Type I Migration in Radiatively Efficient Discs

We study Type I migration of a planet in a radiatively efficient disk using global two dimensional hydrodynamic simulations. The large positive corotation torque is exerted on a planet by an adiabatic disk at early times when the disk has the steep negative entropy gradient. The gas on the horseshoe orbit of the planet is compressed adiabatically during the change of the orbit from the slow orbit to the fast orbit, increasing its density and exerting the positive torque on the planet. The planet would migrate outward in the adiabatic disk before saturation sets in. We further study the effect of energy dissipation by radiation on Type I migration of the planet. The corotation torque decreases when the energy dissipates effectively because the density of the gas on the horseshoe orbit does not increase by the compression compared with the gas of the adiabatic disk. The total torque is mainly determined by the negative Lindblad torque and becomes negative. The planet migrates inward toward the central star in the radiatively efficient disk. The migration velocity is dependent on the radiative efficiency and greatly reduced if the radiative cooling works inefficiently.Comment: 12 pages, 10 figures, 1 table, Accepted for publication in MNRA

Type I migration in optically thick accretion discs

We study the torque acting on a planet embedded in an optically thick accretion disc, using global two-dimensional hydrodynamic simulations. The temperature of an optically thick accretion disc is determined by the energy balance between the viscous heating and the radiative cooling. The radiative cooling rate depends on the opacity of the disc. The opacity is expressed as a function of the temperature. We find the disc is divided into three regions that have different temperature distributions. The slope of the entropy distribution becomes steep in the inner region of the disc with the high temperature and the outer region of the disc with the low temperature, while it becomes shallow in the middle region with the intermediate temperature. Planets in the inner and outer regions move outward owing to the large positive corotation torque exerted on the planet by an adiabatic disc, on the other hand, a planet in the middle region moves inward toward the central star. Planets are expected to accumulate at the boundary between the inner and middle regions of the adiabatic disc. The positive corotation torque decreases with an increase in the viscosity of the disc. We find that the positive corotation torque acting on the planet in the inner region becomes too small to cancel the negative Lindblad torque when we include the large viscosity, which destroys the enhancement of the density in the horseshoe orbit of the planet. This leads to the inward migration of the planet in the inner region of the disc. A planet with 5 Earth masses in the inner region can move outward in a disc with the surface density of 100 g/cm^2 at 1 AU when the accretion rate of a disc is smaller than 2x10^{-8} solar mass/yr.Comment: 17 pages, 15 figure

Recent developments in planet migration theory

Planetary migration is the process by which a forming planet undergoes a drift of its semi-major axis caused by the tidal interaction with its parent protoplanetary disc. One of the key quantities to assess the migration of embedded planets is the tidal torque between the disc and planet, which has two components: the Lindblad torque and the corotation torque. We review the latest results on both torque components for planets on circular orbits, with a special emphasis on the various processes that give rise to additional, large components of the corotation torque, and those contributing to the saturation of this torque. These additional components of the corotation torque could help address the shortcomings that have recently been exposed by models of planet population syntheses. We also review recent results concerning the migration of giant planets that carve gaps in the disc (type II migration) and the migration of sub-giant planets that open partial gaps in massive discs (type III migration).Comment: 52 pages, 18 figures. Review article to be published in "Tidal effects in Astronomy and Astrophysics", Lecture Notes in Physic

Anti-inflammatory recombinant TSG-6 stabilizes the progression of focal retinal degeneration in a murine model

