In silico selection of an ssDNA aptamer against HER2-positive breast cancer cells using computational docking simulation

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Enrichment and characterization of microorganisms capable of degrading various C1 compounds in the Black Sea

Background: Methylated compounds can be used as an energy source to drive interactions between sulfate reducing microorganisms and methanogens. This has potential impact on the current understanding of the global carbon and sulfur cycles. Objectives: The use of methylated compounds by anaerobic microorganisms present in the sulfidic permanently stratified Black Sea sediment and column water and the composition of these communities was investigated through enrichment studies. Methods: Black Sea sediment of three different depths between 5 and 30 centimeters below sea floor, as well as water at 105 meters deep were collected anoxically and used for enrichments, supplemented with 1 mM of either dimethylsulfide (DMS), dimethylsulfoniopropionate (DMSP), trimethylamine (TMA) and methanol as sole energy source. To promote methanogenesis, acetogenesis and sulfate reduction in the different enrichments, 20 mM molybdate, 20 mM bromoerhanosulfonate (BrES) and 20 mM BrES with 20 mM sulfate was added, respectively. Anoxic cultures were incubated at 20ºC in the dark. Uptake of substrate and product formation were monitored over 4 weeks. Active cultures were transferred to fresh medium to promote further enrichment. Analyses of 16s rRNA gene sequencing are ongoing to elucidate the inocula and culture communities. Results: All enrichments grew on the provided substrates. Over four weeks, utilization of substrate ranged between 20% and 100% for all enrichments. Subsequent transfers of the enrichments retained the decrease of substrate although utilization was slower. These results will be complemented with 16s rRNA gene sequencing data and community comparison developed n methanogenic, acetogenic and sulfate-reducing enrichments performed.info:eu-repo/semantics/publishedVersio

Functional analysis of syntrophic LCFA-degrading microbial ecosystems

ICBM 2014 - 2nd International Conference on Biogas Microbiology[Excerpt] Introduction and Aim: Long-chain fatty acids (LCFA) are present in lipid rich wastewater and can be converted to methane anaerobically, coupling wastewater treatment to bioenergy production. Differences in the degradation of saturated and unsaturated long-chain fatty acids (LCFA) by anaerobic consortia are not completely understood. Previous studies showed a segregation on the microbial community composition when the same inoculum sludge was incubated with saturated- or with unsaturated-LCFA (Sousa et al., 2007), suggesting differences in their degradation pathways. In order to get more insights on this and aiming linking microbial community structure to function, a comparative shotgun metaproteomics study of a mesophilic anaerobic sludge incubated with saturated- and unsaturated-LCFA was conducted. Additionally, the metaproteome of a defined co-culture of Syntrophomonas zehnderi and Methanobacterium formicicum growing on saturated- and unsaturated-LCFA to methane was also analyzed. [...]The authors thank the FCT Strategic Project PEst-OE/EQB/LA0023/2013, the project “BioEnv - Biotechnology and Bioengineering for a sustainable world”, REF. NORTE-07-0124-FEDER-000048” co-funded by the Programa Operacional Regional do Norte (ON.2 – O Novo Norte), QREN, FEDER and the project FCOMP-01-0124-FEDER-014784, financed by the FEDER funds through the Operational Competitiveness Programme (COMPETE) and by national funds through the FCT.info:eu-repo/semantics/publishedVersio

Pressurized syngas bioconversion: physiological and microbial characterization

ICBM-3 - 3rd International Conference on Biogas MicrobiologySyngas is composed mainly by CO, H2 and CO2 and its fermentation is a promising biological process to produce fuels or commodity chemicals. Experiments under increased initial syngas pressures, up to 5.2×105 Pa, were carried out to evaluate the effects on metabolites production and microbial communities structure. Two strategies were applied: NB non-adapted biomass and SB successively syngas-fed biomass. The rise of syngas pressure from 1.2×105 Pa up to 5.2×105 Pa led to a decrease on CO and H2 consumption rates and CH4 production rate. Moreover, when methanogenesis was partially inhibited, propionate and butyrate were the main metabolites produced from syngas. DGGE profiles showed differences on diversity and on similarity indices (SI) with changes in pressure. Regardless the syngas pressure employed, the archaeal communities had higher SI (above 70%) than bacterial community (48% to 62%). From the Illumina sequencing analysis, it was observed that the relative abundance of bacterial communities tend to decrease (72% to 46%), and archaeal communities increased (25% to 54%) by raising the pressure of syngas from 1.2×105 Pa to 5.2×105 Pa. In the inoculum and biomass incubated at 1.2×105 Pa syngas, 40% of total population were from Proteobacteria phylum and Deltraproteobacteria class and their abundance was reduced 4-fold at 5.2×105 Pa. As a direct effect of high pressures of syngas, organisms belonging to Firmicutes, Synergistetes and Thermotogae phyla increased over 10-fold. The predominant phylotypes at 3×105 Pa and 5.2×105 Pa were related to Methanobacterium genus (archaea) and to Eubacteriaceae, Synergistaceae and Syntrophobacteraceae families (bacteria). These results showed a microbial population enrichment suggesting a high specialization for the substrate.info:eu-repo/semantics/publishedVersio

