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Continuous discharge of lignin containing colored wastewater from pulp paper mill into the environment has resulted in building up their high level in various aquatic systems. In this study, the chemical texture of kraft lignin in terms of pollution parameters (COD, TOC, BOD, etc.) was quite different and approximately twofold higher as compared to model lignin at same optical density (OD 3.7 at 465 nm) and lignin content (2000 mg/L). For comparative bacterial degradation and detoxification of model and kraft lignin two bacteria Citrobacter freundii and Serratia marcescens were isolated, screened and applied in axenic and mixed condition. Bacterial mixed culture was found to decolorize 87 and 70 % model and kraft lignin (2000 mg/L), respectively; whereas, axenic culture Citrobacter freundii and Serratia marcescens decolorized 64, 60 % model and 50, 55 % kraft lignin, respectively, at optimized condition (34 °C, pH 8.2, 140 rpm). In addition, the mixed bacterial culture also showed the removal of 76, 61 % TOC; 80, 67 % COD and 87, 65 % lignin from model and kraft lignin, respectively. High pollution parameters (like TOC, COD, BOD, sulphate) and toxic chemicals slow down the degradation of kraft lignin as compared to model lignin. The comparative GC–MS analysis has suggested that the interspecies collaboration, i.e., each bacterial strain in culture medium has cumulative enhancing effect on growth, and degradation of lignin rather than inhibition. Furthermore, toxicity evaluation on human keratinocyte cell line after bacterial treatment has supported the degradation and detoxification of model and kraft lignin.

Background Most studies on the paper mulberry are mainly focused on the medicated and pharmacology, fiber quality, leaves feed development, little is known about its mechanism of adaptability to abiotic stress. Physiological measurement, transcriptomics and proteomic analysis were employed to understand its response to cold stress in this study. Methods The second to fourth fully expanded leaves from up to down were harvested at different stress time points forthe transmission electron microscope (TEM) observation. Physiological characteristics measurement included the relative electrolyte leakage (REL), SOD activity assay, soluble sugar content, and Chlorophyll fluorescence parameter measurement. For screening of differentially expressed genes, the expression level of every transcript in each sample was calculated by quantifying the number of Illumina reads. To identify the differentially expressed protein, leaves of plants under 0, 6, 12, 24, 48 and 72 h cold stress wereharvested for proteomic analysis. Finally, real time PCR was used to verify the DEG results of the RNA-seq and the proteomics data. Results Results showed that at the beginning of cold stress, respiratory metabolism was decreased and the transportation and hydrolysis of photosynthetic products was inhibited, leading to an accumulation of starch in the chloroplasts. Total of 5800 unigenes and 38 proteins were affected, including the repressed expression of photosynthesis and the enhanced expression in signal transduction, stress defense pathway as well as secondary metabolism. Although the transcriptional level of a large number of genes has been restored after 12 h, sustained cold stress brought more serious injury to the leaf cells, including the sharp rise of the relative electrolyte leakage, the declined Fv/Fm value, swelled chloroplast and the disintegrated membrane system. Conclusion The starch accumulation and the photoinhibition might be the main adaptive mechanism of the paper mulberry responded to cold stress. Most of important, enhancing the transport and hydrolysis of photosynthetic products could be the potential targets for improving the cold tolerance of the paper mulberry. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2047-6) contains supplementary material, which is available to authorized users.

The EUROFUNG network is a virtual centre of multidisciplinary expertise in the field of fungal biotechnology. The first academic-industry Think Tank was hosted by EUROFUNG to summarise the state of the art and future challenges in fungal biology and biotechnology in the coming decade. Currently, fungal cell factories are important for bulk manufacturing of organic acids, proteins, enzymes, secondary metabolites and active pharmaceutical ingredients in white and red biotechnology. In contrast, fungal pathogens of humans kill more people than malaria or tuberculosis. Fungi are significantly impacting on global food security, damaging global crop production, causing disease in domesticated animals, and spoiling an estimated 10 % of harvested crops. A number of challenges now need to be addressed to improve our strategies to control fungal pathogenicity and to optimise the use of fungi as sources for novel compounds and as cell factories for large scale manufacture of bio-based products. This white paper reports on the discussions of the Think Tank meeting and the suggestions made for moving fungal bio(techno)logy forward.

Background The objective of this study to detect Plasmodium and a subspecies of Plasmodium using filter paper in malaria endemic province, Sanliurfa, in Turkey, compare the results of nested PCR (nPCR) with microscopy for the diagnosis of malaria and present the epidemiological data of malaria. Methods This study was carried out in malaria-endemic Sanliurfa between 2008 and 2011. Finger prick blood samples, thick and thin Giemsa-stained blood smears, were collected from 153 malaria-suspected farmworkers. The Giemsa-stained blood smears were examined microscopically. The obtained DNA products, extracted from blood-spotted filter papers or from the thick blood smears, were analysed by nPCR to amplify the 18S ssrRNA Plasmodium gene with genus and specific primers. The results of the microscopy were compared to the nPCR results. Results Of the specimens, 7.2 % were determined as Plasmodium-positive by microscopy, whereas 9.8 % were determined as Plasmodium-positive by nPCR. Of the positive Plasmodium specimens, 93.33 % were identified as P. vivax. Four out of the 15 specimens that were microscopically diagnosed as negative were Plasmodium-positive with nPCR. When compared to the microscopy, the sensitivity, specificity, and positive predictive values of the nPCR were determined as 100, 97.2 and 73.3 %, respectively. nPCR was determined to be more sensitive and specific than microscopy. Conclusions This study revealed that the accurate diagnosis of malaria by nPCR was compulsory in malaria-endemic Sanliurfa and nPCR should be applied routinely in laboratory studies.

