Perturbation Centrality and Turbine: A Novel Centrality Measure Obtained Using a Versatile Network Dynamics Tool

Analysis of network dynamics became a focal point to understand and predict changes of complex systems. Here we introduce Turbine, a generic framework enabling fast simulation of any algorithmically definable dynamics on very large networks. Using a perturbation transmission model inspired by communicating vessels, we define a novel centrality measure: perturbation centrality. Hubs and inter-modular nodes proved to be highly efficient in perturbation propagation. High perturbation centrality nodes of the Met-tRNA synthetase protein structure network were identified as amino acids involved in intra-protein communication by earlier studies. Changes in perturbation centralities of yeast interactome nodes upon various stresses well recapitulated the functional changes of stressed yeast cells. The novelty and usefulness of perturbation centrality was validated in several other model, biological and social networks. The Turbine software and the perturbation centrality measure may provide a large variety of novel options to assess signaling, drug action, environmental and social interventions.     

SIFamide and SIFamide Receptor Define a Novel Neuropeptide Signaling to Promote Sleep in Drosophila

SIFamide receptor (SIFR) is a Drosophila G protein-coupled receptor for the neuropeptide SIFamide (SIFa). Although the sequence and spatial expression of SIFa are evolutionarily conserved among insect species, the physiological function of SIFa/SIFR signaling remains elusive. Here, we provide genetic evidence that SIFa and SIFR promote sleep in Drosophila. Either genetic ablation of SIFa-expressing neurons in the pars intercerebralis (PI) or pan-neuronal depletion of SIFa expression shortened baseline sleep and reduced sleep-bout length, suggesting that it caused sleep fragmentation. Consistently, RNA interference-mediated knockdown of SIFR expression caused short sleep phenotypes as observed in SIFa-ablated or depleted flies. Using a panel of neuron-specific Gal4 drivers, we further mapped SIFR effects to subsets of PI neurons. Taken together, these results reveal a novel physiological role of the neuropeptide SIFa/SIFR pathway to regulate sleep through sleep-promoting neural circuits in the PI of adult fly brains.     

Staphylococcus aureus Uses a Novel Multidomain Receptor to Break Apart Human Hemoglobin and Steal Its Heme

Staphylococcus aureus is a leading cause of life-threatening infections in the United States. It requires iron to grow, which must be actively procured from its host to successfully mount an infection. Heme-iron within hemoglobin (Hb) is the most abundant source of iron in the human body and is captured by S. aureus using two closely related receptors, IsdH and IsdB. Here we demonstrate that each receptor captures heme using two conserved near iron transporter (NEAT) domains that function synergistically. NMR studies of the 39-kDa conserved unit from IsdH (IsdH^N2N3, Ala³²⁶–Asp⁶⁶⁰) reveals that it adopts an elongated dumbbell-shaped structure in which its NEAT domains are properly positioned by a helical linker domain, whose three-dimensional structure is determined here in detail. Electrospray ionization mass spectrometry and heme transfer measurements indicate that IsdH^N2N3 extracts heme from Hb via an ordered process in which the receptor promotes heme release by inducing steric strain that dissociates the Hb tetramer. Other clinically significant Gram-positive pathogens capture Hb using receptors that contain multiple NEAT domains, suggesting that they use a conserved mechanism.     

Aging: Fruit Flies Break the Chain to a Longer Life

Mitochondria have long had an enigmatic role in the biology of aging. New research in Drosophila reveals an evolutionarily conserved function for the mitochondrial electron transport chain in the modulation of animal lifespan.     

