New Rotation Periods in the Pleiades: Interpreting Activity Indicators

We present results of photometric monitoring campaigns of G, K and M dwarfs in the Pleiades carried out in 1994, 1995 and 1996. We have determined rotation periods for 18 stars in this cluster. In this paper, we examine the validity of using observables such as X-ray activity and amplitude of photometric variations as indicators of angular momentum loss. We report the discovery of cool, slow rotators with high amplitudes of variation. This contradicts previous conclusions about the use of amplitudes as an alternate diagnostic of the saturation of angular momentum loss. We show that the X-ray data can be used as observational indicators of mass-dependent saturation in the angular momentum loss proposed on theoretical grounds

New rotation periods in the Pleiades: Interpreting activity indicators

We present results of photometric monitoring campaigns of G, K and M dwarfs in the Pleiades carried out in 1994, 1995 and 1996. We have determined rotation periods for 18 stars in this cluster. In this paper, we examine the validity of using observables such as X-ray activity and amplitude of photometric variations as indicators of angular momentum loss. We report the discovery of cool, slow rotators with high amplitudes of variation. This contradicts previous conclusions about the use of amplitudes as an alternate diagnostic of the saturation of angular momentum loss. We show that the X-ray data can be used as observational indicators of mass-dependent saturation in the angular momentum loss proposed on theoretical grounds.Comment: 24 pages, LaTex (AASTeX); includes 8 postscript figures and 4 Latex tables. To appear in ApJ, Feb. 1, 1998. Postscript version of preprint can be obtained from http://casa.colorado.edu/~anitak/pubs.htm

The CIDA Variability Survey of Orion OB1. I: the low-mass population of Ori OB 1a and 1b

We present results of a large scale, multi-epoch optical survey of the Ori OB1 association, carried out with the QuEST camera at the Venezuela National Astronomical Observatory. We identify for the first time the widely spread low-mass, young population in the Orion OB1a and OB1b sub-associations. Candidate members were picked up by their variability in the V-band and position in color-magnitude diagrams. We obtained spectra to confirm membership. In a region spanning ~ 68 deg^2 we found 197 new young stars; of these, 56 are located in the Ori OB1a subassociation and 142 in Ori OB1b. Comparison with the spatial extent of molecular gas and extinction maps indicates that the subassociation Ori 1b is concentrated within a ring-like structure of radius ~2 deg (~15 pc at 440 pc), centered roughly on the star epsilon Ori in the Orion belt. The ring is apparent in 13CO and corresponds to a region with an extinction Av>=1. The stars exhibiting strong Ha emission, an indicator of active accretion, are found along this ring, while the center is populated with weak Ha emitting stars. In contrast, Ori OB1a is located in a region devoid of gas and dust. We identify a grouping of stars within a ~3 deg^2 area located in 1a, roughly clustered around the B2 star 25 Ori. The Herbig Ae/Be star V346 Ori is also associated with this grouping, which could be an older analog of sigma Ori. Using using several sets of evolutionary tracks we find an age of 7 - 10 Myr for Ori 1a and of ~4 - 6 Myr for Ori OB1b, consistent with previous estimates from OB stars. Indicators such as the equivalent width of Ha and near-IR excesses show that while a substantial fraction of accreting disks remain at ages ~5 Myr, inner disks are essentially dissipated by 10 Myr.Comment: 44 pages, 12 figures, to appear in the Astronomical Journal. (Abridged abstract - to fit length limit in astroph) Full resolution figures in http://www.cida.ve/~briceno/publications

From Biology to Mathematical Models and Back: Teaching Modeling to Biology Students, and Biology to Math and Engineering Students

