Neurospora from natural populations: Population genomics insights into the Life history of a model microbial Eukaryote

The ascomycete filamentous fungus Neurospora crassa played a historic role in experimental biology and became a model system for genetic research. Stimulated by a systematic effort to collect wild strains initiated by Stanford geneticist David Perkins, the genus Neurospora has also become a basic model for the study of evolutionary processes, speciation, and population biology. In this chapter, we will first trace the history that brought Neurospora into the era of population genomics. We will then cover the major contributions of population genomic investigations using Neurospora to our understanding of microbial biogeography and speciation, and review recent work using population genomics and genome-wide association mapping that illustrates the unique potential of Neurospora as a model for identifying the genetic basis of (potentially adaptive) phenotypes in filamentous fungi. The advent of population genomics has contributed to firmly establish Neurospora as a complete model system and we hope our review will entice biologists to include Neurospora in their research

Gain More for Less: The Surprising Benefits of QoS Management in Constrained NDN Networks

Quality of Service (QoS) in the IP world mainly manages forwarding resources, i.e., link capacities and buffer spaces. In addition, Information Centric Networking (ICN) offers resource dimensions such as in-network caches and forwarding state. In constrained wireless networks, these resources are scarce with a potentially high impact due to lossy radio transmission. In this paper, we explore the two basic service qualities (i) prompt and (ii) reliable traffic forwarding for the case of NDN. The resources we take into account are forwarding and queuing priorities, as well as the utilization of caches and of forwarding state space. We treat QoS resources not only in isolation, but correlate their use on local nodes and between network members. Network-wide coordination is based on simple, predefined QoS code points. Our findings indicate that coordinated QoS management in ICN is more than the sum of its parts and exceeds the impact QoS can have in the IP world

Modified f(G) gravity models with curvature-matter coupling

A modified f(G) gravity model with coupling between matter and geometry is proposed, which is described by the product of the Lagrange density of the matter and an arbitrary function of the Gauss-Bonnet term. The field equations and the equations of motion corresponding to this model show the non-conservation of the energy-momentum tensor, the presence of an extra-force acting on test particles and the non-geodesic motion. Moreover, the energy conditions and the stability criterion at de Sitter point in the modified f(G) gravity models with curvature-matter coupling are derived, which can degenerate to the well-known energy conditions in general relativity. Furthermore, in order to get some insight on the meaning of these energy conditions, we apply them to the specific models of f(G) gravity and the corresponding constraints on the models are given. In addition, the conditions and the candidate for late-time cosmic accelerated expansion in the modified f(G) gravity are studied by means of conditions of power-law expansion and the equation of state of matter less than -1/ 3 .Comment: 13 pages, 4 figure

Signaling of the human P2Y(1) receptor measured by a yeast growth assay with comparisons to assays of phospholipase C and calcium mobilization in 1321N1 human astrocytoma cells

The human P2Y(1) receptor was expressed in the yeast Saccharomyces cerevisiae strain MPY578q5, which is engineered to couple to mammalian G protein-coupled receptors (GPCRs) and requires agonist-induced activation for growth. A range of known P2Y(1) receptor agonists were examined with the yeast growth assay system, and the results were validated by comparing with potencies in the transfected 1321N1 astrocytoma cell line, in which calcium mobilization was measured with a FLIPR (fluorometric-imaging plate reader). The data were also compared with those from phospholipase C activation and radioligand binding with the use of a newly available radioligand [(3)H]MRS2279 (2-chloro-N(6)-methyl-(N)-methanocarba-2’-deoxyadenosine-3’,5’bisphosphate). In the yeast growth assay, the rank order of potency of 2-MeSADP (2-methylthioadenosine 5’-diphosphate), ADP (adenosine 5’-diphosphate), and ATP (adenosine 5’-triphosphate) is the same as those in other assay systems, i.e., 2-MeSADP>ADP>ATP. The P2Y(1)-selective antagonist MRS2179 (N(6)-methyl-2-deoxyadenosine-3’,5’-bisphosphate) was shown to act as an antagonist with similar potency in all systems. The results suggest that the yeast expression system is suitable for screening P2Y(1) receptor ligands, both agonists and antagonists. The yeast system should be useful for random mutagenesis of GPCRs to identify mutants with certain properties, such as selective potency enhancement for small synthetic molecules and constitutive activity

The Mating-Type Chromosome in the Filamentous Ascomycete Neurospora tetrasperma Represents a Model for Early Evolution of Sex Chromosomes

