Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations.

The goal of phylogenetic comparative methods (PCMs) is to study the distribution of quantitative traits among related species. The observed traits are often seen as the result of a Brownian Motion (BM) along the branches of a phylogenetic tree. Reticulation events such as hybridization, gene flow or horizontal gene transfer, can substantially affect a species' traits, but are not modeled by a tree. Phylogenetic networks have been designed to represent reticulate evolution. As they become available for downstream analyses, new models of trait evolution are needed, applicable to networks. We develop here an efficient recursive algorithm to compute the phylogenetic variance matrix of a trait on a network, in only one preorder traversal of the network. We then extend the standard PCM tools to this new framework, including phylogenetic regression with covariates (or phylogenetic ANOVA), ancestral trait reconstruction, and Pagel's $\lambda$ test of phylogenetic signal. The trait of a hybrid is sometimes outside of the range of its two parents, for instance because of hybrid vigor or hybrid depression. These two phenomena are rather commonly observed in present-day hybrids. Transgressive evolution can be modeled as a shift in the trait value following a reticulation point. We develop a general framework to handle such shifts and take advantage of the phylogenetic regression view of the problem to design statistical tests for ancestral transgressive evolution in the evolutionary history of a group of species. We study the power of these tests in several scenarios and show that recent events have indeed the strongest impact on the trait distribution of present-day taxa. We apply those methods to a data set of Xiphophorus fishes, to confirm and complete previous analysis in this group. All the methods developed here are available in the Julia package PhyloNetworks.

Genetic predictors of cardiovascular morbidity in Bardet-Biedl syndrome.

Bardet-Biedl syndrome is a rare ciliopathy characterized by retinal dystrophy, obesity, intellectual disability, polydactyly, hypogonadism and renal impairment. Patients are at high risk of cardiovascular disease. Mutations in BBS1 and BBS10 account for more than half of those with molecular confirmation of the diagnosis. To elucidate genotype-phenotype correlations with respect to cardiovascular risk indicators 50 patients with mutations in BBS1 were compared with 19 patients harbouring BBS10 mutations. All patients had truncating, missense or compound missense/truncating mutations. The effect of genotype and mutation type was analysed. C-reactive protein was higher in those with mutations in BBS10 and homozygous truncating mutations (p = 0.013 and p = 0.002, respectively). Patients with mutations in BBS10 had higher levels of C peptide than those with mutations in BBS1 (p = 0.043). Triglyceride levels were significantly elevated in patients with homozygous truncating mutations (p = 0.048). Gamma glutamyl transferase was higher in patients with homozygous truncating mutations (p = 0.007) and heterozygous missense and truncating mutations (p = 0.002) than those with homozygous missense mutations. The results are compared with clinical cardiovascular risk factors. Patients with missense mutations in BBS1 have lower biochemical cardiovascular disease markers compared with patients with BBS10 and other BBS1 mutations. This could contribute to stratification of the clinical service.

Quantitative determination of the human immune response to immunization with meningococcal vaccines.

Radioactive antigen binding tests have been developed to measure quantitatively the antibody response of 167 adults, 84 children, and 51 infants to several different preparations of group A and group C meningococcal polysaccharides. Almost all the adults injected responded and the geometric mean responses were approximately 15 mug/ml of antibody protein in individuals vaccinated subcutaneously with two preparations of group A vaccine. The geometric mean antibody concentration after immunization with two preparations of group C vaccine was approximately 35 mug/ml. Most children aged 7 yr responded to immunization with two group A vaccines, and their mean response was only slightly less than that seen in adults. There was no difference between the subcutaneous and the intradermal route if both were given with jet gun. The majority of infants aged 6-13 months responded to a preparation of group A vaccine and the geometric mean titer was approximately 1.2 mug/ml. Adults, children, and infants responded significantly less to a preparation of group A polysaccharide which was of low molceular weight.

Premature 3'-end formation of CBP1 mRNA results in the downregulation of cytochrome b mRNA during the induction of respiration in Saccharomyces cerevisiae.

