Understanding the reproductive behavior and population condition of the sandbar shark (Carcharhinus plumbeus) in the western North Atlantic: A molecular approach to conservation and management

The sandbar shark, Carcharhinus plumbeus, has a discontinuous cosmopolitan distribution and is exploited throughout much of its range. In the western North Atlantic, it constitutes the majority of the directed commercial fishery. The stock has declined greatly since the fisheries\u27 inception and has not shown signs of recovery despite the implementation of management practices. Like many highly vagile marine species, it is difficult to obtain information about the sandbar shark through direct observation. Therefore, the goal of this dissertation is to use a molecular approach to examine aspects of behavior and reproduction, providing information useful in conservation and management. to this end, I examine the prevalence of genetic polyandry in the western North Atlantic and estimate effective population size and effective number of breeders for the Delaware Bay and Eastern Shore of Virginia nursery grounds. In addition, I look at patterns of philopatry and reproductive periodicity, while on a worldwide scale, assessing both historical and contemporary gene flow. Paternity analysis using microsatellite markers reveals that most females are mate with multiple males during one reproductive period. Despite the high prevalence of genetic polyandry, no direct benefits are detected. The data, however, suggest that males benefit by excluding other males from mating, intimating strong intrasexual competition. The effective number of breeders per nursery ground, estimated using the linkage disequilibrium method, is fairly consistent across years. Comparisons with census size estimates made for Delaware Bay reveal that the two measurements are tightly coupled. The ratio of effective size to census size is 0.45 or higher. This suggests that monitoring of effective population size may be a useful methodology for tracking abundance, and that exploitation may have a direct negative impact on the level of genetic variance. The results suggest that females may stray between nursery grounds found in Delaware Bay, the Eastern Shore lagoons and Chesapeake Bay, as phi st values are nonsignificant and kin groups are detected between as well as within samples. However, true kin groups can not be distinguished from erroneous kin groups because sample size is too small and the loci employed do not have enough power. Even so, the results suggest that female reproductive periodicity in this species needs to be reevaluated. Different patterns of historical dispersal and contemporary gene flow are observed when markers with different modes of inheritance are used to evaluate historical phylogeography. The results suggest that, although females show regional phylopatry, pulses of female dispersal during the Pleistocene may have created the species\u27 current distribution. This dynamic may have been mediated by the changing distribution of nursery habitat caused by the rise and fall of sea level associated with climate change rather than by fluctuating temperature. This idea is supported by the results, which suggest that male mediated gene flow persists long after female gene flow has stopped

Justices and Presidents: A Political History of Appointments to the Supreme Court (2d edition)

A Review of Justices and Presidents: A Political History of Appointments to the Supreme Court (2d edition) by Henry J. Abraha

Interaction between Polyketide Synthase and Transporter Suggests Coupled Synthesis and Export of Virulence Lipid in M. tuberculosis

Virulent mycobacteria utilize surface-exposed polyketides to interact with host cells, but the mechanism by which these hydrophobic molecules are transported across the cell envelope to the surface of the bacteria is poorly understood. Phthiocerol dimycocerosate (PDIM), a surface-exposed polyketide lipid necessary for Mycobacterium tuberculosis virulence, is the product of several polyketide synthases including PpsE. Transport of PDIM requires MmpL7, a member of the MmpL family of RND permeases. Here we show that a domain of MmpL7 biochemically interacts with PpsE, the first report of an interaction between a biosynthetic enzyme and its cognate transporter. Overexpression of the interaction domain of MmpL7 acts as a dominant negative to PDIM synthesis by poisoning the interaction between synthase and transporter. This suggests that MmpL7 acts in complex with the synthesis machinery to efficiently transport PDIM across the cell membrane. Coordination of synthesis and transport may not only be a feature of MmpL-mediated transport in M. tuberculosis, but may also represent a general mechanism of polyketide export in many different microorganisms

Partially linear censored quantile regression

Censored regression quantile (CRQ) methods provide a powerful and flexible approach to the analysis of censored survival data when standard linear models are felt to be appropriate. In many cases however, greater flexibility is desired to go beyond the usual multiple regression paradigm. One area of common interest is that of partially linear models: one (or more) of the explanatory covariates are assumed to act on the response through a non-linear function. Here the CRQ approach of Portnoy (J Am Stat Assoc 98:1001–1012, 2003) is extended to this partially linear setting. Basic consistency results are presented. A simulation experiment and unemployment example justify the value of the partially linear approach over methods based on the Cox proportional hazards model and on methods not permitting nonlinearity

