pinecone/core-2020-05-10-deduplication huggingface dataset:
Evaluation of electro-coagulation-flocculation for harvesting marine and freshwater microalgae

Although microalgae are considered as a promising feedstock for biofuels, the energy efficiency of the production process needs to be significantly improved. Due to their small size and low concentration in the culture medium, cost efficient harvesting of microalgae is a major challenge. In this study, the use of electro-coagulation-flocculation (ECF) as a method for harvesting a freshwater (Chlorella vulgaris) and a marine (Phaeodactylum tricornutum) microalgal species is evaluated. ECF was shown to be more efficient using an aluminum anode than using an iron anode. Furthermore it could be concluded that the efficiency of the ECF process can be substantially improved by reducing the initial pH and by increasing the turbulence in the microalgal suspension. Although higher current densities resulted in a more rapid flocculation of the microalgal suspension, power consumption, expressed per kg of microalgae harvested, and release of aluminum were lower when a lower current density was used. The aluminum content of the harvested microalgal biomass was less than 1 % while the aluminum concentration in the process water was below 2 mg l-1. Under optimal conditions, power consumption of the ECF process was around 2 kWh kg-1 of microalgal biomass harvested for Chlorella vulgaris and ca. 0.3 kWh kg-1 for Phaeodactylum tricornutum. Compared to centrifugation, ECF is thus more energy efficient. Because of the lower power consumption of ECF in seawater, ECF is a particularly attractive method for harvesting marine microalgae.status: publishe
Production of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) by Ralstonia eutropha in high cell density palm oil fermentations

Improved production costs will accelerate commercialization of polyhydroxyalkanoate (PHA) polymer and PHA-based products. Plant oils are considered favorable feedstocks, due to their high carbon content and relatively low price compared to sugars and other refined carbon feedstocks. Different PHA production strategies were compared using a recombinant strain of Ralstonia eutropha that produces high amounts of P(HB-co-HHx) when grown on plant oils. This R. eutropha strain was grown to high cell densities using batch, extended batch, and fed batch fermentation strategies, in which PHA accumulation was triggered by nitrogen limitation. While extended batch culture produced more biomass and PHA than batch culture, fed batch cultivation was shown to produce the highest levels of biomass and PHA. The highest titer achieved was over 139 g/L cell dry weight (CDW) of biomass with 74% of CDW as PHA containing 19mol% HHx. Our data suggest that the fermentation process is scalable with a space time yield (STY) better than 1 g PHA/L/h. The achieved biomass concentration and PHA yield are among the highest reported for the fermentation of recombinant R. eutropha strains producing P(HB-co-HHx).Malaysia-MIT Biotechnology Partnership Programm
Microflotation performance for algal separation

This is the peer reviewed version of the following article: HANOTU, J., BANDULASENA, H.C.H. and ZIMMERMAN, W.B., 2012. Microflotation performance for algal separation. Biotechnology and Bioengineering, 109 (7), pp. 1663-1673, which has been published in final form at http://dx.doi.org/10.1002/bit.24449.  This article may be used for non-commercial purposes in accordance With Wiley Terms and Conditions for self-archiving'.The performance of microflotation, dispersed air flotation with microbubble clouds with bubble size about 50 µm, for algae separation using fluidic oscillation for microbubble generation is investigated. This fluidic oscillator converts continuous air supply into oscillatory flow with a regular frequency to generate bubbles of the scale of the exit pore. Bubble characterization results showed that average bubble size generated under oscillatory air flow state was 86 µm, approximately twice the size of the diffuser pore size of 38 µm. In contrast, continuous air flow at the same rate through the same diffusers yielded an average bubble size of 1,059 µm, 28 times larger than the pore size. Following microbubble generation, the separation of algal cells under fluidic oscillator generated microbubbles was investigated by varying metallic coagulant types, concentration and pH. Best performances were recorded at the highest coagulant dose (150 mg/L) applied under acidic conditions (pH 5). Amongst the three metallic coagulants studied, ferric chloride yielded the overall best result of 99.2% under the optimum conditions followed closely by ferric sulfate (98.1%) and aluminum sulfate with 95.2%. This compares well with conventional dissolved air flotation (DAF) benchmarks, but has a highly turbulent flow, whereas microflotation is laminar with several orders of magnitude lower energy density. Biotechnol. Bioeng. 2012; 109:1663–1673. © 2012 Wiley Periodicals, Inc
Thermo-responsive non-woven scaffolds for "smart" 3D cell culture