The yeast mitochondrial genome encodes only seven major components of the respiratory chain and ATP synthase; more than 200 other mitochondrial proteins are encoded by nuclear genes. Thus, assembly of functional mitochondria requires coordinate expression of nuclear and mitochondrial genes. One example of coordinate regulation is the stabilization of mitochondrial COB (cytochrome b) mRNA by Cbp1, the product of the nuclear gene CBP1 (cytochrome b processing). CBP1 produces two types of transcripts with different 3' ends: full-length 2.2-kb transcripts and 1.2-kb transcripts truncated within the coding sequence of Cbp1. Upon induction of respiration, the steady-state level of the long transcripts decreases while that of the short transcripts increases reciprocally, an unexpected result since the product of the long transcripts is required for COB mRNA stability and thus for respiration. Here we have tested the hypothesis that the short transcripts, or proteins translated from the short transcripts, are also required for respiration. A protein translated from the short transcripts was not detected by Western analysis, although polysome gradient fractions were shown to contain both long and short CBP1 transcripts. A mutant strain in which production of the short transcripts was abolished showed wild-type growth properties, indicating that the short transcripts are not required for respiration. Due to mutation of the carbon source-responsive element, the long transcript level in the mutant strain did not decrease during induction of respiration. The mutant strain had increased levels of COB RNA, suggestive that production of short CBP1 transcripts is a mechanism for downregulation of the levels of long CBP1 transcripts, Cbp1, and COB mRNA during the induction of respiration.

Computerized Cognitive Testing for Use in Clinical Trials: A Comparison of the NIH Toolbox and Cogstate C3 Batteries.

BACKGROUND: As prevention trials for Alzheimer's disease move into asymptomatic populations, identifying older individuals who manifest the earliest cognitive signs of Alzheimer's disease is critical. Computerized cognitive testing has the potential to replace current gold standard paper and pencil measures and may be a more efficient means of assessing cognition. However, more empirical evidence about the comparability of novel computerized batteries to paper and pencil measures is required. OBJECTIVES: To determine whether two computerized IPad batteries, the NIH Toolbox Cognition Battery and Cogstate-C3, similarly predict subtle cognitive impairment identified using the Preclinical Alzheimer Cognitive Composite (PACC). DESIGN, SETTING, PARTICIPANTS: A pilot sample of 50 clinically normal older adults (Mage=68.5 years±7.6, 45% non-Caucasian) completed the PACC assessment, and the NIH Toolbox and Cogstate-C3 at research centers of Massachusetts General and Brigham and Women's Hospitals. Participants made 3-4 in-clinic visits, receiving the PACC first, then the NIH Toolbox, and finally the Cogstate-C3.>= 0.5SD), versus subtle cognitive impairment (<0.5SD). Composites for each computerized battery were created using principle components analysis, and compared with the PACC using non-parametric Spearman correlations. Logistic regression analyses were used to determine which composite was best able to classify subtle cognitive impairment from typical performance. RESULTS: The NIH Toolbox formed one composite and exhibited the strongest within-battery alignment, while the Cogstate-C3 formed two distinct composites (Learning-Memory and Processing Speed-Attention). The NIH Toolbox and C3 Learning-Memory composites exhibited positive correlations with the PACC (ρ=0.49, p<0.001; ρ=0.58, p<0.001, respectively), but not the C3 Processing Speed-Attention composite, ρ=-0.18, p=0.22. The C3 Learning-Memory was the only composite that classified subtle cognitive impairment, and demonstrated the greatest sensitivity (62%) and specificity (81%) for that subtle cognitive impairment. CONCLUSIONS: Preliminary findings suggest that the NIH Toolbox has the advantage of showing the strongest overall clustering and alignment with standardized paper-and-pencil tasks. By contrast, Learning-Memory tasks within the Cogstate-C3 battery have the greatest potential to identify cross-sectional, subtle cognitive impairment as defined by the PACC.

Pharmacological characterization of multidrug resistant MRP-transfected human tumor cells.

We have previously identified and characterized a novel member of the ATP-binding cassette superfamily of transport proteins, multidrug resistance protein (MRP), and subsequently demonstrated that its overexpression is sufficient to confer multidrug resistance on previously sensitive cells (Cole et al., Science (Washington DC), 258: 1650-1654, 1992; Grant et al., Cancer Res. 54: 357-361, 1994). In the present study, we have transfected two different eukaryotic expression vectors containing MRP complementary DNA into HeLa cells to study the pharmacological phenotype produced exclusively by overexpression of human MRP. The drug resistance patterns of the two MRP-transfected cell populations were similar. They were characterized by a moderate (5- to 15-fold) level of resistance to doxorubicin, daunorubicin, epirubicin, vincristine, and etoposide, and a low (< or = 3-fold) level of resistance to taxol, vinblastine, and colchicine. The transfectants were not resistant to 9-alkyl anthracyclines, mitoxantrone, or cisplatin. The MRP-transfected cells were also resistant to some heavy metal anions including arsenite, arsenate, and trivalent and pentavalent antimonials but were not resistant to cadmium chloride. Accumulation of radiolabeled vincristine was reduced by 45% in the MRP-transfected cells and could be restored to the levels found in sensitive cells by depletion of ATP. Rates of vincristine efflux did not differ greatly in the sensitive and resistant cells. The cytotoxic effects of vincristine and doxorubicin could be enhanced in a dose-dependent fashion by coadministration of verapamil. Cyclosporin A also increased vincristine toxicity but had less effect on doxorubicin toxicity. The degree of chemosensitization by verapamil and cyclosporin A was similar in MRP-transfected cells and in cells transfected with the vector alone, suggesting that sensitization involved mechanisms independent of MRP expression. Verapamil and cyclosporin A caused a modest increase in vincristine accumulation in the resistant cells but did not restore levels to those of the sensitive cells. Taken together, these data indicate that drug-resistant cell lines generated by transfection with MRP complementary DNA display some but not all of the characteristics of MRP-overexpressing cell lines produced by drug selection in vitro. They further demonstrate that the multidrug resistance phenotype conferred by MRP is similar but not identical to that conferred by P-glycoprotein and includes resistance to arsenical and antimonial oxyanions.

