FTIR spectroelectrochemical study of the activation and inactivation processes of [NiFe] hydrogenases: effects of solvent isotope replacement and site-directed mutagenesis

The kinetics of the activation and anaerobic inactivation processes of Desulfovibrio gigas hydrogenase have been measured in D₂O by FTIR spectroelectrochemistry. A primary kinetic solvent isotope effect was observed for the inactivation process but not for the activation step. The kinetics of these processes have been also measured after replacement of a glutamic residue placed near the active site of an analogous [NiFe] hydrogenase from Desulfovibrio fructosovorans. Its replacement by a glutamine affected greatly the kinetics of the inactivation process but only slightly the activation process. The interpretation of the experimental results is that the rate-limiting step for anaerobic inactivation is the formation from water of a -OH^– bridge at the hydrogenase active site, and that Glu25 has a role in this step.Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00775-004-0559-7     

Discovery of superoxide reductase: an historical perspective

For more than 30 years, the only enzymatic system known to catalyze the elimination of superoxide was superoxide dismutase, SOD. SOD has been found in almost all organisms living in the presence of oxygen, including some anaerobic bacteria, supporting the notion that superoxide is a key and general component of oxidative stress. Recently, a new concept in the field of the mechanisms of cellular defense against superoxide has emerged. It was discovered that elimination of superoxide in some anaerobic and microaerophilic bacteria could occur by reduction, a reaction catalyzed by a small metalloenzyme thus named superoxide reductase, SOR. Having played a major role in this discovery, we describe here how the concept of superoxide reduction emerged and how it was experimentally substantiated independently in our laboratory.Abbreviations Dfx desulfoferrodoxin - SOD superoxide dismutase - SOR superoxide reductase     

Temporal requirement for hedgehog signaling in ventral telencephalic patterning

Hedgehog signaling is required for multiple aspects of brain development, including growth, the establishment of both dorsal and ventral midline patterning and the generation of specific cell types such as oligodendrocytes and interneurons. To identify more precisely when during development hedgehog signaling mediates these events, we directed the removal of hedgehog signaling within the brain by embryonic day 9 of development, using a FoxG1(Cre) driver line to mediate the removal of a conditional smoothened null allele. We observed a loss of ventral telencephalic patterning that appears to result from an initial lack of specification of these structures rather than by changes in proliferation or cell death. A further consequence of the removal of smoothened in these mice is the near absence of both oligodendrocytes and interneurons. Surprisingly, the dorsal midline appears to be patterned normally in these mutants. Together with previous analyses, the present results demonstrate that hedgehog signaling in the period between E9.0 and E12 is essential for the patterning of ventral regions and the generation of cell types that are thought to largely arise from them.     

Naming streets for physicians: "l'affaire Carrel"

In the 1970s, Paris and many other French cities named streets in honor of Alexis Carrel, the French physician, scientist, and Nobel laureate. Controversy erupted in the 1990s, when Carrel's right-wing political views were espoused by the National Front party. Honors such as street names require not only respected contributions to society, but also high standards of personal conduct. Paris has recently followed the lead of other French cities and has voted to remove Carrel's name from its streets.     

Antibodies to canine distemper and phocine distemper viruses in polar bears from the Canadian arctic

Serum samples collected from 200 polar bears (Ursus marititnus) from two populations in the Canadian arctic, the western Hudson Bay and Lancaster Sound populations, between 1989 and 1996, were tested for antibodies to canine distemper (CDV) and phocine distemper viruses (PDV) using virus neutralization. Antibodies to CDV and PDV were detected in 48 and six polar bears, respectively. All six bears that tested positive for PDV also tested positive for CDV; in only one case did the antibody titer for PDV exceed that of CDV. Differences in antibody prevalence to CDV were detected between populations and age classes but not sex or year of sampling.     

New stable isotope-mass spectrometric techniques for measuring fluxes through intact metabolic pathways in mammalian systems: introduction of moving pictures into functional genomics and biochemical phenotyping

The thesis of this review is that fully assembled metabolic pathways in living systems, rather than genes or proteins, are the true units of function in biology and biochemistry. A corollary is that measurement of metabolic fluxes (biochemical kinetics) is thereby required to understand biochemical control and gene function. Recent methodologic advances for improving observability of metabolic pathway fluxes in vivo are reviewed. Stable isotope-mass spectrometric techniques discussed here include mass isotopomer distribution analysis (combinatorial analysis), for measurement of polymerization biosynthesis; 2H(2)O administration, for measuring synthesis of DNA (i.e., cell proliferation), RNA, proteins, lipids, glycolipids and other classes of molecules; non-invasive probes of intracellular metabolism, by sampling secreted metabolites in accessible body fluids, after isotopic labeling of the intracellular pathway; and measurement of multiple molecular fluxes concurrently, particularly through use of 2H(2)O. Examples are given of pathway fluxes measured by each of these techniques, noting the often-surprising results. It is concluded that the introduction of "moving pictures" as tools for biochemical phenotyping could radically alter many signature areas of contemporary biology, including functional genomics, drug discovery and development, and disease research.     

the JigCell model builder and run manager

SUMMARY: We describe the JigCell Model Builder (JCMB), a tool for creating biochemical reaction network models. JCMB is designed for ease of use and its interface uses the standard spreadsheet metaphor. The JigCell Run Manager (JCRM) is a tool for organizing the large collections of simulation runs typically required by reaction network modeling activities. AVAILABILITY: JCMB and JCRM are part of the JigCell suite available at http://jigcell.biol.vt.edu.