RNA Interference Analysis of Legionella in Drosophila Cells: Exploitation of Early Secretory Apparatus Dynamics

Legionella pneumophila translocates multiple bacterial effector proteins into host cells to direct formation of a replication vacuole for the bacterium. The emerging consensus is that formation of this compartment involves recruitment of membrane material that traffics between the endoplasmic reticulum (ER) and Golgi. To investigate this model, a targeted approach was used to knock down expression of proteins involved in membrane trafficking, using RNA interference in Drosophila cells. Surprisingly, few single knockdowns of ER–Golgi transport proteins decreased L. pneumophila replication. By analyzing double-stranded RNAs in pairs, combinations were identified that together caused defects in intracellular replication, consistent with the model that membrane traffic funnels into the replication vacuole from multiple sources. In particular, simultaneous depletion of the intermediate compartment and Golgi-tethering factor transport protein particle together with the ER SNARE protein Sec22 reduced replication efficiency, indicating that introduction of lesions at distinct sites in the secretory system reduces replication efficiency. In contrast to knockdowns in secretory traffic, which required multiple simultaneous hits, knockdown of single cytosolic components of ER-associated degradation, including Cdc48/p97 and associated cofactors, was sufficient to inhibit intracellular replication. The requirement for the Cdc48/p97 complex was conserved in mammalian cells, in which replication vacuoles showed intense recruitment of ubiquitinated proteins, the preferred substrates of Cdc48/p97. This complex promoted dislocation of both ubiquitinated proteins and bacterial effectors from the replication vacuole, consistent with the model that maintenance of high-level replication requires surveillance of the vacuole surface. This work demonstrates that L. pneumophila has the ability to gain access to multiple sites in the secretory system and provides the first evidence for a role of the Cdc48/p97 complex in promoting intracellular replication of pathogens and maintenance of replication vacuoles

The Universe out of an Elementary Particle?

We consider a model of an elementary particle as a 2 + 1 dimensional brane evolving in a 3 + 1 dimensional space. Introducing gauge fields that live in the brane as well as normal surface tension can lead to a stable "elementary particle" configuration. Considering the possibility of non vanishing vacuum energy inside the bubble leads, when gravitational effects are considered, to the possibility of a quantum decay of such "elementary particle" into an infinite universe. Some remarkable features of the quantum mechanics of this process are discussed, in particular the relation between possible boundary conditions and the question of instability towards Universe formation is analyzed

A Potent and Effective Suicidal Listeria Vaccine Platform.

Live-attenuated Listeria monocytogenes has shown encouraging potential as an immunotherapy platform in preclinical and clinical settings. However, additional safety measures will enable application across malignant and infectious diseases. Here, we describe a new vaccine platform, termed Lm-RIID (L. monocytogenes recombinase-induced intracellular death), that induces the deletion of genes required for bacterial viability yet maintains potent T cell responses to encoded antigens. Lm-RIID grows normally in broth but commits suicide inside host cells by inducing Cre recombinase and deleting essential genes flanked by loxP sites, resulting in a self-limiting infection even in immunocompromised mice. Lm-RIID vaccination of mice induces potent CD8+ T cells and protects against virulent challenges, similar to live L. monocytogenes vaccines. When combined with α-PD-1, Lm-RIID is as effective as live-attenuated L. monocytogenes in a therapeutic tumor model. This impressive efficacy, together with the increased clearance rate, makes Lm-RIID ideal for prophylactic immunization against diseases that require T cells for protection

These aren’t the loci you’re looking for: Principles of effective SNP filtering for molecular ecologists

Sequencing reduced‐representation libraries of restriction site‐associated DNA (RADseq) to identify single nucleotide polymorphisms (SNPs) is quickly becoming a standard methodology for molecular ecologists. Because of the scale of RADseq data sets, putative loci cannot be assessed individually, making the process of filtering noise and correctly identifying biologically meaningful signal more difficult. Artefacts introduced during library preparation and/or bioinformatic processing of SNP data can create patterns that are incorrectly interpreted as indicative of population structure or natural selection. Therefore, it is crucial to carefully consider types of errors that may be introduced during laboratory work and data processing, and how to minimize, detect and remove these errors. Here, we discuss issues inherent to RADseq methodologies that can result in artefacts during library preparation and locus reconstruction resulting in erroneous SNP calls and, ultimately, genotyping error. Further, we describe steps that can be implemented to create a rigorously filtered data set consisting of markers accurately representing independent loci and compare the effect of different combinations of filters on four RAD data sets. At last, we stress the importance of publishing raw sequence data along with final filtered data sets in addition to detailed documentation of filtering steps and quality control measures