The role of unicellular cyanobacteria in nitrogen fixation and assimilation in subtropical marine waters

Biological N2 fixation constitutes the major source of nitrogen in open ocean systems, regulating the marine nitrogen inventory and primary productivity. Symbiotic relationships between phytoplankton and N2 fixing microorganisms (diazotrophs) have been suggested to play a significant role in the ecology and biogeochemistry in these oceanic regions. The widely distributed, uncultured N2 fixing cyanobacterium UCYN–A was suggested to live in symbiosis since it has unprecedented genome reduction, including the lack of genes encoding for oxygen–evolving photosystem II and the tricarboxylic acid cycle. This thesis aims to study carbon and nitrogen metabolism on field populations of UCYN–A using molecular biology, as well as mass spectrometry tools to visualize metabolic activity on a single cell scale. The development of a 16S rRNA oligonucleotide probe specifically targeting UCYN– A cells and its successful application on environmental samples (Manuscript I and II) revealed a symbiotic partnership with a unicellular prymnesiophyte. We demonstrated a nutrient transfer in carbon and nitrogen compounds between these two partner cells, providing an explanation how these diazotrophs thrive in open ocean systems. Further, UCYN–A can also associate with globally abundant calcifying prymnesiophyte members, e.g. Braarudosphaera bigelowii, indicating that this symbiosis might impact the efficiency of the biological carbon pump. In manuscript III, we provided quantitative information on the cellular abundance and distribution of UCYN–A cells in the North Atlantic Ocean and identified the eukaryotic partner cell as Haptophyta (including prymnesiophyte) via double Catalyzed Reporter Deposition–Fluorescence In Situ Hybridization (CARD–FISH). The UCYN–A–Haptophyta association was the dominant form (87.0±6.1%) over free–living UCYN–A cells. Interestingly, we also detected UCYN–A cells living in association with unknown eukaryotes and non–calcifying Haptophyta cells, raising questions about the host specificity. During a follow up study (Manuscript IV), we conducted various nutrient amendment experiments (including iron, phosphorus, ammonium–nitrate and Saharan Dust) in order to examine physiological interactions between individual UCYN–A and Haptophyta cells. Single cell measurements using nanometer scale secondary ion mass spectrometry (nanoSIMS) revealed a tight physiological coupling in the transfer of carbon (R2 = 0.6232; n = 44) and nitrogen (R2 = 0.9659; n = 44) between host and symbiont. N2 fixation was mainly stimulated when iron–rich Saharan Dust was added, emphasizing on aeolian dust deposition in seawater as a major parameter in constraining N2 fixation of UCYN–A. Moreover, when fixed nitrogen species (ammonium and nitrate) were added, a third unknown microbial partner II cell was observed within individual UCYN–A–Haptophyta associations, but their menaing is unclear. Based on this thesis work we revealed how UCYN–A cells thrive in the environment and established a culture–independent technique to assess the in situ activity in respect to CO2 and N2 fixation of this ecological relevant group of microorganisms. Furthermore, this unusual partnership between a cyanobacterium and a unicellular alga is a model for symbiosis and is analogous to plastid and organismal evolution, and if calcifying, may have important implications for past and present oceanic N2 fixation

Nonlinear magnetic field dependence of the conductance in d-wave NIS tunnel junctions

The ab-plane NIS-tunnelling conductance in d-wave superconductors shows a zero-bias conductance peak which is predicted to split in a magnetic field. In a pure d-wave superconductor the splitting is linear for fields small on the scale of the thermodynamic critical field. The field dependence is shown to be nonlinear, even at low fields, in the vicinity of a surface phase transition into a local time-reversal symmetry breaking state. The field evolution of the conductance is sensitive to temperature, doping, and the symmetry of the sub-dominant pairing channel.Comment: 4 pages, 4 figure

Cancer Biology Data Curation at the Mouse Tumor Biology Database (MTB)

Many advances in the field of cancer biology have been made using mouse models of human cancer. The Mouse Tumor Biology (MTB, "http://tumor.informatics.jax.org":http://tumor.informatics.jax.org) database provides web-based access to data on spontaneous and induced tumors from genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice). These data include standardized tumor names and classifications, pathology reports and images, mouse genetics, genomic and cytogenetic changes occurring in the tumor, strain names, tumor frequency and latency, and literature citations.

Although primary source for the data represented in MTB is peer-reviewed scientific literature an increasing amount of data is derived from disparate sources. MTB includes annotated histopathology images and cytogenetic assay images for mouse tumors where these data are available from The Jackson Laboratory’s mouse colonies and from outside contributors. MTB encourages direct submission of mouse tumor data and images from the cancer research community and provides investigators with a web-accessible tool for image submission and annotation. 

Integrated searches of the data in MTB are facilitated by the use of several controlled vocabularies and by adherence to standard nomenclature. MTB also provides links to other related online resources such as the Mouse Genome Database, Mouse Phenome Database, the Biology of the Mammary Gland Web Site, Festing's Listing of Inbred Strains of Mice, the JAX® Mice Web Site, and the Mouse Models of Human Cancers Consortium's Mouse Repository. 

