pinecone/core-2020-05-10-deduplication huggingface dataset:
Development of image analysis techniques as a tool to detect and quantify morphological changes in anaerobic sludge : I. application to a granulation process

Image analysis techniques were developed and
applied to quantify the process of anaerobic granulation in an expanded granular sludge blanket reactor (EGSB) fed with a synthetic substrate based on glucose [60-30% COD chemical oxygen demand)] and volatile fatty acids
(40-70% COD) over 376 days. In a first operation period that lasted 177 days, the aggregation of dispersed sludge was quantitatively monitored through the recognition and quantification of aggregates and filaments. A parameter
defined as the ratio between the filaments' length and the aggregates projected area (LfA) has proven to be sensitive to detect changes in the aggregation status of the anaerobic
sludge. The aggregation time-defined as the moment when a balance between filaments' length and aggregates' size was establishe-was recognized through the LfA.
The percentage of projected area of aggregates within three size ranges (0.01 -0.1 mm, 0.1 - 1 mm, and >1 mm, equivalent diameter) reflected the granular size spectrum during the aggregation process. When sudden increases on the upflow velocity and on the organic loading rate
were applied to the previously formed granules, the developed image analysis techniques revealed to be good indicators of granular sludge stability, since they were sensitive to detected filaments release, fragmentation, and erosion that usually leads to washout. The specific methanogenic
activities in the presence of acetate, propionate,
butyrate, and H2/CO2 increased along the operation, particularly relevant was the sudden increase in the specific hydrogenophilic activity, immediately after the moment recognized
as aggregation time.Fundação para a Ciência e a Tecnologia (FCT) - SFRH/BD/3187/2000,  PRAXIS XXI/BD/20325/99, POCTI/1999/CTA736524.Instituto Cooperação Científica e Tecnológica Internacional (ICCTI), Ambassade de France in Portugal - Project 203 B4
Physicochemical surface properties of brewing yeast influencing their immobilization onto spent grains in a continuous reactor

Immobilization of brewing yeast onto a cellulosebased carrier obtained from spent grains, a brewing byproduct, by acid/base treatment has been studied in a continuously operating bubble-column reactor. The aim
of this work was to study the mechanisms of brewing yeast immobilization onto spent grain particles through the information on physicochemical surface properties of
brewing yeast and spent grain particles. Three mechanisms of brewing yeast immobilization onto spent grains carrier were proposed: cell-carrier adhesion, cell-cell attachment, and cell adsorption (accumulation) inside natural shelters (carrier’s surface roughness). The possibility
of stable cell-carrier adhesion regarding the free energy of interaction was proved and the relative importance of longrange forces (Derjaguin-Landau-Verwey-Overbeek theory)
and interfacial free energies was discussed. As for the cell-cell attachment leading to a multilayer yeast immobilization, a physicochemical interaction through localized
hydrophobic regions on cell surface was hypothesized.
However, neither flocculation nor chain formation mechanism can be excluded so far. The adsorption of brewing yeast inside sufficiently large crevices (pores) was documented with photomicrographs. A positive effect of higher dilution rate and increased hydrophobicity of base-treated
spent grains on the yeast immobilization rate has also been found.Fundação para Ciência e Tecnologia (FCT
Mineralization of LCFA associated with anaerobic sludge : kinetics, enhancement of methanogenic activity, and effect of VFA