We combined gene divergence data, classical genetics, and phylogenetics to study the evolution of the mating-type chromosome in the filamentous ascomycete Neurospora tetrasperma. In this species, a large non-recombining region of the mating-type chromosome is associated with a unique fungal life cycle where self-fertility is enforced by maintenance of a constant state of heterokaryosis. Sequence divergence between alleles of 35 genes from the two single mating-type component strains (i.e. the homokaryotic mat A or mat a-strains), derived from one N. tetrasperma heterokaryon (mat A+mat a), was analyzed. By this approach we were able to identify the boundaries and size of the non-recombining region, and reveal insight into the history of recombination cessation. The non-recombining region covers almost 7 Mbp, over 75% of the chromosome, and we hypothesize that the evolution of the mating-type chromosome in this lineage involved two successive events. The first event was contemporaneous with the split of N. tetrasperma from a common ancestor with its outcrossing relative N. crassa and suppressed recombination over at least 6.6 Mbp, and the second was confined to a smaller region in which recombination ceased more recently. In spite of the early origin of the first “evolutionary stratum”, genealogies of five genes from strains belonging to an additional N. tetrasperma lineage indicate independent initiations of suppressed recombination in different phylogenetic lineages. This study highlights the shared features between the sex chromosomes found in the animal and plant kingdoms and the fungal mating-type chromosome, despite fungi having no separate sexes. As is often found in sex chromosomes of plants and animals, recombination suppression of the mating-type chromosome of N. tetrasperma involved more than one evolutionary event, covers the majority of the mating-type chromosome and is flanked by distal regions with obligate crossovers

AAV2-Mediated Subretinal Gene Transfer of hIFN-α Attenuates Experimental Autoimmune Uveoretinitis in Mice

BACKGROUND: Recent reports show that gene therapy may provide a long-term, safe and effective intervention for human diseases. In this study, we investigated the effectiveness of adeno-associated virus 2 (AAV2) based human interferon-alpha (hIFN-α) gene therapy in experimental autoimmune uveoretinitis (EAU), a classic model for human uveitis. METHODOLOGY/PRINCIPAL FINDINGS: An AAV2 vector harboring the hIFN-α gene (AAV2.hIFN-α) was subretinally injected into B10RIII mice at two doses (1.5×10(6) vg, 1.5×10(8) vg). AAV2 vector encoding green fluorescent protein (AAV2.GFP) was used as a control (5×10(8) vg). The expression of hIFN-α in homogenized eyes and serum was detected by ELISA three weeks after injection. The biodistribution of vector DNA in the injected eyes, contralateral eyes and distant organs was determined by PCR. EAU was induced by immunization with IRBP(161-180) three weeks following vector injections, and evaluated clinically and pathologically. IRBP-specific proliferation and IL-17 expression of lymphocytes from the spleen and lymph nodes were assayed to test the influence of the subretinal delivery of AAV2.hIFN-α on the systemic immune response. hIFN-α was effectively expressed in the eyes from three weeks to three months following subretinal injection of AAV2.hIFN-α vector. DNA of AAV2.GFP was observed only in the injected eyes, but not in the distant organs or contralateral eyes. Subretinal injection of both doses significantly attenuated EAU activity clinically and histologically. For the lower dose, there was no difference concerning lymphocyte proliferation and IL-17 production among the AAV2.hIFN-α, AAV2.GFP and PBS injected mice. However, the higher dose of AAV2.hIFN-α significantly suppressed lymphocyte proliferation and IL-17 production. CONCLUSIONS/SIGNIFICANCE: Subretinal delivery of AAV2.hIFN-α lead to an effective expression within the eye for at least three months and significantly attenuated EAU activity. AAV2.hIFN-α was shown to inhibit the systemic IRBP-specific immune response

AAV-Mediated Cone Rescue in a Naturally Occurring Mouse Model of CNGA3-Achromatopsia

