Genetic and physical map of the 2,4-dichlorophenoxyacetic acid-degradative plasmid pJP4.

Plasmid pJP4 is an 80-kilobase, IncP1, broad-host-range conjugative plasmid of Alcaligenes eutrophus encoding resistance to mercuric chloride and phenyl mercury acetate and degradation of 2,4-dichlorophenoxyacetic acid, 2-methyl-4-chlorophenoxyacetic acid, and 3-chlorobenzoate. By the use of cloning, transposon mutagenesis, and restriction endonuclease analysis, a biophysical and genetic map of pJP4 was generated.     

Constitutive expression of methyl jasmonate-inducible responses delays reproduction and constrains fitness responses to nutrients in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

The analysis of a suite of traits under a range of environmental conditions is necessary to fully examine costs of resistance. I compared phenological, morphological and reproductive traits of several independent lines of a transgenic methyl jasmonate-overproducing Arabidopsis thaliana plant (JMT plants) to that of vector controls in high and low soil nutrient environments. JMT plants constitutively express a suite of responses normally inducible by wounding or jasmonate. JMT plants showed a marked delay in flowering time, and were larger with more leaves at bolting than vector controls. These traits also responded more positively to increased nutrients in JMT plants than in vector controls. At the end of the season, total seed mass and seed number was lower in JMT plants than in vector controls overall, and these traits responded much less positively to nutrient addition in JMT plants than in vector controls. This study revealed delayed phenology as a novel cost of resistance in Arabidopsis and that overproduction of methyl jasmonate and associate responses can substantially constrain fitness responses to nutrients. These results establish a mechanism whereby costs of resistance can be more apparent under high resource conditions, rather than under low resource conditions, as is widely assumed.     

Viral discovery and sequence recovery using DNA microarrays

Because of the constant threat posed by emerging infectious diseases and the limitations of existing approaches used to identify new pathogens, there is a great demand for new technological methods for viral discovery. We describe herein a DNA microarray-based platform for novel virus identification and characterization. Central to this approach was a DNA microarray designed to detect a wide range of known viruses as well as novel members of existing viral families; this microarray contained the most highly conserved 70mer sequences from every fully sequenced reference viral genome in GenBank. During an outbreak of severe acute respiratory syndrome (SARS) in March 2003, hybridization to this microarray revealed the presence of a previously uncharacterized coronavirus in a viral isolate cultivated from a SARS patient. To further characterize this new virus, approximately 1 kb of the unknown virus genome was cloned by physically recovering viral sequences hybridized to individual array elements. Sequencing of these fragments confirmed that the virus was indeed a new member of the coronavirus family. This combination of array hybridization followed by direct viral sequence recovery should prove to be a general strategy for the rapid identification and characterization of novel viruses and emerging infectious disease.     

Metamorphosis of the olfactory organ of the sea lamprey (Petromyzon marinus L.): Morphological changes and morphometric analysis

In larval sea lampreys (Petromyzon marinus), a small, relatively inconspicuous olfactory organ sac contains small, densely packed olfactory receptor neurons and sustentacular cells. During metamorphosis, the larval organ transforms into a prominent lamellar structure with large distinct olfactory epithelial cells that is characteristic of the adult lamprey. In the present study, scanning electron microscopy and light microscopy are used to examine changes during the seven stages (1–7) of metamorphosis. The magnitude of growth over the course of metamorphosis is evident from the doubling of the relative weight of the nasal sac. During early metamorphosis (stages 1 and 2), the larval olfactory organ enlarges, and by stage 3 specific adult structures begin to form, namely a nasal valve between the nasal tube and the organ, lamellar folds, and diverticuli of the accessory olfactory organ. Subsequent development involves widening of the cells lining the lamellar folds to the form characteristic of postmetamorphic lampreys. Although the cells in the troughs initially retain numerical density values that are significantly higher than those on the lamellar surfaces, by stage 7 values decline both in troughs and along lamellar surfaces to those observed in adults. These results show that although expansion of the olfactory organ is ongoing throughout metamorphosis, remodeling occurs early (by stage 3). This timing provides space for extensive olfactory receptor neuron neurogenesis and differentiation and correlates with the transformation of some organs that were previously examined. This is the first report in any species of olfactory receptor neuron zonation based on morphometric characteristics. J. Morphol. 231:41–52, 1997. © 1997 Wiley-Liss, Inc.     

