An extended RNA binding site for the yeast branch point-binding protein and the role of its zinc knuckle domains in RNA binding

The highly conserved branch point sequence (BPS) of UACUAAC in Saccharomyces cerevisiae is initially recognized by the branch point-binding protein (BBP). Using systematic evolution of ligands by exponential enrichment we have determined that yeast BBP binds the branch point sequence UACUAAC with highest affinity and prefers an additional adenosine downstream of the BPS. Furthermore, we also found that a stem-loop upstream of the BPS enhances binding both to an artificially designed RNA (30-fold effect) and to an RNA from a yeast intron (3-fold effect). The zinc knuckles of BBP are partially responsible for the enhanced binding to the stem-loop but do not appear to have a significant role in the binding of BBP to single-strand RNA substrates. C-terminal deletions of BBP reveal that the linker regions between the two zinc knuckles and between the N-terminal RNA binding domains (KH and QUA2 domains) and the first zinc knuckle are important for binding to RNA. The lack of involvement of the second highly conserved zinc knuckle in RNA binding suggests that this zinc knuckle plays a different role in RNA processing than enhancing the binding of BBP to the BPS.     

Renal autoregulation: new perspectives regarding the protective and regulatory roles of the underlying mechanisms

When the kidney is subjected to acute increases in blood pressure (BP), renal blood flow (RBF) and glomerular filtration rate (GFR) are observed to remain relatively constant. Two mechanisms, tubuloglomerular feedback (TGF) and the myogenic response, are thought to act in concert to achieve a precise moment-by-moment regulation of GFR and distal salt delivery. The current view is that this mechanism insulates renal excretory function from fluctuations in BP. Indeed, the concept that renal autoregulation is necessary for normal renal function and volume homeostasis has long been a cornerstone of renal physiology. This article presents a very different view, at least regarding the myogenic component of this response. We suggest that its primary purpose is to protect the kidney against the damaging effects of hypertension. The arguments advanced take into consideration the unique properties of the afferent arteriolar myogenic response that allow it to protect against the oscillating systolic pressure and the accruing evidence that when this response is impaired, the primary consequence is not a disturbed volume homeostasis but rather an increased susceptibility to hypertensive injury. It is suggested that redundant and compensatory mechanisms achieve volume regulation, despite considerable fluctuations in distal delivery, and the assumed moment-by-moment regulation of renal hemodynamics is questioned. Evidence is presented suggesting that additional mechanisms exist to maintain ambient levels of RBF and GFR within normal range, despite chronic alterations in BP and severely impaired acute responses to pressure. Finally, the implications of this new perspective on the divergent roles of the myogenic response to pressure vs. the TGF response to changes in distal delivery are considered, and it is proposed that in addition to TGF-induced vasoconstriction, vasodepressor responses to reduced distal delivery may play a critical role in modulating afferent arteriolar reactivity to integrate the regulatory and protective functions of the renal microvasculature.     

Bending rigidities of cell surface molecules P-selectin and PSGL-1

P-selectin is a cell adhesion molecule expressed on activated endothelial cells and platelets. P-selectin glycoprotein ligand 1 (PSGL-1) is a mucin expressed on leukocytes. The interaction of P-selectin and PSGL-1 mediates leukocyte tethering to and rolling on the vascular surface, which are initiating events in inflammatory and thrombotic processes. In the hemodynamic environment of the circulation, P-selectin and PSGL-1 are subject to a wide range of forces, which can cause deformation. For P-selectin/PSGL-1 interaction to be physically possible, these molecules may need to project above much of the glycocalyx layers of the respective cell surfaces, suggesting that they are either longer than the thickness of glycocalyx or better able to support compression than the glycocalyx. As such, the mechanical properties of these molecules and their functional implications merit investigation. Here we report determination of the bending rigidities of P-selectin and PSGL-1 by analyzing their thermally excited curvature fluctuations, whose values are of the order of magnitude of 100 pN nm².     

The promise and reality of personal genomics

The publication of the highest-quality and best-annotated personal genome yet tells us much about sequencing technology, something about genetic ancestry, but still little of medical relevance.Which country has published the largest per-capita number of personal genomes? The United States, the United Kingdom? Actually, it is Korea. A recent article in Nature by Kim et al. [1] presents the genome sequence of a Korean male, AK1 - the seventh published sequence of an individual human genome and the second from Korea. The rapid progress in personal genome sequencing is possible because so-called ''next-generation'' sequencing technology has decreased costs by orders of magnitude and increased throughput. But those advantages come at a price: short, error-prone reads derived from single molecules that have to be stitched back together to make a best-guess at the starting sequence. We are still at the stage of working out how to apply the available technologies to coax out biological information: the goal of a US$1,000 genome providing life-changing personal medical insights is still some way off.     

Effect of antenatal peer support on breastfeeding initiation: a systematic review

Background

Our objective was to examine the effect of antenatal peer support on rates of breastfeeding initiation.

