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Elevated serum IgE levels are associated with allergic disorders, parasitosis and specific immunologic abnormalities. In addition, epidemiological and mechanistic evidence indicates an association between IgE-mediated immune surveillance and protection from tumour growth. Intriguingly, recent studies reveal a correlation between IgE deficiency and increased malignancy risk. This is the first review discussing IgE levels and links to pathological conditions, with special focus on the potential clinical significance of ultra-low serum IgE levels and risk of malignancy. In this Position Paper we discuss: (a) the utility of measuring total IgE levels in the management of allergies, parasitosis, and immunodeficiencies, (b) factors that may influence serum IgE levels, (c) IgE as a marker of different disorders, and d) the relationship between ultra-low IgE levels and malignancy susceptibility. While elevated serum IgE is generally associated with allergic/atopic conditions, very low or absent IgE may hamper anti-tumour surveillance, indicating the importance of a balanced IgE-mediated immune function. Ultra-low IgE may prove to be an unexpected biomarker for cancer risk. Nevertheless, given the early stage of investigations conducted mostly in patients with diseases that influence IgE levels, in-depth mechanistic studies and stratification of malignancy risk based on associated demographic, immunological and clinical co-factors are warranted.

A selection of papers prepared by participants of 7th Young Scientists School SBB’15 is presented in three Supplementary Issues to the journals of BMC series, namely, BMC Genomics, BMC Genetics and BMC Microbiology. SBB’15 took place June 22nd-25th in Novosibirsk, Russia (http://conf.nsc.ru/sbb2015). The series of Young Scientists Schools in Systems Biology and Bioinformatics (SBB) started several years ago, in 2008, as educational workshop associated with the large international conference series on bioinformatics known as BGRS\SB (Bioinformatics of Genome Regulation and Structure\Systems Biology) (http://conf.bionet.nsc.ru/bgrssb2016). After its inauguration year of 1998, BGRS/SBB held biannually at the Institute of Cytology and Genetics SB RAS in Novosibirsk. In a recent decade, it became a prime meeting venue for biologists, computer scientists, physicists, mathematicians and biochemists working in an interdisciplinary field of systems biology and computer genomics. Being the largest system biology meeting series in Russia, BGRS\SB-14 attracted participants from 27 countries. In the past BioMedCentral had published series of special issues based on best materials presented at the conference in BMC Genomics (http://www.biomedcentral.com/bmcgenomics/supplements/15/S12), BMC Evolutionary Biology (http://www.biomedcentral.com/bmcevolbiol/supplements/15/S1), BMC Genetics (http://www.biomedcentral.com/bmcgenet/supplements/16/S1) and BMC Systems biology (http://www.biomedcentral.com/bmcsystbiol/supplements/9/S2). In addition, the protein structure related studies presented by BGRS/SBB participants were collated as special issues in Journal of Bioinformatics and Computational Biology (http://www.worldscientific.com/toc/jbcb/4113/01; http://www.worldscientific.com/toc/jbcb/11/01). [1] In addition, the SBB School series has its own history to be proud of. The first generation of its participants already matured enough to substantially advance in the field. A majority of the participants graduated with PhDs, and now are contributing to the school as the lecturers and to a number of world universities as professors. For some students, the conference became instrumental in obtaining their post-doc or first independent position in academic world. In many cases, the informal atmosphere of the school helped to spark a collaboration that later led to publications in leading journals or the dramatic changes in their science career. The Program Committee of the conference and SBB Schools series includes data analysis, bioinformatics and computational biology professionals from different countries. For the last decade, the SBB conference was co-chaired by Academician Prof. Nikolay A. Kolchanov of the Institute of Cytology and Genetics SB RAS, Russia and Prof. Dr. Ralf Hofestadt of Bielefeld University, Germany. System biology and bioinformatics are rapidly developing and wide fields of science knowledge. For Young Scientists Schools, every year is different as it comprises the topics for the trainings that are the hottest at the time of the event. In 2015, the SBB School concentrated on the modern genomics and an analysis of high-throughput sequencing data. The materials presented in the current special issue provide examples of seamless integration of experimental studies performed in the lab and the computer-assisted inquiries into in the complex patterns of the organization and the functioning of biologic systems at the molecular, cell, tissue, organ, and body levels. The scientific topics discussed in 2015 were presented at the following sections: Next generation sequencing (NGS) and data analysis Evolutionary bioinformatics Systems biology and gene network modeling In SBB’15 Supplements to BMC journals Genomics, we collected the best studies presented at the conference. Due to the general breadth of the field of Systems Biology and Bioinformatic, the manuscripts were accepted into three separate tracks, thus forming three Supplementary Issues, BMC Genomics, BMC Genetics and BMC Microbiology. Below we will describe contents of these issues.

Background Validated Internet-based screening tools for cannabis use and abuse are needed. The present study aimed to establish equivalence between the previously validated Alcohol, Smoking and Substance Involvement Screening Test (ASSIST) as a paper-and-pencil (PaP)-administered questionnaire and its online use. Methods Two groups of cannabis users took part in this study and the results were analyzed using structural equation modeling. One group consisted of 150 participants and was assessed with the ASSIST PaP questionnaire in a face-to-face interview (the PaP group). They were recruited from three settings: a primary health care outpatient clinic, a general psychiatric facility, and an ambulatory specialized addiction treatment facility. The other group (the Web group) comprised 1382 persons who answered the online version of the same questionnaire. This sample was drawn from people who naturalistically visited a website dedicated to helping people with cannabis addiction. Results The internal consistency was good for the online questionnaire (0.74) and high for the already validated PaP questionnaire (0.91). The Web group, however, had higher scores on cannabis use than did the PaP group. The results show support for configural invariance, meaning that the one-factor structure was preserved across groups, although measurement equivalence between these two survey modes was not achieved. However, when the Web group was split into two random subsamples, measurement invariance was demonstrated between them by cross-validation. Conclusions Measurement equivalence was not achieved between the two survey modes. Nonetheless, subanalyses of the Web group demonstrated that the cannabis screening questions of the ASSIST can be used for online screening. Differences in ASSIST scores between samples may be due to the sensitive nature of the information surveyed, with possible underreporting in face-to-face interviews, or to the different characteristics of the Web group because of the specialized nature of the website.