Pise: software for building bioinformatics webs

Pise is interface construction software for bioinformatics applications that run by command-line operations. It creates common, easy-to-use interfaces to these applications for the Web, or other uses. It is adaptable to new bioinformatics tools, and offers program chaining, Unix system batch and other controls, making it an attractive method for building and using your own bioinformatics web services.     

Seasonal variation in migration strategies used to cross ecological barriers in a nearctic migrant wintering in Africa

Ecological barriers such as oceans, mountain ranges or glaciers can have a substantial influence on the evolution of animal migration. Along the migration flyway connecting breeding sites in the North American Arctic and wintering grounds in Europe or Africa, nearctic species are confronted with significant barriers such as the Atlantic Ocean and the Greenland icecap. Using geolocation devices, we identified wintering areas used by ringed plovers nesting in the Canadian High‐Arctic and investigated migration strategies used by these nearctic migrants along the transatlantic route. The main wintering area of the ringed plovers (n = 20) was located in western Africa. We found contrasting seasonal migration patterns, with ringed plovers minimizing continuous flight distances over the ocean in spring by making a detour to stop in Iceland. In autumn, however, most individuals crossed the ocean in one direct flight from southern Greenland to western Europe, as far as southern Spain. This likely resulted from prevailing anti‐clockwise winds associated with the Icelandic low‐pressure system. Moreover, the plovers we tracked largely circumvented the Greenland icecap in autumn, but in spring, some plovers apparently crossed the icecap above the 65°N. Our study highlighted the importance of Iceland as a stepping‐stone during the spring migration and showed that small nearctic migrants can perform non‐stop transatlantic flights from Greenland to southern Europe.     

Identification and functional characterization of TMEM16A, a Ca2+-activated Cl- channel activated by extracellular nucleotides, in biliary epithelium

Cl(-) channels in the apical membrane of biliary epithelial cells (BECs) provide the driving force for ductular bile formation. Although a cystic fibrosis transmembrane conductance regulator has been identified in BECs and contributes to secretion via secretin binding basolateral receptors and increasing [cAMP](i), an alternate Cl(-) secretory pathway has been identified that is activated via nucleotides (ATP, UTP) binding apical P2 receptors and increasing [Ca(2+)](i). The molecular identity of this Ca(2+)-activated Cl(-) channel is unknown. The present studies in human, mouse, and rat BECs provide evidence that TMEM16A is the operative channel and contributes to Ca(2+)-activated Cl(-) secretion in response to extracellular nucleotides. Furthermore, Cl(-) currents measured from BECs isolated from distinct areas of intrahepatic bile ducts revealed important functional differences. Large BECs, but not small BECs, exhibit cAMP-stimulated Cl(-) currents. However, both large and small BECs express TMEM16A and exhibit Ca(2+)-activated Cl(-) efflux in response to extracellular nucleotides. Incubation of polarized BEC monolayers with IL-4 increased TMEM16A protein expression, membrane localization, and transepithelial secretion (I(sc)). These studies represent the first molecular identification of an alternate, noncystic fibrosis transmembrane conductance regulator, Cl(-) channel in BECs and suggest that TMEM16A may be a potential target to modulate bile formation in the treatment of cholestatic liver disorders.     

Messenger RNA oxidation occurs early in disease pathogenesis and promotes motor neuron degeneration in ALS

Background

Accumulating evidence indicates that RNA oxidation is involved in a wide variety of neurological diseases and may be associated with neuronal deterioration during the process of neurodegeneration. However, previous studies were done in postmortem tissues or cultured neurons. Here, we used transgenic mice to demonstrate the role of RNA oxidation in the process of neurodegeneration.

Methodology/Principal Findings

We demonstrated that messenger RNA (mRNA) oxidation is a common feature in amyotrophic lateral sclerosis (ALS) patients as well as in many different transgenic mice expressing familial ALS-linked mutant copper-zinc superoxide dismutase (SOD1). In mutant SOD1 mice, increased mRNA oxidation primarily occurs in the motor neurons and oligodendrocytes of the spinal cord at an early, pre-symptomatic stage. Identification of oxidized mRNA species revealed that some species are more vulnerable to oxidative damage, and importantly, many oxidized mRNA species have been implicated in the pathogenesis of ALS. Oxidative modification of mRNA causes reduced protein expression. Reduced mRNA oxidation by vitamin E restores protein expression and partially protects motor neurons.

Conclusion/Significance

These findings suggest that mRNA oxidation is an early event associated with motor neuron deterioration in ALS, and may be also a common early event preceding neuron degeneration in other neurological diseases.