A genomic view on syntrophic versus non-syntrophic lifestyle in anaerobic fatty acid degrading communities

In sulfate-reducing and methanogenic environments complex biopolymers are hydrolyzed and degraded by fermentative micro-organisms that produce hydrogen, carbon dioxide and short chain fatty acids. Degradation of short chain fatty acids can be coupled to methanogenesis or to sulfate-reduction. Here we study from a genome perspective why some of these micro-organisms are able to grow in syntrophy with methanogens and others are not. Bacterial strains were selected based on genome availability and upon their ability to grow on short chain fatty acids alone or in syntrophic association with methanogens. Systematic functional domain profiling allowed us to shed light on this fundamental and ecologically important question. Extra-cytoplasmic formate dehydrogenases (InterPro domain number; IPR006443), including their maturation protein FdhE (IPR024064 and IPR006452) is a typical difference between syntrophic and non-syntrophic butyrate and propionate degraders. Furthermore, two domains with a currently unknown function seem to be associated with the ability of syntrophic growth. One is putatively involved in capsule or biofilm production (IPR019079) and a second in cell division, shape-determination or sporulation (IPR018365). The sulfate-reducing bacteria Desulfobacterium autotrophicum HRM2, Desulfomonile tiedjei and Desulfosporosinus meridiei were never tested for syntrophic growth, but all crucial domains were found in their genomes, which suggests their possible ability to grow in syntrophic association with methanogens. In addition, profiling domains involved in electron transfer mechanisms revealed the important role of the Rnf-complex and the formate transporter in syntrophy, and indicate that DUF224 may have a role in electron transfer in bacteria other than Syntrophomonas wolfei as well. This article was invited for a Special Issue entitled: 18th European Bioenergetic Conference.This research was financed by grants of BE-Basic (project 7.2.3.), the Technology Foundation, the Applied Science Division (STW) (project 11603) and the Divisions CW and ALW (projects 700.55.343 and 819.02.014) of the Netherlands Science Foundation (NWO) and ERC (project 323009). Furthermore, this work was carried out on the Dutch national e-infrastructure with the support of

A Greater Means to the Greater Good: Ethical Guidelines to Meet Social Movement Organization Advocacy Challenges

Existing public relations ethics literature often proves inadequate when applied to social movement campaigns, considering the special communication challenges activists face as marginalized moral visionaries in a commercial public sphere. The communications of counter-hegemonic movements is distinct enough from corporate, nonprofit, and governmental organizations to warrant its own ethical guidelines. The unique communication guidelines most relevant to social movement organizations include promoting asymmetrical advocacy to a greater extent than is required for more powerful organizations and building flexibility into the TARES principles to privilege social responsibility over respect for audience values in activist campaigns serving as ideological critique

Antenatal treatment in two Dutch families with pyridoxine-dependent seizures

Contains fulltext : 88199.pdf (publisher's version ) (Closed access)Incidental reports suggest that antenatal treatment of pyridoxine dependent seizures (PDS) may improve neurodevelopmental outcome of affected patients. Two families with PDS are reported, both with two affected siblings. Antenatal treatment with pyridoxine was instituted during the second pregnancy in each family (50 and 60 mg daily from 3 and 10 weeks of gestation, respectively). Perinatal characteristics and neurodevelopmental outcome at 4 (Family A) and 12 (Family B) years of age were compared between the untreated and treated child within each family. Meconium-stained amniotic fluid was present in both first pregnancies and abnormal foetal movements were noticed in one. In the treated infants, pregnancy and birth were uncomplicated. In family A, postnatal pyridoxine supplementation prevented neonatal seizures. Both children in family A were hypotonic and started walking after 2 years of age; both had white matter changes on MRI, and the first child was treated for squint. IQ was 73 and 98 in the antenatally untreated and treated child, respectively. The second child in family B developed seizures on the seventh day, because pyridoxine maintenance therapy had not been instituted after birth. Seizures responded rapidly to pyridoxine supplementation. MRI showed large ventricles and a mega cisterna magna. IQ was 80 and 106 in the antenatally untreated and treated child respectively. Both children had normal motor development. These results suggest that antenatal pyridoxine supplementation may be effective in preventing intrauterine seizures, decreasing the risk of complicated birth and improving neurodevelopmental outcome in PDS.1 maart 201

