Success of maximum likelihood phylogeny inference in the four-taxon case

We used simulated data to investigate a number of properties of maximum- likelihood (ML) phylogenetic tree estimation for the case of four taxa. Simulated data were generated under a broad range of conditions, including wide variation in branch lengths, differences in the ratio of transition and transversion substitutions, and the absence of presence of gamma-distributed site-to-site rate variation. Data were analyzed in the ML framework with two different substitution models, and we compared the ability of the two models to reconstruct the correct topology. Although both models were inconsistent for some branch-length combinations in the presence of site-to-site variation, the models were efficient predictors of topology under most simulation conditions. We also examined the performance of the likelihood ratio (LR) test for significant positive interior branch length. This test was found to be misleading under many simulation conditions, rejecting too often under some simulation conditions. Under the null hypothesis of zero length internal branch, LR statistics are assumed to be asymptotically distributed chi 2(1); with limited data, the distribution of LR statistics under the null hypothesis varies from chi 2(1).      

Resistance of tomato infected with cucumber mosaic virus satellite RNA to potato spindle tuber viroid

Tomato (Lycopersicon esculentum cvs Rutgers and Lichun) plants were firstly pre-inoculated either with a cucumber mosaic virus (CMV) isolate containing satellite RNA (CMV-S52) or with a CMV isolate without satellite RNA, and then challenged 14 days later with a severe strain of potato spindle tuber viroid (PSTVd). Also, tomato plants transformed with CMV satellite cDNA and non-transgenic control plants were directly inoculated with PSTVd. Protection effects were assessed by the observation of symptoms and by assay of PSTVd accumulation in tomato plants using return polyacrylamide gel electrophoresis and silver staining. The results indicated that the satellite-transgenic plants and plants pre-inoculated with CMV-S52 showed much milder symptoms of PSTVd infection than the respective control plants. The concentration of PSTVd RNA in the satellite-transgenic plants and CMV-S52 pre-inoculated plants was reduced to about 0.02–0.03 of the controls. PSTVd infection did not increase the amount of satellite ds-RNA in plants. It is concluded that the plant resistance to PSTVd is induced by the presence of satellite RNA rather than the CMV infection. It is suggested that as there is considerable sequence similarity between satellite RNA and PSTVd, base pairings may be a cause of reduction of both symptoms and the accumulation of PSTVd.     

Captopril effect on prostaglandin E2, thromboxane B2 and proteinuria in lupus nephritis patients

OBJECTIVE: High urinary Prostaglandin E2 (PGE2) and thromboxane B2 (TxB2) levels have been reported in lupus nephritis (LN). Captopril diminishes proteinuria and improves glomerular filtration rate (GFR), and may have effect on immune function. We evaluate captopril effect on urinary PGE2, and TxB2. METHODS: Eighteen LN patients were randomly assigned to two groups. Group 1 received only prednisone plus cyclophosphamide. Group 2 received also captopril. Serum creatinine, GFR, RPF, urinary proteins, PGE2 and TxB2, were assessed. RESULTS: There were no differences between the initial and final assessments in Group 1. Group 2 showed a significant decrement in proteinuria (p=0.003) and serum creatinine (p=0.01) at the end of the study. PGE2 decreased significantly when compared with the initial value (p=0.02). CONCLUSION: Captopril plus usual treatment, improved serum creatinine and decreased proteinuria in parallel with prostaglandin E2 reduction. This effect is not related to changes in GFR or RPF. Captopril may have an immunomodulatory effect on local inflammatory processes in lupus nephritis.     

High-mobility group box 1 protein is an inflammatory mediator in necrotizing enterocolitis: protective effect of the macrophage deactivator semapimod

High-mobility group box 1 (HMGB1) is a late mediator of endotoxemia known to stimulate the production of proinflammatory cytokines that are putative mediators of intestinal inflammation associated with necrotizing enterocolitis (NEC). We hypothesized that HMGB1 is also involved in the pathogenesis of NEC. We examined the expression of HMGB1 and the effect of the novel drug semapimod on intestinal inflammation in an experimental model of NEC in neonatal rats. Newborn rats were subjected to hypoxia and fed a conventional formula by gavage (FFH) or were breast fed (BF). Rats were killed on day 4, and the distal ileum was harvested for morphological studies and Western blot analysis. FFH newborn rats but not BF controls developed intestinal inflammation similar to the histological changes observed in human NEC. We found that the expression of HMGB1 and its receptor for advanced glycation end products (RAGE) as well as that of other apoptosis/inflammation-related proteins (Bad, Bax, inducible nitric oxide synthase, and cyclooxygenase 2) was upregulated in the ileal mucosa of FFH newborn rats compared with BF animals. Administration of the drug semapimod inhibited the upregulation of those proteins and partially protected the animals against the FFH-induced intestinal injury. Elevated levels of HMGB1 were also found in ileal samples from infants undergoing intestinal resection for acute NEC. Our results implicate HMGB1 and RAGE as important mediators of enterocyte cell death and hypoxia-induced injury in NEC and support the hypothesis that inhibitors such as semapimod might play a therapeutic role in chronic intestinal inflammation characterized by this animal model.     

