PHYCOBILISOMES AND ISOLATED PHYCOBILIPROTEINS. EFFECT OF GLUTARDIALDEHYDE AND BENZOQUINONE ON FLUORESCENCE

The fluorescence of the biliproteins C-phycocyanin from Spirulina platensis, B-phycoerythrin from Porphyridium cruentum and of isolated whole P. cruentum phycobilisomes is quenched in the presence of glutardialdehyde (GA) or benzoquinone (BQ). The kinetics of fluorescence decrease thus induced is biphasic. If GA is used as a quencher, the fluorescence can be recovered at 77 K. Contrary to the GA-effect, only a minor recovery takes place with BQ at 77K, thus demonstrating a different mechanism of action of GA and BQ on biliprotein

FÖRSTER TRANSFER CALCULATIONS BASED ON CRYSTAL STRUCTURE DATA FROM Agmenellum quadruplicatum C-PHYCOCYANIN

Excitation energy transfer in C-phycocyanin is modeled using the Forster inductive resonance mechanism. Detailed calculations are carried out using coordinates and orientations of the chromophores derived from X-ray crystallographic studies of C-phycocyanin from two different species (Schirmer et al, J. Mol. Biol. 184, 257–277 (1985) and ibid., 188, 651-677 (1986)). Spectral overlap integrals are estimated from absorption and fluorescence spectra of C-phycocyanin of Mastigocladus laminosus and its separated subunits. Calculations are carried out for the β-subunit, αβ-monomer, (αβ)3-trimer and (αβ)0-hexamer species with the following chromophore assignments: β155 = 's’(sensitizer), β84 =‘f (fluorescer) and α84 =‘m’(intermediate):]:. The calculations show that excitation transfer relaxation occurs to 3=98% within 200 ps in nearly every case; however, the rates increase as much as 10-fold for the higher aggregates. Comparison with experimental data on fluorescence decay and depolarization kinetics from the literature shows qualitative agreement with these calculations. We conclude that Forster transfer is sufficient to account for all of the observed fluorescence properties of C-phycocyanin in aggregation states up to the hexamer and in the absence of linker polypeptides

Recurrent Hypoglycaemia in a Patient with Metastatic Pancreatic Carcinoma

The patient's recurrent hypoglycaemia was found to be due to non-islet cell tumour hypoglycaemia

Photoproduction of Long-Lived Holes and Electronic Processes in Intrinsic Electric Fields Seen through Photoinduced Absorption and Dichroism in Ca_3Ga_{2-x}Mn_xGe_3O_{12} Garnets

Long-lived photoinduced absorption and dichroism in the Ca_3Ga_{2-x}Mn_xGe_3O_{12} garnets with x < 0.06 were examined versus temperature and pumping intensity. Unusual features of the kinetics of photoinduced phenomena are indicative of the underlying electronic processes. The comparison with the case of Ca_3Mn_2Ge_3O_{12}, explored earlier by the authors, permits one to finally establish the main common mechanisms of photoinduced absorption and dichroism caused by random electric fields of photoproduced charges (hole polarons). The rate of their diffusion and relaxation through recombination is strongly influenced by the same fields, whose large statistical straggling is responsible for a broad continuous set of relaxation components (observed in the relaxation time range from 1 to about 1000 min). For Ca_3Ga_{2-x}Mn_xGe_3O_{12}, the time and temperature dependences of photoinduced absorption and dichroism bear a strong imprint of structure imperfection increasing with x.Comment: 20 pages, 10 figure

Energy densities in the strong-interaction limit of density functional theory

We discuss energy densities in the strong-interaction limit of density functional theory, deriving an exact expression within the definition (gauge) of the electrostatic potential of the exchange-correlation hole. Exact results for small atoms and small model quantum dots are compared with available approximations defined in the same gauge. The idea of a local interpolation along the adiabatic connection is discussed, comparing the energy densities of the Kohn-Sham, the physical, and the strong-interacting systems. We also use our results to analyze the local version of the Lieb-Oxford bound, widely used in the construction of approximate exchange-correlation functionals.Comment: 12 page

De-Novo Discovery of Differentially Abundant Transcription Factor Binding Sites Including Their Positional Preference

Transcription factors are a main component of gene regulation as they activate or repress gene expression by binding to specific binding sites in promoters. The de-novo discovery of transcription factor binding sites in target regions obtained by wet-lab experiments is a challenging problem in computational biology, which has not been fully solved yet. Here, we present a de-novo motif discovery tool called Dispom for finding differentially abundant transcription factor binding sites that models existing positional preferences of binding sites and adjusts the length of the motif in the learning process. Evaluating Dispom, we find that its prediction performance is superior to existing tools for de-novo motif discovery for 18 benchmark data sets with planted binding sites, and for a metazoan compendium based on experimental data from micro-array, ChIP-chip, ChIP-DSL, and DamID as well as Gene Ontology data. Finally, we apply Dispom to find binding sites differentially abundant in promoters of auxin-responsive genes extracted from Arabidopsis thaliana microarray data, and we find a motif that can be interpreted as a refined auxin responsive element predominately positioned in the 250-bp region upstream of the transcription start site. Using an independent data set of auxin-responsive genes, we find in genome-wide predictions that the refined motif is more specific for auxin-responsive genes than the canonical auxin-responsive element. In general, Dispom can be used to find differentially abundant motifs in sequences of any origin. However, the positional distribution learned by Dispom is especially beneficial if all sequences are aligned to some anchor point like the transcription start site in case of promoter sequences. We demonstrate that the combination of searching for differentially abundant motifs and inferring a position distribution from the data is beneficial for de-novo motif discovery. Hence, we make the tool freely available as a component of the open-source Java framework Jstacs and as a stand-alone application at http://www.jstacs.de/index.php/Dispom

Reconstructing the history of ocean wildlife around Ascension Island

1. In 2016, the UK government announced plans for a large-scale Marine Protected Area around Ascension Island, a UK Overseas Territory in the South Atlantic. 2. To improve baselines for marine life to support ambitious conservation and assess change over time, archives were searched for historical accounts of wildlife from Ascension's discovery in 1501 to the present. For more recent changes, 139 interviews with past and present inhabitants were conducted. 3. Ascension's marine life has, from first discovery to the present, been consistently remarked upon for its exceptional abundance. Historical sources indicate declines in seabird and turtle populations from human exploitation and introduction of rats and cats. They are recovering with good management, although still below pre-settlement abundance. 4. Interviews with residents indicate more recent changes, notably declines in catch per unit of fishing effort at popular shore angling sites, a decline in yellowfin tuna (Thunnus albacares) and increase in Galapagos sharks (Carcharhinus galapagensis). 5. What is very notable, however, based on the interviews, was that there was no temporal signal suggestive of recent systemic decline, in marked contrast to many parts of the world where recent wildlife declines have been pervasive and steep. Ascension represents a remarkable and immensely important centre of abundance in a sea of depletion and change, warranting full protection for all the island's waters