Polysaccharides in carob fruit, including carob bean gum (also known as carob gum, locust bean gum) and carob fiber, are widely used in industries such as food, pharmaceuticals, paper, textile, oil well drilling and cosmetics. Carob bean gum is a galactomannan obtained from the seed endosperm of carob tree and the fiber is obtained by removing most of soluble carbohydrates in carob pulp by water extraction. Both the gum and fiber are beneficial to health for many diseases such as diabetes, bowel movements, heart disease and colon cancer. This article reviewed the composition, properties, food applications and health benefits of polysaccharides from carob fruit.

Background The global expansion of dengue (DENV), chikungunya (CHIKV), and Zika viruses (ZIKV) is having a serious impact on public health. Because these arboviruses are transmitted by the same mosquito species and co-circulate in the same area, a sensitive diagnostic assay that detects them together, with discrimination, is needed. Methods We present here a diagnostics panel based on reverse transcription-PCR amplification of viral RNA and an xMap Luminex architecture involving direct hybridization of PCRamplicons and virus-specific probes. Two DNA innovations (“artificially expanded genetic information systems”, AEGIS, and “self-avoiding molecular recognition systems”, SAMRS) increase the hybridization sensitivity on Luminex microspheres and PCR specificity of the multiplex assay compared to the standard approach (standard nucleotides). Results The diagnostics panel detects, if they are present, these viruses with a resolution of 20 genome equivalents (DENV1), or 10 (DENV3–4, CHIKV) and 80 (DENV2, ZIKV) genome equivalents per assay. It identifies ZIKV, CHIKV and DENV RNAs in a single infected mosquito, in mosquito pools comprised of 5 to 50 individuals, and mosquito saliva (ZIKV, CHIKV, and DENV2). Infected mosquitoes and saliva were also collected on a cationic surface (Q-paper), which binds mosquito and viral nucleic acids electrostatically. All samples from infected mosquitoes displayed only target-specific signals; signals from non-infected samples were at background levels. Conclusions Our results provide an efficient and multiplex tool that may be used for surveillance of emerging mosquito-borne pathogens which aids targeted mosquito control in areas at high risk for transmission. Electronic supplementary material The online version of this article (10.1186/s12879-019-3998-z) contains supplementary material, which is available to authorized users.

Background Lignin is a potential biorefinery feedstock for the production of value-added chemicals including vanillin. A huge amount of lignin is produced as a by-product of the paper industry, while cellulosic components of plant biomass are utilized for the production of paper pulp. In spite of vast potential, lignin remains the least exploited component of plant biomass due to its extremely complex and heterogenous structure. Several enzymes have been reported to have lignin-degrading properties and could be potentially used in lignin biorefining if their catalytic properties could be improved by enzyme engineering. The much needed improvement of lignin-degrading enzymes by high-throughput selection techniques such as directed evolution is currently limited, as robust methods for detecting the conversion of lignin to desired small molecules are not available. Results We identified a vanillin-inducible promoter by RNAseq analysis of Escherichia coli cells treated with a sublethal dose of vanillin and developed a genetically programmed vanillin-sensing cell by placing the ‘very green fluorescent protein’ gene under the control of this promoter. Fluorescence of the biosensing cell is enhanced significantly when grown in the presence of vanillin and is readily visualized by fluorescence microscopy. The use of fluorescence-activated cell sorting analysis further enhances the sensitivity, enabling dose-dependent detection of as low as 200 µM vanillin. The biosensor is highly specific to vanillin and no major response is elicited by the presence of lignin, lignin model compound, DMSO, vanillin analogues or non-specific toxic chemicals. Conclusions We developed an engineered E. coli cell that can detect vanillin at a concentration as low as 200 µM. The vanillin-sensing cell did not show cross-reactivity towards lignin or major lignin degradation products including vanillin analogues. This engineered E. coli cell could potentially be used as a host cell for screening lignin-degrading enzymes that can convert lignin to vanillin. Electronic supplementary material The online version of this article (doi:10.1186/s13068-017-0720-5) contains supplementary material, which is available to authorized users.

BackgroundRecent trends in bioprocessing have underlined the significance of lignocellulosic biomass conversions for biofuel production. These conversions demand at least 90% energy upgradation of cellulosic sugars to generate renewable drop-in biofuel precursors (Heff/C ~ 2). Chemical methods fail to achieve this without substantial loss of carbon; whereas, oleaginous biological systems propose a greener upgradation route by producing oil from sugars with 30% theoretical yields. However, these oleaginous systems cannot compete with the commercial volumes of vegetable oils in terms of overall oil yields and productivities. One of the significant challenges in the commercial exploitation of these microbial oils lies in the inefficient recovery of the produced oil. This issue has been addressed using highly selective oil capturing agents (OCA), which allow a concomitant microbial oil production and in situ oil recovery process.ResultsAdsorbent-based oil capturing agents were employed for simultaneous in situ oil recovery in the fermentative production broths.Yarrowia lipolytica, a model oleaginous yeast, was milked incessantly for oil production over 380 h in a media comprising of glucose as a sole carbon and nutrient source. This was achieved by continuous online capture of extracellular oil from the aqueous media and also the cell surface, by fluidizing the fermentation broth over an adsorbent bed of oil capturing agents (OCA). A consistent oil yield of 0.33 g per g of glucose consumed, corresponding to theoretical oil yield over glucose, was achieved using this approach. While the incorporation of the OCA increased the oil content up to 89% with complete substrate consumptions, it also caused an overall process integration.ConclusionThe nondisruptive oil capture mediated by an OCA helped in accomplishing a trade-off between microbial oil production and its recovery. This strategy helped in realizing theoretically efficient sugar-to-oil bioconversions in a continuous production process. The process, therefore, endorses a sustainable production of molecular drop-in equivalents through oleaginous yeasts, representing as an absolute microbial oil factory.