Methods

We performed a systematic review of randomized controlled trials, quasi-randomized trials and cohort studies with concurrent controls. We searched the Cochrane Library, MEDLINE, the Cumulative Index to Nursing and Allied Health Literature (CINAHL), the National Research Register and the British Nursing Index from inception or from 1980 to 2009. We carried out study selection, data abstraction and quality assessment independently and in duplicate. We defined high-quality studies as those that minimized the risk of at least three of the following types of bias: selection, performance, measurement and attrition bias. We calculated risk ratios (RRs) and 95% confidence intervals (CIs) for individual studies and undertook separate meta-analyses for high-quality trials of universal peer support and targeted peer support. We did not include low-quality studies.

Results

We selected 11 studies, which involved 5445 women in total. Seven of these studies (involving 4416 women in total) evaluated universal peer support, and four studies (involving 1029 women in total) targeted antenatal peer support. In the three high-quality studies of universal peer support, all involving low-income women, the relative risk for not initiating breastfeeding was 0.96 (95% CI 0.76–1.22). In the three high-quality studies of antenatal peer support that targeted women considering breastfeeding, the relative risk for not initiating breastfeeding was 0.64 (95% CI 0.41 – 0.99).

Interpretation

Universal antenatal peer support does not appear to improve rates of breastfeeding initiation, but targeted antenatal peer support may be beneficial. This effect may be related to context, however, so any new peer-support program should undergo concurrent high-quality evaluation.Breastfeeding confers numerous benefits for mother and infant,^1–3 yet many women still do not initiate breastfeeding.⁴ The World Health Organization recommends exclusive breastfeeding to six months,⁵ and national governments have implemented initiatives to increase initiation rates.^6,7 Peer support has been examined as one intervention to increase breastfeeding rates, but there have been few high-quality randomized controlled trials (RCTs) examining initiation. One systematic review⁸ (published in 2000) concluded, based only on two nonrandomized studies, that antenatal peer support had a positive effect on breastfeeding initiation. Another⁹ (published in 2005 and updated in 2007) included only RCTs but excluded those whose primary purpose was to affect duration. Based only on one RCT, that review concluded that peer support is likely to result in improvements in initiation of breastfeeding among low-income women where baseline breastfeeding rates are low. These weaknesses in the available evidence make recommendations uncertain. Despite this uncertainty, antenatal peer support for breastfeeding is being incorporated into routine maternity care in some parts of the world.¹⁰Antenatal peer support can be provided as a universal service or targeted to women who are considering breastfeeding. Although trials have made this distinction, previous reviews have not. New evidence has become available, and it appears appropriate to re-examine antenatal peer support through a systematic review. The purpose of our review was to assess the effectiveness of antenatal peer support, as either a universal or a targeted service, including all studies that examined breastfeeding initiation using concurrent controls.     

Characterization of a sialic acid- and P-selectin glycoprotein ligand-1-independent adhesin activity in the granulocytotropic bacterium Anaplasma phagocytophilum

Anaplasma phagocytophilum, the aetiologic agent of human granulocytic anaplasmosis, is an obligate intracellular bacterium that colonizes neutrophils and neutrophil precursors. The granulocytotropic bacterium uses multiple adhesins that cooperatively bind to the N-terminal region of P-selectin glycoprotein ligand-1 (PSGL-1) and to sialyl Lewis x (sLe(x)) expressed on myeloid cell surfaces. Recognition of sLe(x) occurs through interactions with alpha2,3-sialic acid and alpha1,3-fucose. It is unknown whether other bacteria-host cell interactions are involved. In this study, we have enriched for A. phagocytophilum organisms that do not rely on sialic acid for cellular adhesion and entry by maintaining strain NCH-1 in HL-60 cells that are severely undersialylated. The selected bacteria, termed NCH-1A, also exhibit lessened dependencies on PSGL-1 and alpha1,3-fucose. Optimal adhesion and invasion by NCH-1A require interactions with the known determinants (sialic acid, PSGL-1 and alpha1,3-fucose), but none of them is absolutely necessary. NCH-1A binding to sLe(x)-modified PSGL-1 requires recognition of the known determinants in the same manners as other A. phagocytophilum strains. These data suggest that A. phagocytophilum expresses a separate adhesin from those targeting sialic acid, alpha1,3-fucose and the N-terminal region of PSGL-1. We propose that NCH-1A upregulates expression of this adhesin.     

Micro-volume couette flow sample orientation for absorbance and fluorescence linear dichroism

Linear dichroism (LD) can be used to study the alignment of absorbing chromophores within long molecules. In particular, Couette flow LD has been used to good effect in probing ligand binding to DNA and to fibrous proteins. This technique has been previously limited by large sample requirements. Here we report the design and application of a new micro-volume Couette flow cell that significantly enhances the potential applications of flow LD spectroscopy by reducing the sample requirements for flow linear dichroism to 25 microL (with concentrations such that the absorbance maximum of the sample in a 1-cm pathlength cuvette is approximately 1). The micro-volume Couette cell has also enabled the measurement of fluorescence-detected Couette flow linear dichroism. This new technique enables the orientation of fluorescent ligands to be probed even when their electronic transitions overlap with those of the macromolecule and conversely. The potential of flow-oriented fluorescence dichroism and application of the micro-volume Couette LD cell are illustrated by the collection of data for DNA with minor groove and intercalating ligands: DAPI, Hoechst, and ethidium bromide. As with conventional fluorescence, improved sensitivity compared with absorbance LD is to be expected after instrumentation optimization.