RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction

We report the results of a first, collective, blind experiment in RNA three-dimensional (3D) structure prediction, encompassing three prediction puzzles. The goals are to assess the leading edge of RNA structure prediction techniques; compare existing methods and tools; and evaluate their relative strengths, weaknesses, and limitations in terms of sequence length and structural complexity. The results should give potential users insight into the suitability of available methods for different applications and facilitate efforts in the RNA structure prediction community in ongoing efforts to improve prediction tools. We also report the creation of an automated evaluation pipeline to facilitate the analysis of future RNA structure prediction exercises.     

Natural occurrence of microbial sulphur oxidation by long-range electron transport in the seafloor

Recently, a novel mode of sulphur oxidation was described in marine sediments, in which sulphide oxidation in deeper anoxic layers was electrically coupled to oxygen reduction at the sediment surface. Subsequent experimental evidence identified that long filamentous bacteria belonging to the family Desulfobulbaceae likely mediated the electron transport across the centimetre-scale distances. Such long-range electron transfer challenges some long-held views in microbial ecology and could have profound implications for sulphur cycling in marine sediments. But, so far, this process of electrogenic sulphur oxidation has been documented only in laboratory experiments and so its imprint on the seafloor remains unknown. Here we show that the geochemical signature of electrogenic sulphur oxidation occurs in a variety of coastal sediment environments, including a salt marsh, a seasonally hypoxic basin, and a subtidal coastal mud plain. In all cases, electrogenic sulphur oxidation was detected together with an abundance of Desulfobulbaceae filaments. Complementary laboratory experiments in intertidal sands demonstrated that mechanical disturbance by bioturbating fauna destroys the electrogenic sulphur oxidation signal. A survey of published geochemical data and 16S rRNA gene sequences identified that electrogenic sulphide oxidation is likely present in a variety of marine sediments with high sulphide generation and restricted bioturbation, such as mangrove swamps, aquaculture areas, seasonally hypoxic basins, cold sulphide seeps and possibly hydrothermal vent environments. This study shows for the first time that electrogenic sulphur oxidation occurs in a wide range of marine sediments and that bioturbation may exert a dominant control on its natural distribution.     

The chick erythrocyte membrane antigens: characterization and variation during embryonic and postembryonic development.

Chicken erythrocyte plasma membrane antigens were studied by crossed immunoelectrophoresis. An embryonic antigen demonstrated in 12-day-old embryos decreases after hatching and takes 90 to 120 days to disappear. An adult antigen becomes detectable 8 days after hatching and reaches the adult value at the end of the first month of life.In young chickens, induction of anemia produces a decrease of embryonic antigen level followed by an increase during the recovery phase. Correlatively, the adult antigen is precociously detected and maintains a level higher than controls during recovery phase. When adults are rendered anemic, the embryonic antigen is not detected; the adult antigen level, which decreases at first, regains a normal value within a few days.     

Degradation of polycyclic aromatic hydrocarbons by pure strains and by defined strain associations: inhibition phenomena and cometabolism

Six bacterial strains capable of using, as sole carbon and energy source, at least one of the following polycyclic aromatic hydrocarbons (PAH), naphthalene, fluorene, phenanthrene, anthracene, fluoranthene and pyrene, were isolated. The interactions between these PAH during their biodegradation were studied in experiments involving PAH pairs, one PAH at least being used as a carbon source. All individual strains were found capable of cometabolic degradation of PAH in a range varying among strains. Inhibition phenomena, sometimes drastic, were often observed but synergistic interactions were also detected. Naphthalene was toxic to all strains not isolated on this compound. Strain associations were found efficient in relieving inhibition phenomena, including the toxic effect of naphthalene. Accumulation of water-soluble metabolites was consistently observed during PAH degradation.     

The Pre-S1 and Antigenic Loop Infectivity Determinants of the Hepatitis B Virus Envelope Proteins Are Functionally Independent

