The nitrite anion binds to human hemoglobin via the uncommon O-nitrito mode

The nitrite anion is known to oxidize and degrade hemoglobin (Hb). Recent literature reports suggest a nitrite reductase activity for Hb, converting nitrite into nitric oxide. Surprisingly, no structural information about Hb-nitrite interactions has been reported. We have determined the crystal structure of the ferric Hb-nitrite complex at 1.80 A resolution. The nitrite ligand adopts the uncommon O-nitrito binding mode. In addition, the nitrito conformations in the alpha and beta subunits are different, reflecting subtle effects of the distal His in orienting the nitrite ligand in the O-nitrito binding mode.     

Biomarkers: in combination they may do better

The field of biomarkers is a growing one, particularly in osteoarthritis (OA). OA is the most common disabling condition in older persons and a major cause of morbidity. While the debate continues about which of the involved tissues - cartilage, bone or synovium - is the most important in OA aetiology, there is no doubt that the three develop abnormalities in concert; perhaps a truly useful biomarker will reflect just that. While efforts continue to identify reliable biomarkers useful for characterising the status, prognosis and measurement of treatment response in OA, combining existing biomarkers to improve their accuracy looks promising.     

Vitamin D status and determinants of deficiency in non-supplemented athletes during the winter months in Tunisia

Recent reports suggest that hypovitaminosis D in athletes is as common as in the general population. This study was devised to examine vitamin D status and determinants of deficiency in athletes living in a sunny country (Tunisia). One hundred and fifty national elite athletes, training outdoors (n = 83) or indoors (n = 67), were enrolled from January to February 2012. Plasma 25-hydroxyvitamin D was measured by radioimmunoassay. Concentrations were between 50 and 75 nmol · l^-1 in 21.3% of participants, between 25 and 50 nmol · l^-1 in 55.3% of participants and <25 nmol · l^-1 in 14.7% of participants. The concentrations were significantly lower in indoor athletes than outdoor athletes (36.2±19.0 nmol · l^-1 vs. 49.1±19.2 nmol · l^-1; p < 0.001). In multivariate analysis, vitamin D deficiency (25-hydroxyvitamin D <50 nmol · l^-1) was associated with indoor sports [multi-adjusted odds ratio (95% confidence interval), 5.03 (1.64-15.4); p = 0.005], female gender [3.72 (1.44-9.65); p = 0.007] and age < 18 years [2.40 (1.01-5.85); p = 0.05]. Athletes living in sun-rich environments are exposed to a high risk of vitamin D inadequacy. Given the importance of vitamin D in health and athletic ability, targeting sufficient levels of plasma 25-hydroxyvitamin D in athletes is well justified.     

Multiplex quantitative PCR for detection of lower respiratory tract infection and meningitis caused by <Emphasis Type="Italic">Streptococcus pneumoniae</Emphasis>, <Emphasis Type="Italic">Haemophilus influenzae</Emphasis> and <Emphasis Type="Italic">Neisseria meningitidis</Emphasis>

Background  

Streptococcus pneumoniae and Haemophilus influenzae cause pneumonia and as Neisseria meningitidis they are important agents of meningitis. Although several PCR methods have been described for these bacteria the specificity is an underestimated problem. Here we present a quantitative multiplex real-time PCR (qmPCR) for detection of S. pneumoniae (9802 gene fragment), H. influenzae (omp P6 gene) and N. meningitidis (ctrA gene). The method was evaluated on bronchoalveolar lavage (BAL) samples from 156 adults with lower respiratory tract infection (LRTI) and 31 controls, and on 87 cerebrospinal fluid (CSF) samples from meningitis patients.     

Structure and mechanism of Escherichia coli pyridoxine 5'-phosphate oxidase

Escherichia coli pyridoxine 5'-phosphate oxidase (PNPOx) catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP), forming pyridoxal 5'-phosphate (PLP). This reaction serves as the terminal step in the de novo biosynthesis of PLP in E. coli and as a part of the salvage pathway of this coenzyme in both E. coli and mammalian cells. Recent studies have shown that in addition to the active site, PNPOx contains a noncatalytic site that binds PLP tightly. The crystal structures of PNPOx with one and two molecules of PLP bound have been determined. In the active site, the PLP pyridine ring is stacked almost parallel against the re-face of the middle ring of flavin mononucleotide (FMN). A large protein conformational change occurs upon binding of PLP. When the protein is soaked with excess PLP an additional molecule of this cofactor is bound about 11 A from the active site. A possible tunnel exists between the two sites. Site mutants were made of all residues at the active site that make interactions with the substrate. Stereospecificity studies showed that the enzyme is specific for removal of the proR hydrogen atom from the prochiral C4' carbon of PMP. The crystal structure and the stereospecificity studies suggest that the pair of electrons on C4' of the substrate are transferred to FMN as a hydride ion.     

A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates [published erratum appears in Mol Biol Evol 1995 May;12(3):525]

Using simulated data, we compared five methods of phylogenetic tree estimation: parsimony, compatibility, maximum likelihood, Fitch- Margoliash, and neighbor joining. For each combination of substitution rates and sequence length, 100 data sets were generated for each of 50 trees, for a total of 5,000 replications per condition. Accuracy was measured by two measures of the distance between the true tree and the estimate of the tree, one measure sensitive to accuracy of branch lengths and the other not. The distance-matrix methods (Fitch- Margoliash and neighbor joining) performed best when they were constrained from estimating negative branch lengths; all comparisons with other methods used this constraint. Parsimony and compatibility had similar results, with compatibility generally inferior; Fitch- Margoliash and neighbor joining had similar results, with neighbor joining generally slightly inferior. Maximum likelihood was the most successful method overall, although for short sequences Fitch- Margoliash and neighbor joining were sometimes better. Bias of the estimates was inferred by measuring whether the independent estimates of a tree for different data sets were closer to the true tree than to each other. Parsimony and compatibility had particular difficulty with inaccuracy and bias when substitution rates varied among different branches. When rates of evolution varied among different sites, all methods showed signs of inaccuracy and bias.