Determinants within an 18-amino-acid U1A autoregulatory domain that uncouple cooperative RNA binding,inhibition of polyadenylation,and homodimerization

The human U1 snRNP-specific U1A protein autoregulates its own production by binding to and inhibiting the polyadenylation of its own pre-mRNA. Previous work demonstrated that a short sequence of U1A protein is essential for autoregulation and contains three distinct activities, which are (i) cooperative binding of two U1A proteins to a 50-nucleotide region of U1A pre-mRNA called polyadenylation-inhibitory element RNA, (ii) formation of a novel homodimerization surface, and (iii) inhibition of polyadenylation by inhibition of poly(A) polymerase (PAP). In this study, we purified and analyzed 11 substitution mutant proteins, each having one or two residues in this region mutated. In 5 of the 11 mutant proteins, we found that particular amino acids associate with one activity but not another, indicating that they can be uncoupled. Surprisingly, in three mutant proteins, these activities were improved upon, suggesting that U1A autoregulation is selected for suboptimal inhibitory efficiency. The effects of these mutations on autoregulatory activity in vivo were also determined. Only U1A and U170K are known to regulate nuclear polyadenylation by PAP inhibition; thus, these results will aid in determining how widespread this type of regulation is. Our molecular dissection of the consequences of conformational changes within an RNP complex presents a powerful example to those studying more complicated pre-mRNA-regulatory systems.     

Structural and genetic analysis of the BldB protein of Streptomyces coelicolor

We have demonstrated that the bldB gene of Streptomyces coelicolor is required for the formation of aerial hyphae and the synthesis of antibiotics. We also found that BldB forms a higher-order complex (most likely a dimer) and that amino acid residues 20 to 78 are important for this interaction. This region is conserved in the BldB family, suggesting that dimer formation may be a common feature of these proteins.     

Allosteric interactions in sipunculid and brachiopod hemerythrins

Chemical and spectroscopic consequences of allosteric interactions for ligand binding to sipunculid (Phascolopsis gouldii) and brachiopod (Lingula reevii) hemerythrins (Hrs) have been investigated. Possible allosteric effectors for homotropic effects in sipunculid Hrs have been examined, but only reduction in ligand affinity is observed without cooperativity. In contrast to sipunculid Hr, L. reevii Hr binds O2 cooperatively in the pH range 7-8 and exhibits a Bohr effect. Spectroscopic comparisons of the sipunculid and brachiopod Hrs show no significant differences in the active site structures; therefore, modulation of oxygen affinity is attributable to effects linking the site to quaternary structural changes in the octamer. Oxygen equilibria can be fit with a conformational model incorporating a minimum of three states, tensed (T), relaxed (R), and an R-T hybrid. Resonance Raman spectra of L. reevii oxyHr show a shift in the peroxo stretching frequency when the pH is lowered from pH 7.7 (predominantly R oxyHr) to pH 6.3 (a mixture of R, T, and R-T hybrid), but P. gouldii Hr does not have a frequency shift under the same conditions. In contrast to hemoglobins, ligand binding to the deoxy and met forms is noncooperative for brachiopod (and sipunculid) Hrs. It is thus suggested that conformational changes in the protein are linked to the oxidation state change that accompanies oxygenation of the coupled binuclear iron site (deoxy [FeIIFeII]----oxy [FeIIIFeIII]). The total allosteric energy expended in oxygenation is about 1.4 kcal/mol, and such a shift is possible in the relaxed-tense conversion with relatively limited constraints of the iron coordination environment via the protein quaternary structure. The mechanism of cooperativity in the binuclear copper oxygen carrier hemocyanin is discussed in light of these results.     

Do clinicians understand the size of treatment effects? A randomized survey across 8 countries

Background:

Meta-analyses of continuous outcomes typically provide enough information for decision-makers to evaluate the extent to which chance can explain apparent differences between interventions. The interpretation of the magnitude of these differences — from trivial to large — can, however, be challenging. We investigated clinicians’ understanding and perceptions of usefulness of 6 statistical formats for presenting continuous outcomes from meta-analyses (standardized mean difference, minimal important difference units, mean difference in natural units, ratio of means, relative risk and risk difference).

