satFRET: estimation of Forster resonance energy transfer by acceptor saturation

We demonstrate theoretically and experimentally the quantification of Förster resonance energy transfer (FRET) by direct and systematic saturation of the excited state of acceptor molecules. This version of acceptor depletion methods for FRET estimation, denoted as “satFRET” is reversible and suitable for time-resolved measurements. The technique was investigated theoretically using the steady-state solution of the differential equation system of donor and acceptor molecular states. The influence of acceptor photobleaching during measurement was included in the model. Experimental verification was achieved with the FRET-pair Alexa 546- Alexa 633 loaded on particles in different stoichiometries and measured in a confocal microscope. Estimates of energy transfer efficiency by excited state saturation were compared to those obtained by measurements of sensitised emission and acceptor photobleaching. The results lead to a protocol that allows time-resolved FRET measurements of fixed and living cells on a conventional confocal microscope. This procedure was applied to fixed Chinese hamster ovary cells containing a cyan fluorescent protein and yellow fluorescent protein pair. The time resolution of the technique was demonstrated in a live T cell activation assay comparing the FRET efficiencies measured using a genetically encoded green and red fluorescent protein biosensor for GTP/GDP turnover to those measured by acceptor photobleaching of fixed cells

Spitzer observations of the N157B supernova remnant and its surroundings

(Aims): We study the LMC interstellar medium in the field of the nebula N157B, which contains a supernova remnant, an OB association, ionized gas, and high-density dusty filaments in close proximity. We investigate the relative importance of shock excitation by the SNR and photo-ionization by the OB stars, as well as possible interactions between the supernova remnant and its environment. (Methods): We apply multiwavelength mapping and photometry, along with spatially resolved infrared spectroscopy, to identifying the nature of the ISM using new infrared data from the Spitzer space observatory and X-ray, optical, and radio data from the literature. (Results): The N157B SNR has no infrared counterpart. Infrared emission from the region is dominated by the compact blister-type HII region associated with 2MASS J05375027-6911071 and excited by an O8-O9 star. This object is part of an extended infrared emission region that is associated with a molecular cloud. We find only weak emission from the shock-indicator [FeII], and both the excitation and the heating of the extended cloud are dominated by photo-ionization by the early O stars of LH99. (Conclusions): Any possible impact by the expanding SNR does not now affect the extended cloud of molecules and dust, despite the apparent overlap of SNR X-ray emission with infrared and Ha emission from the cloud. This implies that the supernova progenitor cannot have been more massive than about 25 solar masses.Comment: 10 pages, 8 figures, published in A&

Stable and Sporadic Symbiotic Communities of Coral and Algal Holobionts

Coral and algal holobionts are assemblages of macroorganisms and microorganisms, including viruses, Bacteria, Archaea, protists and fungi. Despite a decade of research, it remains unclear whether these associations are spatial-temporally stable of species-specific. We hypothesized that conflicting interpretations of the data arise from high noise associated with sporadic microbial symbionts overwhelming signatures of stable holobiont members. To test this hypothesis, the bacterial communities associated with three coral species (Acropora rosaria, Acropora hyacinthus and Porites lutea) and two algal guilds (crustose coralline algae and turf algae) from 131 samples were analyzed using a novel statistical approach termed the Abundance-Ubiquity (AU) test. The AU test determines whether a given bacterial species would be present given additional sampling effort (that is, stable) versus those species that are sporadically associated with a sample. Using the AU test, we show that coral and algal holobionts have a high-diversity group of stable symbionts. Stable symbionts are not exclusive to one species of coral or algae. No single bacterial species was ubiquitously associated with one host, showing that there is not strict heredity of the microbiome. In addition to the stable symbionts, there was a low-diversity community of sporadice symbionts whose abundance varied widely across individual holobionts of the same species. Identification of these two symbiont communities supports the holobiont model and calls into question the hologenome theory of evolution

New taxa and new synonymy in Muricidae (Neogastropoda: Pagodulinae, Trophoninae, Ocenebrinae) from the Northeast Pacific

The results of an extensive examination of northeast Pacific muricid gastropods ranging from Aleutian Islands, Alaska, to mid-Baja California, is presented. Two new genera and 26 new species are described: In Pagodulinae: Abyssotrophon fusiformis n. sp., A. newmani n. sp., Boreotrophon cascadiensis n. sp., B. cordellensis n. sp., B. cortesianus n. sp., B. obesus n. sp., B. subapolyonis n. sp., B. vancouverensis n. sp., B. aleuticus n. sp., B. pseudotripherus n. sp., B. santarosensis n. sp., B. tannerensis n. sp. In Trophoninae: Warenia, n. gen., Scabrotrophon buldirensis n. sp, S. kantori n. sp., S. lima n. sp., S. macleani n. sp., S. moresbyensis n. sp., S. norafosterae n. sp., S. trifidus n. sp., Nipponotrophon exquisitus n. sp. In Ocenebrinae: Paciocinebrina n. gen., Nucella angustior n. sp., Paciocinebrina benitoensis n. sp., P. macleani n. sp., P. neobarbarensis n. sp., P. pseudomunda n. sp., P. thelmacrowae n. sp. New synonymy: Boreotrophon kamchatkanus Dall, 1902 (+ Trophonopsis nanus Ergorov, 1994); Paciocinebrina atropurpurea (Carpenter, 1865) (+ Tritonalia interfossa var. clathrata Dall, 1919, Ocinebra rubra Baker, 1891, Tritonalia tracheia Dall, 1919); P. barbarensis (Gabb, 1865) (+ Tritonalia interfossa var. beta Dall, 1919, Ocenebra keenae Bormann, 1946); P. circumtexta (Stearns, 1871) (+ Ocinebra circumtexta var. aurantia Stearns, 1895, Tritonalia circumtexta var. citrica Dall, 1919, Tritonalia lurida var. rotunda Dall, 1919); P. foveolata (Hinds, 1844) (+Tritonalia epiphanea Dall, 1919, Tritonalia fusconotata Dall, 1919); P. gracillima (Stearns, 1871) (+ Tritonalia gracillima var. obesa Dall, 1919, Ocinebra stearnsi Hemphill, 1911); P. interfossa (Carpenter, 1864) (+ Tritonalia interfossa alpha Dall, 1921); P. lurida (Middendorff, 1848) (+ Vitularia aspera Baird, 1863), P. sclera (Dall, 1919) (+ Coralliophila (Pseudomurex) kincaidi Dall, 1919). Generic assignments are changed for the following taxa: Boreotrophon kamchatkanus Dall, 1902; Warenia elegantula (Dall, 1907); Scabrotrophon stuarti (E.A. Smith, 1880); Paciocinebrina atropurpurea (Carpenter, 1865), P. barbarensis (Gabb, 1865), P. circumtexta (Stearns, 1871), P. crispatissima (Berry, 1953), P. foveolata (Hinds, 1844), P. fraseri (Oldroyd, 1920), P. gracillima (Stearns, 1871), P. grippi (Dall, 1911), P. interfossa (Carpenter, 1864), P. lurida (Middendorff, 1848), P. minor (Dall, 1919), P. munda (Carpenter, 1864), P. seftoni (Chace, 1958), P. sclera (Dall, 1919). Boreotrophon alborostratus Taki, 1938, is reinstated. Abyssotrophon Egorov, 1993 and Nodulotrophon Habe & Ito, 1965 are here assigned to Pagodulinae Barco et al., 2012, based on radula morphology