MTB provides access to data on mouse models of cancer via the internet and has been designed to facilitate the selection of experimental models for cancer research, the evaluation of mouse genetic models of human cancer, the review of patterns of mutations in specific cancers, and the identification of genes that are commonly mutated across a spectrum of cancers.

MTB is supported by NCI grant CA089713

Ultra-Narrow Faraday Rotation Filter at the Rb D1 Line

We present a theoretical and experimental study of the ultra-narrow bandwidth Faraday anomalous dispersion optical filter (FADOF) operating at the rubidium D1 line (795 nm). This atomic line gives better performance than other lines for the main FADOF figures of merit, e.g. simultaneously 71% transmission, 445 MHz bandwidth and 1.2 GHz equivalent noise bandwidth.Comment: 3 pages, 2 figures. Manuscript same as v1. FADOF calculator (ancillary file) now allows for extension to the D2 lin

Dielectrophoretic assembly of high-density arrays of individual graphene devices for rapid screening

We establish the use of dielectrophoresis for the directed parallel assembly of individual flakes and nanoribbons of few-layer graphene into electronic devices. This is a bottom-up approach where source and drain electrodes are prefabricated and the flakes are deposited from a solution using an alternating electric field applied between the electrodes. These devices are characterized by scanning electron microscopy, atomic force microscopy, Raman spectroscopy, and electron transport measurements. They are electrically active and their current carrying capacity and subsequent failure mechanism is revealed. Akin to carbon nanotubes, we show that the dielectrophoretic deposition is self-limiting to one flake per device and is scalable to ultralarge-scale integration densities, thereby enabling the rapid screening of a large number of devices

Photocurrent study of all-printed photodetectors on paper made of different transition metal dichalcogenide nanosheets

We have inkjet-printed in-plane 'metal-semiconductor-metal' type photodetectors on paper, one of the cheapest flexible substrates, which is also recyclable and foldable, in contrast to traditional plastic substrates. The photodetectors are made by using graphene as electrodes and various transition metal dichalcogenides (TMDs) as photoactive component. In particular, we have tested MoS2, WS2, MoSe2 and MoTe2. Large differences in responsivity and sensitivity were observed for all of the TMDs measured, with MoS2 showing the highest sensitivity and MoTe2 producing the largest response. However, photodetectors made of MoTe2 show large decreases in responsivity after one week of exposure to air. The wavelength dependence of the responsivity in MoS2 based devices was further analyzed using a supercontinuum photocurrent spectroscopy setup, with the results suggesting a bolometric or photoelectric origin of the signal. We also report some simple approaches to enhance the device performance and tune the energy range at which the maximum in responsivity or sensitivity is observed

Probing a Set of Trajectories to Maximize Captured Information

We study a trajectory analysis problem we call the Trajectory Capture Problem (TCP), in which, for a given input set T of trajectories in the plane, and an integer k? 2, we seek to compute a set of k points ("portals") to maximize the total weight of all subtrajectories of T between pairs of portals. This problem naturally arises in trajectory analysis and summarization. We show that the TCP is NP-hard (even in very special cases) and give some first approximation results. Our main focus is on attacking the TCP with practical algorithm-engineering approaches, including integer linear programming (to solve instances to provable optimality) and local search methods. We study the integrality gap arising from such approaches. We analyze our methods on different classes of data, including benchmark instances that we generate. Our goal is to understand the best performing heuristics, based on both solution time and solution quality. We demonstrate that we are able to compute provably optimal solutions for real-world instances

Valley Subband Splitting in Bilayer Graphene Quantum Point Contacts

We report a study of one-dimensional subband splitting in a bilayer graphene quantum point contact in which quantized conductance in steps of 4e$^{2}$/h is clearly defined down to the lowest subband. While our source-drain bias spectroscopy measurements reveal an unconventional confinement, we observe a full lifting of the valley degeneracy at high magnetic fields perpendicular to the bilayer graphene plane for the first two lowest subbands where confinement and Coulomb interactions are the strongest and a peculiar merging or mixing of K and K′ valleys from two nonadjacent subbands with indices (N, N + 2) , which are well described by our semiphenomenological model

New solid state lasers from the ultraviolet to the mid-infrared

The authors discuss three new laser materials that offer improved access to the ultraviolet, near infrared and mid-infrared spectral regions. In order for each of these materials to have been identified, a particular hurdle needed to be overcome with respect to the fundamental laser physics impacting the material. In the case of the 280-320nm Ce:LiSAF laser, the main issue is the need to reduce the loss associated with excited state absorption, while for 1047nm Yb:S-FAP it is the ground state absorption at the laser wavelength that must be minimized. Cr:ZnSe has been down-selected from a number of potential candidates which could lase in the 2200-3000nm region, in order to mitigate the detrimental impact of nonradiative decay. In all three cases the authors discuss how appropriate consideration of fundamental concerns has led to the identification and understanding of the new laser system