The thermo-responsive polymer poly(N-isopropylacrylamide) has received widespread
attention for its in vitro application in the non-invasive, non-destructive release of adherent
cells on two dimensional surfaces. In this study, 3D non-woven scaffolds fabricated from
poly(propylene) (PP), poly(ethylene terephthalate) (PET) and nylon that had been grafted
with PNIPAAm were tested for their ability to support the proliferation and subsequent
thermal release of HC04 and HepG2 hepatocytes. Hepatocyte viability and proliferation was
estimated using the Alamar Blue assay and Hoechst 33258 total DNA quantification. The
assays revealed that the pure and grafted non-woven scaffolds maintained the hepatocytes
within the matrix and promoted 3D proliferation comparable to that of the commercially available AlgimatrixTM alginate scaffold. Albumin production and selected cytochrome P450
genes expression was found to be superior in cells growing on pure and grafted non-woven
PP scaffolds as compared to cells grown as a 2D monolayer. Two scaffolds, namely, PP-g-
PNIPAAm-A and PP-g-PNIPAAm-B were identified as having far superior thermal release
capabilities; releasing the majority of the cells from the matrices within 2 h. This is the first
report for the development of 3D non-woven, thermo-responsive scaffolds able to release
cells from the matrix without the use of any enzymatic assistance or scaffold degradation.The Council for Scientific and Industrial
 Researchhttp://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-0290hb2016Biochemistr
Differential effects of nitrogen and sulfur deprivation on growth and biodiesel feedstock production of chlamydomonas reinhardtii

Cataloged from PDF version of article.Biodiesel production from microalgae is a promising approach for energy production; however, high cost of its process limits the use of microalgal biodiesel. Increasing the levels of triacylglycerol (TAG) levels, which is used as a biodiesel feedstock, in microalgae has been achieved mainly by nitrogen starvation. In this study, we compared effects of sulfur (S) and nitrogen (N) starvation on TAG accumulation and related parameters in wild-type Chlamydomonas reinhardtii CC-124 mt(-) and CC-125 mt(+) strains. Cell division was interrupted, protein and chlorophyll levels rapidly declined while cell volume, total neutral lipid, carotenoid, and carbohydrate content increased in response to nutrient starvation. Cytosolic lipid droplets in microalgae under nutrient starvation were monitored by three-dimensional confocal laser imaging of live cells. Infrared spectroscopy results showed that relative TAG, oligosaccharide and polysaccharide levels increased rapidly in response to nutrient starvation, especially S starvation. Both strains exhibited similar levels of regulation responses under mineral deficiency, however, the degree of their responses were significantly different, which emphasizes the importance of mating type on the physiological response of algae. Neutral lipid, TAG, and carbohydrate levels reached their peak values following 4 days of N or S starvation. Therefore, 4 days of N or S starvation provides an excellent way of increasing TAG content. Although increase in these parameters was followed by a subsequent decline in N-starved strains after 4 days, this decline was not observed in S-starved ones, which shows that S starvation is a better way of increasing TAG production of C. reinhardtii than N starvation. Biotechnol. Bioeng. 2012; 109:19471957. (c) 2012 Wiley Periodicals, In
Methanol-driven enhanced biological phosphorus removal with a syntrophic consortium

The presence of suitable carbon sources for enhanced biological phosphorus removal (EBPR) plays a key role in phosphorus removal from wastewater in urban WWTP. For wastewaters with low volatile fatty acids (VFAs) content, an external carbon addition is necessary. As methanol is the most commonly external carbon source used for denitrification it could be a priori a promising alternative, but previous attempts to use it for EBPR have failed. This study is the first successful report of methanol utilization as external carbon source for EBPR. Since a direct replacement strategy (i.e., supply of methanol as a sole carbon source to a propionic-fed PAO-enriched sludge) failed, a novel process was designed and implemented successfully: development of a consortium with anaerobic biomass and polyphosphate accumulating organisms (PAOs). Methanol-degrading acetogens were (i) selected against other anaerobic methanol degraders from an anaerobic sludge; (ii) subjected to conventional EBPR conditions (anaerobic + aerobic); and (iii) bioaugmented with PAOs. EBPR with methanol as a sole carbon source was sustained in a mid-term basis with this procedure
Recovery of Poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) from Ralstonia eutropha cultures with non-halogenated solvents

