that this new form of money presents both challenges and opportunities for designers. Specifically, we emphasise the potential for Central Bank Digital Currency (CBDC) to either positively or negatively reform values through its design. By considering time, reflecting present values, and promoting inclusion in its deployment, we can strive to ensure that Central Bank Digital Currency (CBDC) represents the diverse needs and perspectives of its users.Comment: 19 pages, 1 figur

A Non-Custodial Wallet for CBDC: Design Challenges and Opportunities

Central Bank Digital Currency (CBDC) is a novel form of money that could be issued and regulated by central banks, offering benefits such as programmability, security, and privacy. However, the design of a CBDC system presents numerous technical and social challenges. This paper presents the design and prototype of a non-custodial wallet, a device that enables users to store and spend CBDC in various contexts. To address the challenges of designing a CBDC system, we conducted a series of workshops with internal and external stakeholders, using methods such as storytelling, metaphors, and provotypes to communicate CBDC concepts, elicit user feedback and critique, and incorporate normative values into the technical design. We derived basic guidelines for designing CBDC systems that balance technical and social aspects, and reflect user needs and values. Our paper contributes to the CBDC discourse by demonstrating a practical example of how CBDC could be used in everyday life and by highlighting the importance of a user-centred approach.Comment: 25 pages, 12 figure

Stemming Epigenetics in Marine Stramenopiles

Epigenetics include DNA methylation, the modification of histone tails that affect chromatin states, and small RNAs that are involved in the setting and maintenance of chromatin modifications. Marine stramenopiles (MAS), which are a diverse assemblage of algae that acquired photosynthesis from secondary endosymbiosis, include single-celled organisms such as diatoms as well as multicellular forms such as brown algae. The recent publication of two diatom genomes that diverged ~90 million years ago (mya), as well as the one of a brown algae that diverged from diatoms ~250 Mya, provide a great system of related, yet diverged set of organisms to compare epigenetic marks and their relationships. For example, putative DNA methyltransferase homologues were found in diatoms while none could be identified in the brown algal genome. On the other hand, no canonical DICER-like protein was found in diatoms in contrast to what is observed in brown algae. A key interest relies in understanding the adaptive nature of epigenetics and its inheritability. In contrast to yeast that lack DNA methylation, homogeneous cultures of diatoms constitute an attractive system to study epigenetic changes in response to environmental conditions such as nutrient-rich to nutrient-poor transitions which is especially relevant because of their ecological importance. P. tricornutum is also of outstanding interest because it is observed as three different morphotypes and thus constitutes a simple and promising model for the study of the epigenetic phenomena that accompany cellular differentiation. In this review we focus on the insights obtained from MAS comparative genomics and epigenomic analyses

The \u3cem\u3ePhaeodactylum\u3c/em\u3e genome reveals the evolutionary history of diatom genomes

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth1,2. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology3,4,5. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (∼40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans

When everything is not everywhere but species evolve: an alternative method to model adaptive properties of marine ecosystems

The functional and taxonomic biogeography of marine microbial systems reflects the current state of an evolving system. Current models of marine microbial systems and biogeochemical cycles do not reflect this fundamental organizing principle. Here, we investigate the evolutionary adaptive potential of marine microbial systems under environmental change and introduce explicit Darwinian adaptation into an ocean modelling framework, simulating evolving phytoplankton communities in space and time. To this end, we adopt tools from adaptive dynamics theory, evaluating the fitness of invading mutants over annual timescales, replacing the resident if a fitter mutant arises. Using the evolutionary framework, we examine how community assembly, specifically the emergence of phytoplankton cell size diversity, reflects the combined effects of bottom-up and top-down controls. When compared with a species-selection approach, based on the paradigm that “Everything is everywhere, but the environment selects”, we show that (i) the selected optimal trait values are similar; (ii) the patterns emerging from the adaptive model are more robust, but (iii) the two methods lead to different predictions in terms of emergent diversity. We demonstrate that explicitly evolutionary approaches to modelling marine microbial populations and functionality are feasible and practical in time-varying, space-resolving settings and provide a new tool for exploring evolutionary interactions on a range of timescales in the ocean.France. Agence nationale de la recherche (grant PHYTBACK (ANR-10-BLAN-7109))European Union (EU Micro B3 project)European Research Council (ERC Diatomite project)Gordon and Betty Moore Foundation (Grant #3778

