Investigating hookworm genomes by comparative analysis of two Ancylostoma species

Background Hookworms, infecting over one billion people, are the mostly closely related major human parasites to the model nematode Caenorhabditis elegans. Applying genomics techniques to these species, we analyzed 3,840 and 3,149 genes from Ancylostoma caninum and A. ceylanicum. Results Transcripts originated from libraries representing infective L3 larva, stimulated L3, arrested L3, and adults. Most genes are represented in single stages including abundant transcripts like hsp-20 in infective L3 and vit-3 in adults. Over 80% of the genes have homologs in C. elegans, and nearly 30% of these were with observable RNA interference phenotypes. Homologies were identified to nematode-specific and clade V specific gene families. To study the evolution of hookworm genes, 574 A. caninum / A. ceylanicum orthologs were identified, all of which were found to be under purifying selection with distribution ratios of nonsynonymous to synonymous amino acid substitutions similar to that reported for C. elegans / C. briggsae orthologs. The phylogenetic distance between A. caninum and A. ceylanicum is almost identical to that for C. elegans / C. briggsae. Conclusion The genes discovered should substantially accelerate research toward better understanding of the parasites' basic biology as well as new therapies including vaccines and novel anthelmintics

Theory of periodic swarming of bacteria: application to Proteus mirabilis

The periodic swarming of bacteria is one of the simplest examples for pattern formation produced by the self-organized collective behavior of a large number of organisms. In the spectacular colonies of Proteus mirabilis (the most common species exhibiting this type of growth) a series of concentric rings are developed as the bacteria multiply and swarm following a scenario periodically repeating itself. We have developed a theoretical description for this process in order to get a deeper insight into some of the typical processes governing the phenomena in systems of many interacting living units. All of our theoretical results are in excellent quantitative agreement with the complete set of available observations.Comment: 11 pages, 8 figure

Developments in Performance Monitoring of Concrete Exposed to Extreme Environments.

The performance of the surface zone of concrete is acknowledged as a major factor governing the rate of deterioration of reinforced concrete structures because it provides the only barrier to the ingress of water containing dissolved ionic species such as chlorides, which ultimately initiate corrosion of the reinforcement. In situ monitoring of cover-zone concrete is therefore critical in attempting to make realistic predictions as to the in-service performance of the structure. To this end, this paper presents developments in a remote interrogation system to allow for continuous, real-time monitoring of the cover-zone concrete from an office setting. Use is made of a multi electrode array embedded within cover-zone concrete to acquire discretized electrical resistivity and temperature measurements, with both parameters monitored spatially and temporally. On-site instrumentation, which allows for the remote interrogation of concrete samples placed at a marine exposure site, is detailed together with data handling and processing procedures. Site measurements highlight the influence of temperature on electrical resistivity and an Arrhenius-based temperature correction protocol is developed using on-site measurements to standardize resistivity data to a reference temperature; this is an advancement over the use of laboratory-based procedures. The testing methodology and interrogation system represent a robust, low-cost, and high-value technique that could be deployed for intelligent monitoring of reinforced concrete structures

Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics

Nematode.net (http://nematode.net) is a publicly available resource dedicated to the study of parasitic nematodes. In 2000, the Genome Center at Washington University (GC) joined a consortium including the Nematode Genomics group in Edinburgh, and the Pathogen Sequencing Unit of the Sanger Institute to generate expressed sequence tags (ESTs) as an inexpensive and efficient solution for gene discovery in parasitic nematodes. As of 2008 the GC, sampling key parasites of humans, animals and plants, has generated over 500 000 ESTs and 1.2 million genome survey sequences from more than 30 non-Caenorhabditis elegans nematodes. Nematode.net was implemented to offer user-friendly access to data produced by this project. In addition to sequence data, the site hosts: assembled NemaGene clusters in GBrowse views characterizing composition and protein homology, functional Gene Ontology annotations presented via the AmiGO browser, KEGG-based graphical display of NemaGene clusters mapped to metabolic pathways, codon usage tables, NemFam protein families which represent conserved nematode-restricted coding sequences not found in public protein databases, a web-based WU-BLAST search tool that allows complex querying and other assorted resources. The primary aim of Nematode.net is the dissemination of this diverse collection of information to the broader scientific community in a way that is useful, consistent, centralized and enduring