Background Reducing fresh water consumption and nutrient addition will be an effective way to reduce the whole cost of bioethanol production. On the other hand, treatment of biogas slurry derived from anaerobic digestion (AD), in which a great amount of nutrients is still left, costs too much to remove these pollutants. It would be beneficial for both digestate valorization and ethanol production if biogas slurry is used for producing bioethanol. However, both hyperosmosis and potential biotoxic components of the biogas slurry can severely inhibit fermentation. Results In this study, two rounds of atmospheric and room temperature plasma (ARTP) mutagenesis combined with adaptive laboratory evolution (ALE) were applied to improve the adaptability and genetic stability of Zymomonas mobilis in biogas slurry. Mutants D95 and S912 were identified. Growth of the mutants was remarkably improved in biogas slurry. The highest ethanol productivity reached 0.63 g/L/h which was 61.7% higher than ZM4 (0.39 g/L/h). Genomic re-sequencing results also revealed that single nucleic variations (SNVs) and Indels occurred in the mutants, which are likely related to inhibitor in biogas slurry and low pH tolerance. Conclusions Our study demonstrated that these mutant strains have great potential to produce ethanol using biogas slurry to replace fresh water and nutrients. Electronic supplementary material The online version of this article (10.1186/s13068-019-1463-2) contains supplementary material, which is available to authorized users.

Background During current submerged fermentation for microbial lipid production, the large-scale reactor operations inevitably consume substantial amounts of water and electricity for aeration, stirring, and temperature control and result in the operational costs almost exceeding the biodiesel value produced. Thus, developing a novel low-cost cultivation strategy is urgently needed by microbial lipid industry. Results The filamentous fungus Phanerochaete chrysosporium can synthesize and accumulate lipids via static solid cultivation. The conversion efficiency of substrates to lipids reaches 0.277 g/g substrate after optimization of the following cultivation factors: humidity, solid medium thickness, temperature, and rotary speed. The lipids obtained by static solid cultivation differ in component and relative content from those achieved by submerged cultivation. Laser scanning confocal microscopy reveals that numerous chlamydospores filled with lipids appear during static solid cultivation, and the fungal morphological change explains why static solid cultivation is superior in lipid yield compared with submerged fermentation. The genes coding the enzymes related to fatty acid elongation and degradation are differently expressed during static solid cultivation, which presents an answer to the appearance of abundant saturated long-chain fatty acids (93.6% in total fatty acids) in chlamydospores. In addition, engineering viability and cost–benefit analysis show that the conversion of wheat bran and glucose to lipid by the fungus is efficient. More importantly, the solid cultivation incurs only a small reactor operational cost because neither cooling water nor electrical equipment, including aerator, stirrer, and the temperature control system, is used. Conclusions This study developed a robust and cost-saving solid fermentation method without an aerator, stirrer, and temperature control system to produce microbial lipids using the chlamydospores of P. chrysosporium. Compared with conventional submerged fermentation, the solid cultivation strategy is promising because it diminishes most of the reactor operational costs, including water and power expenses. Electronic supplementary material The online version of this article (10.1186/s13068-019-1464-1) contains supplementary material, which is available to authorized users.

Background Commercial biogas upgrading facilities are expensive and consume energy. Biological biogas upgrading may serve as a low-cost approach because it can be easily integrated with existing facilities at biogas plants. The microbial communities found in anaerobic digesters typically contain hydrogenotrophic methanogens, which can use hydrogen (H2) as a reducing agent for conversion of carbon dioxide (CO2) into methane (CH4). Thus, biological biogas upgrading through the exogenous addition of H2 into biogas digesters for the conversion of CO2 into CH4 can increase CH4 yield and lower CO2 emission. Results The addition of 4 mol of H2 per mol of CO2 was optimal for batch biogas reactors and increased the CH4 content of the biogas from 67 to 94%. The CO2 content of the biogas was reduced from 33 to 3% and the average residual H2 content was 3%. At molar H2:CO2 ratios > 4:1, all CO2 was converted into CH4, but the pH increased above 8 due to depletion of CO2, which negatively influenced the process stability. Additionally, high residual H2 content in these reactors was unfavourable, causing volatile fatty acid accumulation and reduced CH4 yields. The reactor microbial communities shifted in composition over time, which corresponded to changes in the reactor variables. Numerous taxa responded to the H2 inputs, and in particular the hydrogenotrophic methanogen Methanobacterium increased in abundance with addition of H2. In addition, the apparent rapid response of hydrogenotrophic methanogens to intermittent H2 feeding indicates the suitability of biological methanation for variable H2 inputs, aligning well with fluctuations in renewable electricity production that may be used to produce H2. Conclusions Our research demonstrates that the H2:CO2 ratio has a significant effect on reactor performance during in situ biological methanation. Consequently, the H2:CO2 molar ratio should be kept at 4:1 to avoid process instability. A shift toward hydrogenotrophic methanogenesis was indicated by an increase in the abundance of the obligate hydrogenotrophic methanogen Methanobacterium. Electronic supplementary material The online version of this article (10.1186/s13068-019-1443-6) contains supplementary material, which is available to authorized users.

Background Recently, it has been indicated that anaerobic co-digestion of waste activated sludge with other waste streams at wastewater treatment plants is a promising strategy for enhancing methane production and materials recovery. The enhanced methane production can be used as a renewable source of energy in wastewater treatment plants. It can also reduce the amount of greenhouse gas emission in landfilling of the waste streams. Results According to the results obtained in this study, anaerobic co-digestion of waste activated sludge with mixed fruit waste and cheese whey improves methane production and the quality of digested sludge in comparison to the anaerobic digestion of waste activated sludge individually. It was indicated that carbon/nitrogen ratio (C/N) in the mixture of waste activated sludge, fruit waste and cheese whey improved considerably, leading to better anaerobic organisms’ activity during digestion. With assessing the activity of protease and cellulase, as the main enzymes hydrolyzing organic matter in anaerobic digestion, it was indicated that co-digestion of waste activated sludge with mixed fruit waste and cheese whey enhances the activity of these enzymes by 22 and 9% respectively. At the end of digestion, the amount of cumulative methane production significantly increased by 31% in the reactor with 85% waste activated sludge and 15% mixed fruit waste and cheese whey, compared to the reactor with 100% waste activated sludge. In addition, chemical oxygen demand (COD) and volatile solid (VS) in digested sludge was improved respectively by 9 and 7% when mixed fruit waste and cheese whey was used. Conclusions This study revealed that mixed fruit waste and cheese whey is potentially applicable to anaerobic digestion of waste activated sludge, as fruit waste and cheese whey have high C/N ratio that enhance low C/N in waste activated sludge and provide a better diet for anaerobic organisms. This is of significant importance because not only could higher amount of renewable energy be generated from the enhanced methane production in wastewater treatment plants, but also capital costs of the companies whose waste streams are being transported to wastewater treatments plants could be reduced considerably. Electronic supplementary material The online version of this article (10.1186/s12896-019-0513-y) contains supplementary material, which is available to authorized users.

