Random sampling of constrained phylogenies: conducting phylogenetic analyses when the phylogeny is partially known

Statistical randomization tests in evolutionary biology often require a set of random, computer-generated trees. For example, earlier studies have shown how large numbers of computer-generated trees can be used to conduct phylogenetic comparative analyses even when the phylogeny is uncertain or unknown. These methods were limited, however, in that (in the absence of molecular sequence or other data) they allowed users to assume that no phylogenetic information was available or that all possible trees were known. Intermediate situations where only a taxonomy or other limited phylogenetic information (e.g., polytomies) are available are technically more difficult. The current study describes a procedure for generating random samples of phylogenies while incorporating limited phylogenetic information (e.g., four taxa belong together in a subclade). The procedure can be used to conduct comparative analyses when the phylogeny is only partially resolved or can be used in other randomization tests in which large numbers of possible phylogenies are needed.     

Neurotrophin signaling in oocyte survival and developmental competence: a paradigm for cellular toti-potency

While not fulfilling the criterion of a "stem cell" in being capable of self-renewal, mature and fertilized oocytes are the original "toti-potent" cells, whose capacity for expansion and differentiation can only be approximated by stem cells of embryonic or adult origin in vitro. As such, the mechanisms by which oocytes acquire and manifest competence to support embryo development is of fundamental interest to efforts to control and re-specify somatic cell fate and toti-potency. This is underscored by the unparalleled capacity of oocyte cytoplasm to successfully re-specify the genetic program of animal development following cell nuclear replacement (i.e., cloning). Thus, the knowledge gained by understanding the acquisition of oocyte developmental competence could ultimately facilitate the creation of adult stem cells in vitro from terminally differentiated cells, ex ovo. In this paper, we review the concept of oocyte developmental competence, and focus on our own research and that of others implicating a role for neurotrophins in this process, and that of oocyte cell survival. Lastly we propose a role for neurotrophin signalling in embryo stem cell survival.     

Extracellular cyclic AMP and adenosine appearance in adipose tissue of Sus scrofa: effects of exercise

Cyclic AMP (cAMP) appears extracellularly in a variety of tissues including brain, liver, and kidney; whether it appears in adipose tissue and responds to physiological perturbation is unknown. The purpose of this study was to examine adipose tissue extracellular cAMP appearance and metabolism in situ and in vitro in physiologically challenged animals. Littermate swine were either sedentary or exercise trained on a treadmill for 3 months and subjected to acute exercise on experiment day. In situ, microdialysis probes in subcutaneous back fat were perfused before, during, and after animals performed 20 mins of acute exercise, and dialysate was analyzed for cAMP and adenosine. In vitro, isolated adipocytes were hormonally stimulated to provoke cAMP synthesis and efflux, and plasma membrane phosphodiesterase and 5'-nucleotidase activities were measured. Extracellular cAMP and adenosine levels in adipose tissue of sedentary swine averaged 5.2 +/- 1.7 and 863 +/- 278 nM, respectively. Exercise training tended to increase extracellular cAMP (11.3 +/- 1.7 nM) and reduce extracellular adenosine (438 +/- 303 nM), although neither change was statistically significant. Acute exercise caused a significant 3-fold and 16-fold increase in extracellular cAMP and adenosine, respectively, compared to rest. These changes occurred despite a 2- to 3-fold increase in adipose tissue blood flow during acute exercise. In vitro, cAMP efflux from exercise-trained swine was 42% greater than that from adipocytes of sedentary swine, yet adipocyte plasma membranes from exercise-trained and sedentary swine did not differ in maximal phosphodiesterase and 5'-nucleotidase activities. We conclude that cAMP appears extracellularly in swine adipose tissue and that the levels of extracellular cAMP and adenosine in intact swine adipose tissue are influenced by both acute and chronic exercise. The subsequent impact of the changes in these biochemicals on local cellular metabolism and growth remains to be determined.     

Effects of Cadmium, Lead, Mercury and Zinc on °-Aminolevulinic Acid Dehydratase Activity from Radish Leaves

The purpose of the present study was to investigate the in vitro and the in vivo effects of cadmium, zinc, mercury and lead on -aminolevulinic acid dehydratase (ALA-D) activity from radish leaves. The in vivo effect of these metals on growth, DNA and protein content was also evaluated. The results demonstrated that among the elements studied Cd²⁺ presented the highest toxicity for radish. 50% inhibition of ALA-D activity (IC₅₀) in vitro was at 0.39, 2.39, 2.29, and 1.38 mM Cd²⁺, Zn²⁺, Hg²⁺ and Pb²⁺, respectively. After in vivo exposure Cd²⁺, Zn²⁺, Hg²⁺ and Pb²⁺ inhibited ALA-D by about 40, 26, 34 and 15%, respectively. Growth was inhibited by about 40, 10, 25, and 5% by Cd²⁺, Zn²⁺, Hg²⁺, and Pb²⁺, respectively. DNA content was reduced about 35, 30, 20, and 10% for Cd²⁺, Zn²⁺, Hg²⁺, and Pb²⁺, respectively. The metal concentration in radish leaves exposed to Cd²⁺, Zn²⁺, Hg²⁺, and Pb²⁺ was 18, 13, 6, and 7 mol g^–1, respectively. The marked ability of radish to accumulate Cd²⁺ and Zn²⁺ raises the possibility of using this vegetable as a biomonitor of environmental contamination by these metals.     