Methods:

We invited 610 staff and trainees in internal medicine and family medicine programs in 8 countries to participate. Paper-based, self-administered questionnaires presented summary estimates of hypothetical interventions versus placebo for chronic pain. The estimates showed either a small or a large effect for each of the 6 statistical formats for presenting continuous outcomes. Questions addressed participants’ understanding of the magnitude of treatment effects and their perception of the usefulness of the presentation format. We randomly assigned participants 1 of 4 versions of the questionnaire, each with a different effect size (large or small) and presentation order for the 6 formats (1 to 6, or 6 to 1).

Results:

Overall, 531 (87.0%) of the clinicians responded. Respondents best understood risk difference, followed by relative risk and ratio of means. Similarly, they perceived the dichotomous presentation of continuous outcomes (relative risk and risk difference) to be most useful. Presenting results as a standardized mean difference, the longest standing and most widely used approach, was poorly understood and perceived as least useful.

Interpretation:

None of the presentation formats were well understood or perceived as extremely useful. Clinicians best understood the dichotomous presentations of continuous outcomes and perceived them to be the most useful. Further initiatives to help clinicians better grasp the magnitude of the treatment effect are needed.Health professionals increasingly rely on summary estimates from systematic reviews and meta-analyses to guide their clinical decisions and to provide information for shared decision-making. Meta-analyses of clinical trials typically provide the information necessary for decision-makers to evaluate the extent to which chance can explain apparent intervention effects (i.e., statistical significance). However, interpreting the magnitude of the treatment effect — from trivial to large — particularly for continuous outcome measures, can be challenging.Such challenges include decision-makers’ unfamiliarity with the instruments used to measure the outcome. For instance, without further information, clinicians may have difficulty grasping the importance of a 5-point difference on the Short-Form Health Survey-36 (SF-36) or a 1-point difference on a visual analogue scale for pain.¹ Second, trials often use different instruments to measure the same construct. For instance, investigators may measure physical function among patients with arthritis using 1 of 5 instruments (the Western Ontario and McMaster Universities Arthritis Index using either a visual analogue or Likert scale; the Arthritis Impact Measurement Scale; the SF-36 Physical Function; or the Lequesne index).^2,3Authors have several options for pooling results of continuous outcomes. When all trials have used the same instrument to measure outcomes such as physical function or pain, the most straightforward method is to present the mean difference in natural units between the intervention and control groups. When trialists have used different instruments to measure the same construct, authors of systematic reviews typically report differences between intervention and control groups in standard deviation units, an approach known as the standardized mean difference (SMD). This approach involves dividing the mean difference in each trial by the pooled standard deviation for that trial’s outcome.⁴For meta-analyses of outcomes measured using different instruments, presenting results as an SMD is the longest standing and most widely used approach and is recommended in the Cochrane handbook for systematic reviews of interventions.⁴ Limitations of this approach include, however, statistical bias toward decreased treatment effects,^5,6 the possibility that decision-makers will find the measure difficult to interpret^7,8 and the possibility that the same treatment effect will appear different depending on whether the study population had similar results in the measure of interest (i.e., if homogeneous, a small standard deviation) or varied greatly in the measure of interest (i.e., if heterogeneous, a large standard deviation).^9,10Several research groups have proposed alternative statistical formats for presenting continuous outcomes from meta-analyses that they postulate clinicians will more easily interpret.^{6–8,11–16} The Grading of Recommendations Assessment, Development and Evaluation (GRADE) Working Group recently provided an overview of methods for presenting pooled continuous data.^9,10 These alternatives (Appendix 1, available at www.cmaj.ca/lookup/suppl/doi:10.1503/cmaj.150430/-/DC1), although intuitively compelling, have seen limited use.We conducted a survey to determine clinicians’ understanding of the magnitude of treatment effect for 6 approaches to the presentation of continuous outcomes from meta-analyses, as well as their perceptions of the usefulness of each approach for clinical decision-making. We also evaluated whether their understanding and perceptions of usefulness were influenced by country, medical specialty, clinical experience or training in health research methodology.     

Multi-element analysis of trace element levels in human autopsy tissues by using inductively coupled atomic emission spectrometry technique (ICP-AES).

