Complete Genome Sequence of Raoultella electrica 1GB (DSM 102253T), Isolated from Anodic Biofilms of a Glucose-Fed Microbial Fuel Cell

The type strain Raoultella electrica 1GB (DSM 102253T) was isolated from anodic biofilms of glucose-fed microbial fuel cells. The fully assembled, closed, circular 5.27-Mb genome and corresponding 0.52-Mb plasmid DNA sequences were elucidated. Potential electron transfer and pathogenicity mechanisms were deduced

Intensity-Modulated Radiotherapy in Patients with Cervical Cancer. An intra-individual Comparison of Prone and Supine Positioning

<p>Abstract</p> <p>Background</p> <p>Chemoradiation for cervical cancer patients is associated with considerable gastrointestinal toxicity. Intensity-modulated radiotherapy (IMRT) has demonstrated superiority in terms of target coverage and normal tissue sparing in comparison to conventional 3D planning in gynaecological malignancies. Whether IMRT in prone (PP) or supine position (SP) might be beneficial for cervical cancer patients remains partially unanswered.</p> <p>Methods</p> <p>10 patients on FIGO stage IB-III cervical cancer, 6 patients for definitive and 4 patients for adjuvant external beam pelvic RT, were planned in PP and SP using a 7-field IMRT technique. IMRT plans for PP and SP (mean dose, D_mean50.4 Gy) were optimized in terms of PTV coverage (1^stpriority) and small bowel sparing (2^ndpriority). A comparison of DVH parameters for PTV, small bowel, bladder, and rectum was performed.</p> <p>Results</p> <p>The comparison showed a similar PTV coverage of 95% of the prescribed dose and for target conformity in IMRT plans (PP, SP). PTV, rectum and bladder volumes were comparable for PP and SP. Significantly larger volumes of small bowel were found in PP (436 cc, + 35%, p = 0.01). PP decreased the volume of small bowel at 20-50.4 Gy (p < 0.05) and increased the rectum volumes covered by doses from 10-40 Gy (p < 0.01), the V50.4 was < 5% in both treatment positions. Bladder sparing was significant better at 50.4 Gy (p = 0.03) for PP.</p> <p>Conclusion</p> <p>In this dosimetric study, we demonstrated that pelvic IMRT in prone position for patients with cervical cancer seems to be beneficial in reducing small bowel volume at doses ≥20 Gy while providing similar target coverage and target conformity. The use of frequent image guidance with KV (kilovolt) or MV (megavolt) computertomography can reduce set-up deviations, and treatment in prone position can be done with a higher set-up accuracy. Clinical outcome studies are needed to affirm lower toxicity.</p

Patterns, trends and sex differences in HIV/AIDS reported mortality in Latin American countries: 1996-2007

<p>Abstract</p> <p>Background</p> <p>International cohort studies have shown that antiretroviral treatment (ART) has improved survival of HIV-infected individuals. National population based studies of HIV mortality exist in industrialized settings but few have been presented from developing countries. Our objective was to investigate on a population basis, the regional situation regarding HIV mortality and trends in Latin America (LA) in the context of adoption of public ART policies and gender differences.</p> <p>Methods</p> <p>Cause of death data from vital statistics registries from 1996 to 2007 with "good" or "average" quality of mortality data were examined. Standardized mortality rates and Poisson regression models by country were developed and differences among countries assessed to identify patterns of HIV mortality over time occurring in Latin America.</p> <p>Results</p> <p>Standardized HIV mortality following the adoption of public ART policies was highest in Panama and El Salvador and lowest in Chile. During the study period, three overall patterns were identified in HIV mortality trends- following the adoption of the free ART public policies; a remarkable decrement, a remarkable increment and a slight increment. HIV mortality was consistently higher in males compared to females. Mean age of death attributable to HIV increased in the majority of countries over the study period.</p> <p>Conclusions</p> <p>Vital statistics registries provide valuable information on HIV mortality in LA. While the introduction of national policies for free ART provision has coincided with declines in population-level HIV mortality and increasing age of death in some countries, in others HIV mortality has increased. Barriers to effective ART implementation and uptake in the context of free ART public provision policies should be further investigated.</p

