Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions.

BackgroundN-terminal domains of BVU_4064 and BF1687 proteins from Bacteroides vulgatus and Bacteroides fragilis respectively are members of the Pfam family PF12985 (DUF3869). Proteins containing a domain from this family can be found in most Bacteroides species and, in large numbers, in all human gut microbiome samples. Both BVU_4064 and BF1687 proteins have a consensus lipobox motif implying they are anchored to the membrane, but their functions are otherwise unknown. The C-terminal half of BVU_4064 is assigned to protein family PF12986 (DUF3870); the equivalent part of BF1687 was unclassified.ResultsCrystal structures of both BVU_4064 and BF1687 proteins, solved at the JCSG center, show strikingly similar three-dimensional structures. The main difference between the two is that the two domains in the BVU_4064 protein are connected by a short linker, as opposed to a longer insertion made of 4 helices placed linearly along with a strand that is added to the C-terminal domain in the BF1687 protein. The N-terminal domain in both proteins, corresponding to the PF12985 (DUF3869) domain is a β-sandwich with pre-albumin-like fold, found in many proteins belonging to the Transthyretin clan of Pfam. The structures of C-terminal domains of both proteins, corresponding to the PF12986 (DUF3870) domain in BVU_4064 protein and an unclassified domain in the BF1687 protein, show significant structural similarity to bacterial pore-forming toxins. A helix in this domain is in an analogous position to a loop connecting the second and third strands in the toxin structures, where this loop is implicated to play a role in the toxin insertion into the host cell membrane. The same helix also points to the groove between the N- and C-terminal domains that are loosely held together by hydrophobic and hydrogen bond interactions. The presence of several conserved residues in this region together with these structural determinants could make it a functionally important region in these proteins.ConclusionsStructural analysis of BVU_4064 and BF1687 points to possible roles in mediating multiple interactions on the cell-surface/extracellular matrix. In particular the N-terminal domain could be involved in adhesive interactions, the C-terminal domain and the inter-domain groove in lipid or carbohydrate interactions

Ruprecht 147: a paradigm of dissolving star cluster

We employed recent Gaia/DR2 data to investigate the dynamical status of the nearby (300 pc), old (2.5 Gyr) open cluster Ruprecht~147. We found prominent leading and trailing tails of stars along the cluster orbit, which demonstrates that Ruprecht~147 is losing stars at fast pace. Star counts indicate the cluster has a core radius of 33.3 arcmin, and a tidal radius of 137.5 arcmin. The cluster also possesses an extended corona, which cannot be reproduced by a simple King model. We computed the present-day cluster mass using its luminosity and mass function, and derived an estimate of 234$\pm$52 $M_{\odot}$. We also estimated the cluster original mass using available recipes extracted from N-body simulations obtaining a mass at birth of 50000$\pm$6500 $M_{\odot}$. Therefore dynamical mass loss, mostly caused by tidal interaction with the Milky Way, reduced the cluster mass by about 99\%. We then conclude that Ruprecht~147 is rapidly dissolving into the general Galactic disc.Comment: 13 pages, 10 figure, in press in the Astronomical Journa

High temperature reactive ion etching of iridium thin films with aluminum mask in CF4/O2/Ar plasma

Reactive ion etching (RIE) technology for iridium with CF4/O2/Ar gas mixtures and aluminum mask at high temperatures up to 350 °C was developed. The influence of various process parameters such as gas mixing ratio and substrate temperature on the etch rate was studied in order to find optimal process conditions. The surface of the samples after etching was found to be clean under SEM inspection. It was also shown that the etch rate of iridium could be enhanced at higher process temperature and, at the same time, very high etching selectivity between aluminum etching mask and iridium could be achieved

Optogenetic elevation of endogenous glucocorticoid level in larval zebrafish

The stress response is a suite of physiological and behavioral processes that help to maintain or reestablish homeostasis. Central to the stress response is the hypothalamic-pituitary-adrenal (HPA) axis, as it releases crucial hormones in response to stress. Glucocorticoids (GCs) are the final effector hormones of the HPA axis, and exert a variety of actions under both basal and stress conditions. Despite their far-reaching importance for health, specific GC effects have been difficult to pin-down due to a lack of methods for selectively manipulating endogenous GC levels. Hence, in order to study stress-induced GC effects, we developed a novel optogenetic approach to selectively manipulate the rise of GCs triggered by stress. Using this approach, we could induce both transient hypercortisolic states and persistent forms of hypercortisolaemia in freely behaving larval zebrafish. Our results also established that transient hypercortisolism leads to enhanced locomotion shortly after stressor exposure. Altogether, we present a highly specific method for manipulating the gain of the stress axis with high temporal accuracy, altering endocrine and behavioral responses to stress as well as basal GC levels. Our study offers a powerful tool for the analysis of rapid (non-genomic) and delayed (genomic) GC effects on brain function and behavior, feedbacks within the stress axis and developmental programming by GCs

Detection and sizing of extended partial blockages in pipelines by means of a stochastic successive linear estimator