Contamination rate of Ethiopian paper currency notes handled by various food handlers with Escherichia coli and antimicrobial susceptibility of the isolates was assessed. A total of 384 Ethiopian Birr (ETB) notes were randomly sampled from meat handlers at butchers, bread and the related food handlers at cafeteria, fruit and vegetables handlers at supermarket, and milk sellers both at open market and dairy station. Fifty control new currencies were also sampled from Commercial Bank of Ethiopia. Both surfaces of the currency were swabbed using wet sterile cotton. The swab was overnight incubated in buffered peptone water. A loop full was streaked on eosin methylene blue agar and followed by biochemical test on presumptive E. coli colonies. Randomly selected isolates were exposed to chloramphenicol (C-30 µg), neomycin (N-30 µg), oxytetracycline (OT-30 µg), polymyxin-B (PB-300 IU) and trimethoprim-sulfamethoxazole (SXT-1.25/23.75/µg) susceptibility using disc diffusion techniques. E. coli was not isolated from currency used as control. A total of 288 (75 %) currency notes were found carrying E. coli. E. coli prevalence was ranges from 67.2 % at open market milk sellers to 87.2 % at dairy station milk sellers; from 64.8 % on ETB 100 to 82.9 % on ETB 1. Differences were not observed in E. coli prevalence on currency notes from among almost all food handlers (P > 0.05). Susceptibility of tested isolates to each chloramphenicol, oxytetracycline and trimethoprim-sulfamethoxazole was 100 %, and to polymyxin-B was 97.3 %. High resistance (83.7 %) was observed to neomycin. The finding indicates, contaminated food can be a source of E. coli for further contamination of currency which again transfer through various foods ready for consumption.

Background Paper currency is used for every type of commerce and plays an important role in the life of human beings. However, the combination of its widespread use and constant exchange make paper currency a likely agent for disease transmission. Thus, the aim of this study was to evaluate the microbial load and safety of Ethiopian paper currencies collected from some food vendors in Jimma town. Methods Standard microbiological methods were used for the enumeration of various microbial groups, isolation and characterization of pathogenic bacteria and their growth potential in selected weaning foods. A total of 100 samples of Ethiopian paper currencies, consisting of five denominations, from street food venders, hotels and cafeterias in Jimma town were collected aseptically. Sterile cotton swabs moistened with buffered peptone water solution were used for swabbing and the swabs were separately soaked into 10 ml sterile buffered peptone water solution. Results Mean microbial counts of Aerobic mesophilic bacteria, Staphylococci, Enterobacteriaceae, coliforms and Aerobic bacterial spores were (log CFU/cm2) 6.32, 4.43, 3.14, 2.98 and 3.78, respectively. However, mean counts of Yeasts and Moulds were below detectable levels. There was statistically significant variation (p

Background: Nested PCR is considered a sensitive and specific method for detecting malaria parasites and is especially useful in epidemiological surveys. Howev er, the preparation of DNA templates for PCR is often time-consuming and costly. Methods: A simplified PCR method was developed to directly use a small blood filter paper square (2 × 2 mm) as the DNA template after treatment with saponin. This filter paper-based nested PCR method (FP-PCR) was compared to microscopy and standard nested PCR with DNA extracted by using a Qiagen DNA mini kit from filter paper blood spots of 204 febrile cases. The FP-PCR technique was further applied to evaluate malaria infections in 1,708 participants from cross-sectional epidemiological surveys conducted in Myanmar and Thailand. Results: The FP-PCR method had a detection limit of ~0.2 parasites/μL blood, estimated using cultured Plasmodium falciparum parasites. With 204 field samples, the sensitivity of the FP-PCR method was comparable to that of the standard nested PCR method, which was significantly higher than that of microscopy. Application of the FP-PCR method in large cross-sectional studies conducted in Myanmar and Thailand detected 1.9% (12/638) and 6.2% (66/1,070) asymptomatic Plasmodium infections, respectively, as compared to the detection rates of 1.3% (8/638) and 0.04% (4/1,070) by microscopy. Conclusion: This FP-PCR method was much more sensitive than microscopy in detecting Plasmodium infections. It drastically increased the detection sensitivity of asymptomatic infections in cross-sectional surveys conducted in Thailand and Myanmar, suggesting that this FP-PCR method has a potential for future applications in malaria epidemiology studies.

Methods Nasal secretions from 12 patients with AR to grass pollen and 12 healthy controls were collected. Two preweighed filter discs were placed bilaterally under direct visualization on the anterior third of the nasal septum. Five minutes later, they were removed and weighted again. After adding 2 ml 0,9% NaCl solution to the discs and centrifugation, the nasal secretions were stored in aliquots at -20°C until analysis. Biomarkers such as total IgE, grass pollen specific (gx3) IgE, total IgG, IgG4 and tryptase were measured. Patients with AR were selected based on symptoms during the grass pollen season and based on a positive skin prick test for grass pollen. Control patients were healthy patients without rhinological or allergic disease and with negative skin prick test to the standard panel of allergens.

The microbial H2-producing (hydrogenogenic) carbon monoxide (CO)-oxidizing activity by the membrane-associated CO dehydrogenase (CODH)/energy-converting hydrogenase (ECH) complex is an important metabolic process in the microbial community. However, the studies on hydrogenogenic carboxydotrophs had to rely on inherently cultivation and isolation methods due to their rare abundance, which was a bottleneck in ecological study. Here, we provided gene-targeted sequencing method for the diversity estimation of thermophilic hydrogenogenic carboxydotrophs. We designed six new degenerate primer pairs which effectively amplified the coding regions of CODH genes forming gene clusters with ECH genes (CODHech genes) in Firmicutes which includes major thermophilic hydrogenogenic carboxydotrophs in terrestrial thermal habitats. Amplicon sequencing by these primers using DNAs from terrestrial hydrothermal sediments and CO-gas-incubated samples specifically detected multiple CODH genes which were identical or phylogenetically related to the CODHech genes in Firmictes. Furthermore, we found that phylogenetically distinct CODHech genes were enriched in CO-gas-incubated samples, suggesting that our primers detected uncultured hydrogenogenic carboxydotrophs as well. The new CODH-targeted primers provided us with a fine-grained (~ 97.9% in nucleotide sequence identity) diversity analysis of thermophilic hydrogenogenic carboxydotrophs by amplicon sequencing and will bolster the ecological study of these microorganisms. Supplementary Information The online version contains supplementary material available at 10.1007/s00792-020-01211-y.