Content Factor: A Measure of a Journal's Contribution to Knowledge

Impact Factor, the pre-eminent performance metric for medical journals, has been criticized for failing to capture the true impact of articles; for favoring methodology papers; for being unduly influenced by statistical outliers; and for examining a period of time too short to capture an article's long-term importance. Also, in the era of search engines, where readers need not skim through journals to find information, Impact Factor's emphasis on citation efficiency may be misplaced. A better metric would consider the total number of citations to all papers published by the journal (not just the recent ones), and would not be decremented by the total number of papers published. We propose a metric embodying these principles, "Content Factor", and examine its performance among leading medical and orthopaedic surgery journals. To remedy Impact Factor's emphasis on recent citations, Content Factor considers the total number of citations, regardless of the year in which the cited paper was published. To correct for Impact Factor's emphasis on efficiency, no denominator is employed. Content Factor is thus the total number of citations in a given year to all of the papers previously published in the journal. We found that Content Factor and Impact Factor are poorly correlated. We further surveyed 75 experienced orthopaedic authors and measured their perceptions of the "importance" of various orthopaedic surgery journals. The correlation between the importance score and the Impact Factor was only 0.08; the correlation between the importance score and Content Factor was 0.56. Accordingly, Content Factor better reflects a journal's "importance". In sum, while Content Factor cannot be defended as the lone metric of merit, to the extent that performance data informs journal evaluations, Content Factor- an easily obtained and intuitively appealing metric of the journal's knowledge contribution, not subject to gaming- can be a useful adjunct.     

Migration of Murine Epidermal Langerhans Cells to Regional Lymph Nodes: Engagement of Major Histocompatibility Complex Class II Antigens Induces Migration of Langerhans Cells

Langerhans cells are resident dendritic cells in the epidermis. Once they are loaded with epicutaneously-delivered antigens, they leave the epidermis and migrate to the regional lymph nodes where they initiate primary T cell responses as antigen-presenting cells. However, the stimulus that initiates such migration remains unknown. Because major histocompatibility complex class II (Ia) antigens on B lymphocytes or monocytic cells have been shown to function as signal transducers, we evaluated the effect of the engagement of Ia antigens on the migration of murine epidermal Langerhans cells. The intradermal injection of an anti-Ia monoclonal antibody (mAb) reduced the density of Langerhans cells in epidermis and produced a dose- and time-dependent increase in the frequency of cells reactive with NLDC145 (Langerhans cell- and dendritic cell-specific mAb) within the regional lymph nodes. Injection of a control mAb had no effect. The NLDC145+ cells that were induced to accumulate in the regional lymph nodes were Ia+, large dendritic cells, some of which were positive for both NLDC145 and F4/80, a phenotype corresponding to that of murine epidermal Langerhans cells. Thus, the engagement of Ia antigens on Langerhans cells by mAb induces the migration of Langerhans cells from the epidermis to the regional lymph nodes. Analysis of these changes in Langerhans cells in vitro may help to reveal the biochemical sequence of events involved in the activation and differentiation of Langerhans cells.     

The Relevance of a Novel Quantitative Assay to Detect up to 40 Major Streptococcus pneumoniae Serotypes Directly in Clinical Nasopharyngeal and Blood Specimens

For epidemiological and surveillance purposes, it is relevant to monitor the distribution and dynamics of Streptococcus pneumoniae serotypes. Conventional serotyping methods do not provide rapid or quantitative information on serotype loads. Quantitative serotyping may enable prediction of the invasiveness of a specific serotype compared to other serotypes carried. Here, we describe a novel, rapid multiplex real-time PCR assay for identification and quantification of the 40 most prevalent pneumococcal serotypes and the assay impacts in pneumonia specimens from emerging and developing countries. Eleven multiplex PCR to detect 40 serotypes or serogroups were optimized. Quantification was enabled by reference to standard dilutions of known bacterial load. Performance of the assay was evaluated to specifically type and quantify S. pneumoniae in nasopharyngeal and blood samples from adult and pediatric patients hospitalized with pneumonia (n = 664) from five different countries. Serogroup 6 was widely represented in nasopharyngeal specimens from all five cohorts. The most frequent serotypes in the French, South African, and Brazilian cohorts were 1 and 7A/F, 3 and 19F, and 14, respectively. When both samples were available, the serotype in blood was always present as carriage with other serotypes in the nasopharynx. Moreover, the ability of a serotype to invade the bloodstream may be linked to its nasopharyngeal load. The mean nasopharyngeal concentration of the serotypes that moved to the blood was 3 log-fold higher than the ones only found in the nasopharynx. This novel, rapid, quantitative assay may potentially predict some of the S. pneumoniae serotypes invasiveness and assessment of pneumococcal serotype distribution.     

Factors that Influence the Way Communities Respond to Proposals for Major Changes to Local Emergency Services: A Qualitative Study

Objective

According to policy commentators, decisions about how best to organise care involve trade-offs between factors relating to care quality, workforce, cost, and patient access. In England, proposed changes such as Emergency Department closures often face public opposition. This study examined the way communities respond to plans aimed at reorganising emergency services, including the trade-offs inherent in such decisions.

