Recognizing the forest for the trees: testing temporal patterns of cladogenesis using a null model of stochastic diversification

Computer simulations are developed and employed to examine the expected temporal distributions of nodes under a null model of stochastic lineage bifurcation and extinction. These Markovian models of phylogenetic process were constructed so as to permit direct comparisons against empirical phylogenetic trees generated from molecular or other information available solely from extant species. For replicate simulated phylads with n extant species, cumulative distribution functions (cdf's) of branching times were calculated, and compared (using the Kolmogorov-Smirnov test statistic D) to those from three published empirical trees. Molecular phylogenies for columbine plants and avian cranes showed statistically significant departures from the null expectations, in directions indicating recent and ancient species' radiations, respectively, whereas a molecular phylogeny for the Drosophila virilis species group showed no apparent historical clustering of branching events. Effects of outgroup choice and phylogenetic frame of reference were investigated for the columbines and found to have a predictable influence on the types of conclusions to be drawn from such analyses. To enable other investigators to statistically test for nonrandomness in temporal cladogenetic pattern in empirical trees generated from data on extant species, we present tables of mean cdf's and associated probabilities under the null model for expected branching times in phylads of varying size. The approaches developed in this report complement and extend those of other recent methods for employing null models to assess the statistical significance of pattern in evolutionary trees.      

Involvement of the nitric oxide-cyclic GMP pathway in the desensitization of bradykinin responses of cultured rat sensory neurons.

Bradykinin (BK) excites a subset of dorsal root ganglion neurons by inducing an inward cation current (IBK) that strongly desensitizes and is accompanied by elevations in cGMP. We have examined the links between cGMP metabolism and IBK. The BK dose dependencies of IBK activation, desensitization, and cGMP production are comparable. Stimulation (with sodium nitroprusside [NP] or 8-bromo-cGMP [8Br-cGMP]) or inhibition (with methylene blue, hemoglobin, and nitric oxide synthase [NOS] inhibitors) of cGMP levels did not mimic or diminish IBK. However, desensitization was affected by the following agents: first, desensitization was enhanced by NP and reduced by NOS inhibitors. Second, the effects of NOS inhibitors could be overcome by 8Br-cGMP or L-arginine. Third, 8Br-cGMP modification of desensitization required receptor occupancy. We conclude that the NO-cGMP pathway affects a component of IBK desensitization at the receptor or G protein level.     

Disorder‐Induced Open‐Circuit Voltage Losses in Organic Solar Cells During Photoinduced Burn‐In

The photoinduced open‐circuit voltage (V_oc) loss commonly observed in bulk heterojunction organic solar cells made from amorphous polymers is investigated. It is observed that the total charge carrier density and, importantly, the recombination dynamics are unchanged by photoinduced burn‐in. Charge extraction is used to monitor changes in the density of states (DOS) during degradation of the solar cells, and a broadening over time is observed. It is proposed that the V_oc losses observed during burn‐in are caused by a redistribution of charge carriers in a broader DOS. The temperature and light intensity dependence of the V_oc losses can be described with an analytical model that contains the amount of disorder broadening in a Gaussian DOS as the only fit parameter. Finally, the V_oc loss in solar cells made from amorphous and crystalline polymers is compared and an increased stability observed in crystalline polymer solar cells is investigated. It is found that solar cells made from crystalline materials have a considerably higher charge carrier density than those with amorphous materials. The effects of a DOS broadening upon aging are suppressed in solar cells with crystalline materials due to their higher carrier density, making crystalline materials more stable against V_oc losses during burn‐in.     

Amino acid size, charge, hydropathy indices and matrices for protein structure analysis

Background  

Prediction of protein folding and specific interactions from only the sequence (ab initio) is a major challenge in bioinformatics. It is believed that such prediction will prove possible if Anfinsen's thermodynamic principle is correct for all kinds of proteins, and all the information necessary to form a concrete 3D structure is indeed present in the sequence.     

Integration of DNA sample collection into a multi-site birth defects case-control study

BACKGROUND: Advances in quantitative analysis and molecular genotyping have provided unprecedented opportunities to add biological sampling and genetic information to epidemiologic studies. The purpose of this article is to describe the incorporation of DNA sample collection into the National Birth Defects Prevention Study (NBDPS), an ongoing case-control study in an eight-state consortium with a primary goal to identify risk factors for birth defects. METHODS: Babies with birth defects are identified through birth defects surveillance systems in the eight participating centers. Cases are infants with one or more of over 30 major birth defects. Controls are infants without defects from the same geographic area. Epidemiologic information is collected through an hour-long interview with mothers of both cases and controls. We added the collection of buccal cytobrush DNA samples for case-infants, control-infants, and their parents to this study. RESULTS: We describe here the methods by which the samples have been collected and processed, establishment of a centralized resource for DNA banking, and quality control, database management, access, informed consent, and confidentiality issues. CONCLUSIONS: Biological sampling and genetic analyses are important components to epidemiologic studies of birth defects aimed at identifying risk factors. The DNA specimens collected in this study can be used for detection of mutations, study of polymorphic variants that confer differential susceptibility to teratogens, and examination of interactions among genetic risk factors. Information on the methods used and issues faced by the NBDPS may be of value to others considering the addition of DNA sampling to epidemiologic studies.     

Differential binding of lectins IL-2 and CSL to candida albicans and cancer cells

The demonstration that interleukin 2 (IL-2) is a lectin specific for oligomannosides allows to understand a new function for this cytokine: as a bifunctional molecule when bound to its receptor ss, IL-2 associates the latter which the CD3/TCR complex, interacting with oligosaccharides of CD3 through its carbohydrate-recognition domain (Zanetta et al. , 1996, Biochem. J., 318, 49-53). This induces the tyrosine phosphorylation of the IL-2R beta by ++p56(lck) , the first step of the IL-2-dependent signaling. Since this specific association is disrupted in vitro by oligomannosides with five and six mannose residues, we made the hypothesis that pathogenic cells or microorganisms could bind IL-2, consequently disturbing the IL-2- dependent response. This study shows that the pathogenic yeast Candida albicans (in contrast with nonpathogenic yeasts) binds high amounts of IL-2 as did cancer cells. In contrast with cancer cells, yeasts do not bind the Man6GlcNAc2-specific lectin CSL, an endogenous "amplifier of activation signals" (Zanetta et al. , 1995, Biochem. J., 311, 629-636).      

Understanding and Improving Mechanical Stability in Electrodeposited Cu and Bi for Dynamic Windows Based on Reversible Metal Electrodeposition

Dynamic windows based on reversible metal electrodeposition (RME) can electronically adjust light transmission from ≈70% to <0.1% to improve building aesthetics and energy efficiency by controlling light and heat flow. For RME devices using Cu and Bi, the windows reach “privacy state” (<0.1% transmission) when ≈180 nm of metal is electrodeposited on the transparent conducting electrode. When films with a plated atomic Cu–Bi ratio of ≈2:1 rest in the privacy state, sinusoidal cracks form across the entire film, and the metal delaminates in <1 day. This mechanical failure renders the window unusable as specks of metal are visually unattractive and reduce the dynamic range of the window. The Cu–Bi film is stress free upon deposition, but after 4 h of resting, 38 MPa of tensile stress develops. The tension in Cu–Bi and Cu films combined with the Cu(ClO₄)₂ in the electrolyte results in severe, widespread fractures and delamination due to stress corrosion cracking. In contrast, electrodeposited Bi films have compressive stress, likely due to high self-diffusion and insertion of atoms into grain boundaries while plating, which results in a Bi-based dynamic window with crack-free resting stability that exceeds 9 weeks.