Achromatopsia is a rare autosomal recessive disorder which shows color blindness, severely impaired visual acuity, and extreme sensitivity to bright light. Mutations in the alpha subunits of the cone cyclic nucleotide-gated channels (CNGA3) are responsible for about 1/4 of achromatopsia in the U.S. and Europe. Here, we test whether gene replacement therapy using an AAV5 vector could restore cone-mediated function and arrest cone degeneration in the cpfl5 mouse, a naturally occurring mouse model of achromatopsia with a CNGA3 mutation. We show that gene therapy leads to significant rescue of cone-mediated ERGs, normal visual acuities and contrast sensitivities. Normal expression and outer segment localization of both M- and S-opsins were maintained in treated retinas. The therapeutic effect of treatment lasted for at least 5 months post-injection. This study is the first demonstration of substantial, relatively long-term restoration of cone-mediated light responsiveness and visual behavior in a naturally occurring mouse model of CNGA3 achromatopsia. The results provide the foundation for development of an AAV5-based gene therapy trial for human CNGA3 achromatopsia

The Ninth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the SDSS-III Baryon Oscillation Spectroscopic Survey

The Sloan Digital Sky Survey III (SDSS-III) presents the first spectroscopic data from the Baryon Oscillation Spectroscopic Survey (BOSS). This ninth data release (DR9) of the SDSS project includes 535,995 new galaxy spectra (median z=0.52), 102,100 new quasar spectra (median z=2.32), and 90,897 new stellar spectra, along with the data presented in previous data releases. These spectra were obtained with the new BOSS spectrograph and were taken between 2009 December and 2011 July. In addition, the stellar parameters pipeline, which determines radial velocities, surface temperatures, surface gravities, and metallicities of stars, has been updated and refined with improvements in temperature estimates for stars with T_eff<5000 K and in metallicity estimates for stars with [Fe/H]>-0.5. DR9 includes new stellar parameters for all stars presented in DR8, including stars from SDSS-I and II, as well as those observed as part of the SDSS-III Sloan Extension for Galactic Understanding and Exploration-2 (SEGUE-2). The astrometry error introduced in the DR8 imaging catalogs has been corrected in the DR9 data products. The next data release for SDSS-III will be in Summer 2013, which will present the first data from the Apache Point Observatory Galactic Evolution Experiment (APOGEE) along with another year of data from BOSS, followed by the final SDSS-III data release in December 2014.Comment: 9 figures; 2 tables. Submitted to ApJS. DR9 is available at http://www.sdss3.org/dr

The relevance of WHO injury surveillance guidelines for evaluation: learning from the aboriginal community-centered injury surveillance system (ACCISS) and two institution-based systems

<p>Abstract</p> <p>Background</p> <p>Over the past three decades, the capacity to develop and implement injury surveillance systems (ISS) has grown worldwide and is reflected by the diversity of data gathering environments in which ISS operate. The capacity to evaluate ISS, however, is less advanced and existing evaluation guidelines are ambiguous. Furthermore, the applied relevance of these guidelines to evaluate ISS operating in various settings is unclear. The aim of this paper was to examine how the World Health Organization (WHO) injury surveillance guidelines have been applied to evaluate systems operating in three different contexts.</p> <p>Methods</p> <p>The attributes of a good surveillance system as well as instructions for conducting evaluations, outlined in the WHO injury surveillance guidelines, were used to develop an analytical framework. Using this framework, a comparative analysis of the application of the guidelines was conducted using; the Aboriginal Community-Centered Injury Surveillance System (ACCISS) from Canada, the Shantou-Emergency Department Injury Surveillance Project (S-EDISP) from China, and the Yorkhill-Canadian Hospitals Injury Reporting and Prevention Program (Y-CHIRPP) imported from Canada and implemented in Scotland.</p> <p>Results</p> <p>The WHO guidelines provide only a basic platform for evaluation. The guidelines over emphasize epidemiologic attributes and methods and under emphasize public health and injury prevention perspectives requiring adaptation for context-based relevance. Evaluation elements related to the dissemination and use of knowledge, acceptability, and the sustainability of ISS are notably inadequate. From a public health perspective, alternative reference points are required for re-conceptualizing evaluation paradigms. This paper offers an ISS evaluation template that considers how the WHO guidelines could be adapted and applied.</p> <p>Conclusions</p> <p>Findings suggest that attributes of a good surveillance system, when used as evaluation metrics, cannot be weighted equally across ISS. In addition, the attribute of acceptability likely holds more relevance than previously recognized and should be viewed as a critical underpinning attribute of ISS. Context-oriented evaluations sensitive to distinct operational environments are more likely to address knowledge gaps related to; understanding links between the production of injury data and its use, and the effectiveness, impact, and sustainability of ISS. Current frameworks are predisposed to disassociating epidemiologic approaches from subjective factors and social processes.</p