Design

Cross-sectional study involving in-depth interviews. Participants selected their priorities for emergency care, including aspects they might be prepared to have ‘less’ of (e.g. rapid access) if it meant having ‘more’ of another (e.g. consultant-delivered care). A thematic analysis was carried out, combining inductive and deductive approaches, drawing on theories about risk perception.

Setting

Two urban areas of England; one where changes to emergency services were under consideration (‘Greenville’), and one where they were not (‘Hilltown’).

Participants

28 participants in total. Greenville interviewees included more common emergency service users - parents of young children (n=5) and older people (n=6) - plus patient representatives and individuals campaigning against service closures (n=9). Hilltown interviewees (n=8) received outpatient care for Chronic Obstructive Pulmonary Disease, an important cause of emergency admission.

Results

Most participants, in both areas, were not willing to accommodate the trade-offs involved in consolidating emergency services, principally because of the belief that timely access is associated with better outcomes. Participants did not consider the proposed improvements as gains worth having; interviewees believed care quality would be adversely impact, partly because increased patient numbers would place staff under greater pressure and result in longer waiting times.

Conclusions

Visible clinical leadership and detailed explanation of the case for change were insufficient to overcome opposition to the reconfiguration in Greenville, challenging the assumption that communities can be persuaded by evidence. Commissioners should make explicit credible plans to accommodate changes in patient flows, as well as clarifying the roles played by key staff groups.     

Selection of a Novel Anti-Nicotine Vaccine: Influence of Antigen Design on Antibody Function in Mice

Anti-nicotine vaccines may aid smoking cessation via the induction of anti-nicotine antibodies (Ab) which reduce nicotine entering the brain, and hence the associated reward. Ab function depends on both the quantity (titer) and the quality (affinity) of the Ab. Anti-nicotine vaccines tested previously in clinical studies had poor efficacy despite high Ab titer, and this may be due to inadequate function if Ab of low affinity were induced. In this study, we designed and synthesized a series of novel nicotine-like haptens which were all linked to diphtheria toxoid (DT) as carrier, but which differed in the site of attachment of linker to nicotine, the nature of linker used, and the handle used to attach the hapten to DT. The resulting hapten conjugates were evaluated in a mouse model, using CpG (a TLR9 agonist) and aluminum hydroxide (Al(OH)₃) as adjuvants, whereby Ab titers, affinity and function were evaluated using a radiolabeled nicotine challenge model. A series of additional linkers varying in length, rigidity and polarity were used with a single hapten to generate additional DT-conjugates, which were also tested in mice. Conjugates made with different haptens resulted in various titers of anti-nicotine Ab. Several haptens gave similarly high Ab titers, but among these, Ab affinity and hence function varied considerably. Linker also influenced Ab titer, affinity and function. These results demonstrate that immune responses induced in mice by nicotine-conjugate antigens are greatly influenced by hapten design including site of attachment of linker to nicotine, the nature of linker used, and the handle used to attach the hapten to DT. While both Ab titer and affinity contributed to function, affinity was more sensitive to antigen differences.     

Influence of Phospholipid Species on Membrane Fluidity: A Meta-analysis for a Novel Phospholipid Fluidity Index

Generalized membrane lipid composition determinants of fluidity have been widely investigated, including phospholipid/cholesterol ratio and unsaturation index. Individual phospholipids differ in their physical characteristics, including their interaction with cholesterol and level of unsaturation, emphasizing the importance of examining their individual influence on membrane fluidity. Thus, the purpose of this study was to examine the dominant phospholipids of biological membranes (phosphatidylcholine, PC; phosphatidylethanolamine, PE; sphingomyelin, SM) through a meta-analysis to assess the validity of an inclusive phospholipid fluidity index (PFI = PC/(PE + SM)) as a determinant for membrane fluidity (expressed as polarization of fluorescent probe 1,6 diphenyl-1,3,5-hexatriene) in comparison to previous phospholipid ratios (PC/PE and PC/SM). The results demonstrate that all indices significantly predicted membrane fluidity at 25°C (based on 10–13 data points). In contrast, only PFI approached significance when predicting membrane fluidity at 37°C (P = 0.10 based on five points). As a result, PFI appears to be the only phospholipid index close to significantly predicting membrane fluidity at mammalian physiological temperature. Because this meta-analysis only assessed studies using mammalian membranes, future work should experimentally assess the validity of the PFI utilizing membranes from mammals and a variety of other species and tissues at their respective physiological temperatures.     