Proceedings of the Semantics of African, Asian and Austronesian Languages (TripleA) 2

TripleA is a workshop series founded by linguists from the University of Tübingen and the University of Potsdam. Its aim is to provide a forum for semanticists doing fieldwork on understudied languages, and its focus is on languages from Africa, Asia, Australia and Oceania. The second TripleA workshop was held at the University of Potsdam, June 3-5, 2015

Workshop report. Linear-Scaling Ab Initio Calculations: Applications and Future Directions

The study of properties and of processes in materials, frequently hinges upon understanding phenomena which originate at the atomic level. In such cases the accurate description of the interactions between large numbers of atoms is critical and in turn requires the accurate description of the electrons which play a crucial role in the bonding of atoms into molecules, surfaces and solids. This can only be achieved by solving the equations of quantum mechanics. These equations are too complicated to solve exactly; however their solutions can be approximated by computational techniques. The most accurate ? but also most computationally demanding ? are the “ab initio” techniques which do not use any empirical adjustable parameters. Amongst them, the Density Functional Theory (DFT) formulation of quantum mechanics stands out as an excellent compromise between accuracy and computational efficiency. However, the applicability of ab initio techniques is severely limited by poor scaling: the computational effort needed to perform an ab initio calculation increases with (at least) the third power of the number of atoms, N. This cubic-scaling bottleneck limits the number of atoms we can study to a few hundred at most, even on parallel supercomputers. To overcome this length-scale limitation, a number of researchers worldwide have been pioneering the development of a novel class of ab initio methods with linear-scaling or “Order N” (O(N)) computational cost which nevertheless retain the same high level of accuracy as the conventional approaches. While physically motivated, such methods have proved particularly hard to develop as they introduce highly non-trivial localisation constraints. Nevertheless, many major obstacles have been overcome and a number of O(N) methods (SIESTA, CONQUEST, ONETEP, etc.) for ground state DFT calculations on systems with a gap (e.g. molecules, semiconductors and insulators) are now available and have reached a state of maturity that allows them to be used to study ”real” materials. The particular focus of this workshop is therefore to look forward to what can be achieved in the next few years. Our aim is twofold: (1) As O(N) methods are currently extending the applicability of DFT calculations to problems involving biomolecules and nanostructures they are leading to completely new levels of understanding of these systems. This CECAM meeting will give us the opportunity to make an appraisal of such large-scale simulations and their potential to connect more directly to experiments. (2) We also want to examine the options for extending linear-scaling to problems that cannot be treated by ground-state DFT but require other, more complex approaches. These include methods for treating metallic systems, excited states and wavefunction-based theories for including electronic correlation. Finding ways to transform these methods to linear-scaling cost, and hence extent their applicability to the nano-scale, is the next big challenge that the community of developers of large-scale electronic structure methods is beginning to face. We hope that this workshop will stimulate these major new O(N) methodological developments by bringing together the leading groups in the development of O(N) DFT methods with the leading groups in the development of metal and excited-state or wavefunction-based methods. Strong emphasis during the workshop will be given to discussion in order to promote the exchange of ideas between different communities (Physics, Chemistry, Materials Science, Biochemistry) which are all interested in large-scale applications with ab initio accuracy but are approaching them from different perspectives

Lattice QCD with mixed actions

We discuss some of the implications of simulating QCD when the action used for the sea quarks is different from that used for the valence quarks. We present exploratory results for the hadron mass spectrum and pseudoscalar meson decay constants using improved staggered sea quarks and HYP-smeared overlap valence quarks. We propose a method for matching the valence quark mass to the sea quark mass and demonstrate it on UKQCD clover data in the simpler case where the sea and valence actions are the same.Comment: 15 pages, 10 figures some minor modification to text and figures. Accepted for publicatio