The record of mid Cretaceous oceanic anoxic events from the Ionian zone of southern Albania

Along the Sopoti section of Mali Gjere mountain are found two distinct mid-Cretaceous marly-shaly-siliceous intervals that occur near the top of the Vigla Limestone Formation (Aptian-Albian) of the Ionian zone in southern Albania. The lower interval is relatively rich in carbonate content (36% CaCO₃ on average) and radiolaria (10% on average). It contains black shale levels rich in organic matter (up to 8.5% total organic carbon (TOC)) of marine origin, which did not experience any strong thermal maturation as suggested by their very low T_max values. The age of the lower interval is latest Barremian to Early Aptian based on its calcareous nannofossil and radiolarian assemblages. It is therefore regarded as the equivalent of the Fourcade Level of Greece, reflecting the Oceanic Anoxic Event 1a (OAE1a). The upper interval is richer in both carbonate content (60% CaCO₃ on average) and radiolaria (20% on average) but it is practically devoid of any preserved organic matter. Its age straddles the Aptian-Albian boundary based on integrated biochronologic data of dinoflagellates, calcareous nannofossils and radiolaria. It is tentatively considered as the sedimentary expression of OAE1b (sensu Leckie et al., 2002) in the Ionian zone of Albania. The presence of large Assipetra nannoliths in both shaly-siliceous intervals and the relative abundance of radiolaria suggest that their accumulation took place during periods of higher productivity in the Ionian zone of Albania.     

Converting the prion protein: what makes the protein infectious

The discovery of prion disease transmission in mammals, as well as a non-Mendelian type of inheritance in yeast, has led to the establishment of a new concept in biology, the prion hypothesis. The prion hypothesis postulates that an abnormal protein conformation propagates itself in an autocatalytic manner via recruitment of the normal isoform of the same protein as a substrate, and thereby acts either as a transmissible agent of disease (in mammals) or as a heritable determinant of phenotype (in yeast and fungus). Although reconstitution of fully infectious PrP(Sc)in vitro from synthetic components has not yet been achieved, numerous lines of evidence indicate that the prion protein is the major and essential component, if not the only one, of the prion infectious agent. This article summarizes our current knowledge about the chemical nature of the prion infectious agent, describes potential strategies and challenges related to the generation of prion infectivity de novo, proposes new hypotheses to explain the apparently low infectivity observed in the first synthetic mammalian prions, and describes plausible effects of chemical modifications on prion conversion.     

The ferric-hydroperoxo complex of chloroperoxidase

The hydroperoxo-ferric complex, or Compound 0 (Cpd 0), is an unstable transient intermediate common for oxygen activating heme enzymes such as the cytochromes P450, nitric oxide synthases, and heme oxygenases, as well as the peroxidases and catalases which utilize hydrogen peroxide as a source of oxygen and reducing equivalents. Detailed understanding of the mechanism of oxygen activation and formation of the higher valent catalytically active intermediates in heme enzyme catalysis requires the structural and spectroscopic characterization of this immediate precursor, Cpd 0. Using the method of cryoradiolytic reduction of the oxy-ferrous heme complex, we have prepared and characterized hydroperoxo-ferric complex in chloroperoxidase (CPO) and compared this to the same intermediate generated in cytochrome P450 CYP101. Optical absorption spectrum of Cpd 0 in CPO has a Soret band at 449 nm and poorly resolved α, β bands at 576 and 546 nm.     

Myogenesis in two polyclad platyhelminths with indirect development,Pseudoceros canadensis and Stylostomum sanjuania