We describe the development of a course to teach modeling and mathematical analysis skills to students of biology and to teach biology to students with strong backgrounds in mathematics, physics, or engineering. The two groups of students have different ways of learning material and often have strong negative feelings toward the area of knowledge that they find difficult. To give students a sense of mastery in each area, several complementary approaches are used in the course: 1) a “live” textbook that allows students to explore models and mathematical processes interactively; 2) benchmark problems providing key skills on which students make continuous progress; 3) assignment of students to teams of two throughout the semester; 4) regular one-on-one interactions with instructors throughout the semester; and 5) a term project in which students reconstruct, analyze, extend, and then write in detail about a recently published biological model. Based on student evaluations and comments, an attitude survey, and the quality of the students' term papers, the course has significantly increased the ability and willingness of biology students to use mathematical concepts and modeling tools to understand biological systems, and it has significantly enhanced engineering students' appreciation of biology

The Fueling and Evolution of AGN: Internal and External Triggers

In this chapter, I review the fueling and evolution of active galactic nuclei (AGN) under the influence of internal and external triggers, namely intrinsic properties of host galaxies (morphological or Hubble type, color, presence of bars and other non-axisymmetric features, etc) and external factors such as environment and interactions. The most daunting challenge in fueling AGN is arguably the angular momentum problem as even matter located at a radius of a few hundred pc must lose more than 99.99 % of its specific angular momentum before it is fit for consumption by a BH. I review mass accretion rates, angular momentum requirements, the effectiveness of different fueling mechanisms, and the growth and mass density of black BHs at different epochs. I discuss connections between the nuclear and larger-scale properties of AGN, both locally and at intermediate redshifts, outlining some recent results from the GEMS and GOODS HST surveys.Comment: Invited Review Chapter to appear in LNP Volume on "AGN Physics on All Scales", Chapter 6, in press. 40 pages, 12 figures. Typo in Eq 5 correcte

The dynamics and efficacy of antiviral RNA silencing: A model study

<p>Abstract</p> <p>Background</p> <p>Mathematical modeling is important to provide insight in the complicated pathway of RNA silencing. RNA silencing is an RNA based mechanism that is widely used by eukaryotes to fight viruses, and to control gene expression.</p> <p>Results</p> <p>We here present the first mathematical model that combines viral growth with RNA silencing. The model involves a plus-strand RNA virus that replicates through a double-strand RNA intermediate. The model of the RNA silencing pathway consists of cleavage of viral RNA into siRNA by Dicer, target cleavage of viral RNA via the RISC complex, and a secondary response. We found that, depending on the strength of the silencing response, different viral growth patterns can occur. Silencing can decrease viral growth, cause oscillations, or clear the virus completely. Our model can explain various observed phenomena, even when they seem contradictory at first: the diverse responses to the removal of RNA dependent RNA polymerase; different viral growth curves; and the great diversity in observed siRNA ratios.</p> <p>Conclusion</p> <p>The model presented here is an important step in the understanding of the natural functioning of RNA silencing in viral infections.</p

The Host Galaxies of AGN

We examine the properties of the host galaxies of 22,623 narrow-line AGN with 0.02<z<0.3 selected from a complete sample of 122,808 galaxies from the Sloan Digital Sky Survey. We focus on the luminosity of the [OIII]$\lambda$5007 emission line as a tracer of the strength of activity in the nucleus. We study how AGN host properties compare to those of normal galaxies and how they depend on L[OIII]. We find that AGN of all luminosities reside almost exclusively in massive galaxies and have distributions of sizes, stellar surface mass densities and concentrations that are similar to those of ordinary early-type galaxies in our sample. The host galaxies of low-luminosity AGN have stellar populations similar to normal early-types. The hosts of high- luminosity AGN have much younger mean stellar ages. The young stars are not preferentially located near the nucleus of the galaxy, but are spread out over scales of at least several kiloparsecs. A significant fraction of high- luminosity AGN have strong H$\delta$ absorption-line equivalent widths, indicating that they experienced a burst of star formation in the recent past. We have also examined the stellar populations of the host galaxies of a sample of broad-line AGN. We conclude that there is no significant difference in stellar content between type 2 Seyfert hosts and QSOs with the same [OIII] luminosity and redshift. This establishes that a young stellar population is a general property of AGN with high [OIII] luminosities.Comment: submitted to MNRAS, 44 pages, version with full resolution figures available at http://www.mpa-garching.mpg.de/~gamk/agnpaper/agnpaper.p

