Improving functional annotation for industrial microbes: a case study with Pichia pastoris.

The research communities studying microbial model organisms, such as Escherichia coli or Saccharomyces cerevisiae, are well served by model organism databases that have extensive functional annotation. However, this is not true of many industrial microbes that are used widely in biotechnology. In this Opinion piece, we use Pichia (Komagataella) pastoris to illustrate the limitations of the available annotation. We consider the resources that can be implemented in the short term both to improve Gene Ontology (GO) annotation coverage based on annotation transfer, and to establish curation pipelines for the literature corpus of this organism.We gratefully acknowledge funding from the Wellcome Trust (PomBase and Canto; WT090548MA to SGO), and the EU 7th Framework Programme (BIOLEDGE Contract No: 289126 to SGO).This is the published version distributed under a Creative Commons Attribution License 2.0, which can also be found on the publisher's website at: http://www.sciencedirect.com/science/article/pii/S0167779914001061

Robust Upward Dispersion of the Neutron Spin Resonance in the Heavy Fermion Superconductor Ce1−x_{1-x}Ybx_{x}CoIn5_5

The neutron spin resonance is a collective magnetic excitation that appears in copper oxide, iron pnictide, and heavy fermion unconventional superconductors. Although the resonance is commonly associated with a spin-exciton due to the $d$($s^{\pm}$)-wave symmetry of the superconducting order parameter, it has also been proposed to be a magnon-like excitation appearing in the superconducting state. Here we use inelastic neutron scattering to demonstrate that the resonance in the heavy fermion superconductor Ce$_{1-x}$Yb$_{x}$CoIn$_5$ with $x=0,0.05,0.3$ has a ring-like upward dispersion that is robust against Yb-doping. By comparing our experimental data with random phase approximation calculation using the electronic structure and the momentum dependence of the $d_{x^2-y^2}$-wave superconducting gap determined from scanning tunneling microscopy for CeCoIn$_5$, we conclude the robust upward dispersing resonance mode in Ce$_{1-x}$Yb$_{x}$CoIn$_5$ is inconsistent with the downward dispersion predicted within the spin-exciton scenario.Comment: Supplementary Information available upon reques

Negative Regulation of Hepatitis C Virus Specific Immunity Is Highly Heterogeneous and Modulated by Pegylated Interferon-Alpha/Ribavirin Therapy

Specific inhibitory mechanisms suppress the T-cell response against the hepatitis C virus (HCV) in chronically infected patients. However, the relative importance of suppression by IL-10, TGF-β and regulatory T-cells and the impact of pegylated interferon-alpha and ribavirin (PegIFN-α/ribavirin) therapy on these inhibitory mechanisms are still unclear. We revealed that coregulation of the HCV-specific T-cell responses in blood of 43 chronic HCV patients showed a highly heterogeneous pattern before, during and after PegIFN-α/ribavirin. Prior to treatment, IL-10 mediated suppression of HCV-specific IFN-γ production in therapy-naive chronic HCV patients was associated with higher HCV-RNA loads, which suggests that protective antiviral immunity is controlled by IL-10. In addition, as a consequence of PegIFN-α/ribavirin therapy, negative regulation of especially HCV-specific IFN-γ production by TGF-β and IL-10 changed dramatically. Our findings emphasize the importance of negative regulation for the dysfunctional HCV-specific immunity, which should be considered in the design of future immunomodulatory therapies

Analytical Solution of a Stochastic Content Based Network Model

We define and completely solve a content-based directed network whose nodes consist of random words and an adjacency rule involving perfect or approximate matches, for an alphabet with an arbitrary number of letters. The analytic expression for the out-degree distribution shows a crossover from a leading power law behavior to a log-periodic regime bounded by a different power law decay. The leading exponents in the two regions have a weak dependence on the mean word length, and an even weaker dependence on the alphabet size. The in-degree distribution, on the other hand, is much narrower and does not show scaling behavior. The results might be of interest for understanding the emergence of genomic interaction networks, which rely, to a large extent, on mechanisms based on sequence matching, and exhibit similar global features to those found here.Comment: 13 pages, 5 figures. Rewrote conclusions regarding the relevance to gene regulation networks, fixed minor errors and replaced fig. 4. Main body of paper (model and calculations) remains unchanged. Submitted for publicatio

Biosorption of Cr(VI) by free and immobilized Pediastrum boryanum biomass: equilibrium, kinetic, and thermodynamic studies

15th International Symposium on Toxicity Assessment (ISTA) -- JUL 03-08, 2011 -- City Univ Hong Kong, Hong Kong, PEOPLES R CHINAWOS: 000306790200053PubMed ID: 22374187The biosorption of Cr(VI) from aqueous solution has been studied using free and immobilized Pediastrum boryanum cells in a batch system. The algal cells were immobilized in alginate and alginate-gelatin beads via entrapment, and their algal cell free counterparts were used as control systems during biosorption studies of Cr(VI). The changes in the functional groups of the biosorbents formulations were confirmed by Fourier transform infrared spectra. The effect of pH, equilibrium time, initial concentration of metal ions, and temperature on the biosorption of Cr(VI) ion was investigated. The maximum Cr(VI) biosorption capacities were found to be 17.3, 6.73, 14.0, 23.8, and 29.6 mg/g for the free algal cells, and alginate, alginate-gelatin, alginate-cells, and alginate-gelatin-cells at pH 2.0, which are corresponding to an initial Cr(VI) concentration of 400 mg/L. The biosorption of Cr(VI) on all the tested biosorbents (P. boryanum cells, alginate, alginate-gelatin, and alginate-cells, alginate-gelatin-cells) followed Langmuir adsorption isotherm model. The thermodynamic studies indicated that the biosorption process was spontaneous and endothermic in nature under studied conditions. For all the tested biosorbents, biosorption kinetic was best described by the pseudo-second-order model.PROCORE-France/Hong Kong Joint Res Scheme, Croucher Fdn, KC Wong Educ Fd

