Using RT qPCR for quantifying Mycobacteria marinum from in vitro and in vivo samples

Mycobacterium marinum, the causative agent of fish tuberculosis, is rarely a human pathogen causing a chronic skin infection. It is now wildely used as a model system in animal models, especially in zebra fish model, to study the pathology of tuberculosis and as a means of screening new anti-tuberculosis agent. To facilitate such research, quantifying the viable count of M. marinum bacteria is a crucial step. The main approach used currently is still by counting the number of colony forming units (cfu), a method that has been in place for almost 100 years. Though this method well established, understood and relatively easy to perform, it is time-consuming and labor-intensive. The result can be compromised by failure to grow effectively and the relationship between count and actual numbers is confused by clumping of the bacteria where a single colony is made from multiple organisms. More importantly, this method is not able to detect live but not cultivable bacteria, and there is increasing evidence that mycobacteria readily enter a "dormant" state which confounds the relationship between bacterial number in the host and the number detected in a cfu assay. DNA based PCR methods detect both living and dead organisms but here we describe a method, which utilizes species specific Taq-Man assay and RT-qPCR technology for quantifying the viable M. marinum bacterial load by detecting 16S ribosomal RNA (16S rRNA).Postprin

HTR4 gene structure and altered expression in the developing lung

Background: Meta-analyses of genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) spanning the 5-hydroxytryptamine receptor 4 (5-HT4R) gene (HTR4) associated with lung function. The aims of this study were to i) investigate the expression profile of HTR4 in adult and fetal lung tissue and cultured airway cells, ii) further define HTR4 gene structure and iii) explore the potential functional implications of key SNPs using a bioinformatic approach

Hydrodynamics of the stream-disk impact in interacting binaries

We use hydrodynamic simulations to provide quantitative estimates of the effects of the impact of the accretion stream on disks in interacting binaries. For low accretion rates, efficient radiative cooling of the hotspot region can occur, and the primary consequence of the stream impact is stream overflow toward smaller disk radii. The stream is well described by a ballistic trajectory, but larger masses of gas are swept up and overflow at smaller, but still highly supersonic, velocities. If cooling is inefficient, overflow still occurs, but there is no coherent stream inward of the disk rim. Qualitatively, the resulting structure appears as a bulge extending downstream along the disk rim. We calculate the mass fraction and velocity of the overflowing component as a function of the important system parameters, and discuss the implications of the results for X-ray observations and doppler tomography of cataclysmic variables, low-mass X-ray binaries and supersoft X-ray sources.Comment: 16 pages, including 8 figures. 1 color figure as a jpeg. ApJ, in pres

On the equivalence of strong formulations for capacitated multi-level lot sizing problems with setup times

Several mixed integer programming formulations have been proposed for modeling capacitated multi-level lot sizing problems with setup times. These formulations include the so-called facility location formulation, the shortest route formulation, and the inventory and lot sizing formulation with (l,S) inequalities. In this paper, we demonstrate the equivalence of these formulations when the integrality requirement is relaxed for any subset of binary setup decision variables. This equivalence has significant implications for decomposition-based methods since same optimal solution values are obtained no matter which formulation is used. In particular, we discuss the relax-and-fix method, a decomposition-based heuristic used for the efficient solution of hard lot sizing problems. Computational tests allow us to compare the effectiveness of different formulations using benchmark problems. The choice of formulation directly affects the required computational effort, and our results therefore provide guidelines on choosing an effective formulation during the development of heuristic-based solution procedures

Identifying key research objectives to make European forests greener for bats

Bats are a biodiverse mammal order providing key ecosystem services such as pest suppression, pollination and seed dispersal. Bats are also very sensitive to human actions, and significant declines in many bat populations have been recorded consequently. Many bat species find crucial roosting and foraging opportunities in European forests. Such forests have historically been exploited by humans and are still influenced by harvesting. One of the consequences of this pressure is the loss of key habitat resources, often making forests inhospitable to bats. Despite the legal protection granted to bats across Europe, the impacts of forestry on bats are still often neglected. Because forest exploitation influences forest structure at several spatial scales, economically viable forestry could become more sustainable and even favour bats. We highlight that a positive future for bat conservation that simultaneously benefits forestry is foreseeable, although more applied research is needed to develop sound management. Key future research topics include the detection of factors influencing the carrying capacity of forests, and determining the impacts of forest management and the economic importance of bats in forests. Predictive tools to inform forest managers are much needed, together with greater synergies between forest managers and bat conservationists

Mixed integer programming in production planning with backlogging and setup carryover : modeling and algorithms

This paper proposes a mixed integer programming formulation for modeling the capacitated multi-level lot sizing problem with both backlogging and setup carryover. Based on the model formulation, a progressive time-oriented decomposition heuristic framework is then proposed, where improvement and construction heuristics are effectively combined, therefore efficiently avoiding the weaknesses associated with the one-time decisions made by other classical time-oriented decomposition algorithms. Computational results show that the proposed optimization framework provides competitive solutions within a reasonable time

Evidence for Superhumps in the Radio Light Curve of Algol and a New Model for Magnetic Activity in Algol Systems

Extensive radio data of two Algol systems and two RS CVn binaries were re-analyzed. We found evidence for a new periodicity that we interpret as a superhump in Algol, in which it may have been expected according to its semi-detached nature and low binary mass ratio. This is the first detection of the superhump phenomenon in the radio and the first observation of superhumps in Algol systems. According to our result, the accretion disk in Algol precesses in spite of its non-Keplerian nature and therefore this phenomenon is not restricted to the classical Keplerian disks in compact binaries.We propose that in Algol systems with short orbital periods, the disk is magnetically active as well as the secondary star. The magnetic field in the disk originates from amplification of the seed field in the magnetized material transferred from the secondary. The disk and stellar fields interact with each other, with reconnection of the field lines causing flares and particle acceleration. Relativistic particles are trapped in the field and directed toward the polar regions of the secondary star because of the dipole structure of its magnetic field. Our proposed model for the magnetic activity in Algol systems provides a simple explanation to the observed properties of Algol in the radio wavelengths, and to the presence of quiescent gyrosynchrotron emission near the polar region of the secondary star, where electrons are difficult to be confined if the field lines are open as in normal single magnetic stars. We propose that the superhump variation in the radio is generated by enhanced reconnection when the elongated side of the elliptic disk is the closest to the cool star. This leads to flares and enhancement in particle acceleration and is manifested as stronger gyrosynchrotron radiation.Comment: 8 pages, 5 figures, ApJ, accepted, uses apjfonts.sty and emulateapj5.sty, full abstract in pape

A computational analysis of lower bounds for big bucket production planning problems

In this paper, we analyze a variety of approaches to obtain lower bounds for multi-level production planning problems with big bucket capacities, i.e., problems in which multiple items compete for the same resources. We give an extensive survey of both known and new methods, and also establish relationships between some of these methods that, to our knowledge, have not been presented before. As will be highlighted, understanding the substructures of difficult problems provide crucial insights on why these problems are hard to solve, and this is addressed by a thorough analysis in the paper. We conclude with computational results on a variety of widely used test sets, and a discussion of future research