Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical ...understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized.
Sliding clamps are ring-shaped oligomeric proteins that are essential for processive deoxyribonucleic acid replication. Although crystallographic structures of several clamps have been determined, ...much less is known about clamp structure and dynamics in solution. Here, we characterized the intrinsic solution stability and oligomerization dynamics of the homodimeric Escherichia coli β and the homotrimeric Saccharomyces cerevisiae proliferating cell nuclear antigen (PCNA) clamps using single-molecule approaches. We show that E. coli β is stable in solution as a closed ring at concentrations three orders of magnitude lower than PCNA. The trimeric structure of PCNA results in slow subunit association rates and is largely responsible for the lower solution stability. Despite this large difference, the intrinsic lifetimes of the rings differ by only one order of magnitude. Our results show that the longer lifetime of the E. coli β dimer is due to more prominent electrostatic interactions that stabilize the subunit interfaces.
Transfusion of blood at the limits of approved storage time is associated with lower red blood cell (RBC) post-transfusion recovery and hemolysis, which increases plasma cell-free hemoglobin and ...iron, proposed to induce endothelial dysfunction and impair host defense. There is noted variability among donors in the intrinsic rate of storage changes and RBC post-transfusion recovery, yet genetic determinants that modulate this process are unclear.
We explore RBC storage stability and post-transfusion recovery in murine models of allogeneic and xenogeneic transfusion using blood from humanized transgenic sickle cell hemizygous mice (Hbatm1PazHbbtm1TowTg(HBA-HBBs)41Paz/J) and human donors with a common genetic mutation sickle cell trait (HbAS).
Human and transgenic HbAS RBCs demonstrate accelerated storage time-dependent hemolysis and reduced post-transfusion recovery in mice. The rapid post-transfusion clearance of stored HbAS RBC is unrelated to macrophage-mediated uptake or intravascular hemolysis, but by enhanced sequestration in the spleen, kidney and liver. HbAS RBCs are intrinsically different from HbAA RBCs, with reduced membrane deformability as cells age in cold storage, leading to accelerated clearance of transfused HbAS RBCs by entrapment in organ microcirculation.
The common genetic variant HbAS enhances RBC storage dysfunction and raises provocative questions about the use of HbAS RBCs at the limits of approved storage.
•Sickle cell trait (HbAS) RBC exhibit increased resistance to osmotic shock compared to normal (HbAA) RBCs.•HbAS RBC show accelerated storage-related aging and post-transfusion clearance after cold storage compared to HbAA RBC.•Reduced post-transfusion survival of stored HbAS RBCs is not due to intravascular hemolysis but due to tissue sequestration.
In allogeneic transfusions, red blood cells (RBCs) are collected and stored for up to 42days. Historically, donor RBC genetic background is only considered in the context of major Rh and ABO blood groups. This study shows that donor-specific genetic factors such as sickle cell trait, the benign heterozygote state of sickle cell disease, accelerate storage-related hemolysis and reduces RBC post-transfusion survival in mice. Impaired post-transfusion recovery is due to enhanced sequestration in organ microcirculation. Further studies are warranted to determine an appropriate earlier outdate for HbAS RBC units, particularly in malaria-endemic regions where sickle cell trait prevalence is high.
•Civil society plays different roles in urban sustainability transitions beyond civil advocacy.•Civil society is increasingly recognized as a cog for sustainability transitions.•Civil society is an ...innovator and a self-servicing actor of social needs.•Marketisation of civil society organizations contracts their missions and value propositions.•Civil society activities can (unintentionally) reinforce an uneven neoliberalism.
Understanding the diversifying role of civil society in Europe’s sustainability pathway is a valid proposition both scientifically and socially. Civil society organisations already play a significant role in the reality of cities, what remains to be explored is the question: what is the role of civil society in the future sustainability of European cities? We first examine the novelty of new forms of civil society organization based on a thorough review of recent case studies of civil society initiatives for sustainable transitions across a diversity of European projects and an extensive literature review. We conceptualize a series of roles that civil society plays and the tensions they entail. We argue that, civil society initiatives can pioneer new social relations and practices therefore be an integral part of urban transformations and can fill the void left by a retreating welfare state, thereby safeguarding and servicing social needs but also backing up such a rolling back of the welfare state. It can act as a hidden innovator—contributing to sustainability but remaining disconnected from the wider society. Assuming each of these roles can have unintended effects, such as being proliferated by political agendas, which endanger its role and social mission, and can be peeled off to serve political agendas resulting in its disempowerment and over-exposure. We conclude with a series of implications for future research on the roles of civil society in urban sustainability transitions.