<p>Abstract</p> <p>Background</p> <p>Inflammatory responses are detected in the retina of patients with age-related macular degeneration and <it>Ccl2^-/-/Cx3cr1^-/-</it>mice on rd8 background,(<it>Ccl2^-/-/Cx3cr1^-/-</it>mice) a model that develops progressive age-related macular degeneration-like retinal lesions including focal photoreceptor degeneration, abnormal retinal pigment epithelium and A2E accumulation. Tumor necrosis factor-inducible gene 6 protein is an anti-inflammatory protein and has been shown to improve myocardial infarction outcome and chemically injured cornea in mice by suppressing inflammation. In this study, we evaluated the effect of an intravitreous injection of recombinant TSG-6 on the retinal lesions of <it>Ccl2^-/-/Cx3cr1^-/-</it>mice.</p> <p>Methods</p> <p>Recombinant TSG-6 (400 ng) was administered by intravitreous injection into the right eye of six-week-old C<it>cl2^-/-/Cx3cr1^-/-</it>mice. Their left eye was injected with phosphate-buffered saline as a control. Funduscopic pictures were taken before injection and sequentially once a month after injection. The mice were killed two months after injection and the ocular histology examined. Retinal A2E, a major component of lipofuscin, was measured by high performance liquid chromatography. The microarray of ocular mRNA of 92 immunological genes was performed. The genes showing differentiated expression in microarray were further compared between the injected right eye and the contralateral (control) eye by [real-time quantitative reverse transcription polymerase chain reaction] qRT-PCR.</p> <p>Results</p> <p>The continuous monitoring of the fundus for two months showed a slower progression or alleviation of retinal lesions in the treated right eyes as compared with the untreated left eyes. Among 23 pairs of eyes, the lesion levels improved in 78.3%, stayed the same in 8.7% and progressed in 13.0%. Histology confirmed the clinical observation. Even though there was no difference in the level of A2E between the treated and the untreated eyes, microarray analysis of 92 immune genes showed that <it>IL-17a </it>was substantially decreased after the treatment. Expression of <it>TNF-α </it>showed a similar pattern to <it>IL-17a</it>. The results were consistent in duplicated arrays and confirmed by qRT-PCR.</p> <p>Conclusions</p> <p>We concluded that intravitreous administration of recombinant TSG-6 might stabilize retinal lesions in <it>Ccl2^-/-/Cx3cr1^-/-</it>mice on rd8 background. Modulation of ocular immunological gene expressions, especially IL-17a, could be one of the mechanisms.</p

A mathematical model of quorum sensing regulated EPS production in biofilm communities

<p>Abstract</p> <p>Background</p> <p>Biofilms are microbial communities encased in a layer of extracellular polymeric substances (EPS). The EPS matrix provides several functional purposes for the biofilm, such as protecting bacteria from environmental stresses, and providing mechanical stability. Quorum sensing is a cell-cell communication mechanism used by several bacterial taxa to coordinate gene expression and behaviour in groups, based on population densities.</p> <p>Model</p> <p>We mathematically model quorum sensing and EPS production in a growing biofilm under various environmental conditions, to study how a developing biofilm impacts quorum sensing, and conversely, how a biofilm is affected by quorum sensing-regulated EPS production. We investigate circumstances when using quorum-sensing regulated EPS production is a beneficial strategy for biofilm cells.</p> <p>Results</p> <p>We find that biofilms that use quorum sensing to induce increased EPS production do not obtain the high cell populations of low-EPS producers, but can rapidly increase their volume to parallel high-EPS producers. Quorum sensing-induced EPS production allows a biofilm to switch behaviours, from a colonization mode (with an optimized growth rate), to a protection mode.</p> <p>Conclusions</p> <p>A biofilm will benefit from using quorum sensing-induced EPS production if bacteria cells have the objective of acquiring a thick, protective layer of EPS, or if they wish to clog their environment with biomass as a means of securing nutrient supply and outcompeting other colonies in the channel, of their own or a different species.</p

Deciphering von Hippel-Lindau (VHL/Vhl)-Associated Pancreatic Manifestations by Inactivating Vhl in Specific Pancreatic Cell Populations