Mechanisms of amyloid formation revealed by solution NMR

Amyloid fibrils are proteinaceous elongated aggregates involved in more than fifty human diseases. Recent advances in electron microscopy and solid state NMR have allowed the characterization of fibril structures to different extents of refinement. However, structural details about the mechanism of fibril formation remain relatively poorly defined. This is mainly due to the complex, heterogeneous and transient nature of the species responsible for assembly; properties that make them difficult to detect and characterize in structural detail using biophysical techniques. The ability of solution NMR spectroscopy to investigate exchange between multiple protein states, to characterize transient and low-population species, and to study high molecular weight assemblies, render NMR an invaluable technique for studies of amyloid assembly. In this article we review state-of-the-art solution NMR methods for investigations of: (a) protein dynamics that lead to the formation of aggregation-prone species; (b) amyloidogenic intrinsically disordered proteins; and (c) protein–protein interactions on pathway to fibril formation. Together, these topics highlight the power and potential of NMR to provide atomic level information about the molecular mechanisms of one of the most fascinating problems in structural biology

Visualization of novel virulence activities of the Xanthomonas type III effectors AvrBs1, AvrBs3 and AvrBs4.

International audienceXanthomonas campestris pv. vesicatoria secretes at least 20 effector proteins through the type III secretion system directly into plant cells. In this study, we uncovered virulence activities of the effector proteins AvrBs1, AvrBs3 and AvrBs4 using Agrobacterium-mediated transient expression of the corresponding genes in Nicotiana benthamiana, followed by microscopic analyses. We showed that, in addition to the nuclear-localized AvrBs3, the effector AvrBs1, which localizes to the plant cell cytoplasm, also induces a morphological change in mesophyll cells. Comparative analyses revealed that avrBs3-expressing plant cells contain highly active nuclei. Furthermore, plant cells expressing avrBs3 or avrBs1 show a decrease in the starch content in chloroplasts and an increased number of vesicles, indicating an enlargement of the central vacuole and the cell wall. Both AvrBs1 and AvrBs3 cause an increased ion efflux when expressed in N. benthamiana. By contrast, expression of the avrBs3 homologue avrBs4 leads to large catalase crystals in peroxisomes, suggesting a possible virulence function of AvrBs4 in the suppression of the plant defence responses. Taken together, our data show that microscopic inspection can uncover subtle and novel virulence activities of type III effector proteins

PRODORIC: prokaryotic database of gene regulation

The database PRODORIC aims to systematically organize information on prokaryotic gene expression, and to integrate this information into regulatory networks. The present version focuses on pathogenic bacteria such as Pseudomonas aeruginosa. PRODORIC links data on environmental stimuli with trans-acting transcription factors, cis-acting promoter elements and regulon definition. Interactive graphical representations of operon, gene and promoter structures including regulator-binding sites, transcriptional and translational start sites, supplemented with information on regulatory proteins are available at varying levels of detail. The data collection provided is based on exhaustive analyses of scientific literature and computational sequence prediction. Included within PRODORIC are tools to define and predict regulator binding sites. It is accessible at http://prodoric.tu-bs.de

Backscattering design for a focusing grating coupler with fully etched slots for transverse magnetic modes

Grating couplers are a fundamental building block of integrated optics as they allow light to be coupled from free-space to on-chip components and vice versa. A challenging task in designing any grating coupler is represented by the need for reducing back reflections at the waveguide-grating interface, which introduce additional losses and undesirable interference fringes. Here, we present a design approach for focusing TM grating couplers that minimizes these unwanted reflections by introducing a modified slot that fulfills an anti-reflection condition. We show that this antireflection condition can be met only for the Bloch mode of the grating that concentrates in the dielectric. As a consequence the light is scattered from the grating coupler with a negative angle, referred to as “backscattering design”. Our analytic model shows that the anti-reflection condition is transferrable to grating couplers on different waveguide platforms and that it applies for both TE and TM polarizations. Our experimentally realized focusing grating coupler for TM-modes on the silicon photonics platform has a coupling loss of (3.95 ± 0.15) dB at a wavelength of 1.55 µm. It has feature sizes above 200 nm and fully etched slots. The reflectivity between the grating coupler and the connected waveguide is suppressed to below 0.16%