Effective water system management depends upon knowledge of the current state of a water pipeline system network. For example, in many cases, partial blockages in a water pipeline system are a source of inefficiencies, and result in an increase of pumping costs. These anomalies must be detected and corrected as early as possible. In this study, an algorithm is developed for detecting blockages by means of pressure transient measurements and estimating the diameter distribution resulting from their formation. The algorithm is a stochastic successive linear estimator that provides statistically the best unbiased estimate of diameter distribution due to partial blockages and quantifies the uncertainty associated with these estimates. We first present the theoretical formulation of the algorithm and then test it with a numerical case study

Properties of entangled photon pairs generated in one-dimensional nonlinear photonic-band-gap structures

We have developed a rigorous quantum model of spontaneous parametric down-conversion in a nonlinear 1D photonic-band-gap structure based upon expansion of the field into monochromatic plane waves. The model provides a two-photon amplitude of a created photon pair. The spectra of the signal and idler fields, their intensity profiles in the time domain, as well as the coincidence-count interference pattern in a Hong-Ou-Mandel interferometer are determined both for cw and pulsed pumping regimes in terms of the two-photon amplitude. A broad range of parameters characterizing the emitted down-converted fields can be used. As an example, a structure composed of 49 layers of GaN/AlN is analyzed as a suitable source of photon pairs having high efficiency.Comment: 14 pages, 23 figure

Theory of Slow Light Enhanced Four-Wave Mixing in Photonic Crystal Waveguides

The equations for Four-Wave-Mixing in a Photonic Crystal waveguide are derived accurately. The dispersive nature of slow-light enhancement, the impact of Bloch mode reshaping in the nonlinear overlap integrals and the tensor nature of the third order polarization are therefore taken into account. Numerical calculations reveal substantial differences with simpler models, which increase with decreasing group velocity. We predict that the gain for a 1.3 mm long, unoptimized GaInP waveguide will exceed 10 dB if the pump power exceeds 1 W.Comment: 6 pages, 4 figures; submitted to Optics Expres

Circulating Levels of Cytokines and Their Endogenous Modulators in Patients With Mild to Severe Congestive Heart Failure Due to Coronary Artery Disease or Hypertension

AbstractObjectives. This study sought to determine the circulating levels of cytokines and their respective endogenous modulators in patients with congestive heart failure of variable severity.Background. Activation of immune elements localized in the heart or periphery, or both, may promote release of cytokines in patients with congestive heart failure. Although an increased circulating level of tumor necrosis factor-alpha (TNF-alpha) and its soluble receptor type II (sTNF-RII) is well documented, less is known about other cytokines (i.e., interleukin-1-beta [IL-1-beta], interleukin-6 [IL-6] and interleukin-2 [IL-2] and their soluble receptor/receptor antagonists).Methods. Circulating levels of TNF-alpha and sTNF-RII, IL-1-beta, IL-1 receptor antagonist (IL-1-Ra), IL-6, IL-6 soluble receptor (IL-6-sR), IL-2 and IL-2 soluble receptor-alpha were measured using enzyme-linked immunosorbent assay kits (Quantikine, R&D Systems) in 80 patients with congestive heart failure due to coronary artery disease or hypertension. The severity of their symptoms, which ranged from New York Heart Association functional class I to IV, was confirmed by measurement of peak oxygen consumption.Results. The percentage of patients with elevated levels of cytokines and their corresponding soluble receptor/receptor antagonists significantly increased with functional class. For TNF-alpha and IL-1-beta, the percentage of patients with elevated levels of soluble receptor/receptor antagonists was higher than that of patients with elevated levels of the cytokine itself. For IL-6, the percentage of patients with elevated levels of IL-6-sR tended to be lower than that of patients with elevated levels of IL-6. All but two patients had undetectable levels of IL-2, and all but seven had levels of IL-2-sR within a normal range.Conclusions. In patients with congestive heart failure, circulating levels of cytokines increased with the severity of symptoms. In these patients, circulating levels of sTNF-RII and IL-1-Ra are more sensitive markers of immune activation than are circulating levels of TNF-alpha and IL-1-beta, respectively. Levels of IL-2 and IL-2-sR are not elevated when congestive heart failure is due to coronary artery disease or hypertension

Fiber-bundle illumination: realizing high-degree time-multiplexed multifocal multiphoton microscopy with simplicity

High-degree time-multiplexed multifocal multiphoton microscopy was expected to provide a facile path to scanningless optical-sectioning and the fast imaging of dynamic three-dimensional biological systems. However, physical constraints on typical time multiplexing devices, arising from diffraction in the free-space propagation of light waves, lead to significant manufacturing difficulties and have prevented the experimental realization of high-degree time multiplexing. To resolve this issue, we have developed a novel method using optical fiber bundles of various lengths to confine the diffraction of propagating light waves and to create a time multiplexing effect. Through this method, we experimentally demonstrate the highest degree of time multiplexing ever achieved in multifocal multiphoton microscopy (~50 times larger than conventional approaches), and hence the potential of using simply-manufactured devices for scanningless optical sectioning of biological systems