Modeling Within-Host Dynamics of Influenza Virus Infection Including Immune Responses

Influenza virus infection remains a public health problem worldwide. The mechanisms underlying viral control during an uncomplicated influenza virus infection are not fully understood. Here, we developed a mathematical model including both innate and adaptive immune responses to study the within-host dynamics of equine influenza virus infection in horses. By comparing modeling predictions with both interferon and viral kinetic data, we examined the relative roles of target cell availability, and innate and adaptive immune responses in controlling the virus. Our results show that the rapid and substantial viral decline (about 2 to 4 logs within 1 day) after the peak can be explained by the killing of infected cells mediated by interferon activated cells, such as natural killer cells, during the innate immune response. After the viral load declines to a lower level, the loss of interferon-induced antiviral effect and an increased availability of target cells due to loss of the antiviral state can explain the observed short phase of viral plateau in which the viral level remains unchanged or even experiences a minor second peak in some animals. An adaptive immune response is needed in our model to explain the eventual viral clearance. This study provides a quantitative understanding of the biological factors that can explain the viral and interferon kinetics during a typical influenza virus infection

Novel Small-Molecule Inhibitors of Hepatitis C Virus Entry Block Viral Spread and Promote Viral Clearance in Cell Culture

Combinations of direct-acting anti-virals offer the potential to improve the efficacy, tolerability and duration of the current treatment regimen for hepatitis C virus (HCV) infection. Viral entry represents a distinct therapeutic target that has been validated clinically for a number of pathogenic viruses. To discover novel inhibitors of HCV entry, we conducted a high throughput screen of a proprietary small-molecule compound library using HCV pseudoviral particle (HCVpp) technology. We independently discovered and optimized a series of 1,3,5-triazine compounds that are potent, selective and non-cytotoxic inhibitors of HCV entry. Representative compounds fully suppress both cell-free virus and cell-to-cell spread of HCV in vitro. We demonstrate, for the first time, that long term treatment of an HCV cell culture with a potent entry inhibitor promotes sustained viral clearance in vitro. We have confirmed that a single amino acid variant, V719G, in the transmembrane domain of E2 is sufficient to confer resistance to multiple compounds from the triazine series. Resistance studies were extended by evaluating both the fusogenic properties and growth kinetics of drug-induced and natural amino acid variants in the HCVpp and HCV cell culture assays. Our results indicate that amino acid variations at position 719 incur a significant fitness penalty. Introduction of I719 into a genotype 1b envelope sequence did not affect HCV entry; however, the overall level of HCV replication was reduced compared to the parental genotype 1b/2a HCV strain. Consistent with these findings, I719 represents a significant fraction of the naturally occurring genotype 1b sequences. Importantly, I719, the most relevant natural polymorphism, did not significantly alter the susceptibility of HCV to the triazine compounds. The preclinical properties of these triazine compounds support further investigation of entry inhibitors as a potential novel therapy for HCV infection

Exploring Cell Tropism as a Possible Contributor to Influenza Infection Severity

Several mechanisms have been proposed to account for the marked increase in severity of human infections with avian compared to human influenza strains, including increased cytokine expression, poor immune response, and differences in target cell receptor affinity. Here, the potential effect of target cell tropism on disease severity is studied using a mathematical model for in-host influenza viral infection in a cell population consisting of two different cell types. The two cell types differ only in their susceptibility to infection and rate of virus production. We show the existence of a parameter regime which is characterized by high viral loads sustained long after the onset of infection. This finding suggests that differences in cell tropism between influenza strains could be sufficient to cause significant differences in viral titer profiles, similar to those observed in infections with certain strains of influenza A virus. The two target cell mathematical model offers good agreement with experimental data from severe influenza infections, as does the usual, single target cell model albeit with biologically unrealistic parameters. Both models predict that while neuraminidase inhibitors and adamantanes are only effective when administered early to treat an uncomplicated seasonal infection, they can be effective against more severe influenza infections even when administered late