Autopsy tissue samples from the brain front lobe, cerebellum, heart, kidney (cortex and medulla), liver, pancreas, spleen and ovary were analysed for AL, B, Ba, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, Se, Sr and Zn in 30 (17 women and 13 men) subjects ranging in age from 17 to 96 years at Haukeland University Hospital in Norway. The tissues were selected from macroscopically normal organs and samples were handled according to guidelines recommended to avoid contamination in the pre-analytical phase. Concentration of the trace elements were determined by the inductively coupled plasma atomic emission spectrometry technique (ICP-AES). In most tissues the concentrations of the essential trace elements followed the order Fe> Zn> Cu> Mn> Se> Cr> Co except in the ovary where Se was higher than Mn. The liver was the major site of deposition for Co, Cu and Mn as well as the spleen for Co, brain front lobe for Cu and pancreas for Mn. Ba, Sr and Ni built up in the ovary foLLowed by the kidney. Older subjects accumulated Ba and Sr in most tissues, whereas Al accumulated in the kidney cortex and Cd in the brain cerebellum. Generally males had higher concentrations of trace elements in the different tissue sampLes than females with the exception of Mn in the brain front lobe and heart and Sr in the liver. ICP-AES is a useful method to assess the concentration and the profiLe of trace elements in human autopsy tissues.     

Endothelium Expression of Bcl-2 Is Essential for Normal and Pathological Ocular Vascularization

Bcl–2 is an anti-apoptotic protein with important roles in vascular homeostasis and angiogenesis. Mice globally lacking Bcl–2 (Bcl–2 -/-) are small in stature and succumb to renal failure shortly after weaning as a result of renal hypoplasia/cystic dysplasia. We have shown that Bcl–2 -/- mice displayed attenuated retinal vascular development and neovascularization. In vitro studies indicated that in addition to modulating apoptosis, Bcl–2 expression also impacts endothelial and epithelial cell adhesion, migration and extracellular matrix production. However, studies delineating the cell autonomous role Bcl–2 expression plays in the endothelium during vascular development, pruning and remodeling, and neovascularization are lacking. Here we generated mice carrying a conditional Bcl–2 allele (Bcl-2^Flox/Flox) and VE-cadherin-cre (Bcl-2^EC mice). Bcl-2^EC mice were of normal stature and lifespan and displayed some but not all of the retinal vascular defects previously observed in global Bcl–2 deficient mice. Bcl-2^EC mice had decreased numbers of endothelial cells, decreased retinal arteries and premature primary branching of the retinal vasculature, but unlike the global knockout mice, spreading of the retinal superficial vascular layer proceeded normally. Choroidal neovascularization was attenuated in Bcl-2^EC mice, although retinal neovascularization accompanying oxygen-induced ischemic retinopathy was not. Thus, Bcl–2 expression in the endothelium plays a significant role during postnatal retinal vascularization, and pathological choroidal but not retinal neovascularization, suggesting vascular bed specific Bcl–2 function in the endothelium.     

A Highlights from MBoC Selection: Quantitative Analysis of the Mechanism of Endocytic Actin Patch Assembly and Disassembly in Fission Yeast

We used quantitative confocal microscopy to measure the numbers of 16 proteins tagged with fluorescent proteins during assembly and disassembly of endocytic actin patches in fission yeast. The peak numbers of each molecule that accumulate in patches varied <30–50% between individual patches. The pathway begins with accumulation of 30–40 clathrin molecules, sufficient to build a hemisphere at the tip of a plasma membrane invagination. Thereafter precisely timed waves of proteins reach characteristic peak numbers: endocytic adaptor proteins (∼120 End4p and ∼230 Pan1p), activators of Arp2/3 complex (∼200 Wsp1p and ∼340 Myo1p) and ∼300 Arp2/3 complexes just ahead of a burst of actin assembly into short, capped and highly cross-linked filaments (∼7000 actins, ∼200 capping proteins, and ∼900 fimbrins). Coronin arrives last as all other components disperse upon patch internalization and movement over ∼10 s. Patch internalization occurs without recruitment of dynamins. Mathematical modeling, described in the accompanying paper (Berro et al., 2010, MBoC 21: 2803–2813), shows that the dendritic nucleation hypothesis can account for the time course of actin assembly into a branched network of several hundred filaments 100–200 nm long and that patch disassembly requires actin filament fragmentation in addition to depolymerization from the ends.