Astro-WISE: Chaining to the Universe

The recent explosion of recorded digital data and its processed derivatives threatens to overwhelm researchers when analysing their experimental data or when looking up data items in archives and file systems. While current hardware developments allow to acquire, process and store 100s of terabytes of data at the cost of a modern sports car, the software systems to handle these data are lagging behind. This general problem is recognized and addressed by various scientific communities, e.g., DATAGRID/EGEE federates compute and storage power over the high-energy physical community, while the astronomical community is building an Internet geared Virtual Observatory, connecting archival data. These large projects either focus on a specific distribution aspect or aim to connect many sub-communities and have a relatively long trajectory for setting standards and a common layer. Here, we report "first light" of a very different solution to the problem initiated by a smaller astronomical IT community. It provides the abstract "scientific information layer" which integrates distributed scientific analysis with distributed processing and federated archiving and publishing. By designing new abstractions and mixing in old ones, a Science Information System with fully scalable cornerstones has been achieved, transforming data systems into knowledge systems. This break-through is facilitated by the full end-to-end linking of all dependent data items, which allows full backward chaining from the observer/researcher to the experiment. Key is the notion that information is intrinsic in nature and thus is the data acquired by a scientific experiment. The new abstraction is that software systems guide the user to that intrinsic information by forcing full backward and forward chaining in the data modelling.Comment: To be published in ADASS XVI ASP Conference Series, 2006, R. Shaw, F. Hill and D. Bell, ed

Elimination of adsorptive behaviour of biomolecules at the glass-solution interface in fluorescence correlation spectroscopy

We study adsorptive behaviour of biomolecules at the glass-solution interface in fluorescence correlation spectroscopy (FCS), and propose a negatively charged coating to eliminate the adsorption of molecules. In this article, we demonstrate confocal microscopic measurements on Cy3.5-90-mer-ssDNA and Cy3.5-90-bp-dsDNA in different solutions, and use two polymers – poly (acrylic acid, sodium salt) and poly (sodium 4-styrenesulfonate) to produce the negatively charged coating on glass coverslips. This technology enables more stable FCS measurements in extremely low concentration samples and reveals that the adsorptive behaviour of biomolecules is responsible for sudden disappearance of many iomolecules in low concentration solutions

Possible contribution of olefins and heteroatoms to the Unidentified Infrared Bands

The current assignments of the 11.3 feature are shown to be incompatible with observations. An unbiased survey of correlation charts suggests that the olefinic group R2=CH2 is a good alternative candidate. For the 12.7 feature, the best fits are provided by nitrites, R-O-N=O, and amines, R-N=H2. Sulfones, SO2, exhibit strong features near 7.7 and 8.6 microns, which may contribute to the UIBs. These additional functional groups are likely to be attached to the main hydrocarbon dust skeleton previously hypothesized in the coal/kerogen model. They provide further leeway in modelling the large variety of relative band intensities observed in the sky.Comment: 5 pages, 1 figure, accepted by A and A Letter

Immunological and Clinical Effects of Vaccines Targeting p53-Overexpressing Malignancies

Approximately 50% of human malignancies carry p53 mutations, which makes it a potential antigenic target for cancer immunotherapy. Adoptive transfer with p53-specific cytotoxic T-lymphocytes (CTL) and CD4+ T-helper cells eradicates p53-overexpressing tumors in mice. Furthermore, p53 antibodies and p53-specific CTLs can be detected in cancer patients, indicating that p53 is immunogenic. Based on these results, clinical trials were initiated. In this paper, we review immunological and clinical responses observed in cancer patients vaccinated with p53 targeting vaccines. In most trials, p53-specific vaccine-induced immunological responses were observed. Unfortunately, no clinical responses with significant reduction of tumor-burden have occurred. We will elaborate on possible explanations for this lack of clinical effectiveness. In the second part of this paper, we summarize several immunopotentiating combination strategies suitable for clinical use. In our opinion, future p53-vaccine studies should focus on addition of these immunopotentiating regimens to achieve clinically effective therapeutic vaccination strategies for cancer patients