Macrophages transfer [14C]-labelled fatty acids to pancreatic islets in culture

Macrophages are able to produce, export, and transfer fatty acids to lymphocytes in culture. The purpose of this study was to examine if labelled fatty acids could be transferred from macrophages to pancreatic islets in co-culture. We found that after 3 h of co-culture the transfer of fatty acids to pancreatic islets was: arachidonic > oleic > linoleic = palmitic. Substantial amounts of the transferred fatty acids were found in the phospholipid fraction; 87.6% for arachidonic, 59.9% for oleic, 53.1% for palmitic, and 36.9% for linoleic acids. The remaining radioactivity was distributed among the other lipid fractions analysed (namely polar lipids, cholesterol, fatty acids, triacylglycerol and cholesterol ester), varying with the fatty acid used. For linoleic acid, a significant proportion (63.1%) was almost equally distributed in these lipid fractions. Also, it was observed that transfer of fatty acids from macrophages to pancreatic islets is time-dependent up to 24 h, being constant and linear with time for palmitic acid and remaining constant after 12 h for oleic acid. These results lead us to postulate that in addition to the serum, circulating monocytes may also be a source of fatty acids to pancreatic islets, mainly arachidonic acid.     

Hepatitis C prevalence and risk factors in hemodialysis patients in Central Brazil: a survey by polymerase chain reaction and serological methods

An hemodialysis population in Central Brazil was screened by polymerase chain reaction (PCR) and serological methods to assess the prevalence of hepatitis C virus (HCV) infection and to investigate associated risk factors. All hemodialysis patients (n=428) were interviewed in eight dialysis units in Goiania city. Blood samples were collected and serum samples screened for anti-HCV antibodies by an enzyme-linked immunosorbent assay (ELISA). Positive samples were retested for confirmation with a line immunoassay (LIA). All samples were also tested for HCV RNA by the PCR. An overall prevalence of 46.7% (CI 95%: 42-51.5) was found, ranging from 20.7% (CI 95%: 8.8-38.1) to 90.4% (CI 95%: 79.9-96.4) depending on the dialysis unit. Of the 428 patients, 185 were found to be seropositive by ELISA, and 167 were confirmed positive by LIA, resulting in an anti-HCV prevalence of 39%. A total of 131 patients were HCV RNA-positive. HCV viremia was present in 63.5% of the anti-HCV-positive patients and in 10.3% of the anti-HCV-negative patients. Univariate analysis of risk factors showed that the number of previous blood transfusions, transfusion of blood before mandatory screening for anti-HCV, length of time on hemodialysis, and treatment in multiple units were associated with HCV positivity. However, multivariate analysis revealed that blood transfusion before screening for anti-HCV and length of time on hemodialysis were significantly associated with HCV infection in this population. These data suggest that nosocomial transmission may play a role in the spread of HCV in the dialysis units studied. In addition to anti-HCV screening, HCV RNA detection is necessary for the diagnosis of HCV infection in hemodialysis patients.     

The conserved C2 phospholipid‐binding domain in Delta contributes to robust Notch signalling

Accurate Notch signalling is critical for development and homeostasis. Fine‐tuning of Notch–ligand interactions has substantial impact on signalling outputs. Recent structural studies have identified a conserved N‐terminal C2 domain in human Notch ligands which confers phospholipid binding in vitro. Here, we show that Drosophila ligands Delta and Serrate adopt the same C2 domain structure with analogous variations in the loop regions, including the so‐called β1‐2 loop that is involved in phospholipid binding. Mutations in the β1‐2 loop of the Delta C2 domain retain Notch binding but have impaired ability to interact with phospholipids in vitro. To investigate its role in vivo, we deleted five residues within the β1‐2 loop of endogenous Delta. Strikingly, this change compromises ligand function. The modified Delta enhances phenotypes produced by Delta loss‐of‐function alleles and suppresses that of Notch alleles. As the modified protein is present on the cell surface in normal amounts, these results argue that C2 domain phospholipid binding is necessary for robust signalling in vivo fine‐tuning the balance of trans and cis ligand–receptor interactions.