Magnetic Properties of Magnetotactic Bacteria

This paper reports on the magnetic properties of magnetosomes in the freshwater magnetotactic bacterium Aquaspirillum magnetotacticum. The magnetosomes are well crystallized particles of magnetite with dimensions of 40 to 50 nm, which are arranged within the cells in a single linear chain and are within the single-magnetic-domain (SD) size range for magnetite. A variety of magnetic properties have been measured for two samples of dispersions of freeze-dried cells consisting of (1) whole cells (M-1) and (2) magnetosomes chains separated from cells (M-2). An important result is that the acquisition and demagnetization of various type of remanent magnetizations are markedly different for the two samples and suggest that remanence is substantially affected by magnetostatic interactions. Interactions are likely to be much more important in M-2 because the extracted magnetosome chains are no longer separated from one another by the cell membrane and cytoplasm. Other experimental data for whole cells agree with predictions based on the chain of spheres model for magnetization reversal. This model is consistent with the unique linear arrangement of equidimensional particles in A. magnetotacticum. The magnetic properties of bacterial and synthetic magnetites are compared and the paleomagnetic implications are discussed

Obstructive sleep apnea in heart failure: Review of prevalence, treatment with continuous positive airway pressure, and prognosis

Obstructive sleep apnea is a sleep-related breathing disorder that has a major impact on cardiovascular function. It has been associated with hypertension, coronary artery disease, cardiac arrhythmias, sudden cardiac death, and heart failure. This review focuses on the relationship between obstructive sleep apnea and heart failure with either reduced or preserved ejection fraction. We discuss the pathophysiology of obstructive sleep apnea, as well as its prevalence, treatment outcomes with continuous positive airway pressure, and prognosis in these 2 distinct types of heart failure. We also identify areas in which further work is needed to improve our understanding of this association in heart failure patients

A new approach to generating research-quality data through citizen science: The USA National Phenology Monitoring System

Phenology is one of the most sensitive biological responses to climate change, and recent changes in phenology have the potential to shake up ecosystems. In some cases, it appears they already are. Thus, for ecological reasons it is critical that we improve our understanding of species’ phenologies and how these phenologies are responding to recent, rapid climate change. Phenological events like flowering and bird migrations are easy to observe, culturally important, and, at a fundamental level, naturally inspire human curiosity— thus providing an excellent opportunity to engage citizen scientists. The USA National Phenology Network has recently initiated a national effort to encourage people at different levels of expertise—from backyard naturalists to professional scientists—to observe phenological events and contribute to a national database that will be used to greatly improve our understanding of spatio-temporal variation in phenology and associated phenological responses to climate change.

Traditional phenological observation protocols identify specific dates at which individual phenological events are observed. The scientific usefulness of long-term phenological observations could be improved with a more carefully structured protocol. At the USA-NPN we have developed a new approach that directs observers to record each day that they observe an individual plant, and to assess and report the state of specific life stages (or phenophases) as occurring or not occurring on that plant for each observation date. Evaluation is phrased in terms of simple, easy-to-understand, questions (e.g. “Do you see open flowers?”), which makes it very appropriate for a citizen science audience. From this method, a rich dataset of phenological metrics can be extracted, including the duration of a phenophase (e.g. open flowers), the beginning and end points of a phenophase (e.g. traditional phenological events such as first flower and last flower), multiple distinct occurrences of phenophases within a single growing season (e.g multiple flowering events, common in drought-prone regions), as well as quantification of sampling frequency and observational uncertainties. These features greatly enhance the utility of the resulting data for statistical analyses addressing questions such as how phenological events vary in time and space, and in response to global change. This new protocol is an important step forward, and its widespread adoption will increase the scientific value of data collected by citizen scientists.
&#xa

The structure and function of complex networks

Inspired by empirical studies of networked systems such as the Internet, social networks, and biological networks, researchers have in recent years developed a variety of techniques and models to help us understand or predict the behavior of these systems. Here we review developments in this field, including such concepts as the small-world effect, degree distributions, clustering, network correlations, random graph models, models of network growth and preferential attachment, and dynamical processes taking place on networks.Comment: Review article, 58 pages, 16 figures, 3 tables, 429 references, published in SIAM Review (2003

Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps

The assembly methods used for whole-genome shotgun (WGS) data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of “reliable” overlaps based on identifying repeat k-mers. To demonstrate the benefits of using reliable overlaps, we have created a version of the Phrap assembly program that uses only overlaps from a specific list. We call this version PhrapUMD. Integrating PhrapUMD and our “reliable-overlap” algorithm with the Baylor College of Medicine assembler, Atlas, we assemble the BACs from the Rattus norvegicus genome project. Starting with the same data as the Nov. 2002 Atlas assembly, we compare our results and the Atlas assembly to the 4.3 Mb of rat sequence in the 21 BACs that have been finished. Our version of the draft assembly of the 21 BACs increases the coverage of finished sequence from 93.4% to 96.3%, while simultaneously reducing the base error rate from 4.5 to 1.1 errors per 10,000 bases. There are a number of ways of assessing the relative merits of assemblies when the finished sequence is available. If one views the overall quality of an assembly as proportional to the inverse of the product of the error rate and sequence missed, then the assembly presented here is seven times better. The UMD Overlapper with options for reliable overlaps is available from the authors at http://www.genome.umd.edu. We also provide the changes to the Phrap source code enabling it to use only the reliable overlaps

