Reexamination of the morphological evidence for the cohort Epitheria (Mammalia,Eutheria)

Novacek and co-workers recognized a monophyletic clade Epitheria, comprising all eutherians except edentates and the extinct palaeoryctoids, on the basis of two synapomorphies: a stirrupshaped stapes and a foramen ovale enclosed within the alisphenoid. To evaluate this phylogenetic hypothesis, we reexamined the distributions of stapedial morphologies and positions of the foramen ovale across Recent and extinct mammals and nonmammalian cynodonts. The states and distributions of the stapes and forament ovale characters used by Novacek and coworkers were modified by recognizing two stapedial characters (one relating to shape of the crura, the other to the nature of the foramen) and a single, multistate foramen ovale character (within, behind, and lateral to the alisphenoid). The taxon-character matrix used by Novacek (1989, 1992b), substituting our amended stapedial and foramen ovale characters and adding several previously unscored extinct taxa and three new characters, was subjected to a series of PAUP manipulations. Identified among the most parsimonious trees were three major topologies for the base of Eutheria: (1) a polytomy including an Edentata/Ungulata clade, (2) a polytomy with Edentata and Ungulata as separate clades, and (3) Edentata and (when included) Palaeoryctoidea as the successive outgroups to a monophyletic Epitheria. We conclude that topology 2 best reflects the current state of knowledge. An edentate/ungulate clade is supported by three characters (from the mastoid region and subarcuate fossa); however, other morphological studies require modification of the distributions of these characters in xenarthrans and bassal ungulates, thereby eliminating support for this clade. In nearly all manipulations, obtaining a monophyletic Epitheria required that one or two steps be added to the most parsimonious trees. When a monophyletic Epitheria was obtained, it was supported by a triangular stapes and, in some trees, the reappearance of a stapedial artery (lost earlier at the level of Recent therians) and a transpromontorial internal carotid artery. In the most parsimonious trees, a foramen ovale within the alisphenoid was an equivocal synapomorphy of Recent therians or cutherians, and a stapes with strongly convex crura (our state closest to the stirrup-shaped state of Novacek and co-workers) appeared independently within various eutherian lineages. The reduction or loss of the stapedial foramen was identified as an independent event in monotremes and within marsupials and various eutherian lineages.To whom correspondence should be addressed.     

Two-Dimensional Crystallization of Brush Border Myosin I

Brush border myosin-I (BBMI) is a single-headed unconventional myosin found in the microvilli of intestinal epithelial cells, where it links the core bundle of actin filaments to the plasma membrane. An association of BBMI with anionic phospholipids has been shown to be mediated by a carboxy-terminal domain which is rich in basic amino acids. We have exploited this natural affinity of BBMI for negatively charged lipids to form two-dimensional (2D) crystals of this protein which are suitable for structural analysis by electron crystallographic techniques. The 2D crystals which we have obtained belong to one of two space groups, p22₁2₁or p2. We present here projection maps calculated from images of negatively stained crystals for each of these crystal types to a resolution of 20 Å and show that the asymmetric unit is the same in both crystal types.     

Effect of Agricultural Operations and Precipitation on Vertical Distribution of a Nuclear Polyhedrosis Virus in Soil

TheAnticarsia gemmatalisnuclear polyhedrosis virus (AgNPV) was released in two soybean plots in September, 1991; the soil in the plots was then sampled periodically through July, 1992, to determine the effects of normal agricultural soil manipulations and precipitation on vertical distribution of the polyhedral occlusion bodies (POBs). The amount of AgNPV increased at all depths down to 37.5–50 cm as long as there was virus-contaminated plant matter, even dead soybean refuse, above the soil surface. Agricultural operations (disking, harrowing, mowing, planting, cultivating) had no effect on the amount or vertical distribution of AgNPV in soil. After the crop refuse was disked into the soil in November, the amount of POBs began decreasing at all depths; these decreases continued over winter and at times appeared to be associated with precipitation. The POBs were no longer detected below 37.5 cm by April, 1992, or below 25 cm by July, 1992. However, in July there were still 274 POBs/g in the top 2.5 cm of soil. Thus, agricultural operations should not hinder contamination of soybean leaves by AgNPV from its soil reservoir.     

Immune Evasion by Helicobacter pylori: Gastric Spiral Bacteria Lack Surface Immunoglobulin Deposition and Reactivity with Homologous Antibodies

Background. Helicobacter pylori infection persists in the presence of potent serum and gastric mucosal anti-body responses against bacterial antigens. The aim of this article is to report on a study determine whether there is antibody deposition on H. pylori in vivo in the stomach of infected patients and whether gastric and cultured forms of H. pylori differ in their antibody reactivity.
Materials and Methods. Serum, gastric biopsies, and antral brushings were obtained from 10 patients having endoscopy. H. pylori was cultured from gastric biopsies. Bacterial samples were stained directly for immunoglobulin deposition and indirectly using rabbit antiurease serum or patient serum. Samples were examined by immunofluorescence microscopy and flow cytometry.
Results. Although spiral bacteria could be identified easily by acridine orange staining and antiurease staining of gastric brushings from H. pylori infected patients, gastric bacteria did not have detectable IgG or IgA present, and only one of five samples could be stained for IgG and IgA indirectly using patient serum. In contrast, cultured bacteria could be stained readily with homologous serum for IgG and IgA in the majority of cases. Low pH inhibited immunoglobulin reactivity with cultured H. pylori.
Conclusions. Gastric H. pylori may evade humoral defense owing to poor deposition of immunoglobulin in the gastric environment or failure to express surface antigens that are present on cultured forms of H. pylori.     

