Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins

Background  

Phylogenies capture the evolutionary ancestry linking extant species. Correlations and similarities among a set of species are mediated by and need to be understood in terms of the phylogenic tree. In a similar way it has been argued that biological networks also induce correlations among sets of interacting genes or their protein products.     

Interaction of allosteric effectors (ATP,CO2, H+) modulating oxygen affinity of the hemoglobin in the carp,Cyprinus carpio,in vitro

Summary The interaction of allosteric effectors (CO₂, ATP, H⁺) with respect to the oxygen affinity of carp hemoglobin was analyzed by determining oxygen binding curves spectrophotometrically in dilute solutions of stripped hemoglobin at 20°C. The pH range studied was 6.8–8.2.P _CO2 was 0, 10 and 70 mmHg (0, 1.33 and 9.3 kPa). ATP/Hb₄ was 0, 8 and 24. In the presence of either CO₂ or ATP, the effects of the cofactors onP ₅₀ were as expected over the whole pH range. In contrast to other published data, each cofactor also had a significant effect onP ₅₀ in the presence of the other cofactor. Evidence was obtained that oxylabile carbamate is formed by carp hemoglobin and that the formation of carbamate persists at a lower level in the presence of ATP. The results support the view that the binding of ATP to carp hemoglobin requires only one terminal amino group, leaving the other N-terminal of the -chain free to react with CO₂.     

Delimitation ofPelargonium sect.Glaucophyllum (Geraniaceae)

Pelargonium otaviense Knuth andP. spinosum Willd. are excluded from sect.Glaucophyllum, whileP. grandiflorum (Andr.)Willd.,P. patulum Jacq. andP. tabulare (Burm. f.)L'Hérit. of sect.Eumorpha are included. Sect.Glaucophyllum is characterized by green to glaucous vegetative organs and zygomorphic white to pink corolla with five narrow petals. All the species have an identical pollen and chromosome morphology, the same basic chromosome number (x = 11) and similar flavonoid patterns. A close relationship between sect.Glaucophyllum and sect.Pelargonium is indicated by the occurrence of natural hybrids and concordant characters. Isorhamnetin and luteolin have been detected in the genus for the first time.     

Using jackknife methods for estimating the parameter in dilution series

Dilution assays are quantal dose-response assays that detect a positive or negative response in each individual culture within groups of replicate cultures that vary in the dose of cells/organisms tested. We propose three jackknife versions of the maximum likelihood estimator of the unknown parameter, i.e., the frequency of a well-defined cell within the context of limiting dilution assays or the density of organisms within the context of serial dilution assays. The methods have been evaluated with artificial data from extensive Monte Carlo experiments. As a result of these experiments and theoretical considerations, the jackknife version based on deleting one individual culture at a time is proposed as the statistical procedure of choice. The next best method is the jackknife version based on leaving out the same replicate from each of the culture groups at a time.     

Stimulation of lecithin:cholesterol acyltransferase activity by apolipoprotein A-II in the presence of apolipoprotein A-I

Various combinations of incorporation and addition of apolipoprotein A-I (apo A-I) and apolipoprotein A-II (apo A-II) individually or together to a defined lecithin-cholesterol (250/12.5 molar ratio) liposome prepared by the cholate dialysis procedure were used to study the effect of apo A-II on lecithin:cholesterol acyltransferase (LCAT, EC 2.3.1.43) activity of both purified enzyme preparations and plasma. When apo A-I (0.1-3.0 nmol/assay) alone was incorporated or added to the liposome, apo A-I effectively activated the enzyme. By contrast, when apo A-II (0.1-3.0 nmol/assay) alone was incorporated into or added to the liposome, apo A-II exhibited minimal activation of LCAT activity, approximately 1% of the activity obtained by an equal amount of apo A-I. Addition of apo A-II (0.1-3.0 nmol/assay) together with apo A-I (0.8 nmol/assay) to the liposome reduced the LCAT activity to approximately 30% of the level obtained with addition of apo A-I alone. On the other hand, addition of apo A-II (0.1-3.0 nmol/assay) or addition of lecithin-cholesterol liposome containing apo A-II (0.1-3.0 nmol/assay) to lecithin-cholesterol liposome containing apo A-I (0.8 nmol/assay) did not significantly alter apo A-I activation of LCAT activity. However, when the same amounts (0.1-3.0 nmol/assay) of apo A-II were incorporated together with apo A-I (0.8 nmol/assay) into the liposome, apo A-II significantly stimulated LCAT activity as compared to activity obtained with incorporation of apo A-I alone. The maximal stimulation was obtained with 0.4 nmol apo A-II/assay for both purified and plasma enzyme. At this apo A-II concentration, approximately 4-fold and 1.8-fold stimulation was observed for purified enzyme and plasma enzyme, respectively. These results indicated that apo A-II must be incorporated together with apo A-I into lecithin-cholesterol liposomes to exert its stimulatory effect on LCAT activity and that apo A-II in high-density lipoprotein may play an important role in the regulation of LCAT activity.     

