Evaluating assumptions of scales for subjective assessment of thermal environments – Do laypersons perceive them the way, we researchers believe?

International audienc

Detection of Alpha-Rod Protein Repeats Using a Neural Network and Application to Huntingtin

A growing number of solved protein structures display an elongated structural domain, denoted here as alpha-rod, composed of stacked pairs of anti-parallel alpha-helices. Alpha-rods are flexible and expose a large surface, which makes them suitable for protein interaction. Although most likely originating by tandem duplication of a two-helix unit, their detection using sequence similarity between repeats is poor. Here, we show that alpha-rod repeats can be detected using a neural network. The network detects more repeats than are identified by domain databases using multiple profiles, with a low level of false positives (<10%). We identify alpha-rod repeats in approximately 0.4% of proteins in eukaryotic genomes. We then investigate the results for all human proteins, identifying alpha-rod repeats for the first time in six protein families, including proteins STAG1-3, SERAC1, and PSMD1-2 & 5. We also characterize a short version of these repeats in eight protein families of Archaeal, Bacterial, and Fungal species. Finally, we demonstrate the utility of these predictions in directing experimental work to demarcate three alpha-rods in huntingtin, a protein mutated in Huntington's disease. Using yeast two hybrid analysis and an immunoprecipitation technique, we show that the huntingtin fragments containing alpha-rods associate with each other. This is the first definition of domains in huntingtin and the first validation of predicted interactions between fragments of huntingtin, which sets up directions toward functional characterization of this protein. An implementation of the repeat detection algorithm is available as a Web server with a simple graphical output: http://www.ogic.ca/projects/ard. This can be further visualized using BiasViz, a graphic tool for representation of multiple sequence alignments

Characterization of a putative NsrR homologue in Streptomyces venezuelae reveals a new member of the Rrf2 superfamily

Members of the Rrf2 superfamily of transcription factors are widespread in bacteria but their functions are largely unexplored. The few that have been characterized in detail sense nitric oxide (NsrR), iron limitation (RirA), cysteine availability (CymR) and the iron sulfur (Fe-S) cluster status of the cell (IscR). In this study we combined ChIP-seq with in vitro biochemistry to characterize a putative NsrR homologue in the model organism Streptomyces venezuelae. ChIP seq analysis revealed that rather than regulating the nitrosative stress response like NsrR, Sven6563 binds to a different, much larger regulon of genes with a diverse range of functions, including a range of regulators, genes required for glutamine synthesis, NADH/NAD(P)H metabolism, as well as general DNA/RNA and amino acid/protein turn over. Our biochemical experiments further show that Sven6563 has a [2Fe-2S] cluster and that the switch between oxidized and reduced cluster controls its DNA binding activity in vitro. To our knowledge, both the sensing domain and the target gene regulon are novel for an Rrf2 protein, suggesting Sven6563 represents a new member of the Rrf2 superfamily. Given the redox sensitivity of its Fe-S cluster we have tentatively named the protein RsrR for Redox sensitive response Regulator

The Fission Yeast XMAP215 Homolog Dis1p Is Involved in Microtubule Bundle Organization

Microtubules are essential for a variety of fundamental cellular processes such as organelle positioning and control of cell shape. Schizosaccharomyces pombe is an ideal organism for studying the function and organization of microtubules into bundles in interphase cells. Using light microscopy and electron tomography we analyzed the bundle organization of interphase microtubules in S. pombe. We show that cells lacking ase1p and klp2p still contain microtubule bundles. In addition, we show that ase1p is the major determinant of inter-microtubule spacing in interphase bundles since ase1 deleted cells have an inter-microtubule spacing that differs from that observed in wild-type cells. We then identified dis1p, a XMAP215 homologue, as factor that promotes the stabilization of microtubule bundles. In wild-type cells dis1p partially co-localized with ase1p at regions of microtubule overlap. In cells deleted for ase1 and klp2, dis1p accumulated at the overlap regions of interphase microtubule bundles. In cells lacking all three proteins, both microtubule bundling and inter-microtubule spacing were further reduced, suggesting that Dis1p contributes to interphase microtubule bundling

Evaluation of groundwater quality and its suitability for drinking and agricultural use in Thanjavur city, Tamil Nadu, India

As groundwater is a vital source of water for domestic and agricultural activities in Thanjavur city due to lack of surface water resources, groundwater quality and its suitability for drinking and agricultural usage were evaluated. In this study, 102 groundwater samples were collected from dug wells and bore wells during March 2008 and analyzed for pH, electrical conductivity, temperature, major ions, and nitrate. Results suggest that, in 90% of groundwater samples, sodium and chloride are predominant cation and anion, respectively, and NaCl and CaMgCl are major water types in the study area. The groundwater quality in the study site is impaired by surface contamination sources, mineral dissolution, ion exchange, and evaporation. Nitrate, chloride, and sulfate concentrations strongly express the impact of surface contamination sources such as agricultural and domestic activities, on groundwater quality, and 13% of samples have elevated nitrate content (>45 mg/l as NO3). PHREEQC code and Gibbs plots were employed to evaluate the contribution of mineral dissolution and suggest that mineral dissolution, especially carbonate minerals, regulates water chemistry.Groundwater suitability for drinking usage was evaluated by the World Health Organization and Indian standards and suggests that 34% of samples are not suitable for drinking. Integrated groundwater suitability map for drinking purposes was created using drinking water standards based on a concept that if the groundwater sample exceeds any one of the standards, it is not suitable for drinking. This map illustrates that wells in zones 1, 2, 3, and 4 are not fit for drinking purpose. Likewise, irrigational suitability of groundwater in the study region was evaluated, and results suggest that 20% samples are not fit for irrigation. Groundwater suitability map for irrigation was also produced based on salinity and sodium hazards and denotes that wells mostly situated in zones 2 and 3 are not suitable for irrigation. Both integrated suitability maps for drinking and irrigation usage provide overall scenario about the groundwater quality in the study area. Finally, the study concluded that groundwater quality is impaired by man-made activities, and proper management plan is necessary to protect valuable groundwater resources inThanjavur city

Perennial Forages as Second Generation Bioenergy Crops

The lignocellulose in forage crops represents a second generation of biomass feedstock for conversion into energy-related end products. Some of the most extensively studied species for cellulosic feedstock production include forages such as switchgrass (Panicum virgatum L.), reed canarygrass (Phalaris arundinacea L.), and alfalfa (Medicago sativa L.). An advantage of using forages as bioenergy crops is that farmers are familiar with their management and already have the capacity to grow, harvest, store, and transport them. Forage crops offer additional flexibility in management because they can be used for biomass or forage and the land can be returned to other uses or put into crop rotation. Estimates indicate about 22.3 million ha of cropland, idle cropland, and cropland pasture will be needed for biomass production in 2030. Converting these lands to large scale cellulosic energy farming could push the traditional forage-livestock industry to ever more marginal lands. Furthermore, encouraging bioenergy production from marginal lands could directly compete with forage-livestock production