Risk Perception Mapping: Using Ethnography to Define the Locally Affected Population for a Low-Level Radioactive Waste Storage Facility in Michigan

The concept of a "risk perception shadow" (RPS) has been suggested to describe the geocultural area in which a locally affected population perceives itself to be at risk from a proposed project. Generally such projects involve potentially dangerous substances or activities. The initial conceptualization of an RPS was developed during the social assessment of a proposed Superconducting Super Collider (SSC) in Michigan. This article describes an effort at mapping and analyzing an RPS produced by a proposal to site a low-level radioactive waste (LLRW) storage facility in Michigan. A unique sampling technique was used to define the boundary of the generally concentric RPS. Risk perception mapping (RPM) is suggested as a rapid and efficient method for defining locally affected populations for social impact studies.     

Novel Hydrophobins from <Emphasis Type="Italic">Trichoderma</Emphasis> Define a New Hydrophobin Subclass: Protein Properties,Evolution, Regulation and Processing

Hydrophobins are small proteins, characterised by the presence of eight positionally conserved cysteine residues, and are present in all filamentous asco- and basidiomycetes. They are found on the outer surfaces of cell walls of hyphae and conidia, where they mediate interactions between the fungus and the environment. Hydrophobins are conventionally grouped into two classes (class I and II) according to their solubility in solvents, hydropathy profiles and spacing between the conserved cysteines. Here we describe a novel set of hydrophobins from Trichoderma spp. that deviate from this classification in their hydropathy, cysteine spacing and protein surface pattern. Phylogenetic analysis shows that they form separate clades within ascomycete class I hydrophobins. Using T. atroviride as a model, the novel hydrophobins were found to be expressed under conditions of glucose limitation and to be regulated by differential splicing.     

Influence of Oxygen on Wound Healing Dynamics: Assessment in a Novel Wound Mouse Model under a Variable Oxygen Environment

Introduction

Although oxygen is essential for the wound healing process, tissue hypoxia is known to stimulate angiogenesis. To explore these inconsistent findings, we estimated the influence of the oxygen environment on wound healing with our original model.

Methods

Experiment 1 (Establishment of the model): To modify the topical oxygen tension, oxygen impermeable (polyvinylidene chloride) and permeable (polymethylpentene) membranes were applied to symmetrical excisional wounds in ddy mice (n = 6). Oxygen tension under the membrane was quantified with a device using photo-quenching technique. Experiment 2 (Influence of oxygen environment on wound healing): The wound area, granulation thickness and vascular density were analyzed under different oxygen environments (n = 24).

Results

Experiment 1: The permeable group maintained equivalent oxygen level to atmosphere (114.1±29.8 mmHg on day 7), while the impermeable group showed extremely low oxygen tension (5.72±2.99 mmHg on day 7). Accordingly, each group was defined as the normoxia group and the hypoxia group. Experiment 2: Percent decrease in wound size was significantly enhanced in the normoxia group (11.1±1.66% on day 7) in comparison with the hypoxia group (27.6±3.47% on day 7). The normoxia group showed significantly thicker granulation tissue than the hypoxia group (491.8±243.2 vs. 295.3±180.9 µm). Contrarily, the vascular density of the hypoxia group significantly increased on day 7 (0.046±0.025 vs. 0.011±0.008 mm²/mm²).

Conclusions

Our original model successfully controlled local oxygen concentration around the wound, and the hypoxic wounds showed increased angiogenesis but with a smaller amount of granulation tissue and delayed wound closure. Enhanced neovascularization in the hypoxic group likely implies compensative response to an insufficient ambient oxygen supply.     

Wet-Chemical Etching: a Novel Nanofabrication Route to Prepare Broadband Random Plasmonic Metasurfaces

Plasmonics - Broadband optical metasurfaces are gaining enormous attention owing to their potential applications in optoelectronic devices, sensors, and flat optics. Here, we demonstrate for the...