Microbial diversity of anaerobic syngas-converting enrichments from a multi-orifice baffled bioreactor (MOBB)

Syngas fermentation can be used to produce fuels and chemicals from lignocellulosic biomass or other poorly biodegradable wastes. The aim of this study was to identify and characterize carboxydotrophic microorganisms in enrichments and evaluate their potential for syngas bioconversion. Anaerobic sludge that efficiently converted syngas (60% CO, 30% H2, 10% CO2) to methane, in a multi-orifice baffled bioreactor (MOBB), was used as inoculum to start enrichments with CO as carbon and energy source. Enrichments were started under a headspace containing 40% CO. Bottles amended with vancomycin and/or erythromycin were also inoculated to test the potential for enriching CO-converting methanogens. Methane and acetate were produced in the enrichment, but no growth or methane production was detected in incubation with antibiotics. In the enrichment, organisms related to Acetobacterium and Sporomusa species were the predominant bacterial species and Methanobacterium and Methanospirillum were the dominant archaea. The enrichment was subcultured and pasteurized to select for spore-forming bacteria and to inactivate methanogens. A stable enrichment culture was obtained that converted up to 100% CO. This enrichment produced hydrogen and acetate. The pasteurized culture showed a low microbial diversity; more than 90% of the community was related to Sporomusa ovata (97% identity). The results suggest that methane production from CO in the MOBB is a combined activity of carboxydotrophic acetogenic bacteria and hydrogenotrophic methanogens. Interestingly, growth of S. ovata with high concentrations of CO was never shown before.info:eu-repo/semantics/publishedVersio

Enrichment of syngas-converting communities from a multi-orifice baffled bioreactor

The substitution of natural gas by renewable biomethane is an interesting option to reduce global carbon footprint. Syngas fermentation has potential in this context, as a diverse range of low-biodegradable materials that can be used. In this study, anaerobic sludge acclimatized to syngas in a multi-orifice baffled bioreactor (MOBB) was used to start enrichments with CO. The main goals were to identify the key players in CO conversion and evaluate potential interspecies metabolic interactions conferring robustness to the process. Anaerobic sludge incubated with 0.7 × 105 Pa CO produced methane and acetate. When the antibiotics vancomycin and/or erythromycin were added, no methane was produced, indicating that direct methanogenesis from CO did not occur. Acetobacterium and Sporomusa were the predominant bacterial species in CO-converting enrichments, together with methanogens from the genera Methanobacterium and Methanospirillum. Subsequently, a highly enriched culture mainly composed of a Sporomusa sp. was obtained that could convert up to 1.7 × 105 Pa CO to hydrogen and acetate. These results attest the role of Sporomusa species in the enrichment as primary CO utilizers and show their importance for methane production as conveyers of hydrogen to methanogens present in the culture.Nederlandse Organisatie voor Wetenschappelijk Onderzoek (024.002.002); FP7 Ideas: European Research Council (323009); Norte 2020 - Sistema de Apoio a Investigação Científica e Tecnol ogica (NORTE-01-0145-FEDER-000004); Fundação para a Ciência e a Tecnologia (PD/BD/128030/2016, SFRH/BPD/104837/ 2014).info:eu-repo/semantics/publishedVersio

Microbial systems for conversion of syngas to biobased products

Microbiology Centennial Symposium 2017 - Exploring Microbes for the Quality of Life (Book of Abstracts)Synthesis gas, a mixture of CO, H2, and CO2, can be created via gasification of any carbohydrate material. Fermentation of syngas by carboxydotrophic microbes allows for it to be converted into interesting bio-chemicals. Organisms involved in the fermentation of syngas use the CO or H2 in the gas as electron donor, fixating CO2 into the final end products. Currently acetate and ethanol are relatively well established products from syngas fermentation and there is interest to broaden the scope towards production of more complex products. However, genetic engineering of carboxydotrophic organisms and the knowledge of their metabolism is rather limited, making it difficult to create strains producing these products. A possible way to broaden the scope of products is via co-cultivation of microbes which can make use of each others products. We established a co-cultivation of Clostridium autoethanogenum, a well-known carboxydotrophic acetogen, together with Clostridium kluyveri, a well characterized organism employing the reverse -oxidation pathway. C. autoethanogenum uses the syngas to produce a mixture of acetate and ethanol. C. kluyveri subsequently uses these products to perform chain elongation. This results in a co-culture producing a mixture of C4 and C6 acids and alcohols using carbon monoxide as a sole substrate. This co-culture poses an interesting way for production of more complex and valuable products from syngas. Basic characterization of these co-cultures has been done and currently the research focus lies on how the species interact with each other and how environmental factors influence their production patterns and metabolism.info:eu-repo/semantics/publishedVersio