Percent body fat in obese white females predicted by anthropometric measurements.

The percent body fat (PBF) and 15 anthropometric measurements were measured in 221 obese white females randomly assigned to validation and cross-validation groups. Two new anthropometric equations for the prediction of the percent of body fat were generated by multiple regression. Equation 1 includes the residual lung volume (RV) as a factor and had a correlation coefficient (r) of 0.85 and a standard error of the estimate (SEE) of 3.9%. Equation 2 does not include the RV and has an r of 0.82 and an SEE of 4.3%. Both equations were more precise than two previous widely used equations. In a subgroup of 37 subjects who underwent weight loss, equation 1 gave a more precise estimate of the change in PBF. We conclude that the new equations permit a better prediction of the PBF in obese white females.

Immunochemical analysis of acetaminophen covalent binding to proteins. Partial characterization of the major acetaminophen-binding liver proteins.

A sensitive immunoassay for detecting acetaminophen (APAP) bound to proteins was developed using an affinity purified antibody directed against the N-acetylated end of the APAP molecule. Western blots of electrophoretically resolved liver proteins taken from mice given an hepatotoxic dose of APAP demonstrated that nearly 85% of the total detectable protein-bound APAP was covalently associated with proteins of 44 and 58 kD. Pretreatment of liver extracts with the sulfhydryl-specific reagent, N-ethylmaleimide (NEM), prior to derivatization with the reactive metabolite of APAP, N-acetyl-p-benzoquinone imine (NAPQI), greatly reduced immunochemically detectable APAP-protein adducts and indicated that the antibody detects protein-thiol conjugates of APAP. To investigate the basis of the binding selectivity in vivo, a variety of systems which yielded APAP-protein adducts were analyzed. Systems which activate APAP enzymatically, as in hepatocyte suspensions or in post-mitochondrial (S9) fractions fortified with an NADPH-regenerating system, resulted in a protein binding profile similar to that produced in vivo. Conversely, when extracts or cells were treated with chemically synthesized NAPQI, an alternative protein binding profile was obtained. Two-dimensional electrophoretic analysis of the reduced protein thiol (PSH) content of liver proteins using [3H]NEM labeling revealed that the 58 kD APAP-binding proteins were rich in PSH, whereas the major 44 kD binding protein had virtually no detectable PSH. Many PSH-rich proteins that were not arylated in vivo did bind NAPQI in vitro. However, the 44 kD proteins were not arylated when chemically synthesized NAPQI was added to homogenates or cell suspensions. The present data further suggest that, in addition to the amount and reactivity of free protein sulfhydryls, the cellular localization with respect to the cytochrome P-450 activation site may influence the susceptibility of proteins to NAPQI binding. These findings signal the need for caution in interpreting studies of APAP mechanisms that rely solely on NAPQI addition.

Isolation and characterization of apolipophorin-III from the giant water bug (Lethocerus medius).

Upon injection of synthetic adipokinetic hormone, lipophorin from Lethocerus medius decreased in density and became associated with apolipophorin-III (apoLp-III). ApoLp-III isolated from hemolymph of Lethocerus medius had a M(r) = 19,000 and an amino acid composition high in methionine, in comparison with other apoLp-IIIs. Its circular dichroism spectrum was consistent with a protein with secondary structure of predominantly alpha-helix. NH2-terminal sequence alignment with apoLp-III sequences from other species showed a conservation of the hydrophobic or hydrophilic properties of residues at each position rather than of specific amino acids. ApoLp-III from Lethocerus medius has the potential to form amphipathic alpha-helices, similar to those found in the three-dimensional structure of Locusta migratoria apoLp-III. A portion of the apoLp-III molecules that are not associated with lipophorin contained the blue chromophore, biliverdin.

