G-quadruplex RNA structure as a signal for neurite mRNA targeting

Targeting of messenger RNAs (mRNAs) in neuron processes relies on cis-acting regulatory elements, the nature of which is poorly understood. Here, we report that approximately 30% of the best-known dendritic mRNAs contain a guanine (G)-quadruplex consensus in their 3'-untranslated region. Among these mRNAs, we show by using RNA structure probing that a G-quadruplex is present in the mRNAs of two key postsynaptic proteins: PSD-95 and CaMKIIa. The G-quadruplex structure is necessary and sufficient for the potent and fast localization of mRNAs in cortical neurites and this occurs in a metabotropic glutamate receptor-responsive manner. Thus, G-quadruplex seems to be a common neurite localization signal.     

Engineering aluminum binding affinity in an isolated EF-hand from troponin C: a computational site-directed mutagenesis study

Peptides with the ability to specifically bind aluminum would potentially be of great use in the fields of biochemistry and environmental chemistry. Unfortunately no such peptides are known. An aluminum-specific peptide may be used as an in vivo chelator, for metalloprotein design, for understanding metal-ion induced folding and metal-ion trafficking, and as an environmental sensor to monitor metal pollution in the environment. Plants genetically engineered to produce an aluminum binding peptide might be useful in environmental remediation in areas of high free aluminum ion concentration. In this paper, which is the theoretical complement to the experimental work, we analyzed crystallographic structures of EF-hands bound to various metals in order to determine the ligand distances and identities to compare to metal-ion size, charge, electronegativity, and coordination number and performed energy minimization calculations to identify possible mutations. We then constructed various mutant sequences in silico in an isolated EF-hand from troponin C and analyzed their binding behavior using molecular mechanics for binding to Tb(3+) as compared to Al(3+). As a result of these analyses we were able to isolate some characteristics that could lead to mutant peptides with enhanced aluminum activity that we plan to test experimentally in the future. We also performed metal-ion binding studies with the isolated EF-hand used in the computational work to examine the ability of Al(3+) and comparative metals to bind the peptide. In competition studies, the peptide demonstrated preference for Tb(3+) over Al(3+).     

Abundance and functional roles of intrinsic disorder in the antimicrobial peptides of the NK-lysin family

NK-lysins are antimicrobial peptides (AMPs) that participate in the innate immune response and also have several pivotal roles in various biological processes. Such multifunctionality is commonly found among intrinsically disordered proteins. However, NK-lysins have never been systematically analyzed for intrinsic disorder. To fill this gap, the amino acid sequences of NK-lysins from various species were collected from UniProt and used for the comprehensive computational analysis to evaluate the propensity of these proteins for intrinsic disorder and to investigate the potential roles of disordered regions in NK-lysin functions. We analyzed abundance and peculiarities of intrinsic disorder distribution in all-known NK-lysins and showed that many NK-lysins are expected to have substantial levels of intrinsic disorder. Curiously, high level of intrinsic disorder was also found even in two proteins with known 3D-strucutres (NK-lysin from pig and human granulysin). Many of the identified disordered regions can be involved in protein–protein interactions. In fact, NK-lysins are shown to contain three to eight molecular recognition features; i.e. short structure-prone segments which are located within the long disordered regions and have a potential to undergo a disorder-to-order transition upon binding to a partner. Furthermore, these disordered regions are expected to have several sites of various posttranslational modifications. Our study shows that NK-lysins, which are AMPs with a set of prominent roles in the innate immune response, are expected to abundantly possess intrinsically disordered regions that might be related to multifunctionality of these proteins in the signal transduction pathways controlling the host response to pathogenic agents.     

A Bayesian hierarchical approach to account for left-censored and missing radiation doses prone to classical measurement error when analyzing lung cancer mortality due to γ-ray exposure in the French cohort of uranium miners

Epidemiological data on cohorts of occupationally exposed uranium miners are currently used to assess health risks associated with chronic exposure to low doses of ionizing radiation. Nevertheless, exposure uncertainty is ubiquitous and questions the validity of statistical inference in these cohorts. This paper highlights the flexibility and relevance of the Bayesian hierarchical approach to account for both missing and left-censored (i.e. only known to be lower than a fixed detection limit) radiation doses that are prone to measurement error, when estimating radiation-related risks. Up to the authors’ knowledge, this is the first time these three sources of uncertainty are dealt with simultaneously in radiation epidemiology. To illustrate the issue, this paper focuses on the specific problem of accounting for these three sources of uncertainty when estimating the association between occupational exposure to low levels of γ-radiation and lung cancer mortality in the post-55 sub-cohort of French uranium miners. The impact of these three sources of dose uncertainty is of marginal importance when estimating the risk of death by lung cancer among French uranium miners. The corrected excess hazard ratio (EHR) is 0.81 per 100 mSv (95% credible interval: [0.28; 1.75]). Interestingly, even if the 95% credible interval of the corrected EHR is wider than the uncorrected one, a statistically significant positive association remains between γ-ray exposure and the risk of death by lung cancer, after accounting for dose uncertainty. Sensitivity analyses show that the results obtained are robust to different assumptions. Because of its flexible and modular nature, the Bayesian hierarchical models proposed in this work could be easily extended to account for high proportions of missing and left-censored dose values or exposure data, prone to more complex patterns of measurement error.

