Diatoms from surface sediments of Amurskiy Bay,Sea of Japan

The results of a study of diatoms from surface sediments (0–1 cm) of Amurskiy Bay are presented for the first time. The specific composition (221 species and intraspecific taxa) and ecological structure of the diatom flora were determined. The diatom species composition of phytoplankton, periphyton, and surface sediments is compared.     

Selective activation of adrenergic beta1 receptors induces heme oxygenase 1 production in RAW264.7 cells

We hypothesized that catecholamines through beta-adrenoceptor might modulate macrophage function. We showed that isoproterenol concentration-dependently induced HO-1 production through beta(1)-but not beta(2)-adrenoceptor. Production was increased by forskolin and inhibited by pretreatment with the PKA inhibitor, H-89. Furthermore, induction of HO-1 by isoproterenol effectively protected RAW264.7 cells from effects of glucose oxidase treatment, which was abrogated either by HO-1 inhibitor, ZnPP IX and beta-adenoceptor antagonist, propranolol. Thus, stimulation of HO-1 production through beta(1)-adenoceptors, and via the PKA pathways by isoproterenol, can enable RAW264.7 cells to resist oxidant stress, suggesting that catecholamine hormones may be necessary, at least, to maximize defending role of macrophages.     

Minimal genome encoding proteins with constrained amino acid repertoire

Minimal bacterial gene set comprises the genetic elements needed for survival of engineered bacterium on a rich medium. This set is estimated to include 300–350 protein-coding genes. One way of simplifying an organism with such a minimal genome even further is to constrain the amino acid content of its proteins. In this study, comparative genomics approaches and the results of gene knockout experiments were used to extrapolate the minimal gene set of mollicutes, and bioinformatics combined with the knowledge-based analysis of the structure-function relationships in these proteins and their orthologs, paralogs and analogs was applied to examine the challenges of completely replacing the rarest residue, cysteine. Among several known functions of cysteine residues, their roles in the active centers of the enzymes responsible for deoxyribonucleoside synthesis and transfer RNA modification appear to be crucial, as no alternative chemistry is known for these reactions. Thus, drastic reduction of the content of the rarest amino acid in a minimal proteome appears to be possible, but its complete elimination is challenging.     

Numerical Evaluation and Comparison of Kalantari's Zero Bounds for Complex Polynomials

In this paper, we investigate the performance of zero bounds due to Kalantari and Dehmer by using special classes of polynomials. Our findings are evidenced by numerical as well as analytical results.     

Aging‐related anatomical and biochemical changes in lymphatic collectors impair lymph transport,fluid homeostasis,and pathogen clearance

The role of lymphatic vessels is to transport fluid, soluble molecules, and immune cells to the draining lymph nodes. Here, we analyze how the aging process affects the functionality of the lymphatic collectors and the dynamics of lymph flow. Ultrastructural, biochemical, and proteomic analysis indicates a loss of matrix proteins, and smooth muscle cells in aged collectors resulting in a decrease in contraction frequency, systolic lymph flow velocity, and pumping activity, as measured in vivo in lymphatic collectors. Functionally, this impairment also translated into a reduced ability for in vivo bacterial transport as determined by time‐lapse microscopy. Ultrastructural and proteomic analysis also indicates a decrease in the thickness of the endothelial cell glycocalyx and loss of gap junction proteins in aged lymph collectors. Redox proteomic analysis mapped an aging‐related increase in the glycation and carboxylation of lymphatic's endothelial cell and matrix proteins. Functionally, these modifications translate into apparent hyperpermeability of the lymphatics with pathogen escaping from the collectors into the surrounding tissue and a decreased ability to control tissue fluid homeostasis. Altogether, our data provide a mechanistic analysis of how the anatomical and biochemical changes, occurring in aged lymphatic vessels, compromise lymph flow, tissue fluid homeostasis, and pathogen transport.     

Upscaling methods used in ex ante life cycle assessment of emerging technologies: a review

The International Journal of Life Cycle Assessment - The objective of this paper was to provide LCA practitioners with recommendations and a framework for upscaling emerging technologies by...     

The quality of zero bounds for complex polynomials

In this paper, we evaluate the quality of zero bounds on the moduli of univariate complex polynomials. We select classical and recently developed bounds and evaluate their quality by using several sets of complex polynomials. As the quality of priori bounds has not been investigated thoroughly, our results can be useful to find optimal bounds to locate the zeros of complex polynomials.     

FLIM-FRET analyzer: open source software for automation of lifetime-based FRET analysis

Background

Despite the broad use of FRET techniques, available methods for analyzing protein-protein interaction are subject to high labor and lack of systematic analysis. We propose an open source software allowing the quantitative analysis of fluorescence lifetime imaging (FLIM) while integrating the steady-state fluorescence intensity information for protein-protein interaction studies.

Findings

Our developed open source software is dedicated to fluorescence lifetime imaging microscopy (FLIM) data obtained from Becker & Hickl SPC-830. FLIM-FRET analyzer includes: a user-friendly interface enabling automated intensity-based segmentation into single cells, time-resolved fluorescence data fitting to lifetime value for each segmented objects, batch capability, and data representation with donor lifetime versus acceptor/donor intensity quantification as a measure of protein-protein interactions.

Conclusions

The FLIM-FRET analyzer software is a flexible application for lifetime-based FRET analysis. The application, the C#. NET source code, and detailed documentation are freely available at the following URL: http://FLIM-analyzer.ip-korea.org.

     

Late holocene environmental changes in the Southwestern Chukchi Sea inferred from diatom analysis

The environmental changes in the southern part of the Chukchi Sea over the last 2300 years (two warmings during the ~262 BC–630 AD and ~630–1300 periods AD and 1 cooling ~1300–1840 AD) were inferred from changes in the content of diatoms in sediments (per gram), the ratio of dominant species, and the ecological structure of diatom assemblages. The sediment age was determined based on the recent ²¹⁰Pb sedimentation rates at the sampling point (0.43 mm/yr) and radiocarbon dating of mollusk shells. The environmental changes in the southern Chukchi Sea that were inferred from the diatom analysis correlate with global climate changes, viz., the warming events of the early (Roman) and the middle (Medieval) Subatlantic and the cooling of the late (Little Ice Age) Subatlantic.