Training doctoral students in critical thinking and experimental design using problem-based learning.

BACKGROUND: Traditionally, doctoral student education in the biomedical sciences relies on didactic coursework to build a foundation of scientific knowledge and an apprenticeship model of training in the laboratory of an established investigator. Recent recommendations for revision of graduate training include the utilization of graduate student competencies to assess progress and the introduction of novel curricula focused on development of skills, rather than accumulation of facts. Evidence demonstrates that active learning approaches are effective. Several facets of active learning are components of problem-based learning (PBL), which is a teaching modality where student learning is self-directed toward solving problems in a relevant context. These concepts were combined and incorporated in creating a new introductory graduate course designed to develop scientific skills (student competencies) in matriculating doctoral students using a PBL format. METHODS: Evaluation of course effectiveness was measured using the principals of the Kirkpatrick Four Level Model of Evaluation. At the end of each course offering, students completed evaluation surveys on the course and instructors to assess their perceptions of training effectiveness. Pre- and post-tests assessing students' proficiency in experimental design were used to measure student learning. RESULTS: The analysis of the outcomes of the course suggests the training is effective in improving experimental design. The course was well received by the students as measured by student evaluations (Kirkpatrick Model Level 1). Improved scores on post-tests indicate that the students learned from the experience (Kirkpatrick Model Level 2). A template is provided for the implementation of similar courses at other institutions. CONCLUSIONS: This problem-based learning course appears effective in training newly matriculated graduate students in the required skills for designing experiments to test specific hypotheses, enhancing student preparation prior to initiation of their dissertation research.

Indirect Antioxidant Effects of the Nitrite Anion: Focus on Xanthine Oxidase.

One electron reduction of nitrite (NO2 -) has been determined to be a significant, noncanonical source of nitric oxide (NO) with molybdopterin enzymes being identified as critical to this process. Of the molybdopterin enzymes identified as NO2 - reductases, xanthine oxidoreductase (XOR) is the most extensively studied. Paradoxically, XOR generates oxidants and thus can contribute to oxidative stress under inflammatory conditions when the oxidase form (XO) of XOR is abundant. However, under similar inflammatory conditions XO has been associated with NO generation, especially when NO2 - levels are elevated which begs the question: if reaction of nitrite with XO consumes electrons, then does it subsequently reduce oxidant generation? To address this question, electron paramagnetic resonance (EPR) was used, under controlled O2 tensions, to assess superoxide (O2 •-) generation by endothelial-bound XO plus xanthine and the resultant impact of introducing NO2 -. Nitrite diminished XO-derived O2 •- under hypoxia (1% O2) whereas at 21% O2, it had no impact. To confirm these results and discount contributions from the reaction of NO with O2 •-, molecular O2 consumption was assessed. The presence of NO2 - decreased the rate of XO/xanthine-dependent O2 consumption in a concentration-dependent manner with greater impact under hypoxic conditions (1% O2) compared to 21% O2. In a more biologic setting, NO2 - also diminished XO-dependent H2O2 formation in murine liver homogenates supplemented with xanthine. Interestingly, nitrate (NO3 -) did not alter XO-dependent O2 consumption at either 21% or 1% O2; yet it did slightly impact nitrite-mediated effects when present at 2:1 ratio vs. NO2 -. When combined, these data: 1) show a significant indirect antioxidant function for NO2 - by decreasing oxidant generation from XO, 2) demonstrate that both XO-derived H2O2 and O2 •- production are diminished by the presence of NO2 - and 3) incentivize further exploration of the difference between XO reaction with NO2 - vs. NO3 -.

Bicarbonate and active site zinc modulate the self-peroxidation of bovine copper-zinc superoxide dismutase.

Peroxidation reactions of copper-zinc superoxide dismutase (CuZn-SOD1) or its zinc-depleted form (CuE-SOD1) that likely also involve a component of bicarbonate buffer have been implicated in the pathophysiology of the neurodegenerative diseases amyotrophic lateral sclerosis (ALS), Alzheimer's Disease and Parkinson's Disease. Neither removal of the zinc ion nor adding bicarbonate had large effects on the self-peroxidation reaction of bovine SOD1, but the combination of zinc-deficiency and added bicarbonate caused major changes to the spin trapped SOD1-centred free radical. Removal of the active site zinc ion greatly decreased the formation of an unassigned SOD1-centred free radical in the reaction with the inorganic peroxide peroxynitrite. The results suggest that under cellular conditions ( approximately 5 mM bicarbonate) zinc-deficient SOD1 peroxidation could play a pathogenic role in neurodegenerative diseases.

Expression of a familial amyotrophic lateral sclerosis-associated mutant human superoxide dismutase in yeast leads to decreased mitochondrial electron transport.

