SpecNet: A Spatial Network Algorithm that Generates a Wide Range of Specific Structures

Network measures are used to predict the behavior of different systems. To be able to investigate how various structures behave and interact we need a wide range of theoretical networks to explore. Both spatial and non-spatial methods exist for generating networks but they are limited in the ability of producing wide range of network structures. We extend an earlier version of a spatial spectral network algorithm to generate a large variety of networks across almost all the theoretical spectra of the following network measures: average clustering coefficient, degree assortativity, fragmentation index, and mean degree. We compare this extended spatial spectral network-generating algorithm with a non-spatial algorithm regarding their ability to create networks with different structures and network measures. The spatial spectral network-generating algorithm can generate networks over a much broader scale than the non-spatial and other known network algorithms. To exemplify the ability to regenerate real networks, we regenerate networks with structures similar to two real Swedish swine transport networks. Results show that the spatial algorithm is an appropriate model with correlation coefficients at 0.99. This novel algorithm can even create negative assortativity and managed to achieve assortativity values that spans over almost the entire theoretical range.     

Self-help materials for the prevention of smoking relapse: study protocol for a randomised controlled trial

ABSTRACT: BACKGROUND: Most people who stop smoking successfully for a few weeks will return to smoking again in the medium term. There are few effective interventions to prevent this relapse and none used routinely in clinical practice. A previous exploratory meta-analysis suggested that self-help booklets may be effective but requires confirmation. This trial aims to evaluate the effectiveness and cost-effectiveness of a set of self-help educational materials to prevent smoking relapse in the NHS Stop Smoking Service. METHODS: This is an open, randomised controlled trial. The target population is carbon monoxide (CO) verified quitters at 4 weeks in the NHS stop smoking clinic (total sample size N=1,400). The experimental intervention tested is a set of 8 revised Forever Free booklets, including an introduction booklet and more extensive information on all important issues for relapse prevention. The control intervention is a leaflet that has no evidence to suggest it is effective but is currently given to some patients using NHS stop smoking services. Two follow-up telephone interviews will be conducted at 3 and 12 months after quit date. The primary outcome will be prolonged abstinence from months 4-12 with no more than 5 lapses, confirmed by carbon monoxide test at 12 month assessment. The secondary outcomes will be 7-day self-report point prevalence abstinence at 3 months and 7-day biochemically confirmed point prevalence abstinence at 12 months. To assess cost-effectiveness, costs will be estimated from a health service perspective and the EQ-5D will be used to estimate the QALY (Quality Adjusted Life Year) gain associated with each intervention. The comparison of smoking abstinence rates (and any other binary outcomes) between the two trial arms will be carried out using odds ratio as the outcome statistic and other related statistical tests. Exploratory subgroup analyses, including logistic regression analyses with interaction terms, will be conducted to investigate possible effect modifying variables. DISCUSSION: The possible effect of self-help educational materials for the prevention of smoking relapse has important public health implications. Trial Registration: Current Controlled Trials ISRCTN36980856.     

Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors

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Extensive Antibody Cross-reactivity among Infectious Gram-negative Bacteria Revealed by Proteome Microarray Analysis

