Transurethral Radiofrequency Collagen Denaturation for Treatment of Female Stress Urinary Incontinence: A Review of the Literature and Clinical Recommendations

Stress urinary incontinence is a prevalent condition in women with a significant negative effect on quality of life. Intervention includes behavioral modification, intravaginal devices, pelvic floor muscle exercises, biofeedback, functional electrical stimulation, and surgical procedures. We will review a new in-office procedure for the treatment of SUI that may serve as a viable nonsurgical option

Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection

The accuracy of a homology model based on the structure of a distant relative or other topologically equivalent protein is primarily limited by the quality of the alignment. Here we describe a systematic approach for sequence-to-structure alignment, called ‘K*Sync’, in which alignments are generated by dynamic programming using a scoring function that combines information on many protein features, including a novel measure of how obligate a sequence region is to the protein fold. By systematically varying the weights on the different features that contribute to the alignment score, we generate very large ensembles of diverse alignments, each optimal under a particular constellation of weights. We investigate a variety of approaches to select the best models from the ensemble, including consensus of the alignments, a hydrophobic burial measure, low- and high-resolution energy functions, and combinations of these evaluation methods. The effect on model quality and selection resulting from loop modeling and backbone optimization is also studied. The performance of the method on a benchmark set is reported and shows the approach to be effective at both generating and selecting accurate alignments. The method serves as the foundation of the homology modeling module in the Robetta server

How Our Health Depends on Biodiversity

The eminent Harvard biology Professor Edward O.Wilson once said about ants, “We need them to survive, but they don’t need us at all.” The same, in fact, could be said about countless other insects, bacteria, fungi, plankton, plants, and other organisms. This fundamental truth, however, is largely lost to many of us. Rather, we humans often act as if we are totally independent of Nature, as if our driving thousands of other species to extinction and disrupting the life-giving services they provide will have no effect on us whatsoever. This summary, using concrete examples from our award-winning Oxford University Press book, Sustaining Life: How Human Health Depends on Biodiversity, co-sponsored by the U.N. (CBD Secretariat, UNEP, and UNDP) and the International Union for the Conservation of Nature (IUCN), has been prepared to demonstrate that human beings are an integral, inseparable part of the natural world, and that our health depends ultimately on the health of its species and on the natural functioning of its ecosystems

Climate change and extreme weather events - Implications for food production, plant diseases, and pests

Current and future energy use from burning of fossil fuels and clearing of forests for cultivation can have profound effects on the global environment, agriculture, and the availability of low-cost, high-quality food for humans. Individual farmers and consumers are expected to be affected by changes in global and regional climate. The agricultural sector in both developing and developed areas needs to understand what is at stake and to prepare for the potential for change wisely. Despite tremendous improvements in technology and crop yield potential, food production remains highly dependent on climate, because solar radiation, temperature, and precipitation are the main drivers of crop growth. Plant diseases and pest infestations, as well as the supply of and demand for irrigation water are influenced by climate. For example, in recent decades, the persistent drought in the Sahelian region of Africa has caused continuing deterioration of food production; the 1988 Midwest drought led to a 30% reduction in U.S. corn production and cost taxpayers $3 billion in direct relief payments to farmers and, weather anomalies associated with the 1997-98 El Niño affected agriculture adversely in Nordeste, Brazil and Indonesia. Earlier in the century, the 1930s U.S. Southern Great Plains drought caused some 200,000 farm bankruptcies in the Dust Bowl; yields of wheat and corn were reduced by as much as 50%

GLAMM: Genome-Linked Application for Metabolic Maps

The Genome-Linked Application for Metabolic Maps (GLAMM) is a unified web interface for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic networks and investigating the construction of novel, transgenic pathways. This simple, user-friendly interface is tightly integrated with the comparative genomics tools of MicrobesOnline [Dehal et al. (2010) Nucleic Acids Research, 38, D396–D400]. GLAMM is available for free to the scientific community at glamm.lbl.gov

Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology

Saccharomyces cerevisiae is one of the best-studied model organisms, yet the three-dimensional structure and molecular function of many yeast proteins remain unknown. Yeast proteins were parsed into 14,934 domains, and those lacking sequence similarity to proteins of known structure were folded using the Rosetta de novo structure prediction method on the World Community Grid. This structural data was integrated with process, component, and function annotations from the Saccharomyces Genome Database to assign yeast protein domains to SCOP superfamilies using a simple Bayesian approach. We have predicted the structure of 3,338 putative domains and assigned SCOP superfamily annotations to 581 of them. We have also assigned structural annotations to 7,094 predicted domains based on fold recognition and homology modeling methods. The domain predictions and structural information are available in an online database at http://rd.plos.org/10.1371_journal.pbio.0050076_01

Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron

Tropical forest soils decompose litter rapidly with frequent episodes of anoxia, making it likely that bacteria using alternate terminal electron acceptors (TEAs) such as iron play a large role in supporting decomposition under these conditions. The prevalence of many types of metabolism in litter deconstruction makes these soils useful templates for improving biofuel production. To investigate how iron availability affects decomposition, we cultivated feedstock-adapted consortia (FACs) derived from iron-rich tropical forest soils accustomed to experiencing frequent episodes of anaerobic conditions and frequently fluctuating redox. One consortium was propagated under fermenting conditions, with switchgrass as the sole carbon source in minimal media (SG only FACs), and the other consortium was treated the same way but received poorly crystalline iron as an additional terminal electron acceptor (SG + Fe FACs). We sequenced the metagenomes of both consortia to a depth of about 150 Mb each, resulting in a coverage of 26× for the more diverse SG + Fe FACs, and 81× for the relatively less diverse SG only FACs. Both consortia were able to quickly grow on switchgrass, and the iron-amended consortium exhibited significantly higher microbial diversity than the unamended consortium. We found evidence of higher stress in the unamended FACs and increased sugar transport and utilization in the iron-amended FACs. This work provides metagenomic evidence that supplementation of alternative TEAs may improve feedstock deconstruction in biofuel production

High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater.

Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction