Culture conditions affect the chemical composition of the exopolysaccharide synthesized by the fungus Aureobasidium pullulans

Aims:  To identify if culture conditions affect the chemical composition of exopolysaccharide (EPS) produced by Aureobasidium pullulans .
Methods and Results:  In batch airlift and continuously stirred tank (CSTR) reactors the EPS produced with low (0·13 g l⁻¹ N) initial NaNO₃ or (NH₄)₂SO₄ levels contained pullulan, with maltotriose as its major component, similar to that synthesized in the airlift reactor with high (0·78 g l⁻¹ N) initial NaNO₃ levels. EPS produced by CSTR grown cultures with high (NH₄)₂SO₄ levels contained little pullulan, possibly because of a population shift from unicells to mycelium. This chemical difference may explain why total EPS yields did not fall as they did with cultures grown under identical conditions with high NaNO₃ levels, where the pullulan component of the EPS disappeared. EPS synthesized in N-limiting chemostat cultures of A. pullulans changed little with growth rate or N source, being predominantly pullulan consisting of maltotriose units.
Conclusions:  While the EPS chemical composition changed little under N-limiting conditions, high initial medium N levels determined maltotriose content and/or pullulan content possibly by dictating culture morphology.
Significance and Impact of the Study:  These results emphasize the requirement of all studies to determine EPS chemical composition when examining the influence of culture conditions on EPS yields.     

Herpes Simplex Virus Type 1 Regulatory Protein ICP0 Aids Infection in Cells with a Preinduced Interferon Response but Does Not Impede Interferon-Induced Gene Induction

Several independent lines of evidence indicate that interferon-mediated innate responses are involved in controlling herpes simplex virus type 1 (HSV-1) infection and that the viral immediate-early regulatory protein ICP0 augments HSV-1 replication in interferon-treated cells. However, this is a complex situation in which the experimental outcome is determined by the choice of multiplicity of infection and cell type and by whether cultured cells or animal models are used. It is now known that neither STAT1 nor interferon regulatory factor 3 (IRF-3) play essential roles in the replication defect of ICP0-null mutant HSV-1 in cultured cells. This study set out to investigate the specific role of ICP0 in HSV-1 resistance to the interferon defense. We have used a cell line in which ICP0 expression can be induced at levels similar to those during the early stages of a normal infection to determine whether ICP0 by itself can interfere with interferon or IRF-3-dependent signaling and whether ICP0 enables the virus to circumvent the effects of interferon-stimulated genes (ISGs). We found that the presence of ICP0 was unable to compromise ISG induction by either interferon or double-stranded RNA. On the other hand, ICP0 preexpression reduced but did not eliminate the inhibitory effects of ISGs on HSV-1 infection, with the extent of the relief being highly dependent on multiplicity of infection. The results are discussed in terms of the relationships between ICP0 and intrinsic and innate antiviral resistance mechanisms.The innate immune response mediated through the interferon (IFN) pathway is an important component of antiviral defense mediated by individual cells and whole organisms (10, 28). In turn, many viruses express proteins that counteract the effects of the IFN response (28). In the case of herpes simplex virus type 1 (HSV-1), highly defective HSV-1 mutants activate expression of IFN-stimulated genes (ISGs) through a mechanism that is independent of IFN itself but dependent on IFN regulatory factor 3 (IRF-3) (2, 3, 19, 23, 26). HSV-1 mutants that do not express the immediate-early (IE) regulatory protein ICP0 are more sensitive than the wild-type (wt) virus to IFN pretreatment of cultured cells (13, 20), and ICP0-null mutant HSV-1 is much more pathogenic in mice unable to respond to IFN (12, 15). Furthermore, a number of experimental systems have presented evidence suggesting that a specific function of ICP0 is to interfere with IFN and/or IRF-3-dependent IFN responses (3, 16-18, 21). However, we have reported recently that the replication defect of ICP0-null mutant HSV-1 is not complemented in cultured cells lacking either STAT1 or IRF-3 (9), which raises the question of whether the relative sensitivity of ICP0-null mutant HSV-1 to an IFN-induced antiviral state results from the absence of a specific effect of ICP0 on IFN pathways or is, rather, an indirect consequence of the disabled virus being intrinsically less able to replicate in cells expressing ISGs (9).The investigation of these complex issues is difficult because sensitivity to IFN is highly dependent on multiplicity of infection (MOI) (9) and cell type (20). Therefore, we sought to develop a system in which the specific effects of ICP0 could be examined in the absence of HSV-1 infection and which avoids potential complications arising from the use of viral vectors or plasmid transfection technologies. In an accompanying paper, we describe the construction of a cell line that expresses ICP0 at physiological levels in an inducible manner (7). The cells allow 100% complementation of plaque formation by ICP0-null mutant HSV-1, and induction of ICP0 expression induces efficient reactivation of gene expression from quiescent HSV-1 genomes (7). We have used these cells to investigate whether, by itself, ICP0 is able to impede induction of ISGs in response to IFN (through the normal STAT1 signaling pathway) or to interfere with IRF-3-dependent activation of ISGs induced by double-stranded RNA, the archetypal pathogen-associated molecular pattern (PAMP). We found that preexpression of ICP0 had no deleterious effect on either pathway. On the other hand, preexpression of ICP0 decreased (but did not eliminate) the sensitivity of HSV-1 to an IFN-induced antiviral state. We discuss the relationship between ICP0 and intrinsic and innate cellular defenses to HSV-1 infection.     

