Crystallographic studies of RNA hairpins in complexes with recombinant MS2 capsids: implications for binding requirements.

The coat protein of bacteriophage MS2 is known to bind specifically to an RNA hairpin formed within the MS2 genome. Structurally this hairpin is built up by an RNA double helix interrupted by one unpaired nucleotide and closed by a four-nucleotide loop. We have performed crystallographic studies of complexes between MS2 coat protein capsids and four RNA hairpin variants in order to evaluate the minimal requirements for tight binding to the coat protein and to obtain more information about the three-dimensional structure of these hairpins. An RNA fragment including the four loop nucleotides and a two-base-pair stem but without the unpaired nucleotide is sufficient for binding to the coat protein shell under the conditions used in this study. In contrast, an RNA fragment containing a stem with the unpaired nucleotide but missing the loop nucleotides does not bind to the protein shell.     

Degenerate RNA packaging signals in the genome of Satellite Tobacco Necrosis Virus: implications for the assembly of a T=1 capsid

Using a recombinant, T = 1 Satellite Tobacco Necrosis Virus (STNV)-like particle expressed in Escherichia coli, we have established conditions for in vitro disassembly and reassembly of the viral capsid. In vivo assembly is dependent on the presence of the coat protein (CP) N-terminal region, and in vitro assembly requires RNA. Using immobilised CP monomers under reassembly conditions with “free” CP subunits, we have prepared a range of partially assembled CP species for RNA aptamer selection. SELEX directed against the RNA-binding face of the STNV CP resulted in the isolation of several clones, one of which (B3) matches the STNV-1 genome in 16 out of 25 nucleotide positions, including across a statistically significant 10/10 stretch. This 10-base region folds into a stem-loop displaying the motif ACAA and has been shown to bind to STNV CP. Analysis of the other aptamer sequences reveals that the majority can be folded into stem-loops displaying versions of this motif. Using a sequence and secondary structure search motif to analyse the genomic sequence of STNV-1, we identified 30 stem-loops displaying the sequence motif AxxA. The implication is that there are many stem-loops in the genome carrying essential recognition features for binding STNV CP. Secondary structure predictions of the genomic RNA using Mfold showed that only 8 out of 30 of these stem-loops would be formed in the lowest-energy structure. These results are consistent with an assembly mechanism based on kinetically driven folding of the RNA.     

Monitoring diabetes in patients with and without rheumatoid arthritis: a Medicare study

Introduction

Diabetes mellitus is a key predictor of mortality in rheumatoid arthritis (RA) patients. Both RA and diabetes increase the risk of cardiovascular disease (CVD), yet understanding of how comorbid RA impacts the receipt of guideline-based diabetes care is limited. The purpose of this study was to examine how the presence of RA affected hemoglobin A1C (A1c) and lipid measurement in older adults with diabetes.

Methods

Using a retrospective cohort approach, we identified beneficiaries ≥65 years old with diabetes from a 5% random national sample of 2004 to 2005 Medicare patients (N = 256,331), then examined whether these patients had comorbid RA and whether they received guideline recommended A1c and lipid testing in 2006. Multivariate logistic regression was used to examine the effect of RA on receiving guideline recommended testing, adjusting for baseline sociodemographics, comorbidities and health care utilization.

Results

Two percent of diabetes patients had comorbid RA (N = 5,572). Diabetes patients with comorbid RA were more likely than those without RA to have baseline cardiovascular disease (such as 17% more congestive heart failure), diabetes-related complications including kidney disease (19% higher), lower extremity ulcers (77% higher) and peripheral vascular disease (32% higher). In adjusted models, diabetes patients with RA were less likely to receive recommended A1c testing (odds ratio (OR) 0.84, CI 0.80 to 0.89) than those without RA, but were slightly more likely to receive lipid testing (OR 1.08, CI 1.01 to 1.16).

Conclusions

In older adults with diabetes, the presence of comorbid RA predicted lower rates of A1c testing but slightly improved lipid testing. Future research should examine strategies to improve A1c testing in patients with diabetes and RA, in light of increased CVD and microvascular risks in patients with both conditions.     

Concentration of bronchoalveolar lavage fluid by ultrafiltration: evidence of differential protein loss and functional inactivation of proteinase inhibitors

Bronchoalveolar lavage samples were concentrated using positive-pressure ultrafiltration. The starting material, concentrates, and eluates were assayed for immunoglobulin A (IgA), albumin (Alb), alpha 1-proteinase inhibitor (alpha 1-PI), antileukoprotease (ALP), and total leukocyte elastase inhibitory capacity (LEIC). No enzyme inhibitory capacity or protein was detected in membrane eluates, confirming the selectivity of the membrane used (Mr cutoff 2000 or 500). However, the concentrated lavages showed a generated loss of protein. The proportion of each protein recovered using the 500 Mr cutoff membrane was: IgA, 50.6% (+/- 15%); albumin, 43% (+/- 8.4); alpha 1-PI, 53.6 (+/- 17.3); ALP, 43% (+/- 2.1); and LEIC, 18.4% (+/- 2.6). Similar results were obtained with the 200 Mr cutoff membrane. The alpha 1-PI/Alb and the IgA/alb ratios were higher (2P less than 0.05) in the concentrates than in the starting material, suggesting differential protein loss. Protein losses were due to binding to the membrane since the wash with saline solution improved recoveries: IgA, 80%; Alb, 56%; alpha 1-PI, 64%; ALP, 66%; LEIC, 29%. Concentration of bronchoalveolar lavage fluids therefore resulted in substantial differential losses in elastase inhibitory capacity and protein concentrations, suggesting analysis of these fluids should be performed on unconcentrated samples.     