Antibodies provide a sensitive indicator of proteins displayed by bacteria during sepsis. Because signals produced by infection are naturally amplified during the antibody response, host immunity can be used to identify biomarkers for proteins that are present at levels currently below detectable limits. We developed a microarray comprising ∼70% of the 4066 proteins contained within the Yersinia pestis proteome to identify antibody biomarkers distinguishing plague from infections caused by other bacterial pathogens that may initially present similar clinical symptoms. We first examined rabbit antibodies produced against proteomes extracted from Y. pestis, Burkholderia mallei, Burkholderia cepecia, Burkholderia pseudomallei, Pseudomonas aeruginosa, Salmonella typhimurium, Shigella flexneri, and Escherichia coli, all pathogenic Gram-negative bacteria. These antibodies enabled detection of shared cross-reactive proteins, fingerprint proteins common for two or more bacteria, and signature proteins specific to each pathogen. Recognition by rabbit and non-human primate antibodies involved less than 100 of the thousands of proteins present within the Y. pestis proteome. Further antigen binding patterns were revealed that could distinguish plague from anthrax, caused by the Gram-positive bacterium Bacillus anthracis, using sera from acutely infected or convalescent primates. Thus, our results demonstrate potential biomarkers that are either specific to one strain or common to several species of pathogenic bacteria.Plague is a disease of historical epidemics that remains an important public health problem in limited areas of the world (1). Disease transmission usually occurs through transfer of the bacillus Yersinia pestis by the bite of a flea. However, less frequent direct transfer of viable bacteria by respiratory droplets may result in primary pneumonic infection. A transient intracellular infection of phagocytic cells (2) occurs during the earliest stage of bubonic plague followed by rapid extracellular expansion of bacteria in lymph nodes. The prototypical lymphatic infection of bubonic plague may also progress to bacteremic or pneumonic infection with a very high rate of fatality if there is not rapid intervention by antibiotic treatment (3). Among the reported cases occurring annually in the United States, 15% were fatal in 2006 (4). Although only small numbers of human cases occur each year in North America, a more substantial incidence of plague is found in wild animal populations (5) with seroprevalence rates of up to 100% among mammalian carnivores in endemic areas (6). The geographic range of infection within feral populations is presently unknown but may contribute significantly to the reservoir of potential disease transmission to humans.Diagnostic tests and prophylactic vaccines or therapies must rapidly distinguish or protect against the many infectious diseases that present similar initial symptoms. Specific diagnostic tests and vaccines for plague are public health priorities primarily because of the threat from potential acts of terrorism. Because human deaths may occur within 48 h of infection (7), delays in proper diagnosis have led to disease complications and fatalities from plague (8). Yet the identification of bacterial sepsis at the earliest stage of clinical presentation is challenging because of the generalized nature of disease symptoms and the difficulty in culturing infectious agents or isolating sufficient material to identify the infectious agent by amplification of genetic markers. Although host antibody responses provide a sensitive indicator of current or past infection, insufficient numbers of validated biomarkers are available, and extensive antibody cross-reactivity among Gram-negative pathogens (9–12) complicates the direct analysis of serum.Identification of plague-specific antibody interactions is a daunting task because of the complexity of the bacterial proteome encountered by the host during infection. The chromosome of Y. pestis CO92 encodes ∼3885 proteins, whereas an additional 181 are episomally expressed by pCD1, pMT1, and pPCP1. For comparison, the proteome of Y. pestis KIM¹ contains 4202 individual proteins (13), 87% in common with CO92 (14), and the closely related enteric pathogen Yersinia pseudotuberculosis (15, 16) contains ∼4038 proteins (chromosome plus plasmids). Recent technical advances have facilitated the development of microarrays comprising full-length, functional proteins that represent nearly complete proteomes. For example, Zhu et al. (17) reported the development of a proteome microarray containing the full-length, purified expression products of over 93% of the 6280 protein-coding genes of the yeast Saccharomyces cerevisiae, and Schmid et al. (18) described the human antibody repertoire for vaccinia virus recognition by using a viral proteome microarray. This approach opens the possibility of examining the entire bacterial proteome to elucidate proteins or protein pathways that are essential to pathogenicity or host immunity. We sought to identify biomarkers that could distinguish plague from diseases caused by other bacterial pathogens by measuring host antibody recognition of individual proteins contained within the Y. pestis proteome. The previously reported genomic sequences of Y. pestis strains KIM (13) and CO92 (14), sharing 95% identity, were used for reference. Approximately 77% of the putative Y. pestis proteome can be classified by known homologies. We successfully expressed and purified the majority (70%) of the 4066 ORFs encoded by the chromosome and plasmids of Y. pestis KIM and arrayed these products onto glass slides coated with nitrocellulose. The Y. pestis ORFs subcloned into expression vectors were fully sequenced to confirm quality and identity before use. Different approaches for studying the antibody repertoire for plague in rabbits and non-human primates were compared. Based on results from experiments using the Y. pestis proteome microarray, we identified new candidates for antibody biomarkers of bacterial infections and patterns of cross-reactivity that may be useful diagnostic tools.     