The suitability of paper-based arrays for biofilm formation studies by Staphylococcus aureus is demonstrated. Laboratory-coated papers with different physicochemical properties were used as substrates. The array platform was fabricated by patterning the coated papers with vinyl-substituted polydimethylsiloxane (PDMS) -based ink. The affinity of bacteria onto the flexographically printed hydrophobic and smooth PDMS film was very low whereas bacterial adhesion and biofilm formation occurred preferentially on the unprinted areas, i.e. in the reaction arrays. The concentration of the attached bacteria was quantified by determining the viable colony forming unit (CFU/cm(2)) numbers. The distribution and the extent of surface coverage of the biofilms were determined by atomic force microscopy. In static conditions, the highest bacterial concentration and most highly organized biofilms were observed on substrates with high polarity. On a rough paper surface with low polarity, the biofilm formation was most hindered. Biofilms were effectively removed from a polar substrate upon exposure to (+)-dehydroabietic acid, an anti-biofilm compound.

INTRODUCTION BACKGROUND TO METABOLOMICS: Metabolomics is the comprehensive study of the metabolome, the repertoire of biochemicals (or small molecules) present in cells, tissues, and body fluids. The study of metabolism at the global or "-omics" level is a rapidly growing field that has the potential to have a profound impact upon medical practice. At the center of metabolomics, is the concept that a person's metabolic state provides a close representation of that individual's overall health status. This metabolic state reflects what has been encoded by the genome, and modified by diet, environmental factors, and the gut microbiome. The metabolic profile provides a quantifiable readout of biochemical state from normal physiology to diverse pathophysiologies in a manner that is often not obvious from gene expression analyses. Today, clinicians capture only a very small part of the information contained in the metabolome, as they routinely measure only a narrow set of blood chemistry analytes to assess health and disease states. Examples include measuring glucose to monitor diabetes, measuring cholesterol and high density lipoprotein/low density lipoprotein ratio to assess cardiovascular health, BUN and creatinine for renal disorders, and measuring a panel of metabolites to diagnose potential inborn errors of metabolism in neonates. OBJECTIVES OF WHITE PAPER-EXPECTED TREATMENT OUTCOMES AND METABOLOMICS ENABLING TOOL FOR PRECISION MEDICINE: We anticipate that the narrow range of chemical analyses in current use by the medical community today will be replaced in the future by analyses that reveal a far more comprehensive metabolic signature. This signature is expected to describe global biochemical aberrations that reflect patterns of variance in states of wellness, more accurately describe specific diseases and their progression, and greatly aid in differential diagnosis. Such future metabolic signatures will: (1) provide predictive, prognostic, diagnostic, and surrogate markers of diverse disease states; (2) inform on underlying molecular mechanisms of diseases; (3) allow for sub-classification of diseases, and stratification of patients based on metabolic pathways impacted; (4) reveal biomarkers for drug response phenotypes, providing an effective means to predict variation in a subject's response to treatment (pharmacometabolomics); (5) define a metabotype for each specific genotype, offering a functional read-out for genetic variants: (6) provide a means to monitor response and recurrence of diseases, such as cancers: (7) describe the molecular landscape in human performance applications and extreme environments. Importantly, sophisticated metabolomic analytical platforms and informatics tools have recently been developed that make it possible to measure thousands of metabolites in blood, other body fluids, and tissues. Such tools also enable more robust analysis of response to treatment. New insights have been gained about mechanisms of diseases, including neuropsychiatric disorders, cardiovascular disease, cancers, diabetes and a range of pathologies. A series of ground breaking studies supported by National Institute of Health (NIH) through the Pharmacometabolomics Research Network and its partnership with the Pharmacogenomics Research Network illustrate how a patient's metabotype at baseline, prior to treatment, during treatment, and post-treatment, can inform about treatment outcomes and variations in responsiveness to drugs (e.g., statins, antidepressants, antihypertensives and antiplatelet therapies). These studies along with several others also exemplify how metabolomics data can complement and inform genetic data in defining ethnic, sex, and gender basis for variation in responses to treatment, which illustrates how pharmacometabolomics and pharmacogenomics are complementary and powerful tools for precision medicine. CONCLUSIONS KEY SCIENTIFIC CONCEPTS AND RECOMMENDATIONS FOR PRECISION MEDICINE: Our metabolomics community believes that inclusion of metabolomics data in precision medicine initiatives is timely and will provide an extremely valuable layer of data that compliments and informs other data obtained by these important initiatives. Our Metabolomics Society, through its "Precision Medicine and Pharmacometabolomics Task Group", with input from our metabolomics community at large, has developed this White Paper where we discuss the value and approaches for including metabolomics data in large precision medicine initiatives. This White Paper offers recommendations for the selection of state of-the-art metabolomics platforms and approaches that offer the widest biochemical coverage, considers critical sample collection and preservation, as well as standardization of measurements, among other important topics. We anticipate that our metabolomics community will have representation in large precision medicine initiatives to provide input with regard to sample acquisition/preservation, selection of optimal omics technologies, and key issues regarding data collection, interpretation, and dissemination. We strongly recommend the collection and biobanking of samples for precision medicine initiatives that will take into consideration needs for large-scale metabolic phenotyping studies.