     

Synchrotron analysis of a ‘mummified’ salamander (Vertebrata: Caudata) from the Eocene of Quercy,France

An incomplete ‘mummy’ from the Phosphorites du Quercy (presumed Eocene) was identified as a salamander during the 19^th century. The specimen has now been computed tomography (CT) scanned, and this revealed the incomplete skeleton (with perfectly preserved bones) and soft tissues (lung). The fossil represents a new, well‐characterized taxon. Despite the absence of the skull, several features allow a phylogenetic analysis. The fossil belongs to pseudosaurian caudates; it is tentatively assigned to the Salamandridae, although affinities with Plethodontidae cannot be definitely ruled out.     

The histological structure of glyptosaurine osteoderms (Squamata: Anguidae), and the problem of osteoderm development in squamates

Glyptosaurinae, a fossil clade of anguid lizards, possess robust osteoderms, with granular ornamentation. In this study, the structural and histological features of these osteoderms were described in order to reconstruct their developmental pattern and further document the degree of homology that could exist between vertebrate integumentary skeletons. Glyptosaurine osteoderms have a diploe architecture and display an unusually complex structure that includes four tissue types: a core of woven‐fibered bone intensely remodeled; a peripheral formation of the same tissue containing dense bundles of long Sharpey fibers; a thick basal layer of lamellar bone; and a superficial layer of a non‐osseous material that belongs to the category of hypermineralized tissues such as ganoine, or enameloid and enamel tissues. The growth pattern of glyptosaurine osteoderms involved appositional processes due to osteoblast activity. In early growth stages, osseous metaplasia might have also been involved, but this possibility is not substantiated by histological observations. The superficial layer of the osteoderms must have resulted from epidermal contribution, a conclusion that would support previous hypotheses on the role of epidermal‐dermal interactions in the formation of squamate osteoderms. J. Morphol., 2010. © 2010 Wiley‐Liss, Inc.     

Genome-wide identification of mRNAs associated with the protein SMN whose depletion decreases their axonal localization

Spinal muscular atrophy is a neuromuscular disease resulting from mutations in the SMN1 gene, which encodes the survival motor neuron (SMN) protein. SMN is part of a large complex that is essential for the biogenesis of spliceosomal small nuclear RNPs. SMN also colocalizes with mRNAs in granules that are actively transported in neuronal processes, supporting the hypothesis that SMN is involved in axonal trafficking of mRNPs. Here, we have performed a genome-wide analysis of RNAs present in complexes containing the SMN protein and identified more than 200 mRNAs associated with SMN in differentiated NSC-34 motor neuron-like cells. Remarkably, ∼30% are described to localize in axons of different neuron types. In situ hybridization and immuno-fluorescence experiments performed on several candidates indicate that these mRNAs colocalize with the SMN protein in neurites and axons of differentiated NSC-34 cells. Moreover, they localize in cell processes in an SMN-dependent manner. Thus, low SMN levels might result in localization deficiencies of mRNAs required for axonogenesis.     

An enamel-like tissue,osteodermine, on the osteoderms of a fossil anguid (Glyptosaurinae) lizard

The Glyptosaurinae, a fossil clade of anguid lizards, have robust osteoderms, with a granular ornamentation consisting of tubercles. In this study, the structural and histological features of these osteoderms are described in order to reconstruct their developmental pattern and further document the possible homology that could exist between vertebrate integumentary skeletons. Glyptosaurine osteoderms display a diploe architecture and an unusually complex structure that includes four tissue types: an intensely remodeled core of woven-fibered bone, a thick basal layer of lamellar bone, a peripheral ring exhibiting histological features intermediate between these two tissues and containing dense bundles of long Sharpey fibers, and a superficial layer made of a monorefringent, acellular and highly mineralized material, different from bone, and comparable in many respects to hypermineralized tissues such as ganoine, enameloids and enamel. We call this tissue osteodermine. The growth pattern of glyptosaurine osteoderms is likely to have involved first metaplasia, at an early developmental stage, then appositional growth due to osteoblast activity. The superficial layer that is well developed at the tubercle level must have resulted from epidermal and dermal contributions, a conclusion that would support previous hypotheses on the role of epidermal-dermal interactions in the formation of squamate osteoderms.