Background The industrial conversion of biomass to high-value biofuels and biochemical is mainly restricted by lignocellulose solubilization. Consolidated bio-saccharification (CBS) is considered a promising process for lignocellulose solubilization depending on whole-cell biocatalysts that simultaneously perform effective cellulase production and hydrolysis. However, it usually takes a long time to reach a high saccharification level using the current CBS biocatalyst and process. Results To promote the saccharification efficiency and reduce the cost, a Clostridium thermocellum recombinant strain ∆pyrF::KBm was constructed as a new CBS biocatalyst in this study. The key CBS factors, including the medium, inoculum size and cultivation, and substrate load, were investigated and optimized. The saccharification process was also stimulated by adding free hemicellulases, suggesting the need to further enhance hemicellulase activity of the whole-cell catalyst. Under the optimal conditions, the CBS process was shortened by 50% with pretreated wheat straw as the substrate. The sugar yield reached 0.795 g/g and the saccharification level was 89.3%. Conclusions This work provided a new biocatalyst and an optimized process of CBS and confirmed that CBS is a feasible strategy for cost-efficient solubilization of lignocellulose, which will greatly promote the industrial utilization of lignocellulosic biomass. Electronic supplementary material The online version of this article (10.1186/s13068-019-1374-2) contains supplementary material, which is available to authorized users.

International audience; AbstractMycobacterium avium subspecies paratuberculosis (Map) is the cause of Johne’s disease, a chronic enteritis of cattle. A significant knowledge gap is how persistence of Map within the intestinal tract after infection contributes to progression of disease. To address this, we exposed calves to Map by direct ileocecal Peyer’s patch injection. Our objective was to characterize the persistence of Map in tissues, associated intestinal lesions, fecal Map shedding, and serum antibody responses, through the first 28-weeks post-inoculation (wpi). Previous work using this model showed 100% rate of Map infection in intestine and lymph node by 12 wpi. We hypothesized that direct inoculation of Map into the distal small intestine would induce intestinal Map infection with local persistence and progression towards clinical disease. However, our data show decreased persistence of Map in the distal small intestine and draining lymph nodes. We identified Map in multiple sections of distal ileum and draining lymph node of all calves at 4 and 12 wpi, but then we observed reduced Map in distal ileum at 20 wpi, and by 28 wpi we found that 50% of animals had no detectable Map in intestine or the lymph node. This provides evidence of resilience to Map infection following direct intestinal Map inoculation. Further work examining the immune responses and host–pathogen interactions associated with this infection model are needed to help elicit the mechanisms underlying resilience to Map infection.

Background In this study, a two-step processing method (hydrothermal liquefaction followed by catalytic upgrading) was used to produce upgraded bio-oil. A comprehensive screening analysis of algal species, including four microalgae and four macroalgae, was conducted to bridge the gap between previous accounts of microalgae and macroalgae hydrothermal liquefaction and the upgrading process of the resulting crude bio-oils. Results Hydrothermal liquefaction using eight algal biomasses was performed at 350 °C for 1 h. The microalgae always produced a higher crude bio-oil yield than the macroalgae due to their high lipid content, among which Schizochytrium limacinum provided the maximum crude bio-oil yield of 54.42 wt%. For microalgae, higher amounts of N in the biomass resulted in higher amounts of N in the crude bio-oil; however, contrary results were observed for the macroalgae. The crude bio-oils generated from both the microalgae and macroalgae were characterized as having a high viscosity, total acid number, and heteroatom content, and they were influenced by the biochemical compositions of the feedstocks. Next, all eight-crude bio-oils were treated at 400 °C for 2 h with 10 wt% Ru/C using tetralin as the hydrogen donor. The hydrogen source was provided after tetralin was transformed to naphthalene. All the upgraded bio-oils had higher energy densities and significantly lower N, O, and S contents and viscosities than their corresponding crude bio-oils. However, the H/C molar ratio of the upgraded bio-oils decreased due to the absence of external hydrogen relative to the crude bio-oils. The S content of the upgraded bio-oil produced from upgrading the Schizochytrium limacinum crude bio-oil was even close to the 50 ppm requirement of China IV diesel. Conclusions Microalgae are better feedstocks than macroalgae for liquid fuel production. Biochemical components have a significant impact on the yield and composition of crude bio-oil. Tetralin does not perform as well as external hydrogen for controlling coke formation. The S content of the upgraded bio-oil can be reduced to 76 ppm for the crude bio-oil produced from Schizochytrium limacinum. Upgraded bio-oils have similar properties to those of naphtha and jet fuel. Electronic supplementary material The online version of this article (10.1186/s13068-018-1083-2) contains supplementary material, which is available to authorized users.