SUMMARY Myogenesis of two representatives of Platyhelminthes, Stylostomum sanjuania and Pseudoceros canadensis, was followed from egg deposition until well‐differentiated free‐swimming larval stages, using F‐actin staining and confocal laserscanning microscopy. Zonulae adhaerentes are the only structures to stain before 50% of development between egg deposition and hatching in S. sanjuania, and before 67% of development in P. canadenis. Subsequently, irregular fibers appear in the embryo, followed by a helicoid muscle close to the apical pole. Three longitudinal muscle pairs form, of which the dorsal pair remains more pronounced than the others. Gradually, new muscles form by branching or from double‐stranded muscle zones adjacent to existing muscles. This results in an elaborate muscular bodywall that consists of a single helicoid muscle as well as multiple circular and longitudinal muscles. Diverse retractor muscles insert at the sphincter muscles around the stomodeum. The overall arrangement and formation mode of the larval musculature appears very similar in both species, although only P. canadensis has a primary circular muscle posterior to the helicoid muscle. Muscle formation in the apical region of the embryo precedes that at the abapical pole and the primary longitudinal muscles form slightly later than the primary circular muscles. Myogenesis and larval myoanatomy appears highly conserved among polyclad flatworms, but differs significantly from that of other trochozoan clades. Our data suggest that the larval muscular ground pattern of polyclad larvae comprises a bodywall consisting of a helicoid muscle, circular and longitudinal muscles, several retractor muscles, and sphincter muscles around the stomodeum.     

Increased efficacy of HIV-1 neutralization by antibodies at low CCR5 surface concentration

It has been observed that some antibodies, including the CD4-induced (CD4i) antibody IgG X5 and the gp41-specific antibody IgG 2F5, exhibit higher neutralizing activity in PBMC-based assays than in cell line based assays [J.M. Binley, T. Wrin, B. Korber, M.B. Zwick, M. Wang, C. Chappey, G. Stiegler, R. Kunert, S. Zolla-Pazner, H. Katinger, C.J. Petropoulos, D.R. Burton, Comprehensive cross-clade neutralization analysis of a panel of anti-human immunodeficiency virus type 1 monoclonal antibodies, J. Virol. 78 (2004) 13232-13252]. It has been hypothesized that the lower CCR5 concentration on the surface of the CD4 T lymphocytes compared to that on cell lines used for the neutralization assays could be a contributing factor to the observed differences in neutralizing activity. To test this hypothesis and to further elucidate the contribution of CCR5 concentration differences on antibody neutralizing activity, we used a panel of HeLa cell lines with well-defined and differential surface concentrations of CCR5 and CD4 in a pseudovirus-based assay. We observed that the CCR5 cell surface concentration but not the CD4 concentration had a significant effect on the inhibitory activity of X5 and several other CD4i antibodies including 17b and m9, as well as that of the gp41-specifc antibodies 2F5 and 4E10 but not on that of the CD4 binding site antibody (CD4bs), b12. The 50% inhibitory concentration (IC50) decreased up to two orders of magnitude in cell lines with low CCR5 concentration corresponding to that in CD4 T cells used in PBMC-based assays (about 10(3) per cell) compared to cell lines with high CCR5 concentration (about 10(4) or more). Our results suggest that the CCR5 cell surface concentration could be a contributing factor to the high neutralizing activities of some antibodies in PBMC-based-assays but other factors could also play an important role. These findings could have implications for development of vaccine immunogens based on the epitopes of X5 and other CD4i antibodies, for elucidation of the mechanisms of HIV-1 neutralization by antibodies, and for design of novel therapeutic approaches.     

Mechanisms that contribute to differences in motor performance between young and old adults.

This paper examines the physiological mechanisms responsible for differences in the amplitude of force fluctuations between young and old adults. Because muscle force is a consequence of motor unit activity, the potential mechanisms include both motor unit properties and the behavior of motor unit populations. The force fluctuations, however, depend not only on the age of the individual but also on the muscle group performing the task, the type and intensity of the muscle contraction, and the physical activity status of the individual. Computer simulations and experimental findings performed on tasks that involved single agonist and antagonist muscles suggest that differences in force fluctuations are not attributable to motor unit twitch force, motor unit number, or nonuniform activation of the agonist muscle, but that they are influenced by the variability and common modulation of motor unit discharge in both the agonist and antagonist muscles. Because the amplitude of the force fluctuations does not vary linearly with muscle activation, these results suggest that multiple mechanisms contribute to the differences in force fluctuations between young and old adults, although the boundary conditions for each mechanism remain to be determined.     

Cofilin produces newly polymerized actin filaments that are preferred for dendritic nucleation by the Arp2/3 complex.

