Protoanthropoidea (Primates, Simiiformes): A New Primate Higher Taxon and a Solution to the Rooneyia Problem

As a derivative of the hypothesis that anthropoids evolved from omomyid-like primates, the enigmatic North American fossil Rooneyia viejaensis, from the latest Eocene of Texas, is placed in a new higher taxon, Protoanthropoidea, which is proposed as the sister-group of Anthropoidea. Rooneyia and anthropoids share synapomorphically a pattern of character states relating to the unique orbital morphology of higher primates, including; highly convergent and frontated orbits roofed above by an extended frontal bone; funnel-shaped orbital fossae; orbital apices that are recessed beneath the forebrain; a deep, large lateral process of the frontal bone (upper portion of the postorbital bar) that may presage closure of the orbit by an enlarged ascending process of the zygomatic. If the sister-group of anthropoids occupied North America as part of a Laurasian geographic distribution during the Paleogene, as some primate genera did, ancestral anthropoids may likewise have occurred across Laurasia, prestaging them to enter Africa and Central/South America in two independent episodes of dispersal—without having the ancestral platyrrhines crossing the daunting Atlantic Ocean.     

Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72

Azoarcus sp. strain BH72, a mutualistic endophyte of rice and other grasses, is of agrobiotechnological interest because it supplies biologically fixed nitrogen to its host and colonizes plants in remarkably high numbers without eliciting disease symptoms. The complete genome sequence is 4,376,040-bp long and contains 3,992 predicted protein-coding sequences. Genome comparison with the Azoarcus-related soil bacterium strain EbN1 revealed a surprisingly low degree of synteny. Coding sequences involved in the synthesis of surface components potentially important for plant-microbe interactions were more closely related to those of plant-associated bacteria. Strain BH72 appears to be 'disarmed' compared to plant pathogens, having only a few enzymes that degrade plant cell walls; it lacks type III and IV secretion systems, related toxins and an N-acyl homoserine lactones-based communication system. The genome contains remarkably few mobile elements, indicating a low rate of recent gene transfer that is presumably due to adaptation to a stable, low-stress microenvironment.     

Hypoxemia in the absence of blood loss upregulates iNOS expression and activity in macrophages

Regional hypoxia,associated with hemorrhage, is thought to induce a variety ofalterations in immune cell function, including upregulation ofmacrophage-inducible nitric oxide synthase (iNOS) expression andactivity (NO production). Furthermore, NO may cause immune celldysfunction similar to that associated with hemorrhagic shock. However,it remains unknown whether hypoxia per se in the absence of any bloodloss is a sufficient stimulus to cause iNOS expression and NOproduction by macrophages. To study this, male Sprague-Dawley rats(275-325 g) were placed in a plastic box flushed with a gasmixture containing 5% O₂-95%N₂ for 60 min. Peritoneal andsplenic macrophages were isolated 0-5.5 h thereafter, and bloodsamples were obtained. Nitrite and nitrate (stable degradation productsof NO) production by splenic and peritoneal macrophages cultured for 48 h was significantly increased 3 and 5.5 h after hypoxemia. The increasein NO production by macrophages was preceded by elevated expression ofiNOS mRNA at 1.5 h after hypoxia. Additionally, interferon-(IFN-) levels in plasma from rats subjected to hypoxemia weresignificantly elevated soon after the insult (0-1.5 hposthypoxemia), suggesting a causal relationship between IFN-production and upregulation of iNOS activity. We propose that ahypoxemia-induced increase in macrophage iNOS activity followinghemorrhage may in part be responsible for the observed immunedysfunction. Thus attempts to suppress macrophage iNOS activity afterthis form of trauma may be helpful in improving immune function underthose conditions.     