Background Environmental issues, such as the fossil energy crisis, have resulted in increased public attention to use bioethanol as an alternative renewable energy. For ethanol production, water and nutrient consumption has become increasingly important factors being considered by the bioethanol industry as reducing the consumption of these resources would decrease the overall cost of ethanol production. Biogas slurry contains not only large amounts of wastewater, but also the nutrients required for microbial growth, e.g., nitrogen, ammonia, phosphate, and potassium. Therefore, biogas slurry is an attractive potential resource for bioethanol production that could serve as an alternative to process water and nitrogen sources. Results In this study, we propose a method that replaces the process water and nitrogen sources needed for cellulosic ethanol production by Zymomonas mobilis with biogas slurry. To test the efficacy of these methods, corn straw degradation following pretreatment with diluted NaOH and enzymatic hydrolysis in the absence of fresh water was evaluated. Then, ethanol fermentation using the ethanologenic bacterial strain Z. mobilis ZMT2 was conducted without supplementing with additional nitrogen sources. After pretreatment with 1.34% NaOH (w/v) diluted in 100% biogas slurry and continuous enzymatic hydrolysis for 144 h, 29.19 g/L glucose and 12.76 g/L xylose were generated from 30 g dry corn straw. The maximum ethanol concentration acquired was 13.75 g/L, which was a yield of 72.63% ethanol from the hydrolysate medium. Nearly 94.87% of the ammonia nitrogen was depleted and no nitrate nitrogen remained after ethanol fermentation. The use of biogas slurry as an alternative to process water and nitrogen sources may decrease the cost of cellulosic ethanol production by 10.0–20.0%. By combining pretreatment with NaOH diluted in biogas slurry, enzymatic hydrolysis, and ethanol fermentation, 56.3 kg of ethanol was produced by Z. mobilis ZMT-2 through fermentation of 1000 kg of dried corn straw. Conclusions In this study, biogas slurry replaced process water and nitrogen sources during cellulosic ethanol production. The results suggest that biogas slurry is a potential alternative to water when pretreating corn straw and, thus, has important potential applications in cellulosic ethanol production from corn straw. This study not only provides a novel method for utilizing biogas slurry, but also demonstrates a means of reducing the overall cost of cellulosic ethanol.

Background Single cell oil (SCO) production from lignocelluloses by oleaginous microorganisms is still high in production cost, making the subsequent production of biofuels inviable economically in such an era of low oil prices. Therefore, how to upgrade the final products of lignocellulose-based bioprocess to more valuable ones is becoming a more and more important issue. Results Differently sourced cellulases were compared in the enzymatic hydrolysis of the steam-exploded corn stover (SECS) and the cellulase from the mixed culture of Trichoderma reesei and Aspergillus niger was found to have the highest enzymatic hydrolysis yield 86.67 ± 4.06%. Three-stage enzymatic hydrolysis could greatly improve the efficiency of the enzymatic hydrolysis of SECS, achieving a yield of 74.24 ± 2.69% within 30 h. Different bioprocesses from SECS to SCO were compared and the bioprocess C with the three-stage enzymatic hydrolysis was the most efficient, producing 57.15 g dry cell biomass containing 31.80 g SCO from 327.63 g SECS. An efficient and comprehensive process from corn stover to long-chain α,ω-dicarboxylic acids (DCAs) was established by employing self-metathesis, capable of producing 6.02 g long-chain DCAs from 409.54 g corn stover and 6.02 g alkenes as byproducts. Conclusions On-site cellulase production by the mixed culture of T. reesei and A. niger is proven the most efficient in providing cellulase to the lignocellulose-based bioprocess. Three-stage enzymatic hydrolysis was found to have very good application value in SCO production by Trichosporon cutaneum from SECS. A whole process from corn stover to long-chain DCAs via a combination of biological and chemical approaches was successfully established and it is an enlightening example of the comprehensive utilization of agricultural wastes.

Background Recent advances in the development of enzyme cocktails for degradation of lignocellulosic biomass, especially the discovery of lytic polysaccharide monooxygenases (LPMOs), have opened new perspectives for process design and optimization. Softwood biomass is an abundant resource in many parts of the world, including Scandinavia, but efficient pretreatment and subsequent enzymatic hydrolysis of softwoods are challenging. Sulfite pulping-based pretreatments, such as in the BALI™ process, yield substrates that are relatively easy to degrade. We have assessed how process conditions affect the efficiency of modern cellulase preparations in processing of such substrates. Results We show that efficient degradation of sulfite-pulped softwoods with modern, LPMO-containing cellulase preparations requires the use of conditions that promote LPMO activity, notably the presence of molecular oxygen and sufficient reducing power. Under LPMO activity-promoting conditions, glucan conversion after 48-h incubation with Cellic® CTec3 reached 73.7 and 84.3% for Norway spruce and loblolly pine, respectively, at an enzyme loading of 8 mg/g of glucan. The presence of free sulfite ions had a negative effect on hydrolysis efficiency. Lignosulfonates, produced from lignin during sulfite pretreatment, showed a potential to activate LPMOs. Spiking of Celluclast®, a cellulase cocktail with low LPMO activity, with monocomponent cellulases or an LPMO showed that the addition of the LPMO was clearly more beneficial than the addition of any classical cellulase. Addition of the LPMO in reactions with spruce increased the saccharification yield from approximately 60% to the levels obtained with Cellic® CTec3. Conclusions In this study, we have demonstrated the importance of LPMOs for efficient enzymatic degradation of sulfite-pulped softwood. We have also shown that to exploit the full potential of LPMO-rich cellulase preparations, conditions promoting LPMO activity, in particular the presence of oxygen and reducing equivalents are necessary, as is removal of residual sulfite from the pretreatment step. The use of lignosulfonates as reductants may reduce the costs related to the addition of small molecule reductants in sulfite pretreatment-based biorefineries. Electronic supplementary material The online version of this article (doi:10.1186/s13068-017-0862-5) contains supplementary material, which is available to authorized users.

Background: Molasses is a dense and saline by-product of the sugar agroindustry. Its high organic content potentially fuels a myriad of renewable products of industrial interest. However, the biotechnological exploitation of molasses is mainly hampered by the high concentration of salts, an issue that is nowadays tackled through dilution. In the present study, the performance of microbial communities derived from marine sediment was compared to that of communities from a terrestrial environment (anaerobic digester sludge). The aim was to test whether adaptation to salinity represented an advantage for fermenting molasses into renewable chemicals such as volatile fatty acids (VFAs) although high sugar concentrations are uncommon to marine sediment, contrary to anaerobic digesters. Results: Terrestrial and marine microbial communities were enriched in consecutive batches at different initial pH values (pHi; either 6 or 7) and molasses dilutions (equivalent to organic loading rates (OLRs) of 1 or 5 gCOD L-1 d-1) to determine the best VFA production conditions. Marine communities were supplied with NaCl to maintain their native salinity. Due to molasses inherent salinity, terrestrial communities experienced conditions comparable to brackish or saline waters (20-47 mS cm-1), while marine conditions resembled brine waters (>47 mS cm-1). Enrichments at optimal conditions of OLR 5 gCOD L-1 d-1 and pHi 7 were transferred into packed-bed biofilm reactors operated continuously. The reactors were first operated at 5 gCOD L-1 d-1, which was later increased to OLR 10 gCOD L-1 d-1. Terrestrial and marine reactors had different gas production and community structures but identical, remarkably high VFA bioconversion yields (above 85%) which were obtained with conductivities up to 90 mS cm-1. COD-to-VFA conversion rates were comparable to the highest reported in literature while processing other organic leftovers at much lower salinities. Conclusions: Although salinity represents a major driver for microbial community structure, proper acclimation yielded highly efficient systems treating molasses, irrespective of the inoculum origin. Selection of equivalent pathways in communities derived from different environments suggests that culture conditions select for specific functionalities rather than microbial representatives. Mass balances, microbial community composition, and biochemical analysis indicate that biomass turnover rather than methanogenesis represents the main limitation to further increasing VFA production with molasses. This information is relevant to moving towards molasses fermentation to industrial application.

