Extraction of regulatory gene/protein networks from Medline

MOTIVATION: We have previously developed a rule-based approach for extracting information on the regulation of gene expression in yeast. The biomedical literature, however, contains information on several other equally important regulatory mechanisms, in particular phosphorylation, which we now expanded for our rule-based system also to extract. RESULTS: This paper presents new results for extraction of relational information from biomedical text. We have improved our system, STRING-IE, to capture both new types of linguistic constructs as well as new types of biological information [i.e. (de-)phosphorylation]. The precision remains stable with a slight increase in recall. From almost one million PubMed abstracts related to four model organisms, we manage to extract regulatory networks and binary phosphorylations comprising 3,319 relation chunks. The accuracy is 83-90% and 86-95% for gene expression and (de-)phosphorylation relations, respectively. To achieve this, we made use of an organism-specific resource of gene/protein names considerably larger than those used in most other biology related information extraction approaches. These names were included in the lexicon when retraining the part-of-speech (POS) tagger on the GENIA corpus. For the domain in question, an accuracy of 96.4% was attained on POS tags. It should be noted that the rules were developed for yeast and successfully applied to both abstracts and full-text articles related to other organisms with comparable accuracy. AVAILABILITY: The revised GENIA corpus, the POS tagger, the extraction rules and the full sets of extracted relations are available from http://www.bork.embl.de/Docu/STRING-IE     

A Novel Anti-Inflammatory and Pro-Resolving Role for Resolvin D1 in Acute Cigarette Smoke-Induced Lung Inflammation

Introduction

Cigarette smoke is a profound pro-inflammatory stimulus that contributes to acute lung injuries and to chronic lung disease including COPD (emphysema and chronic bronchitis). Until recently, it was assumed that resolution of inflammation was a passive process that occurred once the inflammatory stimulus was removed. It is now recognized that resolution of inflammation is a bioactive process, mediated by specialized lipid mediators, and that normal homeostasis is maintained by a balance between pro-inflammatory and pro-resolving pathways. These novel small lipid mediators, including the resolvins, protectins and maresins, are bioactive products mainly derived from dietary omega-3 and omega-6 polyunsaturated fatty acids (PUFA). We hypothesize that resolvin D1 (RvD1) has potent anti-inflammatory and pro-resolving effects in a model of cigarette smoke-induced lung inflammation.

Methods

Primary human lung fibroblasts, small airway epithelial cells and blood monocytes were treated with IL-1β or cigarette smoke extract in combination with RvD1 in vitro, production of pro-inflammatory mediators was measured. Mice were exposed to dilute mainstream cigarette smoke and treated with RvD1 either concurrently with smoke or after smoking cessation. The effects on lung inflammation and lung macrophage populations were assessed.

Results

RvD1 suppressed production of pro-inflammatory mediators by primary human cells in a dose-dependent manner. Treatment of mice with RvD1 concurrently with cigarette smoke exposure significantly reduced neutrophilic lung inflammation and production of pro-inflammatory cytokines, while upregulating the anti-inflammatory cytokine IL-10. RvD1 promoted differentiation of alternatively activated (M2) macrophages and neutrophil efferocytosis. RvD1 also accelerated the resolution of lung inflammation when given after the final smoke exposure.

Conclusions

RvD1 has potent anti-inflammatory and pro-resolving effects in cells and mice exposed to cigarette smoke. Resolvins have strong potential as a novel therapeutic approach to resolve lung injury caused by smoke and pulmonary toxicants.     

Nutritional and hormonal control of lipolysis in isolated gilthead seabream (Sparus aurata) adipocytes

We examined the effects of diet composition and fasting on lipolysis of freshly isolated adipocytes from gilthead seabream (Sparus aurata). We also analyzed the effects of insulin, glucagon, and growth hormone (GH) in adipocytes isolated from fish fed with different diets. Basal lipolysis, measured as glycerol release, increased proportionally with cell concentration and time of incubation, which validates the suitability of these cell preparations for the study of hormonal regulation of this metabolic process. Gilthead seabream were fed two different diets, FM (100% of fish meal) and PP (100% of plant protein supplied by plant sources) for 6 wk. After this period, each diet group was divided into two groups: fed and fasted (for 11 days). Lipolysis was significantly higher in adipocytes from PP-fed fish than in adipocytes from FM-fed fish. Fasting provoked a significant increase in the lipolytic rate, about threefold in isolated adipocytes regardless of nutritional history. Hormone effects were similar in the different groups: glucagon increased the lipolytic rate, whereas insulin had almost no effect. GH was clearly lipolytic, although the relative increase in glycerol over control was lower in isolated adipocytes from fasted fish compared with fed fish. Together, we demonstrate for the first time that lipolysis, measured in isolated seabream adipocytes, is affected by the nutritional state of the fish. Furthermore, our data suggest that glucagon and especially GH play a major role in the control of adipocyte lipolysis.     

Structural basis of pyrrole polymerization in human porphobilinogen deaminase

Human porphobilinogen deaminase (PBGD), the third enzyme in the heme pathway, catalyzes four times a single reaction to convert porphobilinogen into hydroxymethylbilane. Remarkably, PBGD employs a single active site during the process, with a distinct yet chemically equivalent bond formed each time. The four intermediate complexes of the enzyme have been biochemically validated and they can be isolated but they have never been structurally characterized other than the apo- and holo-enzyme bound to the cofactor. We present crystal structures for two human PBGD intermediates: PBGD loaded with the cofactor and with the reaction intermediate containing two additional substrate pyrrole rings. These results, combined with SAXS and NMR experiments, allow us to propose a mechanism for the reaction progression that requires less structural rearrangements than previously suggested: the enzyme slides a flexible loop over the growing-product active site cavity. The structures and the mechanism proposed for this essential reaction explain how a set of missense mutations result in acute intermittent porphyria.     