Clinal genetic variation and the 'rare allele phenomenon' in random mating populations of <Emphasis Type="Italic">Urophora cardui</Emphasis> (Diptera: Tephritidae)

In the present study we investigate a contact zone between two population groups of the tephritid fly Urophora cardui. We investigate scenarios that may have produced the genetic differentiation of the two groups, and we describe the 'rare allele phenomenon' from the contact zone. The rare allele phenomenon refers to alleles that are found at high frequency in contact zones but are rare or lacking outside the contact zone. The phenomenon is often observed in hybrid zones between subspecies of limited reproductive compatibility, but seldom in populations with random mating. Clinal genetic variation was observed at three loci in the contact zone. Three alleles at the locus Aat showed steep clines, between 20--70 km wide. A rare Aat-A allele occurred at high frequency in the centre of the contact zone. Two further loci, Hk and Pgd, showed less steep clinal genetic variation, the transition being in and slightly south of the centre of the Aat cline. Populations showed Hardy--Weinberg proportions and there was no evidence for linkage dis-equlibrium. These findings suggest random mating and gradual introgression between the population systems, which may originate from at least two range expansions. Aat's steep clines and rare allele may indicate selection on Aat alleles, although we presently can not quantify any agents. Because U. cardui experiences random mating in the contact zone with no apparent 'hybrid' incompatibility, mating experiments offer the possibility for future enquiries about the genetic basis of the rare allele phenomenon.     

Identification and characterization of rain, a novel Ras-interacting protein with a unique subcellular localization

The Ras small GTPase functions as a signaling node and is activated by extracellular stimuli. Upon activation, Ras interacts with a spectrum of functionally diverse downstream effectors and stimulates multiple cytoplasmic signaling cascades that regulate cellular proliferation, differentiation, and apoptosis. In addition to the association of Ras with the plasma membrane, recent studies have established an association of Ras with Golgi membranes. Whereas the effectors of signal transduction by activated, plasma membrane-localized Ras are well characterized, very little is known about the effectors used by Golgi-localized Ras. In this study, we report the identification of a novel Ras-interacting protein, Rain, that may serve as an effector for endomembrane-associated Ras. Rain does not share significant sequence similarity with any known mammalian proteins, but contains a Ras-associating domain that is found in RalGDS, AF-6, and other characterized Ras effectors. Rain interacts with Ras in a GTP-dependent manner in vitro and in vivo, requires an intact Ras core effector-binding domain for this interaction, and thus fits the definition of a Ras effector. Unlike other Ras effectors, however, Rain is localized to perinuclear, juxta-Golgi vesicles in intact cells and is recruited to the Golgi by activated Ras. Finally, we found that Rain cooperates with activated Raf and causes synergistic transformation of NIH3T3 cells. Taken together, these observations support a role for Rain as a novel protein that can serve as an effector of endomembrane-localized Ras.     

DNA recognition by the homing endonuclease PI-SceI involves a divalent metal ion cofactor-induced conformational change

PI-SceI, a homing endonuclease of the LAGLIDADG family, consists of two domains involved in DNA cleavage and protein splicing, respectively. Both domains cooperate in binding the recognition sequence. Comparison of the structures of PI-SceI in the absence and presence of substrate reveals major conformational changes in both the protein and DNA. Notably, in the protein-splicing domain the loop comprising residues 53-70 and adopts a "closed" conformation, thus enabling it to interact with the DNA. We have studied the dynamics of DNA binding and subsequent loop movement by fluorescence techniques. Six amino acids in loop53-70 were individually replaced by cysteine and modified by fluorescein. The interaction of the modified PI-SceI variants with the substrate, unlabeled or labeled with tetramethylrhodamine, was analyzed in equilibrium and stopped-flow experiments. A kinetic scheme was established describing the interaction between PI-SceI and DNA. It is noteworthy that the apparent hinge-flap motion of loop53-70 is only observed in the presence of a divalent metal ion cofactor. Substitution of the major Mg2+-binding ligands in PI-SceI, Asp-218 and Asp-326, by Asn or "nicking" PI-SceI with trypsin at Arg-277, which interferes with formation of an active enzyme.substrate complex, both prevent the conformational change of loop53-70. Deletion of the loop inactivates the enzyme. We conclude that loop53-70 is an important structural element that couples DNA recognition by the splicing domain with DNA cleavage by the catalytic domain and as such "communicates" with the Mg2+ binding sites at the catalytic centers.     