Towards a mechanistic understanding of linguistic diversity

Our species displays remarkable linguistic diversity. While the uneven distribution of this diversity demands explanation, the drivers of these patterns have not been conclusively determined. We address this issue in two steps. First, we review previous empirical studies that have suggested environmental, geographical, and socio-cultural drivers of linguistic diversification. However, contradictory results and methodological variation make it difficult to draw general conclusions. Second, we outline a program for future research. We suggest that future analyses should account for interactions among causal factors, lack of spatial and phylogenetic independence of data, and transitory patterns. Recent analytical advances in biogeography and evolutionary biology, such as simulation modeling of diversity patterns, hold promise for testing four key mechanisms of language diversification proposed here: neutral change, population movement, contact, and selection. Future modeling approaches should also evaluate how the outcomes of these processes are influenced by demography, environmental heterogeneity, and time

ASL expression in ALDH1A1+ neurons in the substantia nigra metabolically contributes to neurodegenerative phenotype

Argininosuccinate lyase (ASL) is essential for the NO-dependent regulation of tyrosine hydroxylase (TH) and thus for catecholamine production. Using a conditional mouse model with loss of ASL in catecholamine neurons, we demonstrate that ASL is expressed in dopaminergic neurons in the substantia nigra pars compacta, including the ALDH1A1 + subpopulation that is pivotal for the pathogenesis of Parkinson disease (PD). Neuronal loss of ASL results in catecholamine deficiency, in accumulation and formation of tyrosine aggregates, in elevation of α-synuclein, and phenotypically in motor and cognitive deficits. NO supplementation rescues the formation of aggregates as well as the motor deficiencies. Our data point to a potential metabolic link between accumulations of tyrosine and seeding of pathological aggregates in neurons as initiators for the pathological processes involved in neurodegeneration. Hence, interventions in tyrosine metabolism via regulation of NO levels may be therapeutic beneficial for the treatment of catecholamine-related neurodegenerative disorders

MAPK feedback encodes a switch and timer for tunable stress adaptation in yeast

Signaling pathways can behave as switches or rheostats, generating binary or graded responses to a given cell stimulus. We evaluated whether a single signaling pathway can simultaneously encode a switch and a rheostat. We found that the kinase Hog1 mediated a bifurcated cellular response: Activation and commitment to adaptation to osmotic stress are switch-like, whereas protein induction and the resolution of this commitment are graded. Through experimentation, bioinformatics analysis, and computational modeling, we determined that graded recovery is encoded through feedback phosphorylation and a gene induction program that is both temporally staggered and variable across the population. This switch-to-rheostat signaling mechanism represents a versatile stress adaptation system, wherein a broad range of inputs generate an “all-in” response that is later tuned to allow graded recovery of individual cells over time

Production of highly-polarized positrons using polarized electrons at MeV energies

The Polarized Electrons for Polarized Positrons experiment at the injector of the Continuous Electron Beam Accelerator Facility has demonstrated for the first time the efficient transfer of polarization from electrons to positrons produced by the polarized bremsstrahlung radiation induced by a polarized electron beam in a high-$Z$ target. Positron polarization up to 82\% have been measured for an initial electron beam momentum of 8.19~MeV/$c$, limited only by the electron beam polarization. This technique extends polarized positron capabilities from GeV to MeV electron beams, and opens access to polarized positron beam physics to a wide community.Comment: 5 pages, 4 figure

A Galvanic Sensor for Monitoring the Corrosion Condition of the Concrete Reinforcing Steel: Relationship Between the Galvanic and the Corrosion Currents

This work reports a study carried out on the design and performance of galvanic and polarization resistance sensors to be embedded in concrete systems for permanent monitoring of the corrosion condition of reinforcing steel, aiming to establish a correlation between the galvanic currents, Igal, and the corrosion currents, Icorr, estimated from the polarization resistance, Rp. Sensors have been tested in saturated Ca(OH)2 aqueous solutions, under a variety of conditions, simulating the most important parameters that can accelerate the corrosion of concrete reinforcing steel, such as carbonation, ingress of chloride ions, presence or absence of O2. For all the conditions, the influence of temperature (20 to 55 °C) has also been considered. From this study, it could be concluded that the galvanic currents are sensitive to the various parameters following a trend similar to that of the Rp values. A relationship between the galvanic and the corrosion current densities was obtained and the limiting values of the Igal, indicative of the state condition of the reinforcing steel for the designed sensor, were established