Long-chain fatty acids (LCFA) associated with
anaerobic sludge by mechanisms of precipitation, adsorption, or entrapment can be biodegraded to methane. The mineralization kinetics of biomass-associated LCFA were established according to an inhibition model based on Haldane’s enzymatic inhibition kinetics. A value around
1,000 mg COD-LCFA g VSS-1 was obtained for the optimal specific LCFA content that allowed the maximal mineralization rate. For sludge with specific LCFA contents of 2838 ± 63 and 4571 ± 257 mg COD-LCFA g VSS-1, the specific methanogenic activities in the presence of
acetate, butyrate, and H2/CO2 were significantly enhanced
after the mineralization of the biomass-associated LCFA.
For sludge with a specific LCFA content near the optimal
value defined by the kinetic model, the effect of adding
VFA to the medium was studied during the mineralization
of the biomass-associated LCFA. Different patterns were
obtained for each individual substrate. Acetate and butyrate
were preferentially consumed by the consortium, but
in the case of propionate no evidence of a sequential consumption
pattern could be withdrawn. It was concluded
that LCFA do not exert a bactericidal neither a permanent
toxic effect toward the anaerobic consortia. A discussion is
addressed to the relative roles of a reversible inhibitory effect
and a transport limitation effect imposed by the LCFA
surrounding the cells.Fundação para a Ciência e Tecnologia (FCT) - PRAXIS XXI/BD/20326/99, SFRH/BD/8726/2002.
Fundo Social Europeu (FSE)
Monitoring the biological activity of the composting process: oxygen uptake rate (OUR), respirometric index (RI) and respiratory quotient (RQ)

Composting of several organic wastes of different chemical composition (source-separated organic fraction of municipal solid waste, dewatered raw sludge, dewatered anaerobically digested sludge and paper sludge) was carried out under controlled conditions to study the suitability of different biological indexes (oxygen uptake rate, respirometric index, and respiratory quotient) to monitor the biological activity of the composting process. Among the indexes tested, oxygen uptake rate (also referred to as dynamic respirometric index) provided the most reliable values of microbial activity in a compost environment. On the other hand, values of the static respirometric index measured at process temperature, especially in the early stages of the composting process, were significantly lower than those of the dynamic index, which was probably due to oxygen diffusion limitations present in static systems. Both static and dynamic indexes were similar during the maturation phase. Static respirometric index measured at 37°C should not be used with samples obtained during the thermophilic phase, since it resulted in an underestimation of the respiration values. Respiratory quotient presented only slight variations when changing the process temperature or the waste considered, and its use should be restricted to ensure aerobic conditions in the composting matrix
Relationships between hydrodynamics and rheology of flocculating yeast suspensions in a high-cell-density airlift bioreactor

In this article a hydrodynamic and rheological
analysis of a continuous airlift bioreactor with high-celldensity
system is presented. A highly flocculating recombinant
strain of Sacharomyces cerevisiae containing genes
for lactose transport (lactose permease) and hydrolysis
(β-galactosidase) was exploited to ferment lactose from
cheese whey to ethanol. The magnetic particle-tracer
method was used to assess the effect of operational
conditions (air-flow rate, biomass concentration) on hydrodynamic
behavior of an airlift bioreactor during the fermentation
process. Measurements of liquid circulation
velocity showed the existence of a critical value of biomass
concentration at which a dramatic deceleration of
net liquid flow appeared with increasing biomass quantity.
Rheological analysis revealed exponential increase of
viscosity of the yeast floc suspension at the same biomass
concentration of about 73 g/dm³ corresponding to
42.8% v/v of solid fraction. These facts have a particular
importance for the successful processing of a high-celldensity
airlift bioreactor as only a circulated flow regime
will be favorable to keep the solid particles in suspension
state and evenly distributed throughout the bioreactor.União Europeia (UE). Marie Curie Fellowship of the European Community Programme - grant number HPMF-CT-2002-01643
Fluorene and phenanthrene uptake by Pseudomonas putida ATCC 17514 : kinetics and physiological aspects