Laccase (p-diphenol:dioxygen oxidoreductase, EC 1.10.3.2) is a member of the multicopper oxidases and catalyzes the one-electron oxidation of a wide range of substrates, coupled with the reduction of oxygen to water. It is widely distributed in bacteria, fungi, plants and insects. Laccases are encoded by multigene family, and have been characterized mostly from fungi till now, with abundant industrial applications in pulp and paper, textile, food industries, organic synthesis, bioremediation and nanobiotechnology, while limited researches have been performed in plants, and no application has been reported. Plant laccases share the common molecular architecture and reaction mechanism with fungal ones, despite of difference in redox potential and pH optima. Plant laccases are implicated in lignin biosynthesis since genetic evidence was derived from the Arabidopsis LAC4 and LAC17. Manipulation of plant laccases has been considered as a promising and innovative strategy in plant biomass engineering for desirable lignin content and/or composition, since lignin is the major recalcitrant component to saccharification in biofuel production from lignocellulose, and therefore directly limits the fermentation yields. Moreover, plant laccases have been reported to be involved in wound healing, maintenance of cell wall structure and integrity, and plant responses to environmental stresses. Here, we summarize the properties and functions of plant laccase, and discuss the potential of biotechnological application, thus providing a new insight into plant laccase, an old enzyme with a promising beginning in lignocellulose biofuel production. Electronic supplementary material The online version of this article (doi:10.1186/s13068-015-0331-y) contains supplementary material, which is available to authorized users.

Background DNA copy number profiles from microarray and sequencing experiments sometimes contain wave artefacts which may be introduced during sample preparation and cannot be removed completely by existing preprocessing methods. Besides, large derivative log ratio spread (DLRS) of the probes correlating with poor DNA quality is sometimes observed in genome screening experiments and may lead to unreliable copy number profiles. Depending on the extent of these artefacts and the resulting misidentification of copy number alterations/variations (CNA/CNV), it may be desirable to exclude such samples from analyses or to adapt the downstream data analysis strategy accordingly. Results Here, we propose a method to distinguish reliable genomic copy number profiles from those containing heavy wave artefacts and/or large DLRS. We define four features that adequately summarize the copy number profiles for reliability assessment, and train a classifier on a dataset of 1522 copy number profiles from various microarray platforms. The method can be applied to predict the reliability of copy number profiles irrespective of the underlying microarray platform and may be adapted for those sequencing platforms from which copy number estimates could be computed as a piecewise constant signal. Further details can be found at https://github.com/baudisgroup/CNARA. Conclusions We have developed a method for the assessment of genomic copy number profiling data, and suggest to apply the method in addition to and after other state-of-the-art noise correction and quality control procedures. CNARA could be instrumental in improving the assessment of data used for genomic data mining experiments and support the reliable functional attribution of copy number aberrations especially in cancer research. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3074-7) contains supplementary material, which is available to authorized users.

Background Biohythane is a new and high-value transportation fuel present as a mixture of biomethane and biohydrogen. It has been produced from different organic matters using anaerobic digestion. Bioenergy can be recovered from waste activated sludge through methane production during anaerobic digestion, but energy yield is often insufficient to sludge disposal. Microbial electrolysis cell (MEC) is also a promising approach for bioenergy recovery and waste sludge disposal as higher energy efficiency and biogas production. The systematic understanding of microbial interactions and biohythane production in MEC is still limited. Here, we report biohythane production from waste sludge in biocathode microbial electrolysis cells and reveal syntrophic interactions in microbial communities based on high-throughput sequencing and quantitative PCR targeting 16S rRNA gene. Results The alkali-pretreated sludge fed MECs (AS-MEC) showed the highest biohythane production rate of 0.148 L·L−1-reactor·day−1, which is 40 and 80 % higher than raw sludge fed MECs (RS-MEC) and anaerobic digestion (open circuit MEC, RS-OCMEC). Current density, metabolite profiles, and hydrogen-methane ratio results all confirm that alkali-pretreatment and microbial electrolysis greatly enhanced sludge hydrolysis and biohythane production. Illumina Miseq sequencing of 16S rRNA gene amplicons indicates that anode biofilm was dominated by exoelectrogenic Geobacter, fermentative bacteria and hydrogen-producing bacteria in the AS-MEC. The cathode biofilm was dominated by fermentative Clostridium. The dominant archaeal populations on the cathodes of AS-MEC and RS-MEC were affiliated with hydrogenotrophic Methanobacterium (98 %, relative abundance) and Methanocorpusculum (77 %), respectively. Multiple pathways of gas production were observed in the same MEC reactor, including fermentative and electrolytic H2 production, as well as hydrogenotrophic methanogenesis and electromethanogenesis. Real-time quantitative PCR analyses showed that higher amount of methanogens were enriched in AS-MEC than that in RS-MEC and RS-OCMEC, suggesting that alkali-pretreated sludge and MEC facilitated hydrogenotrophic methanogen enrichment. Conclusion This study proves for the first time that biohythane could be produced directly in biocathode MECs using waste sludge. MEC and alkali-pretreatment accelerated enrichment of hydrogenotrophic methanogen and hydrolysis of waste sludge. The results indicate syntrophic interactions among fermentative bacteria, exoelectrogenic bacteria and methanogenic archaea in MECs are critical for highly efficient conversion of complex organics into biohythane, demonstrating that MECs can be more competitive than conventional anaerobic digestion for biohythane production using carbohydrate-deficient substrates. Biohythane production from waste sludge by MEC provides a promising new way for practical application of microbial electrochemical technology. Electronic supplementary material The online version of this article (doi:10.1186/s13068-016-0579-x) contains supplementary material, which is available to authorized users.