Mixed Infection with cagA-Positive and cagA-Negative Strains of Helicobacter pylori

Background Helicobacter pylori infection has been implicated strongly in the pathogenesis of gastritis, peptic ulcer disease, gastric adenocarcinoma, and gastric lymphoma, but the reasons for these widely different clinical outcomes are unknown. The aim of this study was to determine whether these differences could be due in part to mixed infection in the same individual, with bacteria having differences in pathogenic factors associated with ulcers.
Materials and Methods. The cagA gene of H. pylori was used to test for mixed infection because it is present in only some strains, and its presence has been associated with ulcers. Polymerase chain reaction (PCR) assays for the cagA gene were applied to H. pylori culture isolates and endoscopic gastric aspirates. Individual bacterial clones were tested for genetic similarity by random primer amplification and restriction endonuclease digestion of urease gene PCR products.
Results. The majority of H. pylori -positive patients had strongly cagA -positive culture isolates and endoscopic samples (62.5% and 69.6%, respectively). However, many of these patients had evidence of mixed infection with cagA negative and cagA positive strais in cultures isolates and endoscopic samples (25% and 17.4%, respectively). Mixed infection was found to be due to genetically unrelated strains in two patients in whom genetic analysis was performed.
Conclusion. Mixed infection with differences in substrain pathogenic factors might occur in H. pylori infection and might contribute to differences in clinical outcome.     

Limits to Catalysis by Ribonuclease A

Bovine pancreatic ribonuclease A (RNase A) catalyzes the cleavage of the P-O(5') bond in RNA. Although this enzyme has been the object of much landmark work in bioorganic chemistry, the nature of its rate-limiting transition state and its catalytic rate enhancement had been unknown. Here, the value of k(cat)/K(m) for the cleavage of UpA by wild-type RNase A was found to be inversely related to the concentration of added glycerol. In contrast, the values of k(cat)/K(m) for the cleavage of UpA by a sluggish mutant of RNase A and the cleavage of the poor substrate UpOC(6)H(4)-p-NO(2) by wild-type RNase A were found to be independent of glycerol concentration. Yet, UpA cleavage by the wild-type and mutant enzymes was found to have the same dependence on sucrose concentration, indicating that catalysis of UpA cleavage by RNase A is limited by desolvation. The rate of UpA cleavage by RNase A is maximal at pH 6.0, where k(cat) = 1.4 × 10(3) s(-1) and k(cat)/K(m) = 2.3 × 10(6) M(-1)s(-1) at 25°C. At pH 6.0 and 25°C, the uncatalyzed rate of [5,6-(3)H]Up[3,5,8-(3)H]A cleavage was found to be k(uncat) = 5 × 10(-9) s(-1) (t(1/2) = 4 years). Thus, RNase A enhances the rate of UpA cleavage by 3 × 10(11)-fold by binding to the transition state for P-O(5') bond cleavage with a dissociation constant of <2 × 10(-15) M.     

Morphological responses by Bosmina longirostris and Eubosmina tubicen to changes in copepod predator populations during a whole-lake acidification experiment

Changes in zooplankton populations during the experimental acidilicationof Little Rock Lake provided an opportunity to examine specificmechanisms underlying the morphological responses of bosminidsto changing predation pressure. Two large copepods, Epischuralacustris and Mesocyclops edax, disappeared from the lake'sacidified basin in 1986 and 1989, respectively, while a smallercopepod predator, Tropocyclops extensus, increased during laterstages of acidification. The two bosminid species showed distinctlydifferent responses coinciding with the changes in copepod predation.Bosmina longirostris exhibited a significant decrease in mucrolength with the decline of M.edax and E.lacustris. Its meanbody and antennule length, however, did not change. We suggestthat the decoupling of B.longirostris mucro length and antennulelength may have been related to the persistence of the smallercopepod predator, T.extensus. Eubosmina tubicen showed no apparentresponse to declines in M.edax and E.lacustris abundance ineither mean mucro, antennule or body length. Allometric analysesindicated, however, that mucro length was related to size-dependentcopepod predation for both B.longirostris and E.tubicen.     

Isotopic fractionation during nitrate uptake by phytoplankton grown in continuous culture

The isotopic fractionation associated with uptake of NO₃^–by six species of phytoplankton (two diatoms, one cryptophyte,one chlorophyte and two haptophytes) was measured at a varietyof steady-state growth rates in nitrogen-limited continuousculture. The magnitude of the isotopic fractionation factor(