An effort to make sense of antisense transcription in bacteria

Analysis of bacterial transcriptomes have shown the existence of a genome-wide process of overlapping transcription due to the presence of antisense RNAs, as well as mRNAs that overlapped in their entire length or in some portion of the 5'- and 3'-UTR regions. The biological advantages of such overlapping transcription are unclear but may play important regulatory roles at the level of transcription, RNA stability and translation. In a recent report, the human pathogen Staphylococcus aureus is observed to generate genome-wide overlapping transcription in the same bacterial cells leading to a collection of short RNA fragments generated by the endoribonuclease III, RNase III. This processing appears most prominently in Gram-positive bacteria. The implications of both the use of pervasive overlapping transcription and the processing of these double stranded templates into short RNAs are explored and the consequences discussed

Photo-excited semiconductor superlattices as constrained excitable media: Motion of dipole domains and current self-oscillations

A model for charge transport in undoped, photo-excited semiconductor superlattices, which includes the dependence of the electron-hole recombination on the electric field and on the photo-excitation intensity through the field-dependent recombination coefficient, is proposed and analyzed. Under dc voltage bias and high photo-excitation intensities, there appear self-sustained oscillations of the current due to a repeated homogeneous nucleation of a number of charge dipole waves inside the superlattice. In contrast to the case of a constant recombination coefficient, nucleated dipole waves can split for a field-dependent recombination coefficient in two oppositely moving dipoles. The key for understanding these unusual properties is that these superlattices have a unique static electric-field domain. At the same time, their dynamical behavior is akin to the one of an extended excitable system: an appropriate finite disturbance of the unique stable fixed point may cause a large excursion in phase space before returning to the stable state and trigger pulses and wave trains. The voltage bias constraint causes new waves to be nucleated when old ones reach the contact.Comment: 19 pages, 8 figures, to appear in Phys. Rev.

What Matters Most to Patients and Rheumatologists? A Discrete Choice Experiment in Rheumatoid Arthritis

Introduction: To determine patient and rheumatologist preferences for rheumatoid arthritis (RA) treatment attributes in Spain and to evaluate their attitude towards shared decision-making (SDM). Methods: Observational, descriptive, exploratory and cross-sectional study based on a discrete choice experiment (DCE). To identify the attributes and their levels, a literature review and two focus groups (patients [P] = 5; rheumatologists [R] = 4) were undertaken. Seven attributes with 2–4 levels were presented in eight scenarios. Attribute utility and relative importance (RI) were assessed using a conditional logit model. Patient preferences for SDM were assessed using an ad hoc questionnaire. Results: Ninety rheumatologists [52.2% women; mean years of experience 18.1 (SD: 9.0); seeing an average of 24.4 RA patients/week (SD: 15.3)] and 137 RA patients [mean age: 47.5 years (SD: 10.7); 84.0% women; mean time since diagnosis of RA: 14.2 years (SD: 11.8) and time in treatment: 13.2 years (SD: 11.2), mean HAQ score 1.2 (SD: 0.7)] participated in the study. In terms of RI, rheumatologists and RA patients viewed: time with optimal QoL: R: 23.41%/P: 35.05%; substantial symptom improvement: R: 13.15%/P: 3.62%; time to onset of treatment action: R: 16.24%/P: 13.56%; severe adverse events: R: 10.89%/P: 11.20%; mild adverse events: R: 4.16%/P: 0.91%; mode of administration: R: 25.23%/P: 25.00%; and added cost: R: 6.93%/P: 10.66%. Nearly 73% of RA patients were involved in treatment decision-making to a greater or lesser extent; however, 27.4% did not participate at all. Conclusion: Both for rheumatologists and patients, the top three decision-making drivers are time with optimal quality, treatment mode of administration and time to onset of action, although in different ranking order. Patients were willing to be more involved in the treatment decision-making process

Embalse subterráneo, Brasil.

Se tiene conocimiento de la técnica de almacenamiento de agua através del uso de embalses subterráneos en varias partes del mundo; en Arizona, Estados Unidos; en el desierto de Negev, en Israel; en las rcgiones áridas de Africa del Norte y en el desierto del Sahara. en Irán

The impact of deep-sea fisheries and implementation of the UNGA Resolutions 61/105 and 64/72. Report of an international scientific workshop

The scientific workshop to review fisheries management, held in Lisbon in May 2011, brought together 22 scientists and fisheries experts from around the world to consider the United Nations General Assembly (UNGA) resolutions on high seas bottom fisheries: what progress has been made and what the outstanding issues are. This report summarises the workshop conclusions, identifying examples of good practice and making recommendations in areas where it was agreed that the current management measures fall short of their target