Background Anaerobic digesters become unstable when operated at a high organi c loading rate (OLR). Investigating the microbial community response to OLR disturbance is helpful for achieving efficient and stable process operation. However, previous studies have only focused on community succession during different process stages. How does community succession influence process stability? Is this kind of succession resilient? Are any key microbial indicator closely related to process stability? Such relationships between microbial communities and process stability are poorly understood. Results In this study, a mesophilic anaerobic digester for treating food waste (FW) was operated to study the microbial diversity and dynamicity due to OLR disturbance. Overloading resulted in proliferation of acidogenic bacteria, and the resulting high volatile fatty acid (VFA) yield triggered an abundance of acetogenic bacteria. However, the abundance and metabolic efficiency of hydrogenotrophic methanogens decreased after disturbance, and as a consequence, methanogens and acetogenic bacteria could not efficiently complete the syntrophy. This stress induced the proliferation of homoacetogens as alternative hydrogenotrophs for converting excessive H2 to acetate. However, the susceptible Methanothrix species also failed to degrade the excessive acetate. This metabolic imbalance finally led to process deterioration. After process recovery, the digester gradually returned to its original operational conditions, reached close to its original performance, and the microbial community profile achieved a new steady-state. Interestingly, the abundance of Syntrophomonas and Treponema increased during the deteriorative stage and rebounded after disturbance, suggesting they were resilient groups. Conclusions Acidogenic bacteria showed high functional redundancy, rapidly adapted to the increased OLR, and shaped new microbial community profiles. The genera Syntrophomonas and Treponema were resilient groups. This observation provides insight into the key microbial indicator that are closely related to process stability. Moreover, the succession of methanogens during the disturbance phase was unsuitable for the metabolic function needed at high OLR. This contradiction resulted in process deterioration. Thus, methanogenesis is the main step that interferes with the stable operation of digesters at high OLR. Further studies on identifying and breeding high-efficiency methanogens may be helpful for breaking the technical bottleneck of process instability and achieving stable operation under high OLR.

Background Emerging evidence suggests beneficial effects of omega-3 fatty acids on diabetic complications. The present study compared the progressive effects of metformin and flax/fish oil on lipid metabolism, inflammatory markers, and liver and renal function test markers in streptozotocin-nicotinamide-induced diabetic rats. Methods Streptozotocin-induced diabetic rats were randomized into control and four diabetic groups: streptozotocin (STZ), metformin (200 mg/kg body weight (b.w)/day (D)), flax and fish oil (500 mg/kg b.w/D). Results Metformin and flax and fish oil exhibited increased expression of transcription factor peroxisome proliferator-activated receptor γ while the treatment downregulated sterol regulatory element-binding protein 1 and nuclear factor kβ as compared to those of the STZ group. Apart from modulation of transcription factor expression, the expression of fatty acid synthase, long chain acyl CoA synthase, and malonyl-CoA-acyl carrier protein transacylase was lowered by flax/fish oil treatment. Serum cholesterol, triglycerides, and VLDL were also significantly reduced in the treatment groups as compared to those in the STZ group. Although pathological abnormalities were seen in the liver and kidneys of rats on metformin, no significant changes in liver/renal function markers were observed at day 15 and day 30 of the treatment groups. Flax/fish oil had protective effects toward pathological abnormalities in the liver and kidney. Flax/fish oil improved lipid profile and alkaline phosphatase at day 30 as compared to that at day 15. Conclusions The present study demonstrates potential beneficial effects of metformin and flax/fish oil intervention in improving serum lipid profile by regulating the expression of transcription factors and genes involved in lipid metabolism in diabetic rats. In addition, these interventions also lowered the expression of atherogenic cytokines. The protective effects of flax/fish oil are worth investigating in human subjects on metformin monotherapy.

Background: Marine long-chain polyunsaturated fatty acids are susceptible to oxidation, generating a range of different oxidation products with suggested negative health effects. The aim of the present study was to utilize sensitive high-throughput transcriptome analyses to investigate potential unfavorable effects of oxidized fish oil (PV: 18 meq/kg; AV: 9) compared to high-quality fish oil (PV: 4 meq/kg; AV: 3). Methods: In a double-blinded randomized controlled study for seven weeks, 35 healthy subjects were assigned to 8 g of either oxidized fish oil or high quality fish oil. The daily dose of EPA+DHA was 1.6 g. Peripheral blood mononuclear cells were isolated at baseline and after 7 weeks and transcriptome analyses were performed with the illuminaHT-12 v4 Expression BeadChip. Results: No gene transcripts, biological processes, pathway or network were significantly changed in the oxidized fish oil group compared to the fish oil group. Furthermore, gene sets related to oxidative stress and cardiovascular disease were not differently regulated between the groups. Within group analyses revealed a more prominent effect after intake of high quality fish oil as 11 gene transcripts were significantly (FDR < 0.1) changed from baseline versus three within the oxidized fish oil group. Conclusion: The suggested concern linking lipid oxidation products to short-term unfavorable health effects may therefore not be evident at a molecular level in this explorative study. © 2016 The Author(s). This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Background Methane is a feedstock of interest for the future, both from natural gas and from renewable biogas sources. Methanotrophic bacteria have the potential to enable commercial methane bioconversion to value-added products such as fuels and chemicals. A strain of interest for such applications is Methylomicrobium buryatense 5GB1, due to its robust growth characteristics. However, to take advantage of the potential of this methanotroph, it is important to generate comprehensive bioreactor-based datasets for different growth conditions to compare bioprocess parameters. Results Datasets of growth parameters, gas utilization rates, and products (total biomass, extracted fatty acids, glycogen, excreted acids) were obtained for cultures of M. buryatense 5GB1 grown in continuous culture under methane limitation and O2 limitation conditions. Additionally, experiments were performed involving unrestricted batch growth conditions with both methane and methanol as substrate. All four growth conditions show significant differences. The most notable changes are the high glycogen content and high formate excretion for cells grown on methanol (batch), and high O2:CH4 utilization ratio for cells grown under methane limitation. Conclusions The results presented here represent the most comprehensive published bioreactor datasets for a gamma-proteobacterial methanotroph. This information shows that metabolism by M. buryatense 5GB1 differs significantly for each of the four conditions tested. O2 limitation resulted in the lowest relative O2 demand and fed-batch growth on methane the highest. Future studies are needed to understand the metabolic basis of these differences. However, these results suggest that both batch and continuous culture conditions have specific advantages, depending on the product of interest. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0372-8) contains supplementary material, which is available to authorized users.