Banana production generates significant amounts of agricultural wastes, being fiber extraction one of the most relevant alternatives for their valorization. This process produces banana’s pseudostem pulp (BPP) as a byproduct, which shows an interesting composition for the biorefinery’s biochemical platform, with high polysaccharides (68%) and low lignin contents. This work deals with the enzymatic hydrolysis (EH) of raw and hydrothermally pre-treated BPP, focusing on the production of oligosaccharides (OS). Raw BPP hydrolysis with cellulase at different dosages rendered only 3.2% OS yields (OSY). Pectinase addition has not affected EH performance. On the other hand, EH of hydrothermally pre-treated BPP at 150 °C and 170 °C (P150 and P170) allowed to increase OSY up to 28% (P150, 1 FPU of cellulase/g dry biomass, 12 h), being 72% of the solubilized sugars in the form of cello-oligosaccharides. This last condition was subjected to a multi-stage EH strategy without improvements in OSY. An endo-glucanase was also tested, but obtained OSY were lower than cellulase results. Finally, obtained OS demonstrated to stimulate the growth of two Lactobacilli strains. The results show that BPP pre-treated under mild operational conditions is a good candidate for cello-oligosaccharides production by EH using 1 FPU/g DB of cellulase with a simple strategy. Graphical abstract

Early issues of the Standards in Genomic Sciences (SIGS) journal have focused heavily on building a strong collection of genome notes compliant with the Minimum Information about a Genome Sequence (MIGS) checklist [1], in particular from the Genomic Encyclopedia for Bacteria and Archaea project (GEBA) [2]. This has resulted in SIGS quickly becoming the 3rdth ranked journal of all time in terms of total number of newly published genome sequences. SIGS is now branching out to also include descriptions of metagenomes and pan-genomes. As SIGS evolves it is now becoming a unique forum for publishing standards-compliant literature. Joint publication is a key step in the defining the shared interests and goals of communities. The November/December 2010 issue was a special issue containing meeting reports from five communities, including four from the Genomic Standards Consortium (GSC) [3]. In this issue, we present two types of articles new to SIGS that we believe will pave the way for similar submissions. Duhaime et al. review our current knowledge of a collection of marine phage genomes through the lens of MIGS-compliant fields, including habitat, geographic location, and host [4]. These authors contribute the first curation-based review paper to show that adherence to the GSC MIGS checklist enables a rich set of contextual data to be captured for marine phage. Likewise, SIGS now offers a forum for publishing multi-author, consensus-building papers that help define the work of the GSC and, hopefully in the future, related communities. Morrison et al. provide such a roadmap for the use of ontologies to mark up and interpret related data sources in new ways and introduce the Ontogrator software and website [5]. In a separate article, Castoe et al. present arguments from a consortium of zoologists advocating the sequencing of the garter-snake genome (Thamnophis sirtalis) [6].

Carotenoids are health promoting compounds which bioavailability depends on their release from the intracellular compartments. The aim of this study was to evaluate the effect of the application of different levels of pressure, time and temperature in High Hydrostatic Pressure-Assisted Extraction (HHPAE) processes, and the use of soybean and sunflower oils on the extraction yield of carotenoids present in papaya pulp and peel. . Papaya (pulp and peel) as source of carotenoids and soybean and sunflower oils as eco-friendly solvents were used. The effects of temperature, pressure and time (20–40 °C, 300–500 MPa and 2–8 min) on the carotenoid extraction yield were studied applying a central composite experimental design. Carotenoids and esters in papaya were analysed by high performance liquid chromatography (HPLC-DAD-MS/MS) and by spectrophotometric methods. The main carotenoids found in carotenoid-rich oils were (all-E)-lycopene, (13Z)-lycopene isomer, β-carotene, (all-E)-β-cryptoxanthin and xanthophyll esters as (all-E)-β-cryptoxanthin caprate, (all-E)-β-cryptoxanthin laurate and (all-E)-β-cryptoxanthin myristate. The optimal extraction condition was obtained at 400 MPa, 40.5 °C for 5 min, with the highest (all-E)-lycopene extraction yield (99.1%) from papaya pulp using soybean oil. The highest (all-E)-β-carotene (14.0%) and (all-E)-β-cryptoxanthin (19.3%) extraction yields were obtained from peel extracts at 500 MPa, 35 °C for 2 min using soybean oil and 400 MPa, 27.5 °C for 5 min using sunflower oil, respectively. The results showed that carotenoid extraction yields in papaya pulp and peel extracts were higher applying mild pressures (300–400 MPa). Low xanthophyll and xanthophyll esters extraction efficiency (0.8–3.1%) was observed due to the low polarity of the vegetable oils., This research was funded by the Spanish Ministry of Science and Innovation (Spain), through project number RTA2015-00044-C02-02 and the Tecnológico de Monterrey, Mexico (FunFoodEmertec). Author Sara Lara-Abia received financial support from Tecnológico de Monterrey (México) (Research Chair Funds CAT-200) and CONACYT-SEP (Research Project 101700 and Doctoral Scholarship no. 895077).

Background Consolidated bioprocessing, which combines saccharolytic and fermentative abilities in a single microorganism, is receiving increased attention to decrease environmental and economic costs in lignocellulosic biorefineries. Nevertheless, the economic viability of lignocellulosic ethanol is also dependent of an efficient utilization of the hemicellulosic fraction, which contains xylose as a major component in concentrations that can reach up to 40% of the total biomass in hardwoods and agricultural residues. This major bottleneck is mainly due to the necessity of chemical/enzymatic treatments to hydrolyze hemicellulose into fermentable sugars and to the fact that xylose is not readily consumed by Saccharomyces cerevisiaethe most used organism for large-scale ethanol production. In this work, industrial S. cerevisiae strains, presenting robust traits such as thermotolerance and improved resistance to inhibitors, were evaluated as hosts for the cell-surface display of hemicellulolytic enzymes and optimized xylose assimilation, aiming at the development of whole-cell biocatalysts for consolidated bioprocessing of corn cob-derived hemicellulose. Results These modifications allowed the direct production of ethanol from non-detoxified hemicellulosic liquor obtained by hydrothermal pretreatment of corn cob, reaching an ethanol titer of 11.1 g/L corresponding to a yield of 0.328 g/g of potential xylose and glucose, without the need for external hydrolytic catalysts. Also, consolidated bioprocessing of pretreated corn cob was found to be more efficient for hemicellulosic ethanol production than simultaneous saccharification and fermentation with addition of commercial hemicellulases. Conclusions These results show the potential of industrial S. cerevisiae strains for the design of whole-cell biocatalysts and paves the way for the development of more efficient consolidated bioprocesses for lignocellulosic biomass valorization, further decreasing environmental and economic costs., This work has been carried out at the Biomass and Bioenergy Research Infrastructure (BBRI)-LISBOA-01-0145-FEDER-022059, supported by Operational Programme for Competitiveness and Internationalization (PORTUGAL2020), by Lisbon Portugal Regional Operational Programme (Lisboa 2020) and by North Portugal Regional Operational Programme (Norte 2020) under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (ERDF) and has been supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UIDB/04469/2020, the “Contrato-Programa” UIDB/04050/2020, the MIT-Portugal Program (Ph.D. Grant PD/BD/128247/2016 to Joana T. Cunha) and through Project FatVal (POCI-01-0145-FEDER-032506) and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do Norte., info:eu-repo/semantics/publishedVersion