The von Hippel-Lindau (VHL) syndrome is a pleomorphic familial disease characterized by the development of highly vascularized tumors, such as hemangioblastomas of the central nervous system, pheochromocytomas, renal cell carcinomas, cysts and neuroendocrine tumors of the pancreas. Up to 75% of VHL patients are affected by VHL-associated pancreatic lesions; however, very few reports in the published literature have described the cellular origins and biological roles of VHL in the pancreas. Since homozygous loss of Vhl in mice resulted in embryonic lethality, this study aimed to characterize the functional significance of VHL in the pancreas by conditionally inactivating Vhl utilizing the Cre/LoxP system. Specifically, Vhl was inactivated in different pancreatic cell populations distinguished by their roles during embryonic organ development and their endocrine lineage commitment. With Cre recombinase expression directed by a glucagon promoter in α-cells or an insulin promoter in β-cells, we showed that deletion of Vhl is dispensable for normal functions of the endocrine pancreas. In addition, deficiency of VHL protein (pVHL) in terminally differentiated α-cells or β-cells is insufficient to induce pancreatic neuroendocrine tumorigenesis. Most significantly, we presented the first mouse model of VHL-associated pancreatic disease in mice lacking pVHL utilizing Pdx1-Cre transgenic mice to inactivate Vhl in pancreatic progenitor cells. The highly vascularized microcystic adenomas and hyperplastic islets that developed in Pdx1-Cre;Vhl f/f homozygous mice exhibited clinical features similar to VHL patients. Establishment of three different, cell-specific Vhl knockouts in the pancreas have allowed us to provide evidence suggesting that VHL is functionally important for postnatal ductal and exocrine pancreas, and that VHL-associated pancreatic lesions are likely to originate from progenitor cells, not mature endocrine cells. The novel model systems reported here will provide the basis for further functional and genetic studies to define molecular mechanisms involved in VHL-associated pancreatic diseases

Genome Sequence of the Versatile Fish Pathogen Edwardsiella tarda Provides Insights into its Adaptation to Broad Host Ranges and Intracellular Niches

BACKGROUND:Edwardsiella tarda is the etiologic agent of edwardsiellosis, a devastating fish disease prevailing in worldwide aquaculture industries. Here we describe the complete genome of E. tarda, EIB202, a highly virulent and multi-drug resistant isolate in China. METHODOLOGY/PRINCIPAL FINDINGS:E. tarda EIB202 possesses a single chromosome of 3,760,463 base pairs containing 3,486 predicted protein coding sequences, 8 ribosomal rRNA operons, and 95 tRNA genes, and a 43,703 bp conjugative plasmid harboring multi-drug resistant determinants and encoding type IV A secretion system components. We identified a full spectrum of genetic properties related to its genome plasticity such as repeated sequences, insertion sequences, phage-like proteins, integrases, recombinases and genomic islands. In addition, analysis also indicated that a substantial proportion of the E. tarda genome might be devoted to the growth and survival under diverse conditions including intracellular niches, with a large number of aerobic or anaerobic respiration-associated proteins, signal transduction proteins as well as proteins involved in various stress adaptations. A pool of genes for secretion systems, pili formation, nonfimbrial adhesions, invasions and hemagglutinins, chondroitinases, hemolysins, iron scavenging systems as well as the incomplete flagellar biogenesis might feature its surface structures and pathogenesis in a fish body. CONCLUSION/SIGNIFICANCE:Genomic analysis of the bacterium offered insights into the phylogeny, metabolism, drug-resistance, stress adaptation, and virulence characteristics of this versatile pathogen, which constitutes an important first step in understanding the pathogenesis of E. tarda to facilitate construction of a practical effective vaccine used for combating fish edwardsiellosis

The great screen anomaly—a new frontier in product discovery through functional metagenomics

Functional metagenomics, the study of the collective genome of a microbial community by expressing it in a foreign host, is an emerging field in biotechnology. Over the past years, the possibility of novel product discovery through metagenomics has developed rapidly. Thus, metagenomics has been heralded as a promising mining strategy of resources for the biotechnological and pharmaceutical industry. However, in spite of innovative work in the field of functional genomics in recent years, yields from function-based metagenomics studies still fall short of producing significant amounts of new products that are valuable for biotechnological processes. Thus, a new set of strategies is required with respect to fostering gene expression in comparison to the traditional work. These new strategies should address a major issue, that is, how to successfully express a set of unknown genes of unknown origin in a foreign host in high throughput. This article is an opinionating review of functional metagenomic screening of natural microbial communities, with a focus on the optimization of new product discovery. It first summarizes current major bottlenecks in functional metagenomics and then provides an overview of the general metagenomic assessment strategies, with a focus on the challenges that are met in the screening for, and selection of, target genes in metagenomic libraries. To identify possible screening limitations, strategies to achieve optimal gene expression are reviewed, examining the molecular events all the way from the transcription level through to the secretion of the target gene product