Fourier transform infrared spectroscopy on the Rap.RapGAP reaction, GTPase activation without an arginine finger

GTPase activating proteins (GAPs) down-regulate Ras-like proteins by stimulating their GTP hydrolysis, and a malfunction of this reaction leads to disease formation. In most cases, the molecular mechanism of activation involves stabilization of a catalytic Gln and insertion of a catalytic Arg into the active site by GAP. Rap1 neither possesses a Gln nor does its cognate Rap-GAP employ an Arg. Recently it was proposed that RapGAP provides a catalytic Asn, which substitutes for the Gln found in all other Ras-like proteins (Daumke, O., Weyand, M., Chakrabarti, P. P., Vetter, I. R., and Wittinghofer, A. (2004) Nature 429, 197-201). Here, RapGAP-mediated activation has been investigated by time-resolved Fourier transform infrared spectroscopy. Although the intrinsic hydrolysis reactions of Rap and Ras are very similar, the GAP-catalyzed reaction shows unique features. RapGAP binding induces a GTP(*) conformation in which the three phosphate groups are oriented such that they are vibrationally coupled to each other, in contrast to what was seen in the intrinsic and the Ras.RasGAP reactions. However, the charge shift toward beta-phosphate observed with RasGAP was also observed for RapGAP. A GDP.P(i) intermediate accumulates in the GAP-catalyzed reaction, because the release of P(i) is eight times slower than the cleavage reaction, and significant GTP synthesis from GDP.P(i) was observed. Partial steps of the cleavage reaction are correlated with structural changes of protein side groups and backbone. Thus, the Rap.RapGAP catalytic machinery compensates for the absence of a cis-Gln by a trans-Asn and for the catalytic Arg by inducing a different GTP conformation that is more prone to be attacked by a water molecule.     

Sex-specific p38 MAP kinase activation following trauma-hemorrhage: involvement of testosterone and estradiol

Although immune functions are markedly depressed in males and not in proestrous females following trauma-hemorrhage (T-H), the mechanisms responsible for the divergent responses remain unknown. Because sex steroids modulate the activation of p38, our aim was to determine whether differences in the activation of p38 by phosphorylation (p38-P) might contribute to the sex-dimorphic immune response following T-H. The effects of testosterone and estradiol on the activation of p38 were also examined. Intact male mice (C3H/HeN), castrated males treated with vehicle, 5alpha-dihydrotestosterone (DHT), or 17beta-estradiol, and proestrous females were subjected to trauma (i.e., midline laparotomy) and hemorrhagic shock (35 +/- 5 mmHg for 90 min and resuscitation) or sham operation. At 2 h thereafter, splenic (SMphi) and peritoneal macrophages (PMphi) were harvested and cultured (with 10 microg/ml LPS), and Western blot analysis was carried out for quantification of p38 and p38-P. Sex, testosterone and estradiol plasma levels, and T-H did not alter the constitutive expression of p38 in SMphi and PMphi. In contrast, the activated form of p38 (p38-P) was markedly increased in SMphi and PMphi from female shams compared with male shams. Moreover, the phosphorylation of p38-P increased in males after T-H, whereas it decreased in females under those conditions. Castration before T-H prevented the increase in p38-P in males. Castrated animals treated with DHT displayed increased p38-P following T-H, whereas 17beta-estradiol had no effect on p38-P in castrated mice. Thus 1) sex influences the activation of p38 MAP kinase, 2) DHT is responsible for the increased activation of p38 in male mice, and 3) this sex-specific activation of p38 might be responsible for the sexually dimorphic immune response following T-H.