IgG specific antibodies to rye grass and ragweed pollen antigens in the tear secretions of patients with vernal conjunctivitis.

We studied the tears of 30 patients (25 males and five females, ranging in age from 8 to 34 years) with vernal conjunctivitis for pollen-specific IgG antibodies to rye grass and ragweed antigen E by an enzyme-linked immunosorbent assay (ELISA). Eighteen of 30 (60%) and 20 of 30 (67%) patients with vernal conjunctivitis had significant levels (more than 2 S.D. from the mean of control tears) of IgG antibodies in their tear secretions to rye grass (geometric mean = 68.7 ELISA units) and ragweed antigen E (geometric mean = 50 ELISA units), respectively. In contrast, the control groups (eight atopic individuals, four with seasonal rhinitis, and 12 with allergic conjunctivitis) had low amounts of specific IgG antibodies to these two pollen antigens in their tears. Total IgG and IgM were also increased in the tears of patients with vernal conjunctivitis. To evaluate whether these immunoglobulins and specific IgG antibodies were locally produced by the conjunctival tissues, we used transferrin as a marker for the leakage of plasma proteins into tears. We found that the specific IgG antibodies to rye grass or ragweed antigen E, or both, in the tears were locally produced by the conjunctival tissues. The local production ranged from 20% to 99.9%. Of 17 patients with vernal conjunctivitis and undetectable pollen-specific IgE antibodies in their tears, 14 (82.4%) had tear specific IgG antibodies to rye grass or ragweed antigen E or both, whereas of those with measurable tear IgE antibodies, only nine of 13 (69%) had tear IgG antibodies to rye grass or antigen E or both. These results suggested that both IgE- and IgG-mediated immune mechanisms may be important in the pathogenesis of vernal conjunctivitis.

Alternatives for cardiac rehabilitation patients unable to return to a hospital-based program.

OBJECTIVE: To determine the effectiveness of a home exercise program using transtelephonic exercise monitoring (TEM). DESIGN: Prospective, two-group experimental, random assignment. SETTING: Urban centered hospital and surrounding community. SUBJECTS: Twenty cardiac rehabilitation patients entering a Phase II cardiac rehabilitation program. OUTCOME MEASURES: Maximal oxygen consumption, blood pressure, pressure-rate product, workload. INTERVENTION: Twenty male cardiac patients were randomly enrolled in either a 12-week home- or hospital-based exercise program. Maximal exercise tolerance tests were conducted, before and after exercise intervention, on a computer-driven bicycle ergometer. Subjects trained 3 days per week for 12 weeks on a bicycle ergometer for a maximum of 35 minutes at 75% of maximum heart rate reserve or functional capacity. RESULTS: Posttraining results showed significant improvement in cardiac function for both groups. Two patients in the TEM group developed new arrhythmias while exercising that required medication changes; however, no medical emergencies arose in either exercise group. Independent Student t test showed no significant difference between groups before or after training. CONCLUSIONS: We conclude that TEM is an effective alternative for the rehabilitation of patients who are unable to return to a hospital-based program.

A self-correcting method for improving the precision of beam blocks.

A technique for manufacturing precise custom blocks is described. Using the tracing stylus of the mold making machine, reference markers are cut into the lateral borders of the polystyrene mold after the cavities for the blocks have been made. These markers are aligned with the central ray cross hair of the shadow tray when the blocks are mounted on the tray. The ability of the technique to enhance precision has been verified in laboratory tests by intentionally introducing small imperfections into a mold making machine and checking the positional accuracy of the mounted blocks. The clinical performance has been tested by evaluating 47 check films of blocks for 16 randomly selected patients. The average positional error of individual blocks, projected to the isocenter, was less than one mm. The average time needed to cut the reference markers was 25 seconds. Implementing the technique required only minor modifications of a commercial mold making machine.

Ethanol isotope method (EIM) for uncovering illegal wine.

Isotopic methods have proven to be a powerful analytical tool for the determination of origin and authenticity of wine. In addition, measuring the stable isotope ratio provides useful information for the detection of many illegal practices in the production of wine. The determinations of the stable isotope composition of compounds are based on measuring the relative ratios using isotope ratio mass spectrometry. This article describes a new isotopic method for measuring the δD value of non-exchangeable hydrogen stable isotopes in ethanol for investigating adulteration practices in wine making. With this new method, we are able to determine the addition of water and sugar in wine with higher accuracy, repeatability and reliability.