Reduced downstream costs, together with high purity recovery of polyhydroxyalkanoate (PHA), will accelerate the commercialization of high quality PHA-based products. In this work, a process was designed for effective recovery of the copolymer poly(hydroxybutyrate-co-hydroxyhexanoate) (P(HB-co-HHx)) containing high levels of HHx (>15 mol%) from Ralstonia eutropha biomass using non-halogenated solvents. Several non-halogenated solvents (methyl isobutyl ketone, methyl ethyl ketone, and butyl acetate and ethyl acetate) were found to effectively dissolve the polymer. Isoamyl alcohol was found to be not suitable for extraction of polymer. All PHA extractions were performed from both dry and wet cells at volumes ranging from 2 mL to 3 L using a PHA to solvent ratio of 2% (w/v). Ethyl acetate showed both high recovery levels and high product purities (up to 99%) when using dry cells as starting material. Recovery from wet cells, however, eliminates a biomass drying step during the downstream process, potentially saving time and cost. When wet cells were used, methyl isobutyl ketone (MIBK) was shown to be the most favorable solvent for PHA recovery. Purities of up to 99% and total recovery yields of up to 84% from wet cells were reached. During polymer recovery with either MIBK or butyl acetate, fractionation of the extracted PHA occurred, based on the HHx content of the polymer. PHA with higher HHx content (17–30 mol%) remained completely in solution, while polymer with a lower HHx content (11–16 mol%) formed a gel-like phase. All PHA in solution could be precipitated by addition of threefold volumes of n-hexane or n-heptane to unfiltered PHA solutions. Effective recycling of the solvents in this system is predicted due to the large differences in the boiling points between solvent and precipitant. Our findings show that two non-halogenated solvents are good candidates to replace halogenated solvents like chloroform for recovery of high quality PHA. Biotechnol. Bioeng. 2013; 110: 461–470. © 2012 Wiley Periodicals, Inc.Malaysia-MIT Biotechnology Partnership Programm
Multi-cycle recovery of lactoferrin and lactoperoxidase from crude whey using fimbriated high-capacity magnetic cation exchangers and a novel "rotor-stator" high-gradient magnetic separator

This is the peer reviewed version of the following article: BROWN, G.N. ... et al, 2013. Multi-cycle recovery of lactoferrin and lactoperoxidase from crude whey using fimbriated high-capacity magnetic cation exchangers and a novel "rotor-stator" high-gradient magnetic separator. Biotechnology and Bioengineering, 110 (6), pp. 1714–1725, which has been published in final form at http://dx.doi.org/10.1002/bit.24842. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.Cerium (IV) initiated "graft-from" polymerization reactions were employed to convert M-PVA magnetic particles into polyacrylic acid-fimbriated magnetic cation exchange supports displaying ultra-high binding capacity for basic target proteins. The modifications, which were performed at 25mg and 2.5g scales, delivered maximum binding capacities (Q) for hen egg white lysozyme in excess of 320mgg, combined with sub-micromolar dissociation constants (0.45-0.69μm) and "tightness of binding" values greater than 49Lg. Two batches of polyacrylic acid-fimbriated magnetic cation exchangers were combined to form a 5g pooled batch exhibiting Q values for lysozyme, lactoferrin, and lactoperoxidase of 404, 585, and 685mgg, respectively. These magnetic cation exchangers were subsequently employed together with a newly designed "rotor-stator" type HGMF rig, in five sequential cycles of recovery of lactoferrin and lactoperoxidase from 2L batches of a crude sweet bovine whey feedstock. Lactoferrin purification performance was observed to remain relatively constant from one HGMF cycle to the next over the five operating cycles, with yields between 40% and 49% combined with purification and concentration factors of 37- to 46-fold and 1.3- to 1.6-fold, respectively. The far superior multi-cycle HGMF performance seen here compared to that observed in our earlier studies can be directly attributed to the combined use of improved high capacity adsorbents and superior particle resuspension afforded by the new "rotor-stator" HGMS design. © 2013 Wiley Periodicals, Inc
Oxyfunctionalization of aliphatic compounds by a recombinant peroxygenase from coprinopsis cinerea