Pollution associated with crude oil (CO) extraction degrades the quality of waters, threatens drinking water sources and may ham air quality. The systems biology approach aims at learning the kinetics of substrate utilization and bacterial growth for a biological process for which very limited knowledge is available. This study uses the Pseudomonas aeruginosa to degrade CO and determines the kinetic parameters of substrate utilization and bacterial growth modeled from a completely mixed batch reactor. The ability of Pseudomonas aeruginosa can remove 91 % of the total petroleum hydrocarbons and 83 % of the aromatic compounds from oily environment. The value k of 9.31 g of substrate g(-1) of microorganism d(-1) could be far higher than the value k obtained for petrochemical wastewater treatment and that for municipal wastewater treatment. The production of new cells of using CO as the sole carbon and energy source can exceed 2(3) of the existing cells per day. The kinetic parameters are verified to contribute to improving the biological removal of CO from oily environment.

Background Cellulosic biomass especially agricultural/wood residues can be utilized as feedstock to cost-effectively produce fuels, chemicals and bulk industrial enzymes, which demands xylose utilization from microbial cell factories. While previous works have made significant progress in improving microbial conversion of xylose into fuels and chemicals, no study has reported the engineering of efficient xylose utilizing protein expression systems for the purpose of producing industrial enzymes. Results In this work, using Pichia pastoris as an example, we demonstrated the successful engineering of xylose metabolizing ability into of protein expression systems. A heterologous XI (xylose isomerase) pathway was introduced into P. pastoris GS115 by overexpressing the Orpinomyces spp. XI or/and the endogenous XK (xylulokinase) gene, and evolutionary engineering strategies were also applied. Results showed that the XI pathway could be functionally expressed in P. pastoris. After 50 generation of sequential batch cultivation, a set of domesticated recombinant P. pastoris strains with different performance metrics on xylose were obtained. One evolved strain showed the highest xylose assimilation ability, whose cell yield on xylose can even be comparable to that on glucose or glycerol. This strain also showed significantly increased β-mannanase production when cultured on xylose medium. Furthermore, transcription analysis of xylose pathway genes suggested that overexpression of XI and XK might be the key factors affecting effective xylose assimilation. Conclusions To our best knowledge, this study is the first work demonstrating the construction of efficient xylose utilizing P. pastoris strains, thus providing a basis for using cellulosic biomass for bulk industrial enzyme production.

Background Caldicellulosiruptor species have gained a reputation as being among the best microorganisms to produce hydrogen (H2) due to possession of a combination of appropriate features. However, due to their low volumetric H2 productivities (QH2), Caldicellulosiruptor species cannot be considered for any viable biohydrogen production process yet. In this study, we evaluate biofilm forming potential of pure and co-cultures of Caldicellulosiruptor saccharolyticus and Caldicellulosiruptor owensensis in continuously stirred tank reactors (CSTR) and up-flow anaerobic (UA) reactors. We also evaluate biofilms as a means to retain biomass in the reactor and its influence on QH2. Moreover, we explore the factors influencing the formation of biofilm. Results Co-cultures of C. saccharolyticus and C. owensensis form substantially more biofilm than formed by C. owensensis alone. Biofilms improved substrate conversion in both of the reactor systems, but improved the QH2 only in the UA reactor. When grown in the presence of each other’s culture supernatant, both C. saccharolyticus and C. owensensis were positively influenced on their individual growth and H2 production. Unlike the CSTR, UA reactors allowed retention of C. saccharolyticus and C. owensensis when subjected to very high substrate loading rates. In the UA reactor, maximum QH2 (approximately 20 mmol · L−1 · h−1) was obtained only with granular sludge as the carrier material. In the CSTR, stirring negatively affected biofilm formation. Whereas, a clear correlation was observed between elevated (>40 μM) intracellular levels of the secondary messenger bis-(3′-5′)-cyclic dimeric guanosine monophosphate (c-di-GMP) and biofilm formation. Conclusions In co-cultures C. saccharolyticus fortified the trade of biofilm formation by C. owensensis, which was mediated by elevated levels of c-di-GMP in C. owensensis. These biofilms were effective in retaining biomass of both species in the reactor and improving QH2 in a UA reactor using granular sludge as the carrier material. This concept forms a basis for further optimizing the QH2 at laboratory scale and beyond. Electronic supplementary material The online version of this article (doi:10.1186/s13068-015-0201-7) contains supplementary material, which is available to authorized users.

Indigenous microflora community changes during six months of co-composting of activated sewage sludge and date palm waste was investigated using two different culture approaches. In order to evaluate the co-composting process evolution for mixture A and B, growth standard media (GSM) and Compost Time Extract Agar (CTEA) are used. Enumeration for indigenous flora abundance on GSM medium shows that the colony-forming unit (CFU) total number was 100 fold higher than on CTEA. The thermophilic phase is determined at 30 day for both mixtures A and B. Nevertheless this stage is limited only at 22 and 30 days, respectively for mixture A and B on CTEA medium, which indicate a similar temperature profile at versus time of co-composting. The results suggest that the GSM medium approach can be used for monitoring the microbial cultivable presence. However, CTEA act as a natural selective medium to enumerate the indigenous functional microflora. This technique was successful in assessing the process evolution and determination of a real succession thermophilic and maturation co-composting stages.