Four-dimensional hierarchical structure of love constructs in a cross-cultural perspective

This article reports new methodology for cross-cultural exploration of psychometric properties of a four-dimensional hierarchical love scale. We collected data from 2831 participants from nine regional locations from six countries and assessed their responses to the love scale as well as several other love feelings. We applied a new methodological approach using recently advanced statistical methods to the comparison of forty love attitudes underscoring four distinct latent attitudes associated with love to another person in romantic relationships across these samples. The results demonstrate the importance of measurement invariance tests for cross-cultural comparison of scores on love scales. To properly assess measurement invariance, we suggest five statistical procedures, which we investigated in this study: (1) making corrections for acquiescence and extreme response biases; (2) taking into consideration cultural uniqueness in how participants respond to the measures, which may contribute to poor model fit; (3) accounting for such cultural uniqueness to make cross-cultural comparisons more valid; (4) removing items, which substantially contribute to poor model fit; and (5) shortening the subscales when scoring and analyzing the data. The results of the studies propose two shortened versions (33 and 30 items) of the love scale as two cross-culturally valid and invariant alternatives to the original 40-item scale

Single Cell Analysis of Blood Mononuclear Cells Stimulated Through Either LPS or Anti-CD3 and Anti-CD28.

Immune cell activation assays have been widely used for immune monitoring and for understanding disease mechanisms. However, these assays are typically limited in scope. A holistic study of circulating immune cell responses to different activators is lacking. Here we developed a cost-effective high-throughput multiplexed single-cell RNA-seq combined with epitope tagging (CITE-seq) to determine how classic activators of T cells (anti-CD3 coupled with anti-CD28) or monocytes (LPS) alter the cell composition and transcriptional profiles of peripheral blood mononuclear cells (PBMCs) from healthy human donors. Anti-CD3/CD28 treatment activated all classes of lymphocytes either directly (T cells) or indirectly (B and NK cells) but reduced monocyte numbers. Activated T and NK cells expressed senescence and effector molecules, whereas activated B cells transcriptionally resembled autoimmune disease- or age-associated B cells (e.g., CD11c, T-bet). In contrast, LPS specifically targeted monocytes and induced two main states: early activation characterized by the expression of chemoattractants and a later pro-inflammatory state characterized by expression of effector molecules. These data provide a foundation for future immune activation studies with single cell technologies (https://czi-pbmc-cite-seq.jax.org/)

Phase transitions in contagion processes mediated by recurrent mobility patterns

Human mobility and activity patterns mediate contagion on many levels, including the spatial spread of infectious diseases, diffusion of rumors, and emergence of consensus. These patterns however are often dominated by specific locations and recurrent flows and poorly modeled by the random diffusive dynamics generally used to study them. Here we develop a theoretical framework to analyze contagion within a network of locations where individuals recall their geographic origins. We find a phase transition between a regime in which the contagion affects a large fraction of the system and one in which only a small fraction is affected. This transition cannot be uncovered by continuous deterministic models due to the stochastic features of the contagion process and defines an invasion threshold that depends on mobility parameters, providing guidance for controlling contagion spread by constraining mobility processes. We recover the threshold behavior by analyzing diffusion processes mediated by real human commuting data.Comment: 20 pages of Main Text including 4 figures, 7 pages of Supplementary Information; Nature Physics (2011

Quadrupolar Susceptibility and Magnetic Phase Diagram of PrNi2_2Cd20_{20} with Non-Kramers Doublet Ground State

In this study, ultrasonic measurements were performed on a single crystal of cubic PrNi$_2$Cd$_{20}$, down to a temperature of 0.02 K, to investigate the crystalline electric field ground state and search for possible phase transitions at low temperatures. The elastic constant $(C_{11}-C_{12})/2$, which is related to the $\Gamma_3$-symmetry quadrupolar response, exhibits the Curie-type softening at temperatures below $\sim$30 K, which indicates that the present system has a $\Gamma_3$ non-Kramers doublet ground state. A leveling-off of the elastic response appears below $\sim$0.1 K toward the lowest temperatures, which implies the presence of level splitting owing to a long-range order in a finite-volume fraction associated with $\Gamma_3$-symmetry multipoles. A magnetic field-temperature phase diagram of the present compound is constructed up to 28 T for $H \parallel$ [110]. A clear acoustic de Haas-van Alphen signal and a possible magnetic-field-induced phase transition at $H \sim$26 T are also detected by high-magnetic-field measurements.Comment: 13 pages, 7 figure