Nature and Extent of the Deep Biosphere

In the last three decades we have learned a great deal about microbes in subsurface environments. Once, these habitats were rarely examined, perhaps because so much of the life that we are concerned with exists at the surface and seems to pace its metabolic and evolutionary rhythms with the overt planetary, solar, and lunar cycles that dictate our own lives. And it certainly remains easier to identify with living beings that are in our midst, most obviously struggling with us or against us for survival over time scales that are easiest to track using diurnal, monthly or annual periods. Yet, research efforts are drawn again and again to the subsurface to consider life there. No doubt this has been due to our parochial interests in the resources that exist there (the water, minerals, and energy) that our society continues to require and that in some cases are created or modified by microbes. However, we also continue to be intrigued by the scientific curiosities that might only be solved by going underground and examining life where it does and does not exist. But really, is life underground just a peculiarity of most life on the planet and only a recently discovered figment of life? Or is it actually a more prominent and fundamental, if unseen, theme for life on our planet? Our primary purpose in this chapter is to provide an incremental assembly of knowledge of subsurface life with the aim of moving us towards a more complete conceptual model of deep life on the planet. We aim to merge the consideration of the subseafloor and the continental subsurface because it is only through such a unified treatment that we can reach a comprehensive view of this underground life. We also provide some thoughts on a way forward with what we consider to be interesting new research areas, along with the methods by which they might be addressed as we seek new knowledge about life in this Stygian realm.This is the publisher’s final pdf. The published article is copyrighted by Mineralogical Society of America and can be found at: http://www.minsocam.org/.Keywords: Subsurface sediments, Subseafloor sediments, Sea floor, Basalt aquifer, Terrestrial subsurface, Monitoring bacterial transport, In-situ hybridization, Push pull test, Lithoautotrophic microbial ecosystems, In-situ hybridization, Ocean crus

A science-based approach to tackle invasive alien species in Belgium – the role of the ISEIA protocol and the Harmonia information system as decision support tools

A coherent response to biological invasions involves science-based, up-to-date prioritization tools alongside information transfer to relevant authorities and stakeholders. Here, we describe how the collaboration between scientists and policy makers in Belgium has allowed the development of decision support tools regarding invasive alien species. We present the environmental impact assessment protocol ISEIA and comment on its applications. Furthermore, we describe and provide metadata for the information system Harmonia which was developed to disseminate this information to a diverse audience. Using several examples of initiatives addressing the threat of invasive alien species in Belgium, we show how these tools have been instrumental in strengthening capacity of the scientific community, authorities and stakeholders in Belgium on addressing the invasive alien species issue

Ogre and Pythia: An Invariance Proof Method for Weak Consistency Models

We design an invariance proof method for concurrent programs parameterised by a weak consistency model. The calculational design of the invariance proof method is by abstract interpretation of a truly parallel analytic semantics. This generalises the methods by Lamport and Owicki-Gries for sequential consistency. We use cat as an example of language to write consistency specifications of both concurrent programs and machine architectures

Generalised quantum weakest preconditions

Generalisation of the quantum weakest precondition result of D'Hondt and Panangaden is presented. In particular the most general notion of quantum predicate as positive operator valued measure (POVM) is introduced. The previously known quantum weakest precondition result has been extended to cover the case of POVM playing the role of a quantum predicate. Additionally, our result is valid in infinite dimension case and also holds for a quantum programs defined as a positive but not necessary completely positive transformations of a quantum states.Comment: 7 pages, no figures, added references, changed conten

Physiological and transcriptomic evidence for a close coupling between chloroplast ontogeny and cell cycle progression in the pennate diatom <i>Seminavis robusta</i>

Despite the growing interest in diatom genomics, detailed time series of gene expression in relation to key cellular processes are still lacking. Here, we investigated the relationships between the cell cycle and chloroplast development in the pennate diatom Seminavis robusta. This diatom possesses two chloroplasts with a well-orchestrated developmental cycle, common to many pennate diatoms. By assessing the effects of induced cell cycle arrest with microscopy and flow cytometry, we found that division and reorganization of the chloroplasts are initiated only after S-phase progression. Next, we quantified the expression of the S. robusta FtsZ homolog to address the division status of chloroplasts during synchronized growth and monitored microscopically their dynamics in relation to nuclear division and silicon deposition. We show that chloroplasts divide and relocate during the S/G2 phase, after which a girdle band is deposited to accommodate cell growth. Synchronized cultures of two genotypes were subsequently used for a cDNA-amplified fragment length polymorphism-based genome-wide transcript profiling, in which 917 reproducibly modulated transcripts were identified. We observed that genes involved in pigment biosynthesis and coding for light-harvesting proteins were up-regulated during G2/M phase and cell separation. Light and cell cycle progression were both found to affect fucoxanthin-chlorophyll a/c-binding protein expression and accumulation of fucoxanthin cell content. Because chloroplasts elongate at the stage of cytokinesis, cell cycle-modulated photosynthetic gene expression and synthesis of pigments in concert with cell division might balance chloroplast growth, which confirms that chloroplast biogenesis in S. robusta is tightly regulated

Path Selection for Quantum Repeater Networks

Quantum networks will support long-distance quantum key distribution (QKD) and distributed quantum computation, and are an active area of both experimental and theoretical research. Here, we present an analysis of topologically complex networks of quantum repeaters composed of heterogeneous links. Quantum networks have fundamental behavioral differences from classical networks; the delicacy of quantum states makes a practical path selection algorithm imperative, but classical notions of resource utilization are not directly applicable, rendering known path selection mechanisms inadequate. To adapt Dijkstra's algorithm for quantum repeater networks that generate entangled Bell pairs, we quantify the key differences and define a link cost metric, seconds per Bell pair of a particular fidelity, where a single Bell pair is the resource consumed to perform one quantum teleportation. Simulations that include both the physical interactions and the extensive classical messaging confirm that Dijkstra's algorithm works well in a quantum context. Simulating about three hundred heterogeneous paths, comparing our path cost and the total work along the path gives a coefficient of determination of 0.88 or better.Comment: 12 pages, 8 figure

A short review of constructing noise map using crowdsensing technology

The advent of crowdsensing technology has provided a promising possibility for monitoring noise pollution in large-scale areas. Constructing noise map by using mobile smart phones in a cost-effective manner is being widely used in the city and industrial plants. In this short paper, the state-of-the-art crowdsensing-based noise map applications are first summarized. Furthermore, open research challenges associated with building up noise map are highlighted