Carbon monoxide protects against the development of experimental necrotizing enterocolitis

Necrotizing enterocolitis (NEC) is a disease of neonates that is increasing in incidence and often results in significant morbidity and mortality. Carbon monoxide (CO), a byproduct of the catabolism of heme, is known to have anti-inflammatory and antiapoptotic properties. In this study, we aimed to demonstrate that inhaled CO protects against the development of intestinal inflammation in a model of experimental NEC as well as decreases enterocyte cell death in vitro. Additionally, we also aimed to demonstrate that CO decreases enterocyte production of inducible nitric oxide synthase (iNOS) and nitric oxide (NO). Neonatal rats were exposed to intermittent hypoxia exposure and formula feeding to induce experimental NEC. Animals randomized to CO treatment were put in an environment containing 0.025% CO for 1 h/day on days 1-3 of life. All animals were killed on day 4 of life. In vitro experiments were performed with IEC-6 cells, a rat enterocyte cell line. Cells were examined for viability, iNOS production, and elaboration of NO. We found that CO diminished levels of serum inflammatory cytokines and nitrites, protected against intestinal inflammation, and decreased ileal iNOS production and protein nitration in a model of experimental NEC. In vitro, CO decreased cytokine- or hypoxia/endotoxin-induced iNOS and NO production. CO also abrogated TNF-alpha- and actinomycin D-induced apoptosis or hypoxia/endotoxin-induced cell death. In conclusion, 1 h of daily low-dose inhaled CO protected against the development of intestinal inflammation in a model of experimental NEC. iNOS and NO production were decreased by CO both in vivo and in vitro. CO may prove to be a useful clinical adjunct in the treatment of NEC.     

Rh(I) complexes containing tris(pyrazolyl)amine and bis(pyrazolyl)amine ligands: synthesis and NMR studies

The tris(pyrazolyl)amine ligands: tris[2-(1-pyrazolyl)methyl]amine (tpma), tris [3,5-dimethyl-1-pyrazolyl)methyl]amine (tdma), tris[2-(1-pyrazolyl)ethyl]amine (tpea), tris[2-(3,5-dimethyl-1-pyrazolyl)ethyl]amine (tdea) and bis(pyrazolyl)amine ligands: bis[2-(1-pyrazolyl)ethyl]amine (bpea) and bis[2-(3,5-dimethyl-1-pyrazolyl)ethyl]amine (bdea) react with [RhCl(cod)]₂ in presence of NaBF₄ (tpma, tdma and bdea) or AgBF₄ (tpea, tdea and bpea) to lead to [Rh(cod)L] (BF₄) (L=tpma (1), tdma (2), bdea (3), tpea (4), tdea (5) and bpea (6)). These complexes have been characterised by elemental analyses, conductivity, IR, ¹H and ¹³C NMR spectroscopy and liquid mass (with electrospray) spectrometry. The ¹H NMR spectra of 1, 2 show the presence of two isomers in solution in a 3:1 ratio (coordination κ² or κ³ type) in a thermodynamic equilibrium. The steric bulk of cyclo-octa-1,5-diene causes it to prefer the κ² mode of bonding as majority. Similar to previous published results, complexes 4 and 5 exist in a sole form in solution (probably κ² isomer). Finally, the complexes 3 and 6 are fluxional. A NMR study shows that this fluxional process is not frozen at 183 K.     

Determination of pyrrolized phospholipids in oxidized phospholipid vesicles and lipoproteins

The Ehrlich reaction was optimized to determine pyrrolized phospholipids produced as a consequence of oxidative stress. The procedure consisted of the treatment of the modified phospholipids with p-(dimethylamino)benzaldehyde at a controlled acidity temperature and the spectrophotometric determination of adducts produced. The extinction coefficient of Ehrlich adducts was calculated by using 1-[1-(2-hydroxyethyl)-1H-pyrrol-2-yl]propan-1-ol (compound 1) as standard and was 56,500 M(-1)cm(-1). The response was linear and reproducible within the range of 0.051-7.65 microM of compound 1. When the assay was applied to determination of pyrrole content in ethanolamine incubated in the presence of 0.25-1mM of 4,5(E)-epoxy-2(E)-heptenal, the complete conversion of the aldehyde into the pyrrole ring was observed and the results obtained were similar to those found when compound 1 was determined by gas chromatography. When phosphatidylethanolamine was incubated in the presence of 0.5-40 mM of 4,5(E)-epoxy-2(E)-heptenal, the phospholipid was pyrrolized similarly to ethanolamine, although there was not a quantitative conversion and the amount of pyrroles produced depended on the pH of the media. Pyrrolized phospholipids were also produced when phosphatidylethanolamine multilamellar vesicles where oxidized in the presence of either Fe(3+)/ascorbic acid or ABAP (2,2'-azobis(2-methylpropionamide) dihydrochloride) and when high-density lipoproteins were incubated in the presence of Cu(2+), thereby confirming that phospholipid pyrrolization is a common consequence of oxidative stress and that Ehrlich adducts may be valid for determining this pyrrolization.