To define the contribution of the corneal epithelium in corneal topography in keratoconus and discuss the implications regarding combined topography-guided photorefractive keratectomy and corneal ...collagen crosslinking (CXL).
French National Reference Center for Keratoconus, Bordeaux, France.
Case series.
Specular topographies were performed before and immediately after epithelial removal during conventional CXL surgery in patients with keratoconus.
The study included 1 eye with forme fruste keratoconus, 4 eyes in Krumeich stage I, and 3 eyes in stage II. The mean simulated maximum keratometry (K) increased by 2.87 diopters (D) after epithelial removal. The mean effective refractive power increased by a mean of 4.01 D and the astigmatic refractive power, by a mean of 2.17 D. The difference in mean axis deviation was not significant. The mean inferior-superior ratio irregularity index increased 1.51 units. All K and refractive readings except astigmatic refractive axis were significantly increased after epithelial removal. All regularity indices increased significantly without the epithelium. The amplitude of variations in K readings made it difficult to predict the refractive changes after custom laser photoablation based on epithelial-based topography.
The astigmatism refractive axis did not change significantly; therefore, this axis could be useful for astigmatic corrections, whereas the spherical component would not be useful. Topographic changes after epithelial removal can be important but not intuitive in keratoconus eyes. This should be considered in custom topography-guided photoablation strategies when attempting to correct refractive errors at the time of CXL.
As a mediator between lipid metabolism dysfunction, oxidative stress and inflammation, oxidized low-density lipoprotein (oxLDL) is a promising therapeutical target in a wide range of metabolic ...diseases. In mice, pneumococcal immunization increases anti-phosphorylcholine and oxLDL antibody levels, and reduces atherosclerosis, non-alcoholic steatohepatitis and Niemann-Pick disease burden. These findings suggest that pneumococcal vaccination may be a useful preventive and therapeutical strategy in metabolic disease patients. In this pilot clinical trial, our aim was to determine whether the administration of a pneumococcal vaccine increases anti-phosphorylcholine and anti-oxLDL antibody levels in metabolic disease patients. The following patients were enrolled: four patients with familial partial lipodystrophy (all women, mean age 32 years old); three familial hypercholesterolemia patients (one girl, two boys; mean age 13 years); and two Niemann-Pick type B (NP-B) patients (two men, mean age 37.5 years old). Participants received one active dose of a 13-valent conjugated pneumococcal vaccine (Prevenar 13) and were followed-up for four weeks. Four weeks after Prevenar 13 vaccination, no differences were observed in patients' levels of anti-oxLDL IgM or IgG antibodies. In addition, we observed a reduction in anti-phosphorylcholine (anti-PC) IgM antibody levels, whereas no differences were observed in anti-PC IgG antibody titers. These findings indicate that Prevenar 13 vaccination does not induce an immune response against oxLDL in patients with metabolic diseases. Therefore, Prevenar 13 is not suited to target the metabolic disruptor and pro-inflammatory mediator oxLDL in patients.
Lake whitefish Coregonus clupeaformisare a native coldwater species supporting important recreational and commercial fisheries in the Laurentian Great Lakes. Climate-related changes in water ...temperature may have important implications for the future sustainability of these fisheries. However, projecting future habitat availability is difficult because limited information is available on lake whitefish thermal ecology in the region. In this study, archival temperature loggers were implanted into 400 lake whitefish from northwestern Lake Michigan, including Green Bay, during October–November 2017. Loggers recorded temperature for 11 months at 4-hr intervals. Thirteen recovered temperature loggers were used in analyses. In winter (1 December–31 March), temperatures occupied by lake whitefish ranged from 0 to 8.0 °C, while in spring (1 April–31 May) temperatures ranged from 0 to 20.0 °C. In summer (1 June–15 September) and fall (16 September–7 November), lake whitefish occupied temperatures of 4–21.5 and 4–21.0 °C, respectively. Average temperatures in summer (10.8 °C) were within the previously proposed optimal temperature range (10–14 °C) and broad thermal niche (7–17 °C); however, 58% of observations were outside the optimal temperature range and 11% of observations were outside the broad thermal niche. Our results suggest that lake whitefish from northwestern Lake Michigan inhabit temperatures both above and below previously reported expected temperature ranges. This study provides initial insights on lake whitefish thermal ecology in Lake Michigan and can be used as a baseline for future work aimed at determining how lake whitefish habitat availability may change in the future.
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