The use of phytoremediation to remove metals of contaminated soils is an interesting technique that is usually limited by adverse physical and chemical properties of this type of soils. The addition of biochar produced from manure waste could improve soil properties due to its nutrient content, high cation exchange capacity or water holding capacity. However, the high water content of manure wastes precludes its pyrolysis treatment use for biochar production, without a previous drying step. Indeed, hydrothermal carbonization (HTC) of manure wastes could be an adequate treatment method as it takes place in water solution. The product obtained after HTC of biomass, named hydrochar, exhibits different physiochemical properties than biochar that could affect their potential application. The objective of the present work is to study the effect of chars obtained by pyrolysis or HTC of manure wastes in mining soil phytoremediation with Sinapis alba. Two selected mining soils (PORT and GAM) were treated with two manure biochars prepared at 450 °C (BMW450) and 600 °C (BMW600), two hydrochars prepared by HTC of manure at 190 °C (HWM190) and 240 °C (HMW240) and raw manure waste (MW) at a rate of 10% in mass. Later, different soil samples were incubated with or without Sinapis alba growth. Experimental results shown that properties of chars have a great influence on the efficiency of the use of Sinapis alba in the phytoremediation of mining soils. The addition of BMW600 and raw material (MW) increased the production of aerial and root biomass for GAM soil. For PORT soil, HMW190, two biochars and MW increases root and aerial biomass whereas HMW240 only produces an increment on aerial biomass. Addition of two hydrochars and MW had a positive effect on the biochemical soil activities and the highest microbial biomass carbon of GAM and PORT soil samples was observed after addition of HMW190. Finally, the addition of biochars and hydrochars could improve the phytoremediation of mining soils by Sinapis alba. However, the heavy metal uptake greatly depends on the type of soil, the amendment and the target metal. The accumulation of As, Pb and Zn in the aerial part of Sinapis alba was very low. However, Sinapis alba acts as accumulator for As in the presence of BMW600 and HMW190, for Zn after amendment with HM190 and for Pb after BMW600 addition to PORT soil. For GAM soil, only the addition of BMW450 and BM600 improves the capacity of accumulation of As in roots., Authors want to thank to Spanish Ministerio de Economía y Competitividad “Retos Investigación 2014” for the economic support (CGL2014-58322-R).

Reindeer (Rangifer tarandus) have evolved elaborate nasal turbinate structures that are perfused via a complex vascular network. These are subject to thermoregulatory control, shifting between heat conservation and dissipation, according to the animal’s needs. The three-dimensional design of the turbinate structures is essential in the sense that they determine the efciency with which heat and water are transferred between the structure and the respired air. The turbinates have already a relatively large surface area at birth, but the structures have yet not reached the complexity of the mature animal. The aim of this study was to elucidate the structure–function relationship of the heat exchange process. We have used morphometric and physiological data from newborn reindeer calves to construct a thermodynamic model for respiratory heat and water exchange and present novel results for the simulated respiratory energy losses of calves in the cold. While the mature reindeer efectively conserves heat and water through nasal counter-current heat exchange, the nose of the calf has not yet attained a similar efciency. We speculate that this is probably related to structure-size limitations and more favourable climate conditions during early life. The fully developed structure–function relationship may serve as inspiration for engineering design. Simulations of diferent extents of mucosal vascularization suggest that the abundance and pattern of perfusion of veins in the reindeer nasal mucosa may contribute to the control of temperature profles, such that nasal cavity tissue is sufciently warm, but not excessively so, keeping heat dissipation within limits. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00449-019-02245-z) contains supplementary material, which is available to authorized users., Laccases are very interesting biocatalysts of recognized importance for several industrial applications. Its production by Trametes versicolor, a white-rot fungus, was induced by a combination of cotton gin wastes (1\%), a lignocellulosic waste, and vinasse (15\%), an industrial by-product from sugarcane industry. The use of these agro-industrial wastes are interesting, since it helps in reducing the enzyme production costs, due to their low cost and wide availability, as well as the environmental contamination issues, due to their improper disposal. Thus, laccase production was studied in submerged fermentation of T. versicolor using these agro-industrial wastes (cotton gin waste and vinasse) as carbon source and an additional nitrogen source (0.1\\% peptone). Three different bioreactors were evaluated for laccase production, such as BioFlo 310 bioreactor, aluminium tray and Erlenmeyer flasks to achieve high levels of laccase production. The highest specific production of laccase was found in BioFlo 310 bioreactor with 12 days of fermentation (55.24 U/mg prot.), which has been shown to be closely related to the oxygen supply to the microorganism through aeration of the fermentation medium. This study brings new insights into green biotechnology regarding vinasse utilization, which is frequently discharged in soils, rivers, and lakes causing adverse effects on agricultural soils and biota, as well as the cotton gin waste recovery., The authors are grateful to Mariana Cereia and Maurício de Oliveira for their technical assistance. This work was supported by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP, processes 2010/52322-3; 2014/50884-5; 2018/07522-6), and V. E. P. was the recipient of a FAPESP fellowship (Process 2015/23200-0)., info:eu-repo/semantics/publishedVersion