The distribution of fitness effects among beneficial mutations in Fisher's geometric model of adaptation

Recent models of adaptation at the DNA sequence level assume that the fitness effects of new mutations show certain statistical properties. In particular, these models assume that the distribution of fitness effects among new mutations is in the domain of attraction of the so-called Gumbel-type extreme value distribution. This assumption has not, however, been justified on any biological or theoretical grounds. In this note, I study random mutation in one of the simplest models of mutation and adaptation-Fisher's geometric model. I show that random mutation in this model yields a distribution of mutational effects that belongs to the Gumbel type. I also show that the distribution of fitness effects among rare beneficial mutations in Fisher's model is asymptotically exponential. I confirm these analytic findings with exact computer simulations. These results provide some support for the use of Gumbel-type extreme value theory in studies of adaptation and point to a surprising connection between recent phenotypic- and sequence-based models of adaptation: in both, the distribution of fitness effects among rare beneficial mutations is approximately exponential.     

ACAT-1, Cav-1 and PrP expression in scrapie susceptible and resistant sheep

Scrapie is a prion disease for which no means of ante-mortem diagnosis is available. We recently found a relationship between cell susceptibility to scrapie and altered cholesterol homeostasis. In brains and in skin fibroblasts and peripheral blood mononuclear cells from healthy and scrapie-affected sheep carrying a scrapie-susceptible genotype, the levels of cholesterol esters were consistently higher than in tissues and cultures derived from animals with a scrapie-resistant genotype. Here we show that intracellular accumulation of cholesterol esters (CE) in fibroblasts derived from scrapie-susceptible sheep was accompanied by parallel alterations in the expression level of acyl-coenzymeA: cholesterol-acyltransferase (ACAT1) and caveolin-1 (Cav-1) that are involved in the pathways leading to intracellular cholesterol esterification and trafficking. Comparative analysis of cellular prion protein (PrPc) mRNA, showed an higher expression level in cells from animals carrying a susceptible genotype, with or without Scrapie. These data suggest that CE accumulation in peripheral cells, together with the altered expression of some proteins implicated in intracellular cholesterol homeostasis, might serve to identify a distinctive lipid metabolic profile associated with increased susceptibility to develop prion disease following infection.     

Using Evolutionary Conserved Modules in Gene Networks as a Strategy to Leverage High Throughput Gene Expression Queries

Background

Large-scale gene expression studies have not yielded the expected insight into genetic networks that control complex processes. These anticipated discoveries have been limited not by technology, but by a lack of effective strategies to investigate the data in a manageable and meaningful way. Previous work suggests that using a pre-determined seed-network of gene relationships to query large-scale expression datasets is an effective way to generate candidate genes for further study and network expansion or enrichment. Based on the evolutionary conservation of gene relationships, we test the hypothesis that a seed network derived from studies of retinal cell determination in the fly, Drosophila melanogaster, will be an effective way to identify novel candidate genes for their role in mouse retinal development.