Engineering seed dormancy by the modification of zeaxanthin epoxidase gene expression

Abscisic acid (ABA) is a plant hormone synthesized during seed development that is involved in the induction of seed dormancy. Delayed germination due to seed dormancy allows long-term seed survival in soil but is generally undesirable in crop species. Freshly harvested seeds of wild-type Nicotiana plumbaginifolia plants exhibit a clear primary dormancy that results in delayed germination, the degree of primary dormancy being influenced by environmental culture conditions of the mother plant. In contrast, seeds, obtained either from ABA-deficient mutant aba2-s1 plants directly or aba2-s1 plants grafted onto wild-type plant stocks, exhibited rapid germination under all conditions irrespective of the mother plant culture conditions. The ABA biosynthesis gene ABA2 of N. plumbaginifolia, encoding zeaxanthin epoxidase, was placed under the control of the constitutive 35S promoter. Transgenic plants overexpressing ABA2 mRNA exhibited delayed germination and increased ABA levels in mature seeds. Expression of an antisense ABA2 mRNA, however, resulted in rapid seed germination and in a reduction of ABA abundance in transgenic seeds. It appears possible, therefore, that seed dormancy can be controlled in this Nicotiana model species by the manipulation of ABA levels.     

Evidence of dietary feedback in a facultative association between deep-sea gastropods and sea anemones

While epibiotic associations between macrobenthic invertebrates are common, the role they play in the feeding ecology of intervening species is often incompletely understood. The diets of epibiotic sea anemones Allantactis parasitica and their gastropod hosts were analyzed using digestive tract contents, lipid biomarkers and observations of live specimens in an attempt to detect dietary feedback from the facultative association. Comparisons were made using symbiotic individuals and asymbiotic counterparts collected at depths of 191-627 m from three neighbouring areas in the northwest Atlantic. Gastropods carrying one or two epibionts had higher stomach indices than those harbouring three epibionts or no epibiont. The diet of symbiotic gastropods was also more diversified based on stomach contents and lipid analysis. Among other things, symbiotic gastropods contained four times more lipids and a greater proportion of Σn−3 fatty acids. Gastrovascular cavity content indices of asymbiotic sea anemones were generally lower than those of symbiotic counterparts. Their cavities were more often empty, and their diet less diversified with fewer benthic items, suggesting that foraging of gastropods through the sediments makes more food available to sea anemones living as epibionts. Lipid analysis showed some disparities between symbiotic and asymbiotic sea anemones at the regional scale, including in percent phospholipids and in the proportion of certain fatty acids. Together these findings indicate that mutual protection against predators leads to prolonged and more efficient foraging for gastropods and increased time spent deployed (feeding) in food-rich areas for sea anemones, thus enabling both partners to fully exploit food resources that may be limited at bathyal depths.     

Role of RNA structure and susceptibility to RNase E in regulation of a cold shock mRNA, cspA mRNA

Degradation of the cspA mRNA in vivo is very rapid at temperatures greater than 30 degrees C and is moderately dependent on RNase E. Investigations in vitro show that degradosomes prepared from normal or cold-shocked cultures cleave the cspA mRNA preferentially at a single site in vitro between two stem-loops approximately 24 residues 3' to the termination codon and approximately 31 residues from the 3' end. The site of cleavage is independent of the temperature and largely independent of the phosphorylation status of the 5' end of cspA mRNA. A 5' stem-loop, potential occlusion of the initiation and termination codons, temperature-dependent translational efficiency, and the position of the RNase E cleavage site can explain the differential stability of the cspA mRNA.     

A plasminogen-like protein, present in the apical extracellular environment of thyroid epithelial cells, degrades thyroglobulin in vitro

The prothyroid hormone, thyroglobulin (Tg), is stored at high concentrations in the thyroid follicular lumen as a soluble 19S homo-dimer and as heavier soluble (27S and 37S) and insoluble (Tgm) forms. Follicular degradation of Tg may contribute to maintaining Tg concentrations compatible with follicle integrity. Here, we report on the presence of a plasminogen-like protein in the follicular lumen of normal human thyroids and its synthesis and apical secretion by cultured epithelial thyroid cells. Since all the main luminal forms of Tg are cleaved by this plasminogen-like protein, we suggest that it contributes to Tg degradation in the follicular lumen.