Planctomycetes are ubiquitous bacteria with environmental and biotechnological relevance. Axenic cultures of planctomycetal strains are the basis to analyse their unusual biology and largely uncharacterised metabolism in more detail. Here, we describe strain Mal4T isolated from marine sediments close to Palma de Mallorca, Spain. Strain Mal4T displays common planctomycetal features, such as division by polar budding and the presence of fimbriae and crateriform structures on the cell surface. Cell growth was observed at ranges of 10–39 °C (optimum at 31 °C) and pH 6.5–9.0 (optimum at 7.5). The novel strain shows as pear-shaped cells of 2.0 ± 0.2 × 1.4 ± 0.1 µm and is one of the rare examples of orange colony-forming Planctomycetes. Its genome has a size of 7.7 Mb with a G+C content of 63.4%. Phylogenetically, we conclude that strain Mal4T (= DSM 100296T = LMG 29133T) is the type strain representing the type species of a novel genus, for which we propose the name Maioricimonas rarisocia gen. nov., sp. nov., Open Access funding provided by Projekt DEAL. Part of this research was funded by the Deutsche Forschungsgemeinschaft (DFG) Grants KA 4967/1-1 and JO 893/4-1, Grant ALWOP.308 of the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO), SIAM (Soehngen Institute for Anaerobic Microbiology) Grant No. 024002002 and the Radboud Excellence fellowship.

Edible insects have been advocated as a means to combat food insecurity, which is prevalent in West Africa. In this study we look at the contribution of the shea caterpillar Cirina butyrospermi, colloquially known as ‘chitoumou’, to the food security of smallholder households in rural southwestern Burkina Faso. We used a mixed methods approach to understand the relationship between caterpillar collection, consumption, and sale by smallholder households, and their seasonal food security status. We found that caterpillars are an important source of food and income for households, significantly increasing the household consumption of animal protein and, with shea nuts, representing the main income source for the majority of women. We also found that food security is higher during caterpillar season, and that household-level food security during this season can be predicted by the amount of caterpillars collected, consumed and sold. However, this relationship holds only during the caterpillar season, suggesting that the positive impact of caterpillars on food security is temporally limited. We conclude that the shea caterpillar is an example of an edible insect that is crucial for seasonal food security in a widespread agricultural system.

The common glow-worms (Lampyris noctiluca) are best known for emission of green light by their larvae and sexually active adult females. However, both their DNA and RNA viruses remain unknown. Glow-worms are virologically interesting, as they are non-social and do not feed as adults, and hence their viral transmission may be limited. We identified viral sequences from 11 different virus taxa by the RNA-sequencing of two Finnish populations of adult glow-worms. The viruses represent nine different virus families and have negative, positive, or double-stranded RNA genomes. We also found a complete retroviral genome. Similar viral sequences were found from the sequencing data of common eastern firefly of North America, a species belonging to the same family (Lampyridae) as that of the common glow-worm. On average, an individual glow-worm had seven different RNA virus types and most of them appeared to establish a stable infection since they were found from glow-worms during two consecutive years. Here we present the characterization of load, prevalence, and interactions for each virus. Most of the glow-worm RNA viruses seem to be transmitted vertically, which may reflect the biology of glow-worms as non-social capital breeders, i.e., they invest stored resources in reproduction. Electronic supplementary material The online version of this article (10.1007/s11262-019-01724-5) contains supplementary material, which is available to authorized users.

4 Tablas.-- 3 Figuras, The aim of the present work was to compare the mesophilic anaerobic digestion of untreated olive mill solid waste (OMSW), soft hydrothermal pre-treated OMSW (SHP OMSW), and a co-digestion mixture of 95% OMSW and 5% microalga Dunaliella salina (co-OMSW). During the co-digestion experiment, the volatile fatty acid accumulation decreased in comparison with that obtained for OMSW and SHP OMSW, reducing the slight inhibition observed during the OMSW and SHP OMSW experiments. Final values of methane yield of 380 ± 1 mL CH4 g−1 VSadded for the OMSW, 424 ± 2 mL CH4 g−1 VSadded for the SHP OMSW, and 491 ± 1 mL CH4 g−1 VSadded for the co-OMSW were determined. Two mathematical models, first-order kinetics and modified Gompertz model, were employed to fit the experimental data with the aim of elucidating the anaerobic biodegradation and obtain the kinetic constants. Both models allowed for adequately fitting the experimental results of methane production with time. The kinetic constant, k, of the first-order model increased by 12% for the co-OMSW compared with the values achieved for OMSW and SHP OMSW. The modified Gompertz model revealed that the maximum methane production rate, Rm, for the co-OMSW and SHP OMSW increased by 34.7% and 10.3% compared with the value obtained for OMSW., This study was funded by: - The Project of Excellence RNM-1970 funded by the regional government of Andalucía, Junta de Andalucía, Consejería de Economía, Innovación, Ciencia y Empleo, Andalucía, Spain. - The Ramón y Cajal Program (RYC-2011-08783 contract) funded by the Spanish Ministry of Economy and Competitiveness, providing financial support to Dr. Rincón.