The hepatitis B virus (HBV) envelope proteins bear two determinants of viral entry: a receptor-binding site (RBS) in the pre-S1 domain of the large envelope protein and a conformation-dependent determinant, of unknown function, in the antigenic loop (AGL) of the small, middle, and large envelope proteins. Using an in vitro infection assay consisting of susceptible HepaRG cells and the hepatitis delta virus (HDV) as a surrogate of HBV, we first investigated whether subelements of the pre-S1 determinant (amino acids 2 to 75), i.e., the N-terminal myristoyl anchor, subdomain 2-48 (RBS), and subdomain 49-75, were functionally separable. In transcomplementation experiments, coexpression of two distinct infectivity-deficient pre-S1 mutants at the surface of HDV virions failed to restore infectivity, indicating that the myristoyl anchor, the 2-48 RBS, and the 49-75 sequence, likely cooperate in cis at viral entry. Furthermore, we showed that as much as 52% of total pre-S1 in the HDV envelope could bear infectivity-deficient lesions without affecting entry, indicating that a small number of pre-S1 polypeptides—estimated at three to four per virion—is sufficient for infectivity. We next investigated the AGL activity in the small or large envelope protein background (S- and L-AGL, respectively) and found that lesions in S-AGL were more deleterious to infectivity than in L-AGL, a difference that reflects the relative stoichiometry of the small and large envelope proteins in the viral envelope. Finally, we showed that C147S, an AGL infectivity-deficient substitution, exerted a dominant-negative effect on infectivity, likely reflecting an involvement of C147 in intermolecular disulfide bonds.Hepatitis B virus (HBV) remains a major public health concern worldwide, affecting more than 350 millions of chronically infected individuals. Since the discovery of HBV, substantial information has been gathered on the viral replication cycle, but our understanding of the viral entry mechanism remains limited, and the identity of the receptor(s) for HBV is still unknown (15). HBV displays a very narrow host range, which is likely determined at viral entry by a highly specific interaction between the HBV envelope proteins and receptors at the surface of human hepatocytes. The envelope proteins designated large (L-HBsAg), middle (M-HBsAg), and small (S-HBsAg) are membrane-spanning glycoproteins that differ from each other by the size of their N-terminal ectodomain (21). L-HBsAg contains a N-terminal pre-S1, central pre-S2, and C-terminal S domains. M-HBsAg is shorter than L-HBsAg in lacking pre-S1, whereas S-HBsAg consists of the S domain only (Fig. ​(Fig.1).1). Envelope protein synthesis occurs at the endoplasmic reticulum (ER) membrane. Empty subviral particles (SVPs) assemble from aggregates at a pre-Golgi membrane and exit the cell through the secretory pathway (36). Assembly of mature HBV virions requires, in addition to S-HBsAg, the presence of L-HBsAg as a matrix protein for nucleocapsid envelopment (6). Recent findings indicate that HBV virions and SVPs follow distinct pathways for budding: the late endosomal multivesicular bodies (MVBs) for HBV virions, and the MVB-independent secretory pathway for SVPs (26, 28, 46). The HBV envelope proteins can also package the hepatitis delta virus (HDV) ribonucleoprotein (RNP), in case of HBV/HDV coinfection (5, 45), leading to the formation of HDV virions. Whether HDV uses the SVP secretion pathway rather than an MVB-dependent route is uncertain.Open in a separate windowFIG. 1.Schematic representation of HBV envelope proteins. The topology of the L-, M-, and S-HBsAg proteins at the viral membrane is represented. The pre-S2 domain of L- and M-HBsAg, and the determinants of viral entry, pre-S1 and AGL, are indicated. The M-HBsAg protein, represented in gray, is dispensable for infectivity. The myristic acid (Myr) linked to the L-HBsAg N terminus is indicated (closed box). Subdomains 2-48 and 49-75 of the pre-S1 infectivity determinant are indicated. Open boxes represent transmembrane regions in the S domain.L-HBsAg, but not M-HBsAg, is crucial to infectivity of both HBV and HDV particles (13, 31, 41, 42). L-HBsAg contains a major infectivity determinant located between amino acid residues 2 and 75 of its N-terminal pre-S1 domain (4, 30), including a myristoyl anchor linked to glycine-2 (1, 8, 18), a putative receptor binding site (RBS) between positions 2 and 48, and a domain of unknown function between amino acids 49 and 75. To date, the most compelling evidence that pre-S1 mediates receptor binding comes from studies demonstrating that myristoylated synthetic peptides specific for the N-terminal 2-to-48 pre-S1 domain can bind to hepatocyte plasma membranes and block infection in vitro (3, 16, 17) and in vivo (37). Beside pre-S1, a second determinant was recently identified in the antigenic loop (AGL) borne by the three HBV envelope proteins (Fig. ​(Fig.1).1). The AGL participation in viral entry was first established in the HDV model (23) and more recently directly in the HBV model (39). Interestingly, serine substitutions for the AGL cysteine residues, which prove detrimental to the conserved immunodominant “a” determinant, could also block viral entry. Note that the “a” determinant consists in conformational epitopes, which elicit highly neutralizing antibodies (22). Infectivity and the “a” determinant were also lost when virions were treated with membrane-impermeable inhibitors of thiol/disulfide isomerization (2). These findings clearly established a correlation between the AGL cysteine disulfide bonds network, the conformation of the “a” determinant, and infectivity. Hence, the strict conservation of the “a” determinant among all HBV genotypes is related to the AGL function at viral entry. The AGL determinant may operate in association with, or independently of pre-S1, in binding to receptors at the early step of entry and/or in the mechanism of envelope disassembly postentry.In the present study, we investigated the pre-S1 determinant by performing transcomplementation experiments between mutants of 3 pre-S1 subelements: the myristoyl anchor, subdomain 2-48, and subdomain 49-75. We analyzed the activity of the AGL determinant in the S- or L-HBsAg background (S- and L-AGL, respectively), and we examined the effect of introducing increasing amounts of infectivity-deficient pre-S1, or AGL, in the virion''s envelope on infectivity.     

Broad-scale determinants of non-native fish species richness are context-dependent

Identifying the factors determining the non-native species richness (NNSR) in a given area is essential for preventing species invasions. The relative importance of human-related and natural factors considered for explaining NNSR might depend upon both the spatial scale (i.e. the extent of the gradients sampled) and the historical context of the area surveyed. Here, using a worldwide database of freshwater fish occurrences, we tested whether the relative influence of human and ecological determinants of non-native fish species establishment at the scale of the biogeographic realm was consistent (i) with that observed worldwide, and (ii) among the different biogeographical realms. The prominent role of human activity in shaping the global (i.e. worldwide) pattern of NNSR cannot be directly extrapolated to the biogeographic realms. Furthermore, the relationships between human and ecological determinants and NNSR vary strikingly across biogeographic realms, revealing a strong context dependency of the determinants of NNSR. In particular, the human-related factors play a predominant role in explaining the establishment of non-native species in economically developed realms, while in the other realms environmental characteristics of the river basins best explained geographical patterns of NNSR. In the face of future biological invasions, considering both the spatial scale and the historical context of the surveyed area is crucial to adopt effective conservation strategies.