A Multi-Compartment, Single and Multiple Dose Pharmacokinetic Study of the Vaginal Candidate Microbicide 1% Tenofovir Gel

Background: Tenofovir (TFV) gel is being evaluated as a microbicide with pericoital and daily regimens. To inhibit viral replication locally, an adequate concentration in the genital tract is critical. Methods and Findings: Forty-nine participants entered a two-phase study: single-dose (SD) and multi-dose (MD), were randomized to collection of genital tract samples (endocervical cells [ECC], cervicovaginal aspirate and vaginal biopsies) at one of seven time points [0.5, 1, 2, 4, 6, 8, or 24 hr(s)] post-dose following SD exposure of 4 mL 1% TFV gel and received a single dose. Forty-seven were randomized to once (QD) or twice daily (BID) dosing for 2 weeks and to collection of genital tract samples at 4, 8 or 24 hrs after the final dose, but two discontinued prior to gel application. Blood was collected during both phases at the seven times post-dose. TFV exposure was low in blood plasma for SD and MD; median C max was 4.0 and 3.4 ng/mL, respectively (C≤29 ng/mL). TFV concentrations were high in aspirates and tissue after SD and MD, ranging from 1.2×10 4 to 9.9×10 6 ng/mL and 2.1×10 2 to 1.4×10 6 ng/mL, respectively, and did not noticeably differ between proximal and distal tissue. TFV diphosphate (TFV-DP), the intracellular active metabolite, was high in ECC, ranging from 7.1×10 3 to 8.8×10 6 ng/mL. TFV-DP was detectable in approximately 40% of the tissue samples, ranging from 1.8×10 2 to 3.5×10 4 ng/mL. AUC for tissue TFV-DP was two logs higher after MD compared to SD, with no noticeable differences when comparing QD and BID. Conclusions: Single-dose and multiple-dose TFV gel exposure resulted in high genital tract concentrations for at least 24 hours post-dose with minimal systemic absorption. These results support further study of TFV gel for HIV prevention. Trial registration: ClinicalTrials.gov NCT00561496. © 2011 Schwartz et al

Review Mechanisms of Mechanotransduction

Essentially all organisms from bacteria to humans are mechanosensitive. Physical forces regulate a large array of physiological processes, and dysregulation of mechanical responses contributes to major human diseases. A survey of both specialized and widely expressed mechanosensitive systems suggests that physical forces provide a general means of altering protein conformation to generate signals. Specialized systems differ mainly in having acquired efficient mechanisms for transferring forces to the mechanotransducers. The conversion of physical force into biochemical information is fundamental to development and physiology. It provides a simple means by which cells and organisms can ensure structural stability, as well as a way to regulate morphogenetic movements to generate precise three-dimensional structures. In the vascular system, pressure and shear stress from pumping blood influence the morphology and pathology of the heart and vasculature. Bone is shaped by forces from gravity and muscle contraction. Hearing and touch are based on neural responses to pressure. Inflation and deflation of the lungs regulate their physiology. Coordinated growth of tissues is guided by mechanical forces, and failure of these mechanisms contributes to cancer. Mechanosensitivity in one form or another appears to be a property shared by all cells of the body and by all phyla from mammals to bacteria

Multi-wavelength analysis of high energy electrons in solar flares: a case study of August 20, 2002 flare

A multi-wavelength spatial and temporal analysis of solar high energy electrons is conducted using the August 20, 2002 flare of an unusually flat (gamma=1.8) hard X-ray spectrum. The flare is studied using RHESSI, Halpha, radio, TRACE, and MDI observations with advanced methods and techniques never previously applied in the solar flare context. A new method to account for X-ray Compton backscattering in the photosphere (photospheric albedo) has been used to deduce the primary X-ray flare spectra. The mean electron flux distribution has been analysed using both forward fitting and model independent inversion methods of spectral analysis. We show that the contribution of the photospheric albedo to the photon spectrum modifies the calculated mean electron flux distribution, mainly at energies below 100 keV. The positions of the Halpha emission and hard X-ray sources with respect to the current-free extrapolation of the MDI photospheric magnetic field and the characteristics of the radio emission provide evidence of the closed geometry of the magnetic field structure and the flare process in low altitude magnetic loops. In agreement with the predictions of some solar flare models, the hard X-ray sources are located on the external edges of the Halpha emission and show chromospheric plasma heated by the non-thermal electrons. The fast changes of Halpha intensities are located not only inside the hard X-ray sources, as expected if they are the signatures of the chromospheric response to the electron bombardment, but also away from them.Comment: 26 pages, 9 figures, accepted to Solar Physic