Reliable detection of <it>Bacillus anthracis</it>, <it>Francisella tularensis </it>and <it>Yersinia pestis </it>by using multiplex qPCR including internal controls for nucleic acid extraction and amplification

Abstract Background Several pathogens could seriously affect public health if not recognized timely. To reduce the impact of such highly pathogenic micro-organisms, rapid and accurate diagnostic tools are needed for their detection in various samples, including environmental samples. Results Multiplex real-time PCRs were designed for rapid and reliable detection of three major pathogens that have the potential to cause high morbidity and mortality in humans: B. anthracis, F. tularensis and Y. pestis. The developed assays detect three pathogen-specific targets, including at least one chromosomal target, and one target from B. thuringiensis which is used as an internal control for nucleic acid extraction from refractory spores as well as successful DNA amplification. Validation of the PCRs showed a high analytical sensitivity, specificity and coverage of diverse pathogen strains. Conclusions The multiplex qPCR assays that were developed allow the rapid detection of 3 pathogen-specific targets simultaneously, without compromising sensitivity. The application of B. thuringiensis spores as internal controls further reduces false negative results. This ensures highly reliable detection, while template consumption and laboratory effort are kept at a minimum</p

Development and Comparison of Two Assay Formats for Parallel Detection of Four Biothreat Pathogens by Using Suspension Microarrays

Microarrays provide a powerful analytical tool for the simultaneous detection of multiple pathogens. We developed diagnostic suspension microarrays for sensitive and specific detection of the biothreat pathogens Bacillus anthracis, Yersinia pestis, Francisella tularensis and Coxiella burnetii. Two assay chemistries for amplification and labeling were developed, one method using direct hybridization and the other using target-specific primer extension, combined with hybridization to universal arrays. Asymmetric PCR products for both assay chemistries were produced by using a multiplex asymmetric PCR amplifying 16 DNA signatures (16-plex). The performances of both assay chemistries were compared and their advantages and disadvantages are discussed. The developed microarrays detected multiple signature sequences and an internal control which made it possible to confidently identify the targeted pathogens and assess their virulence potential. The microarrays were highly specific and detected various strains of the targeted pathogens. Detection limits for the different pathogen signatures were similar or slightly higher compared to real-time PCR. Probit analysis showed that even a few genomic copies could be detected with 95 % confidence. The microarrays detected DNA from different pathogens mixed in different ratios and from spiked or naturally contaminated samples. The assays that were developed have a potential for applicatio

Detection limits of the DH and TSPE-UH suspension array formats.

a<p>Values displayed represent the lowest DNA concentration at which 95% of the positive samples are detected, as calculated by using probit analysis. ND = not determined.</p

Detection of mixed pathogens by using DH and TSPE-UH suspension microarrays.

<p>Genomic DNA from <i>B. anthracis</i> (Ba), <i>F. tularensis</i> (Ft), <i>Y. pestis</i> (Yp), <i>C. burnetii</i> (Cb) was mixed in different ratios and measured by using DH (<b>A</b>) and TSPE-UH (<b>B</b>) microarrays. Mean fluorescence intensity (MFI) is displayed for the different pathogen-specific probes (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031958#pone-0031958-t001" target="_blank">Table 1</a>). The detection of one pathogen is not impeded by the detection of the other targeted pathogens.</p

DH suspension microarray measurement showing minor cross-reactivity.

<p>Three <i>Y. pestis</i> strains (Yp) and the no template control (NTC) are shown from a DH measurement. Probe <i>isf</i> showed a minor signal when a high load of <i>Y. pestis</i> genomic DNA was amplified.</p

Typical results from DH and TSPE-UH suspension microarrays detecting select pathogens.

<p>Two 17-plex bead arrays were developed for the detection of <i>B. anthracis</i> (Ba), <i>F. tularensis</i> (Ft), <i>Y. pestis</i> (Yp), <i>C. burnetii</i> (Cb) and an internal control for DNA extraction and microarray detection (Bt). The microarrays were based on (<b>A</b>) direct hybridization (DH), or (<b>B</b>) target specific primer extension combined with universal microarray hybridization (TSPE-UH) assay formats. Both microarrays make use of identical amplification products from a 16-plex asymmetric PCR. Mean fluorescence intensity (MFI) is displayed for the different probes that are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031958#pone-0031958-t001" target="_blank">Table 1</a>.</p