The anthraquinone dye Remazol Brilliant Blue R is largely used in the textile industry. However, its removal from wastewaters is costly and complex. Many methods have been tested to solve this ecological problem, but there is still a need for efficient methods. We propose here an alternative use of a two-chambered microbial fuel cell (MFC), fuelled with domestic wastewater in the anodic chamber, to degrade a simulated textile dye effluent made of Remazol Brilliant Blue R inoculated with an immobilised fungal strain, Pleurotus ostreatus URM 4809, as a laccase producer, in the cathodic chamber. The MFC showed continuous synthesis of laccase in the cathodic chamber, which, in turn, promoted the rapid decolourisation, of more than 86\% of the textile dye effluent. The yield was further increased by the addition of glycerol. Electrochemical monitoring also indicated an increase in power density and current density. After 20Â days of MFC operation, 62.1\\% of organic matter was removed in the anodic compartment, thus leaving the effluent with a much lower toxicity., Authors would like to acknowledge the technician and fnancial support of Programa Novos Talentos provided by the Instituto de Pesquisa Tecnológica do Estado de São Paulo (IPT) and Instituto de Estudos Avançados do Mar (IEAMar)., info:eu-repo/semantics/publishedVersion

This study has compared the harvesting efficiency of four flocculation methods, namely, induced by pH, FeCl3, AlCl3 and chitosan. No changes were observed on M. aeruginosa cells. Flocculation assays performed at pH 3 and 4 have shown the best harvesting efficiency among the pH-induced tests, reaching values above 90% after 8 h. The adjustment of zeta potential (ZP) to values comprised between 6.7 and 20.7 mV enhanced significantly the settling rates using flocculant agents, being FeCl3 the best example where increments up to 88% of harvesting efficiency were obtained. Although all the four methods tested have presented harvesting efficiencies above 91% within the first 8 h after the optimization process, the highest performance was obtained using 3.75 mg L1 of FeCl3, which allowed reaching 92% in 4 h., This research work was supported by the grants SFRH/BPD/98694/2013 (Bruno Fernandes) and SFRH/BD/52335/2013 (Pedro Geada) from Fundação para a Ciência e a Tecnologia (Portugal). Luís Loureiro is recipient of a fellowship supported by a doctoral advanced training (call NORTE-69-2015-15) funded by the European Social Fund under the scope of Norte2020 - Programa Operacional Regional do Norte. This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the FCT Strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684) and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do Norte. This study was also supported by the Project UID/Multi/04423/2013, the Project RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-027462), and the project NOVELMAR (reference NORTE-01-0145-FEDER-000035) co-financed by the North Portugal Regional Operational Programme (Norte 2020) under the National Strategic Reference Framework (NSRF) through the ERDF., info:eu-repo/semantics/publishedVersion

The genus Leptosphaeria contains numerous fungi that cause the symptoms of asthma and also parasitize wild and crop plants. In search of a robust and universal forecast model, the ascospore concentration in air was measured and weather data recorded from 1 March to 31 October between 2006 and 2012. The experiment was conducted in three European countries of the temperate climate, i.e., Ukraine, Poland, and the UK. Out of over 150 forecast models produced using artificial neural networks (ANNs) and multivariate regression trees (MRTs), we selected the best model for each site, as well as for joint two-site combinations. The performance of all computed models was tested against records from 1 year which had not been used for model construction. The statistical analysis of the fungal spore data was supported by a comprehensive study of both climate and land cover within a 30-km radius from the air sampler location. High-performance forecasting models were obtained for individual sites, showing that the local micro-climate plays a decisive role in biology of the fungi. Based on the previous epidemiological studies, we hypothesized that dew point temperature (DPT) would be a critical factor in the models. The impact of DPT was confirmed only by one of the final best neural models, but the MRT analyses, similarly to the Spearman’s rank test, indicated the importance of DPT in all but one of the studied cases and in half of them ranked it as a fundamental factor. This work applies artificial neural modeling to predict the Leptosphaeria airborne spore concentration in urban areas for the first time. Electronic supplementary material The online version of this article (10.1007/s00484-018-1500-z) contains supplementary material, which is available to authorized users.

Humans show impaired recognition of faces that are presented upside down, a phenomenon termed face inversion effect, which is thought to reflect the special relevance of faces for humans. Here, we investigated whether a phylogenetically distantly related avian species, the carrion crow, with similar socio-cognitive abilities to human and non-human primates, exhibits a face inversion effect. In a delayed matching-to-sample task, two crows had to differentiate profiles of crow faces as well as matched controls, presented both upright and inverted. Because crows can discriminate humans based on their faces, we also assessed the face inversion effect using human faces. Both crows performed better with crow faces than with human faces, and performed worse when responding to inverted pictures in general compared to upright pictures. However, neither of the crows showed a face inversion effect. For comparative reasons, the tests were repeated with human subjects. As expected, humans showed a face-specific inversion effect. Therefore, we did not find any evidence that crows – like humans – process faces as a special visual stimulus. Instead, individual recognition in crows may be based on cues other than a conspecific’s facial profile, such as their body, or on processing of local features rather than holistic processing.

Human disturbance modifies selection regimes, depressing native species fitness and enabling the establishment of non-indigenous species with suitable traits. A major impediment to test the effect of disturbance on invasion success is the lack of long-term data on the history of invasions. Here, we overcome this problem and reconstruct the effect of disturbance on the invasion of the bivalve Anadara transversa from sediment cores in the Adriatic Sea. We show that (1) the onset of major eutrophication in the 1970s shifted communities towards species tolerating hypoxia, and (2) A. transversa was introduced in the 1970s but failed to reach reproductive size until the late 1990s because of metal contamination, resulting in an establishment and detection lag of ~25 years. Subfossil assemblages enabled us to (1) disentangle the distinct stages of invasion, (2) quantify time-lags and (3) finely reconstruct the interaction between environmental factors and the invasion process, showing that while disturbance does promote invasions, a synergism of multiple disturbances can shift selection regimes beyond tolerance limits and induce significant time lags in establishment. The quantification of these time lags enabled us to reject the hypothesis that aquaculture was an initial vector of introduction, making shipping the most probable source. Electronic supplementary material The online version of this article (10.1007/s10530-017-1634-7) contains supplementary material, which is available to authorized users.