The goal of this study is the selective oxyfunctionalization of aliphatic compounds under mild and environmentally friendly conditions using a low-cost enzymatic biocatalyst. This could be possible taking advantage from a new peroxidase type that catalyzes monooxygenase reactions with H2O2 as the only cosubstrate (peroxygenase). With this purpose, recombinant peroxygenase, from gene mining in the sequenced genome of Coprinopsis cinerea and heterologous expression using an industrial fungal host, is tested for the first time on aliphatic substrates. The reaction on free and esterified fatty acids and alcohols, and long-chain alkanes was followed by gas chromatography, and the different reaction products were identified by mass spectrometry. Regioselective hydroxylation of saturated/unsaturated fatty acids was observed at the w-1 and w-2 positions (only at the w-2 position in myristoleic acid). Alkyl esters of fatty acids and monoglycerides were also w-1 or w-2 hydroxylated, but di- and tri-glycerides were not modified. Fatty alcohols yielded hydroxy derivatives at the w-1 or w-2 positions (diols) but also fatty acids and their\ud
hydroxy derivatives. Interestingly, the peroxygenase was able to oxyfunctionalize alkanes giving, in addition to alcohols at\ud
positions 2 or 3, dihydroxylated derivatives at both sides of the molecule. The predominance of mono- or di-hydroxylated\ud
derivatives seems related to the higher or lower proportion of acetone, respectively, in the reaction medium. The recombinant C. cinerea peroxygenase appears as a promising biocatalyst for alkane activation and production of aliphatic oxygenated derivatives, with better properties than the previously reported peroxygenase from Agrocybe aegerita, and advantages related to its recombinant nature for enzyme engineering and industrial production.This study was funded by the PEROXICATS (KBBE-2010-4-265397) EU project. E.D. Babot thanks the Spanish CSIC for a JAE fellowship co-financed by FSE. R. Ullrich and M. Hofrichter are acknowledged for providing wild-type A. aegerita peroxygenase preparation.Peer reviewe
Understanding mild acid pretreatment of sugarcane bagasse through particle scale modeling

Sugarcane bagasse is an abundant and sustainable resource, generated as a by-product of sugarcane milling. The cellulosic material within bagasse can be broken down into glucose molecules and fermented to produce ethanol, making it a promising feedstock for biofuel production. Mild acid pretreatment hydrolyses the hemicellulosic component of biomass, thus allowing enzymes greater access to the cellulosic substrate during saccharification. A particle-scale mathematical model describing the mild acid pretreatment of sugarcane bagasse has been developed, using a volume averaged framework. Discrete population-balance equations are used to characterise the polymer degradation kinetics, and diffusive effects account for mass transport within the cell wall of the bagasse. As the fibrous material hydrolyses over time, variations in the porosity of the cell wall and the downstream effects on the reaction kinetics are accounted for using conservation of volume arguments. Non-dimensionalization of the model equations reduces the number of parameters in the system to a set of four dimensionless ratios that compare the timescales of different reaction and diffusion events. Theoretical yield curves are compared to macroscopic experimental observations from the literature and inferences are made as to constraints on these “unknown” parameters. These results enable connections to be made between experimental data and the underlying thermodynamics of acid pretreatment. Consequently, the results suggest that data-fitting techniques used to obtain kinetic parameters should be carefully applied, with prudent consideration given to the chemical and physiological processes being modeled
Regulated expression of polysaccharide utilization and capsular biosynthesis loci in biofilm and planktonic  Bacteroides thetaiotaomicron  during growth in chemostats