Methodology/Principal Findings

Our results demonstrate that a number of gene relationships regulating retinal cell differentiation in the fly are identifiable as pairwise correlations between genes from developing mouse retina. In addition, we demonstrate that our extracted seed-network of correlated mouse genes is an effective tool for querying datasets and provides a context to generate hypotheses. Our query identified 46 genes correlated with our extracted seed-network members. Approximately 54% of these candidates had been previously linked to the developing brain and 33% had been previously linked to the developing retina. Five of six candidate genes investigated further were validated by experiments examining spatial and temporal protein expression in the developing retina.

Conclusions/Significance

We present an effective strategy for pursuing a systems biology approach that utilizes an evolutionary comparative framework between two model organisms, fly and mouse. Future implementation of this strategy will be useful to determine the extent of network conservation, not just gene conservation, between species and will facilitate the use of prior biological knowledge to develop rational systems-based hypotheses.     

Development and function of CD94-deficient natural killer cells

The CD94 transmembrane-anchored glycoprotein forms disulfide-bonded heterodimers with the NKG2A subunit to form an inhibitory receptor or with the NKG2C or NKG2E subunits to assemble a receptor complex with activating DAP12 signaling proteins. CD94 receptors expressed on human and mouse NK cells and T cells have been proposed to be important in NK cell tolerance to self, play an important role in NK cell development, and contribute to NK cell-mediated immunity to certain infections including human cytomegalovirus. We generated a gene-targeted CD94-deficient mouse to understand the role of CD94 receptors in NK cell biology. CD94-deficient NK cells develop normally and efficiently kill NK cell-susceptible targets. Lack of these CD94 receptors does not alter control of mouse cytomegalovirus, lymphocytic choriomeningitis virus, vaccinia virus, or Listeria monocytogenes. Thus, the expression of CD94 and its associated NKG2A, NKG2C, and NKG2E subunits is dispensable for NK cell development, education, and many NK cell functions.     

Substitution by Inosine at the 3��-Ultimate and Penultimate Positions of 16S rRNA Gene Universal Primers

Universal 16S rRNA gene primers (8F and 518R) bearing inosine substitutions at either the 3??-ultimate or the 3??-ultimate and penultimate base positions were exploited for the first time to study the bacterial community associated with coral polymicrobial Black Band Disease (BBD). Inosine-modified universal primer pairs display some shifting in the composition of 16S rRNA gene libraries, as well as expanding the observed diversity of a BBD bacterial community at the family/class level. Possible explanations for the observed shifts are discussed. These results thus point to the need for adopting multiple approaches in designing 16S rRNA universal primers for PCR amplification and subsequent construction of 16S rRNA gene libraries or pyrosequencing in the exploration of complex microbial communities.     

Probing conformational changes of gramicidin ion channels by single-molecule patch-clamp fluorescence microscopy

Complex conformational changes influence and regulate the dynamics of ion channels. Such conformational changes are stochastic and often inhomogeneous, which makes it extremely difficult, if not impossible, to characterize them by ensemble-averaged experiments or by single-channel recordings of the electric current that report the open-closed events but do not specifically probe the associated conformational changes. Here, we report our studies on ion channel conformational changes using a new approach, patch-clamp fluorescence microscopy, which simultaneously combines single-molecule fluorescence spectroscopy and single-channel current recordings to probe the open-closed transitions and the conformational dynamics of individual ion channels. We demonstrate patch-clamp fluorescence microscopy by measuring gramicidin ion channel conformational changes in a lipid bilayer formed at a patch-clamp micropipette tip under a buffer solution. By measuring single-pair fluorescence resonance energy transfer and fluorescence self-quenching from dye-labeled gramicidin channels, we observed that the efficiency of single-pair fluorescence resonance energy transfer and self-quenching is widely distributed, which reflects a broad distribution of conformations. Our results strongly suggest a hitherto undetectable correlation between the multiple conformational states of the gramicidin channel and its closed and open states in a lipid bilayer.