Cellulose is the most widely used biopolymer on Earth. Its large-scale production is mainly from lignocellulosic material (plant origin), however, this plant material is not the only source of this valuable polymer, since microorganisms, like bacteria, naturally produce cellulose, especially those of the genus Komagateibacter (formerly Gluconacetobacter). This type of cellulose is of great interest because of its unique properties such as high purity and resistance, nevertheless, it has not been produced in a large-scale industrial process to date using low-cost substrates, one of the key aspects that should be considered for the industrial obtaining of any biotechnological product. As a main finding we found that the majority of low-cost culture media discussed could have the potential to produce bacterial cellulose on an industrial scale, since in most cases they yield more cellulose (with similar physical chemical characteristics) to those obtained in standard media. However, for an appropriate large-scale production, a specific knowledge about these by-products (since their composition and characteristics, which have a direct impact on the productivity of this biopolymer, are quite heterogeneous) and a proper standardization of them would also be required. Research staff of many industries could use the information presented here to help design a process to use their respective byproducts as substrate to obtain a product with a high added value as bacterial cellulose.

Bioconversion of organic waste into value-added products by a process called syngas fermentation is gaining considerable interest during the last years. Syngas is a gaseous mixture composed mainly of hydrogen and carbon monoxide and smaller quantities of other gases like CO2 that can be fermented by Rhodospirillum rubrum, a natural producer of polyhydroxybutyrate (PHB). R. rubrum is a highly versatile, purple, non-sulfur bacterium that can grow in a broad range of anaerobic and aerobic conditions. In anaerobiosis, it can utilize CO as carbon and energy source in the presence or absence of light. When exposed to CO, CO dehydrogenase, which catalyzes oxidation of CO into CO2, is induced. Part of the CO2 produced is assimilated into cell material and the remaining CO2, along with the H2, is released into the environment. The protocol below provides detailed information of PHB production during syngas fermentation by R. rubrum at lab scale., The design of this protocol was supported by the project European Commission SYNPOL no. 311815 [http:\crwww.sympol.org].

Cytotoxic lymphocyte protease granzyme M (GrM) is a potent inducer of tumor cell death. The apoptotic phenotype and mechanism by which it induces cell death, however, remain poorly understood and controversial. Here, we show that GrM-induced cell death was largely caspase-dependent with various hallmarks of classical apoptosis, coinciding with caspase-independent G2/M cell cycle arrest. Using positional proteomics in human tumor cells, we identified the nuclear enzyme topoisomerase II alpha (topoIIα) as a physiological substrate of GrM. Cleavage of topoIIα by GrM at Leu(1280) separated topoIIα functional domains from the nuclear localization signals, leading to nuclear exit of topoIIα catalytic activity, thereby rendering it nonfunctional. Similar to the apoptotic phenotype of GrM, topoIIα depletion in tumor cells led to cell cycle arrest in G2/M, mitochondrial perturbations, caspase activation, and apoptosis. We conclude that cytotoxic lymphocyte protease GrM targets topoIIα to trigger cell cycle arrest and caspase-dependent apoptosis.

Biochemical oxygen demand (BOD) is a widely used index of water-quality assessment. Since bioelectrochemical BOD biosensors require anaerobic conditions for anodic reactions, they are not directly used in aerobic environments such as aeration tanks. Normally, the BOD biosensors are closed-type, where the anode is packed inside a closed chamber to avoid exposure to oxygen. In this study, a novel bioelectrochemical open-type biosensor was designed for in-situ monitoring of BOD during intermittent aeration. The open-type anode, without any protection against exposure to oxygen, was directly inserted into an intermittently aerated tank filled with livestock wastewater. Anodic potential was controlled using a potentiostat. Interestingly, this novel biosensor generated similar levels of current under both aerating and non-aerating conditions, and showed a logarithmic correlation (R2 > 0.9) of current with BOD concentrations up to 250 mg/L. Suspended solids in the wastewater attached to and covered the whole anode, presumably leading to the production of anaerobic conditions inside the covered anode via biological oxygen removal. Exoelectrogenic anaerobes (Geobacter spp.) were detected inside the covered anode using the 16S-rRNA gene. This biosensor will have various practical applications, such as the automatic control of aeration intensity and the in-situ monitoring of natural water environments.

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) can induce apoptosis in many cancer cells without causing toxicity in vivo. However, to date, TRAIL-receptor agonists have only shown limited therapeutic benefit in clinical trials. This can, most likely, be attributed to the fact that 50% of all cancer cell lines and most primary human cancers are TRAIL resistant. Consequently, future TRAIL-based therapies will require the addition of sensitizing agents that remove crucial blocks in the TRAIL apoptosis pathway. Here, we identify PIK-75, a small molecule inhibitor of the p110α isoform of phosphoinositide-3 kinase (PI3K), as an exceptionally potent TRAIL apoptosis sensitizer. Surprisingly, PI3K inhibition was not responsible for this activity. A kinome-wide in vitro screen revealed that PIK-75 strongly inhibits a panel of 27 kinases in addition to p110α. Within this panel, we identified cyclin-dependent kinase 9 (CDK9) as responsible for TRAIL resistance of cancer cells. Combination of CDK9 inhibition with TRAIL effectively induced apoptosis even in highly TRAIL-resistant cancer cells. Mechanistically, CDK9 inhibition resulted in downregulation of cellular FLICE-like inhibitory protein (cFlip) and Mcl-1 at both the mRNA and protein levels. Concomitant cFlip and Mcl-1 downregulation was required and sufficient for TRAIL sensitization by CDK9 inhibition. When evaluating cancer selectivity of TRAIL combined with SNS-032, the most selective and clinically used inhibitor of CDK9, we found that a panel of mostly TRAIL-resistant non-small cell lung cancer cell lines was readily killed, even at low concentrations of TRAIL. Primary human hepatocytes did not succumb to the same treatment regime, defining a therapeutic window. Importantly, TRAIL in combination with SNS-032 eradicated established, orthotopic lung cancer xenografts in vivo. Based on the high potency of CDK9 inhibition as a cancer cell-selective TRAIL-sensitizing strategy, we envisage the development of new, highly effective cancer therapies.