Secretion of a lipid transfer protein by human monocyte-derived macrophages

Human monocyte-derived macrophages in culture were shown to synthesize and secrete a lipid transfer protein. The human monocyte-derived macrophage transfer protein showed the following characteristics: (i) linear secretion rate over a 24-h period, which was blocked completely by cycloheximide and stimulated by phorbol myristate acetate (67% increase over nonstimulated values); (ii) apparent Mr = approximately 62,000 off Sephacryl S-200; (iii) isoelectric point of 5.0; (iv) binding to phenyl-Sepharose, but not to heparin-Sepharose; (v) facilitation of the transfer of both neutral lipids (cholesteryl esters and triglycerides) and phosphatidylcholine between high density lipoproteins and d less than 1.063 g/ml lipoproteins; and (vi) thermal stability (stable for 1 h at 56 degrees C). The last five of these properties are similar to those of the plasma lipid transfer protein. Thus, macrophages secrete a lipid transfer protein that closely resembles the neutral lipid transfer protein found in human plasma and may be a source of this plasma protein in vivo.     

南瓜雌蕊与自花及远缘花粉的相互作用

南瓜柱头表面经去垢剂、蛋白酶及Con A处理后花粉不能萌发或花粉管生长受阻,Con A能专一地与柱头表面结合。柱头块加入培养液可促进花粉萌发。不同的远缘花粉授粉后在雌蕊不同部位受阻。在成熟南瓜雌蕊提取液中检测到血凝活性,凝集素可能参与雌蕊对远缘花粉的抑制。     

Effects of oligomycin on the partial reactions of the sodium plus potassium-stimulated adenosine triphosphatase

The effects on phosphoenzyme (E-P) formation of ligands which activate Electrophorus (Na,K)-ATPase were investigated in the presence of oligomycin. When the enzyme was allowed to bind oligomycin in the presence of NaCl and MgCl2, subsequent addition of ATP plus KCl produced a monoexponential time course of E-P formation with a rate of 56 s-1, similar to the rate obtained in the uninhibited enzyme phosphorylated by ATP in the absence of KCl. Pi liberation under these conditions was slow and showed no initial burst phase, consistent with the inhibitory effect oligomycin has on the E1-P to E2-P conformational transition. Addition to KCl to a preincubation medium containing oligomycin, NaCl, and MgCl2 had no further effect on E-P formation. However, equilibration with oligomycin, KCl, and MgCl2 prior to the addition of NaCl plus ATP gave a much slower rate of E-P formation (5 s-1) and resulted in an initial rapid release of Pi similar to that found in the uninhibited enzyme. The slow increase in E-P level observed after incubation with oligomycin, KCl, and MgCl2 may be due to secondary formation of an inhibition complex following rapid binding of oligomycin. In contrast to the monophasic behavior which resulted from pre-exposure to NaCl or KCl, preincubation with oligomycin in the presence of MgCl2 plus Tris or Tris alone gave a biphasic pattern of E-P formation in which about 50% of the intermediate accumulated at a rate of 56 s-1 and the remainder at a rate of 5 s-1. In addition, the Pi burst amplitude was reduced, indicating partial inhibition of the enzyme. These results suggest that in the absence of Na+ and K+ only half of the enzyme is inhibited by oligomycin while the remainder undergoes inhibition subsequent to initiation of phosphorylation. Since the oligomycin concentration was saturating, the partial inhibition reflected in the biphasic pattern of E-P formation may be due to half-of-the-sites reactivity in which only half of the subunits bind oligomycin in the absence of monovalent cations.