Consequences of sperm displacement for female dung flies,Scatophaga stercoraria

Displacement of stored sperm during copulation occurs in many insects. This process provides direct benefits for males via increased fertilization success, but the fitness consequences of sperm displacement for females are less clear. Here we investigate potential benefits of sperm displacement for female yellow dung flies, Scatophaga stercoraria. We find no evidence that female dung flies gain direct benefits from displacement of previously stored sperm in terms of increased fertility or fecundity. There was no difference in the relative survival rate, development time, size or fluctuating asymmetry of offspring produced by females that had previously stored sperm displaced before oviposition and those that did not. Females using previously stored sperm to fertilize their eggs produced significantly higher ratios of male to female offspring. These novel findings have important implications for understanding the evolutionary dynamics of male–female interactions in sperm competition.     

A novel model and molecular therapy for Z alpha-1 antitrypsin deficiency

Animal models that closely resemble human disease can present a challenge. Particularly so in alpha-1 antitrypsin deficiency (α(1)ATD), as the mouse alpha-1 antitrypsin (α(1)AT) cluster encodes five highly related genes compared with the one in humans. The mouse PI2 homologue is closest to the α(1)AT human gene. We have changed the equivalent mouse site that results in the Z variant in man (Glu342Lys) and made both the "M" and "Z" mouse PI2 α(1)AT proteins. We have tested the ability of a small-molecular-weight compound CG to alleviate polymerisation of these mouse α(1)AT proteins as it has been shown to reduce aggregates of Z α(1)AT in man. We found that (1) CG specifically reduces the formation of polymers of recombinant mouse "Z" protein but not "M" protein; (2) whereas there is significantly more α(1)AT secreted from Chinese Hamster Ovary cells transfected with the mouse "M" α(1)AT gene than with the "Z" (20.8?±?3.9 and 6.7?±?3.6, respectively; P?相似文献   

Isolation of an asymmetric RNA uncoating intermediate for a single-stranded RNA plant virus

We have determined the three-dimensional structures of both native and expanded forms of turnip crinkle virus (TCV), using cryo-electron microscopy, which allows direct visualization of the encapsidated single-stranded RNA and coat protein (CP) N-terminal regions not seen in the high-resolution X-ray structure of the virion. The expanded form, which is a putative disassembly intermediate during infection, arises from a separation of the capsid-forming domains of the CP subunits. Capsid expansion leads to the formation of pores that could allow exit of the viral RNA. A subset of the CP N-terminal regions becomes proteolytically accessible in the expanded form, although the RNA remains inaccessible to nuclease. Sedimentation velocity assays suggest that the expanded state is metastable and that expansion is not fully reversible. Proteolytically cleaved CP subunits dissociate from the capsid, presumably leading to increased electrostatic repulsion within the viral RNA. Consistent with this idea, electron microscopy images show that proteolysis introduces asymmetry into the TCV capsid and allows initial extrusion of the genome from a defined site. The apparent formation of polysomes in wheat germ extracts suggests that subsequent uncoating is linked to translation. The implication is that the viral RNA and its capsid play multiple roles during primary infections, consistent with ribosome-mediated genome uncoating to avoid host antiviral activity.     

Evidence that avian reovirus σNS is an RNA chaperone: implications for genome segment assortment

Reoviruses are important human, animal and plant pathogens having 10–12 segments of double-stranded genomic RNA. The mechanisms controlling the assortment and packaging of genomic segments in these viruses, remain poorly understood. RNA–protein and RNA–RNA interactions between viral genomic segment precursors have been implicated in the process. While non-structural viral RNA-binding proteins, such as avian reovirus σNS, are essential for virus replication, the mechanism by which they assist packaging is unclear. Here we demonstrate that σNS assembles into stable elongated hexamers in vitro, which bind single-stranded nucleic acids with high affinity, but little sequence specificity. Using ensemble and single molecule fluorescence spectroscopy, we show that σNS also binds to a partially double-stranded RNA, resulting in gradual helix unwinding. The hexamer can bind multiple RNA molecules and exhibits strand-annealing activity, thus mediating conversion of metastable, intramolecular stem-loops into more stable heteroduplexes. We demonstrate that the ARV σNS acts as an RNA chaperone facilitating specific RNA–RNA interactions between genomic precursors during segment assortment and packaging.     

Sperm competition games: a prospective analysis of risk assessment.

We develop the logic of assessment of sperm competition risk by individual males where the mechanism of sperm competition follows a ''loaded raffle'' (first and second inseminates of a female have unequal prospects). Male roles (first or second to mate) are determined randomly. In model 1, males have no information about the risk associated with individual females and ejaculation strategy depends only on the probability, q, that females mate twice. Evolutionarily stable strategy (ESS) ejaculate expenditure increases linearly from zero with q, and reduces with increasing inequality between ejaculates, though the direction of the loading (which role is favoured) is unimportant. In model 2, males have perfect information and can identify each of three risk states: females that will (1) mate just once (''no risk''), (2) mate twice but have not yet mated (''future risk''), and (3) mate twice and have already mated (''past risk''). The ESS is to ejaculate minimally with ''no risk'' females, and to expand equally with ''past'' and ''future'' risk females; the direction of the competitive loading is again unimportant. Expenditure again increases with risk, but is now non-zero at extremely low risk. Model 3 examines three cases of partial information where males can identify only one of the three risk states and cannot distinguish between the other two: they therefore have just two information sets or ''contexts''. Expenditure in both contexts typically rises non-linearly from zero with q, but (whatever the loading direction) expenditure is higher in the context with higher risk (e.g. if contexts are ''mated'' and ''virgin'', males spend more with mated females). However, in highly loaded raffles, sperm expenditure can decrease over part of the range of risk. Also, the direction of the loading now affects expenditure. Biological evidence for the predictions of the models is summarized and discussed.