DETAILED CHEMICAL KINETIC MODELING OF JP-8/JET-A IGNITION AND COMBUSTION

ABSTRACT Significant progress towards development and validation of a detailed chemical kinetic mechanism for the US Air Force JP-8 fuel is presented in this article. Three detailed chemical kinetic mechanisms for three JP-8 surrogate fuels, as given i

Long term measurements of aerosol optical properties at a primary forest site in Amazonia

A long term experiment was conducted in a primary forest area in Amazonia, with continuous in-situ measurements of aerosol optical properties between February 2008 and April 2011, comprising, to our knowledge, the longest database ever in the Amazon Basin. Two major classes of aerosol particles, with significantly different optical properties were identified: coarse mode predominant biogenic aerosols in the wet season (January–June), naturally released by the forest metabolism, and fine mode dominated biomass burning aerosols in the dry season (July–December), transported from regional fires. Dry particle median scattering coefficients at the wavelength of 550 nm increased from 6.3 Mm−1 to 22 Mm−1, whereas absorption at 637 nm increased from 0.5 Mm−1 to 2.8 Mm−1 from wet to dry season. Most of the scattering in the dry season was attributed to the predominance of fine mode (PM2) particles (40–80% of PM10 mass), while the enhanced absorption coefficients are attributed to the presence of light absorbing aerosols from biomass burning. As both scattering and absorption increased in the dry season, the single scattering albedo (SSA) did not show a significant seasonal variability, in average 0.86 ± 0.08 at 637 nm for dry aerosols. Measured particle optical properties were used to estimate the aerosol forcing efficiency at the top of the atmosphere. Results indicate that in this primary forest site the radiative balance was dominated by the cloud cover, particularly in the wet season. Due to the high cloud fractions, the aerosol forcing efficiency absolute values were below −3.5 W m−2 in 70% of the wet season days and in 46% of the dry season days. Besides the seasonal variation, the influence of out-of-Basin aerosol sources was observed occasionally. Periods of influence of the Manaus urban plume were detected, characterized by a consistent increase on particle scattering (factor 2.5) and absorption coefficients (factor 5). Episodes of biomass burning and mineral dust particles advected from Africa were observed between January and April, characterized by enhanced concentrations of crustal elements (Al, Si, Ti, Fe) and potassium in the fine mode. During these episodes, median particle absorption coefficients increased by a factor of 2, whereas median SSA values decreased by 7%, in comparison to wet season conditions

CD98hc facilitates B cell proliferation and adaptive humoral immunity.

The proliferation of antigen-specific lymphocytes and resulting clonal expansion are essential for adaptive immunity. We report here that B cell-specific deletion of the heavy chain of CD98 (CD98hc) resulted in lower antibody responses due to total suppression of B cell proliferation and subsequent plasma cell formation. Deletion of CD98hc did not impair early B cell activation but did inhibit later activation of the mitogen-activated protein kinase Erk1/2 and downregulation of the cell cycle inhibitor p27. Reconstitution of CD98hc-deficient B cells with CD98hc mutants showed that the integrin-binding domain of CD98hc was required for B cell proliferation but that the amino acid-transport function of CD98hc was dispensable for this. Thus, CD98hc supports integrin-dependent rapid proliferation of B cells. We propose that the advantage of adaptive immunity favored the appearance of CD98hc in vertebrates

Low-fidelity DNA synthesis by human DNA polymerase theta

Human DNA polymerase theta (pol θ or POLQ) is a proofreading-deficient family A enzyme implicated in translesion synthesis (TLS) and perhaps in somatic hypermutation (SHM) of immunoglobulin genes. These proposed functions and kinetic studies imply that pol θ may synthesize DNA with low fidelity. Here, we show that when copying undamaged DNA, pol θ generates single base errors at rates 10- to more than 100-fold higher than for other family A members. Pol θ adds single nucleotides to homopolymeric runs at particularly high rates, exceeding 1% in certain sequence contexts, and generates single base substitutions at an average rate of 2.4 × 10−3, comparable to inaccurate family Y human pol κ (5.8 × 10−3) also implicated in TLS. Like pol κ, pol θ is processive, implying that it may be tightly regulated to avoid deleterious mutagenesis. Pol θ also generates certain base substitutions at high rates within sequence contexts similar to those inferred to be copied by pol θ during SHM of immunoglobulin genes in mice. Thus, pol θ is an exception among family A polymerases, and its low fidelity is consistent with its proposed roles in TLS and SHM