Strains of Saccharomyces cerevisiae that express either the wild type or the amyotrophic lateral sclerosis-associated mutant human copper-zinc superoxide dismutase (SOD1) proteins A4V and G93A, respectively, in a yeast SOD1-deficient parent strain were used to investigate the hypothesis that expression of a mutant SOD1 protein causes deficient mitochondrial electron transport as a possible mechanism for disease induction. Mitochondria isolated from the wild type SOD1-expressing yeast were identical to mitochondria from the parent strain in heme content and activities of complexes II, III, and IV. Mitochondria isolated from the A4V-expressing yeast had decreased rates of electron transport in complexes II+III, III, and IV and corresponding decreases in hemes b, c-c1, and a-a3 content compared to mitochondria from wild type human SOD1-expressing yeast. Mitochondria isolated from G93A-expressing yeast had decreased rates of electron transport in complex IV and probably in complex II with a corresponding decrease in heme a-a3 content. These results suggest that mutant SOD1-expression causes defective electron transport complex assembly and that the yeast system will provide an excellent model for the study of the mechanism of mutant SOD1-induced mitochondrial electron transport defects.

Probing the free radicals formed in the metmyoglobin-hydrogen peroxide reaction.

The reaction between metmyoglobin and hydrogen peroxide results in the two-electron reduction of H2O2 by the protein, with concomitant formation of a ferryl-oxo heme and a protein-centered free radical. Sperm whale metmyoglobin, which contains three tyrosine residues (Tyr-103, Tyr-146, and Tyr-151) and two tryptophan residues (Trp-7 and Trp-14), forms a tryptophanyl radical at residue 14 that reacts with O2 to form a peroxyl radical and also forms distinct tyrosyl radicals at Tyr-103 and Tyr-151. Horse metmyoglobin, which lacks Tyr-151 of the sperm whale protein, forms an oxygen-reactive tryptophanyl radical and also a phenoxyl radical at Tyr-103. Human metmyoglobin, in addition to the tyrosine and tryptophan radicals formed on horse metmyoglobin, also forms a Cys-110-centered thiyl radical that can also form a peroxyl radical. The tryptophanyl radicals react both with molecular oxygen and with the spin trap 3,5-dibromo-4-nitrosobenzenesulfonic acid (DBNBS). The spin trap 5,5-dimethyl-1-pyrroline N-oxide (DMPO) traps the Tyr-103 radicals and the Cys-110 thiyl radical of human myoglobin, and 2-methyl-2-nitrosopropane (MNP) traps all of the tyrosyl radicals. When excess H2O2 is used, DBNBS traps only a tyrosyl radical on horse myoglobin, but the detection of peroxyl radicals and the loss of tryptophan fluorescence support tryptophan oxidation under those conditions. Kinetic analysis of the formation of the various free radicals suggests that tryptophanyl radical and tyrosyl radical formation are independent events, and that formation of the Cys-110 thiyl radical on human myoglobin occurs via oxidation of the thiol group by the Tyr-103 phenoxyl radical. Peptide mapping studies of the radical adducts and direct EPR studies at low temperature and room temperature support the conclusions of the EPR spin trapping studies.

Tryptophan-14 is the preferred site of DBNBS spin trapping in the self-peroxidation reaction of sperm whale metmyoglobin with a single equivalent of hydrogen peroxide.

The 3,5-dibromo-4-nitrosobenzenesulfonate (DBNBS)-metmyoglobin adduct formed following the horse metmyoglobin-H(2)O(2) reaction has been assigned to both a tyrosyl and a tryptophanyl residue radical. At low H(2)O(2), hyperfine coupling to a (13)C atom in sperm whale metmyoglobin labeled at the tryptophan residues with (13)C allowed the unequivocal assignment of the primary adduct to a tryptophanyl radical. Trapping at Trp-14 of sperm whale myoglobin was indicated by greatly decreased electron paramagnetic resonance (EPR) spectral intensity of the DBNBS adducts of the Trp-14-Phe recombinant proteins. Complex EPR spectra with partially resolved hyperfine splittings from several atoms were obtained by pronase treatment of the DBNBS/*W14F metmyoglobin adducts. The EPR spectra of authentic DBNBS/*Tyr adducts were incubation time-dependent; the late time spectra resembled the spectra of pronase-treated DBNBS/*W14F sperm whale myoglobin adducts, suggesting formation of an unstable tyrosyl radical adduct in the latter proteins. When the H(2)O(2):metmyoglobin ratio was increased to 5:1, the EPR spectrum after pronase treatment supported trapping of a tyrosyl radical, although similar decreases in tryptophan content were detected at H(2)O(2):metmyoglobin ratios of 1:1 and 5:1.

Nitric oxide trapping of the tyrosyl radical-chemistry and biochemistry.