One of the earliest events in the process of cell motility is the massive generation of free actin barbed ends, which elongate to form filaments adjacent to the plasma membrane at the tip of the leading edge. Both cofilin and Arp2/3 complex have been proposed to contribute to barbed end formation during cell motility. Attempts to assess the functions of cofilin and Arp 2/3 complex in vivo indicate that both cofilin and Arp2/3 complex contribute to actin polymerization: cofilin by severing and Arp2/3 by nucleating and branching. In order to determine if the activities of cofilin and Arp2/3 complex interact, we employed a light microscope-based assay to visualize actin polymerization directly in the presence of both proteins. The results indicate that cofilin generates barbed ends to increase the mass of freshly polymerized F-actin but does not directly affect the activity of Arp2/3 complex. However, while ADP, ADP-Pi, and newly polymerized ATP-filaments are all capable of supporting Arp2/3-mediated branching, newly polymerized F-actin supports most of the Arp2/3-induced branch formation. The results suggest that, in vivo, cofilin contributes to barbed end formation by inducing the initial increase in the number of barbed ends leading to increased ATP-F-actin, which in turn supports higher levels of dendritic nucleation by active Arp2/3 complex.     

Polymorphism and ultrastructural organization of prion protein amyloid fibrils: an insight from high resolution atomic force microscopy

Amyloid fibrils were produced from the full-length mouse prion protein (PrP) under solvent conditions similar to those used for the generation of synthetic prions from PrP 89-230. Analysis of the ultrastructure by atomic force microscopy revealed extremely broad polymorphism in fibrils formed under a single growth condition. Fibrils varied with respect to the number of constitutive filaments and the manner in which the filaments were assembled. PrP polymerization was found to show several peculiar features: (i) the higher-order fibrils/ribbons were formed through a highly hierarchical mechanism of assembly of lower-order fibrils/ribbons; (ii) the lateral assembly proceeded stepwise; at each step, a semi-stable fibrillar species were generated, which were then able to enter the next level of assembly; (iii) the assembly of lower into higher-order fibrils occurred predominantly in a vertical dimension via stacking of ribbons on top of each other; (iv) alternative modes of lateral association co-existed under a single growth condition; (iv) the fibrillar morphology changed even within individual fibrils, illustrating that alternative modes of filament assembly are inter-convertible and thermodynamically equivalent. The most predominant fibrillar types were classified into five groups according to their height, each of which was divided in up to three subgroups according to their width. Detailed analysis of ultrastructure revealed that the fibrils of the major subtype (height 3.61(+/-0.28)nm, width 31.1(+/-2.0)nm) were composed of two ribbons, each of which was composed of two filaments. The molecular volume calculations indicated that a single PrP molecule occupied a distance of approximately 1.2 nm within a single filament. High polymorphism in fibrils generated in vitro is reminiscent of high morphological diversity of scrapie-associated fibrils isolated from scrapie brains, suggesting that polymorphism is peculiar for polymerization of PrP regardless of whether fibrils are formed in vitro or under pathological conditions in vivo.     

Magnetic field effects in Arabidopsis thaliana cryptochrome-1

The ability of some animals, most notably migratory birds, to sense magnetic fields is still poorly understood. It has been suggested that this "magnetic sense" may be mediated by the blue light receptor protein cryptochrome, which is known to be localized in the retinas of migratory birds. Cryptochromes are a class of photoreceptor signaling proteins that are found in a wide variety of organisms and that primarily perform regulatory functions, such as the entrainment of circadian rhythm in mammals and the inhibition of hypocotyl growth in plants. Recent experiments have shown that the activity of cryptochrome-1 in Arabidopsis thaliana is enhanced by the presence of a weak external magnetic field, confirming the ability of cryptochrome to mediate magnetic field responses. Cryptochrome's signaling is tied to the photoreduction of an internally bound chromophore, flavin adenine dinucleotide. The spin chemistry of this photoreduction process, which involves electron transfer from a chain of three tryptophans, can be modulated by the presence of a magnetic field in an effect known as the radical-pair mechanism. Here we present and analyze a model of the flavin-adenine-dinucleotide-tryptophan chain system that incorporates realistic hyperfine coupling constants and reaction rate constants. Our calculations show that the radical-pair mechanism in cryptochrome can produce an increase in the protein's signaling activity of approximately 10% for magnetic fields on the order of 5 G, which is consistent with experimental results. These calculations, in view of the similarity between bird and plant cryptochromes, provide further support for a cryptochrome-based model of avian magnetoreception.