Perspectives on syngas fermentation

Book of Abstracts of CEB Annual Meeting 2017The replacement of fossil fuels by renewable energy sources is, nowadays, a worldwide priority. Gasification processes and further bioconversion of syngas appears to be a promising alternative compared to the existing chemical techniques, since this process convert renewable sources into alternative fuels and commodity chemicals, such as CH4, fatty acids, alcohols, etc., additionally contributing to the reduction of greenhouse gases [1]. Nearly any form of organic matter can be transformed through gasification, into syngas, mainly composed of CO, H2 and CO2. The biological conversion of syngas offers several advantages over catalytic processes, specifically the greater resistance to catalyst poisoning and the higher specificity for the substrates [2]. Syngas- and CO-fermenting microorganisms use the Wood-Ljungdahl pathway to produce several multi-carbon compounds such as short- and medium-fatty acids and alcohols. Even though many studies were performed in the last few years, fermentation of syngas still involves practical challenges due to limitations of the process. The major bottleneck of syngas fermentation that blocks the commercialization of this technology is gas-to-liquid mass transfer limitations, since it reduces the microorganisms access to the substrate and consequently reduces the productivity rates. It is of utmost importance the development of alternatives that promote the enhancement of mass transfer, the improvement on the productivity rates from syngas fermentation and the deep study of the biocatalysts involved in syngas bioconversion pathways. Biological syngas conversion has been a research topic at the BRIDGE group since 2009, by studying both technological and microbiological aspects of the process. Previous work developed in our group focused on the use of anaerobic complex microbial communities to obtain enriched cultures and/or pure cultures that could convert syngas or CO into mainly acetate, CH4 and H2. Regarding to the technological aspects of syngas bioconversion process, a multi-orifice baffled bioreactor was used to study the effect of using different reactors designs to improve the gas-liquid mass transfer. Moreover, recent studies conducted at BRIDGE group with collaboration of BIOSYSTEMS group showed that the use of increased pressure (up to 5 bar) to increase gas-liquid mass transfer, leads to different metabolic routes on microorganisms. These results represent a step forward to direct the biochemical pathways of microbial community towards the specific products from syngas. As future perspectives, we aimed to continue a research line on syngas fermentation, by studying different operational approaches for this process and focusing on the production of butanol, 2,3-butanediol and propionate.info:eu-repo/semantics/publishedVersio

Conversion of Cn-unsaturated into Cn-2-saturated LCFA can occur uncoupled from methanogenesis in anaerobic bioreactors

Fat, oils, and grease present in complex wastewater can be readily converted to methane, but the energy potential of these compounds is not always recyclable, due to incomplete degradation of long chain fatty acids (LCFA) released during lipids hydrolysis. Oleate (C18:1) is generally the dominant LCFA in lipid-containing wastewater, and its conversion in anaerobic bioreactors results in palmitate (C16:0) accumulation. The reason why oleate is continuously converted to palmitate without further degradation via β-oxidation is still unknown. In this work, the influence of methanogenic activity in the initial conversion steps of unsaturated LCFA was studied in 10 bioreactors continuously operated with saturated or unsaturated C16- and C18-LCFA, in the presence or absence of the methanogenic inhibitor bromoethanesulfonate (BrES). Saturated Cn-2-LCFA accumulated both in the presence and absence of BrES during the degradation of unsaturated Cn-LCFA, and represented more than 50\% of total LCFA. In the presence of BrES further conversion of saturated intermediates did not proceed, not even when prolonged batch incubation was applied. As the initial steps of unsaturated LCFA degradation proceed uncoupled from methanogenesis, accumulation of saturated LCFA can be expected. Analysis of the active microbial communities suggests a role for facultative anaerobic bacteria in the initial steps of unsaturated LCFA biodegradation. Understanding this role is now imperative to optimize methane production from LCFA.European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement No 323009, and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684), and Project RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-027462). We also thank the Gravitation grant (project 024.002.002) of the Netherlands Ministry of Education, Culture and Science and the Netherlands Science Foundation (NWO

Effect of sulfate and iron (III) on LCFA degradation by a methanogenic community

[Excerpt] Under anaerobic conditions long chain fatty acids (LCFA) can be converted to methane by syntrophic bacteria and methanogenic archaea. LCFA degradation was also reported in the presence of alternative hydrogenotrophic partners, such as sulfate-reducing bacteria (SRB) and iron-reducing bacteria (IRB), which generally show higher affinity for H2 than methanogens and are more resistant to LCFA [1,2,3]. Their presence in a microbial culture degrading LCFA can be advantageous to reduce LCFA toxicity towards methanogens, although high concentrations of external electron acceptor (EEA) can lead to outcompetition of methanogens and cease methane production. In this work, we tested the effect of adding sub-stoichiometric concentrations of sulfate and iron(III) to methanogenic communities degrading LCFA. (...