The quenching of the Y(D) tyrosyl radical in photosystem II by nitric oxide was reported to result from the formation of a weak tyrosyl radical-nitric oxide complex. This radical/radical reaction is expected to generate an electron spin resonance (ESR)-silent nitrosocyclohexadienone species that can reversibly regenerate the tyrosyl radical and nitric oxide or undergo rearrangement to form 3-nitrosotyrosine. It has been proposed that 3-nitrosotyrosine can be oxidized by one electron to form the tyrosine iminoxyl radical (>C=N-O.). This proposal was put forth as a result of ESR detection of the iminoxyl radical intermediate when photosystem II was exposed to nitric oxide. Although the detection of the iminoxyl radical in photosystem II strongly suggested a mechanism involving 3-nitrosotyrosine, the iminoxyl radical ESR spectrum was not unequivocally identified as originating from tyrosine. Subsequently, non-protein L-tyrosine iminoxyl radical was generated by two methods: (1) peroxidase oxidation of synthetic 3-nitroso-N-acetyl-L-tyrosine; and (2) peroxidase oxidation of free L-tyrosine in the presence of nitric oxide. The determination of protein nitrotyrosine content has become a frequently used technique for the detection of nitrosative tissue damage. Protein nitration has been suggested to be a final product of the production of highly reactive nitrogen oxide intermediates (e.g. peroxynitrite) formed in reactions between nitric oxide (NO.) and oxygen-derived species such as superoxide. The enzyme prostaglandin H synthase-2 also forms a tyrosyl radical during its enzymatic catalysis of prostaglandin formation. In the presence of the NO.-generator diethylamine nonoate, the tyrosyl radical of prostaglandin H synthase-2 also changes to that of an iminoxyl radical. Western blot analysis of prostaglandin H synthase-2 after exposure to the NO.-generator revealed nitrotyrosine formation. The results provide a mechanism for nitric oxide-dependent tyrosine nitration that does not require formation of more highly reactive nitrogen oxide intermediates such as peroxynitrite or nitrogen dioxide.

Peroxyl adduct radicals formed in the iron/oxygen reconstitution reaction of mutant ribonucleotide reductase R2 proteins from Escherichia coli.

Catalytically important free radicals in enzymes are generally formed at highly specific sites, but the specificity is often lost in point mutants where crucial residues have been changed. Among the transient free radicals earlier found in the Y122F mutant of protein R2 in Escherichia coli ribonucleotide reductase after reconstitution with Fe2+ and O2, two were identified as tryptophan radicals. A third radical has an axially symmetric EPR spectrum, and is shown here using 17O exchange and simulations of EPR spectra to be a peroxyl adduct radical. Reconstitution of other mutants of protein R2 (i.e. Y122F/W48Y and Y122F/W107Y) implicates W48 as the origin of the peroxyl adduct. The results indicate that peroxyl radicals form on primary transient radicals on surface residues such as W48, which is accessible to oxygen. However, the specificity of the reaction is not absolute since the single mutant W48Y also gives rise to a peroxyl adduct radical. We used density functional calculations to investigate residue-specific effects on hyperfine coupling constants using models of tryptophan, tyrosine, glycine and cysteine. The results indicate that any peroxyl adduct radical attached to the first three amino acid alpha-carbons gives similar 17O hyperfine coupling constants. Structural arguments and experimental results favor W48 as the major site of peroxyl adducts in the mutant Y122F. Available molecular oxygen can be considered as a spin trap for surface-located protein free radicals.

Histidinyl radical formation in the self-peroxidation reaction of bovine copper-zinc superoxide dismutase.

In the absence of suitable oxidizable substrates, the peroxidase reaction of copper-zinc superoxide dismutase (SOD) oxidizes SOD itself, ultimately resulting in its inactivation. A SOD-centered free radical adduct of 2-methyl-2-nitrosopropane (MNP) was detected upon incubation of SOD with the spin trap and a hydroperoxide (either H(2)O(2) or peracetic acid). Proteolysis by Pronase converted the anisotropic electron paramagnetic resonance (EPR) spectrum of MNP/(center dot)SOD to a nearly isotropic spectrum with resolved hyperfine couplings to several atoms with non-zero nuclear spin. Authentic histidinyl radical (from histidine + HO(center dot)) formed a MNP adduct with a very similar EPR spectrum to that of the Pronase-treated MNP/(center dot)SOD, suggesting that the latter was centered on a histidine residue. An additional hyperfine coupling was detected when histidine specifically (13)C-labeled at C-2 of the imidazole ring was used, providing evidence for trapping at that atom. All of the experimental spectra were convincingly simulated assuming hyperfine couplings to 2 nearly equivalent nitrogen atoms and 2 different protons, also consistent with trapping at C-2 of the imidazole ring. Free histidinyl radical consumed oxygen, implying peroxyl radical formation. MNP-inhibitable oxygen consumption was also observed when cuprous SOD but not cupric SOD was added to a H(2)O(2) solution. Formation of 2-oxohistidine, the stable product of the SOD-hydroperoxide reaction, required oxygen and was inhibited by MNP. These results support formation of a transient SOD-peroxyl radical.