Bacteroides thetaiotaomicron  is a prominent member of the human distal gut microbiota that specializes in breaking down diet and host‐derived polysaccharides. While polysaccharide utilization has been well studied in  B. thetaiotaomicron , other aspects of its behavior are less well characterized, including the factors that allow it to maintain itself in the gut. Biofilm formation may be a mechanism for bacterial retention in the gut. Therefore, we used custom GeneChips to compare the transcriptomes of biofilm and planktonic  B. thetaiotaomicron  during growth in mono‐colonized chemostats. We identified 1,154 genes with a fold‐change greater than 2, with confidence greater than or equal to 95%. Among the prominent changes observed in biofilm populations were: (i) greater expression of genes in polysaccharide utilization loci that are involved in foraging of O‐glycans normally found in the gut mucosa; and (ii) regulated expression of capsular polysaccharide biosynthesis loci. Hierarchical clustering of the data with different datasets, which were obtained during growth under a range of conditions in minimal media and in intestinal tracts of gnotobiotic mice, revealed that within this group of differentially expressed genes, biofilm communities were more similar to the in vivo samples than to planktonic cells and exhibited features of substrate limitation. The current study also validates the use of chemostats as an in vitro “gnotobiotic” model to study gene expression of attached populations of this bacterium. This is important to gut microbiota research, because bacterial attachment and the consequences of disruptions in attachment are difficult to study in vivo. Biotechnol. Bioeng. 2014;111: 165–173. © 2013 Wiley Periodicals, Inc.     The authors used GeneChips to compare the transcriptomes of biofilm and planktonic populations of the human gut symbiont  Bacteroides thetaiotaomicron . The biofilm population showed a relative increase in expression of polysaccharide utilization loci, particularly those involved in host‐derived glycan degradation. Comparison to data from other studies with this organism revealed that these changes made the biofilm population more similar to cells grown in mouse ceca than to cells grown planktonically in vitro
Mechanistic modeling of sulfur-deprived photosynthesis and hydrogen production in suspensions of Chlamydomonas Reinhardtii

The ability of unicellular green algal species such as Chlamydomonas reinhardtii to produce hydrogen gas via iron-hydrogenase is well known. However, the oxygen-sensitive hydrogenase is closely linked to the photosynthetic chain in such a way that hydrogen and oxygen production need to be separated temporally for sustained photo-production. Under illumination, sulfur-deprivation has been shown to accommodate the production of hydrogen gas by partially-deactivating O2 evolution activity, leading to anaerobiosis in a sealed culture. As these facets are coupled, and the system complex, mathematical approaches potentially are of significant value since they may reveal improved or even optimal schemes for maximizing hydrogen production. Here, a mechanistic model of the system is constructed from consideration of the essential pathways and processes. The role of sulfur in photosynthesis (via PSII) and the storage and catabolism of endogenous substrate, and thus growth and decay of culture density, are explicitly modeled in order to describe and explore the complex interactions that lead to H2 production during sulfur-deprivation. As far as possible, functional forms and parameter values are determined or estimated from experimental data. The model is compared with published experimental studies and, encouragingly, qualitative agreement for trends in hydrogen yield and initiation time are found. It is then employed to probe optimal external sulfur and illumination conditions for hydrogen production, which are found to differ depending on whether a maximum yield of gas or initial production rate is required. The model constitutes a powerful theoretical tool for investigating novel sulfur cycling regimes that may ultimately be used to improve the commercial viability of hydrogen gas production from microorganism
Rate-limiting step analysis of the microbial desulfurization of dibenzothiophene in a model oil system

A mechanistic analysis of the various mass transport and kinetic steps in the microbial desulfurization of dibenzothiophene (DBT) by Rhodococcus erythropolis IGTS8 in a model biphasic (oil–water), small-scale system was performed. The biocatalyst was distributed into three populations, free cells in the aqueous phase, cell aggregates and oil–adhered cells, and the fraction of cells in each population was measured. The power input per volume (P/V) and the impeller tip speed (v[subscript tip]) were identified as key operating parameters in determining whether the system is mass transport controlled or kinetically controlled. Oil–water DBT mass transport was found to not be limiting under the conditions tested. Experimental results at both the 100 mL and 4 L (bioreactor) scales suggest that agitation leading to P/V greater than 10,000 W/ m3 and/or v[subscript tip] greater than 0.67 m/s is sufficient to overcome the major mass transport limitation in the system, which was the diffusion of DBT within the biocatalyst aggregates.National Institutes of Health (U.S.). Biotechnology Training Program (Grant T32GM008334)Saudi Aramc