Physiological state influences the antennal response of Anastrepha obliqua to male and host volatiles

The sexual and host‐related behaviours of the fruit fly Anastrepha obliqua Macquart (Diptera: Tephritidae) are mediated by volatile compounds. However, whether the physiological state of this species affects its antennal and behavioural responses to semiochemicals is unknown. The effects of age, mating status, diet and the topical application of methoprene, a Juvenile hormone analogue (JHA), on the antennal sensitivity of this tephritid fruit fly species to selected male [(Z)‐3‐nonenol] and host fruit volatiles (ethyl benzoate, ethyl hexanoate, ethyl butyrate and trans‐β‐ocimene) are investigated using electroantennography (EAG). Overall, (Z)‐3‐nonenol and ethyl benzoate elicit the highest EAG responses in both sexes. Flies of both sexes aged 1, 5 and 10 days old show higher EAG responses to the tested compounds compared with flies aged 20 days old. Virgin females and males show higher EAG responses to volatile compounds than mated flies. Females and males fed with sugar plus protein show higher antennal responses to volatiles compared with flies fed sugar or protein alone. Flies of both sexes treated with methoprene show higher antennal responses than flies treated with acetone (control). These results suggest that the peripheral olfactory system in A. obliqua is modulated by the physiological state of the flies.     

Estimating Neospora caninum prevalence in wildlife populations using Bayesian inference

Prevalence of disease in wildlife populations, which is necessary for developing disease models and conducting epidemiologic analyses, is often understudied. Laboratory tests used to screen for diseases in wildlife populations often are validated only for domestic animals. Consequently, the use of these tests for wildlife populations may lead to inaccurate estimates of disease prevalence. We demonstrate the use of Bayesian latent class analysis (LCA) in determining the specificity and sensitivity of a competitive enzyme‐linked immunosorbent assay (cELISA; VMRD^®, Inc.) serologic test used to identify exposure to Neospora caninum (hereafter N. caninum) in three wildlife populations in southeastern Ohio, USA. True prevalence of N. caninum exposure in these populations was estimated to range from 0.1% to 3.1% in American bison (Bison bison), 51.0% to 53.8% in Père David's deer (Elaphurus davidianus), and 40.0% to 45.9% in white‐tailed deer (Odocoileus virginianus). The accuracy of the cELISA in American bison and Père David's deer was estimated to be close to the 96% sensitivity and 99% specificity reported by the manufacturer. Sensitivity in white‐tailed deer, however, ranged from 78.9% to 99.9%. Apparent prevalence of N. caninum from the test results is not equal to the true prevalence in white‐tailed deer and Père David's deer populations. Even when these species inhabit the same community, the true prevalence in the two deer populations differed from the true prevalence in the American bison population. Variances in prevalence for some species suggest differences in the epidemiology of N. caninum for these colocated populations. Bayesian LCA methods could be used as in this example to overcome some of the constraints on validating tests in wildlife species. The ability to accurately evaluate disease status and prevalence in a population improves our understanding of the epidemiology of multihost pathogen systems at the community level.     

Immune humoral response in pigs infected with eggs and posoncospheres of Taenia solium

Due to the importance of cysticercosis in Mexico and Latin America and to the fact that in the last years another mechanism of infection for this disease has been proposed, i.e. through postoncospheres and immunosuppression of the host, we have considered relevant to perform the present work, which consisted in assessing the immune response induced by dexamethasone as well as that produced by parasites in pigs infected with T. solium eggs, or postoncosphere-infected, and in postoncosphere-infected and dexamethasone-treated animals. We used 10 recently weaned pigs, three were used as controls, two of them without the drug and one with it; two were infected with T. solium eggs; five with postoncospheres receiving also dexamethasone three of them. We evaluated the humoral response against parasite antigen using indirect haemagglutination (IH) and ELISA methods. Results of the immune humoral response revealed titres of up to 1:128 in T. solium eggs infected animals, of 1:16 in postoncosphere infected animals, and of 1:32 towards the end of the experiment in postoncosphere plus dexamethasone animals. Absorbance titres with ELISA confirmed these findings. Data obtained by IH show that the antibody titres of the pigs challenged with postoncospheres and postoncospheres plus dexamethasone are positive as compared to the titres obtained in the pigs infected with T. solium eggs. Results from the ELISA confirmed this finding, since, from weeks 14 to 17, the pigs became positive, behaving as those pigs that developed cysticercosis. This is relevant as it indicates that the antiposcosphere antibodies recognized antigens of T. solium larvae.     

Cryopreserved Morulae can be used to Efficiently Generate Germline-transmitting Chimeras by Blastocyst Injection

The production of chimeric mice is a complex process, requiring the careful coordination of tissue culture cell growth, production of a large number (30–75) of competent blastocysts and the availability of appropriately timed pseudo pregnant female mice. Failure at any of these steps can impinge upon the rapid production of chimeras. One potential improvement for the efficient generation of chimeric mice would be the utilization of cryopreserved embryos suitable for injection. C57Bl/6 morulae were frozen using a standard 2-step protocol with ethylene glycol as the cryopreservation agent. We determined that cryopreserved morulae could thaw, culture to blastocyst stage in KSOM media and survive injection at rates equivalent to control embryos. Cryopreserved morulae were also equivalent to controls at all later stages in the process of production of chimeric mice, including birth rate, percentage chimerism of resulting animals and ability to produce germline progeny. Hence, cryopreservation of morulae for blastocyst injection is a suitable option to enhance the efficiency of chimeric mouse generation.