Pseudomonas putida ATCC 17514 was used as
a model strain to investigate the characteristics of bacterial
growth in the presence of solid fluorene and phenanthrene.
Despite the lower water-solubility of phenanthrene, P.
putida degraded this polycyclic aromatic hydrocarbon
(PAH) at a maximum observed rate of 1.4 ± 0.1 mg Lˉ¹
hˉ¹, higher than the apparent degradation rate of fluorene,
0.8 ± 0.07 mg Lˉ¹ hˉ¹. The role of physiological processes
on the biodegradation of these PAHs was analyzed and
two different uptake strategies were identified. Zeta potential
measurements revealed that phenanthrene-grown
cells were slightly more negatively charged (–57.5 ±
4.7 mV) than fluorene-grown cells (–51.6 ± 4.9 mV), but
much more negatively charged than glucose-grown cells
(–26.8 ± 3.3 mV), suggesting that the PAH substrate
induced modifications on the physical properties of bacterial
surfaces. Furthermore, protein-to-exopolysaccharide
ratios detected during bacterial growth on phenanthrene
were typical of biofilms developed under physicochemical
stress conditions, caused by the presence of sparingly
water-soluble chemicals as the sole carbon and energy
source for growth, the maximum value for TP/EPS during
growth on phenanthrene (1.9) being lower than the one
obtained with fluorene (5.5). Finally, confocal laser microscopy
observations using a gfp-labeled derivative strain
revealed that, in the presence of phenanthrene, P.
putida::gfp cells formed a biofilm on accessible crystal
surfaces, whereas in the presence of fluorene the strain
grew randomly between the crystal clusters. The results
showed that P. putida was able to overcome the lower
aqueous solubility of phenanthrene by adhering to the solid
PAH throughout the production of extracellular polymeric
substances, thus promoting the availability and uptake of
such a hydrophobic compound.Fundação para a Ciência e a Tecnologia (FCT) – PRAXISXXI/BD/15944/98.EC Biotech program - BIO4-CT97-2015
Nonconventional hydrolytic dehalogenation of 1-chlorobutane by dehydrated bacteria in a continuous solid-gas biofilter

Rhodococcus erythropolis NCIMB 13064 and Xanthobacter autotrophicus GJ10 are able to catalyze the conversion of halogenated hydrocarbons to their corresponding alcohols. These strains are attractive biocatalysts for gas phase remediation of polluted gaseous effluents because of their complementary specificity for short or medium and for mono-, di-, or trisubstituted halogenated hydrocarbons (C2-C8 for Rhodococcus erythropolis and C1-C4 for Xanthobacter autotrophicus). After dehydration, these bacteria can catalyze the hydrolytic dehalogenation of 1-chlorobutane in a nonconventional gas phase system under a controlled water thermodynamic activity (aw). This process makes it possible to avoid the problems of solubility and bacterial development due to the presence of water in the traditional biofilters. In the aqueous phase, the dehalogenase activity of Rhodococcus erythropolis is less sensitive to thermal denaturation and the apparent Michaelis-Menten constants at 30°C were 0.4 mM and 2.40 μmol min−1 g−1 for Km and Vmax, respectively. For Xanthobacter autotrophicus they were 2.8 mM and 0.35 μmol min−1 g−1. In the gas phase, the behavior of dehydrated Xanthobacter autotrophicus cells is different from that observed with Rhododcoccus erythropolis cells. The stability of the dehalogenase activity is markedly lower. It is shown that the HCl produced during the reaction is responsible for this low stability. Contrary to Rhodococcus erythropolis cells, disruption of cell walls does not increase the stability of the dehalogenase activity. The activity and stability of lyophilized Xanthobacter autotrophicus GJ10 cells are dependant on various parameters. Optimal dehalogenase activity was determined for water thermodynamic activity (aw) of 0.85. A temperature of 30°C offers the best compromise between activity and stability. The pH control before dehydration plays a role in the ionization state of the dehalogenase in the cells. The apparent Michaelis-Menten constants Km and Vmax for the dehydrated Xanthobacter autotrophicus cells were 0.07 (1-chlorobutane thermodynamic activity) and 0.08 μmol min−1 g−1 of cells, respectively. A maximal transformation capacity of 1.4 g of 1-chlorobutane per day was finally obtained using 1g of lyophilized Xanthobacter autotrophicus GJ10 cell
Anaerobic biodegradation of oleic and palmitic acids : evidence of mass transfer limitations caused by long chain fatty acid accumulation onto the anaerobic sludge

Palmitic acid was the main long chain fatty
acids (LCFA) that accumulated onto the anaerobic sludge when oleic acid was fed to an EGSB reactor. The conversion between oleic and palmitic acid was linked to the biological activity. When palmitic acid was fed to an EGSB reactor it represented also the main LCFA that accumulated onto the sludge. The way of palmitic acid accumulation
was different in the oleic and in the palmitic acid fed reactors.Whenoleic acid was fed, the biomass-associated LCFA (83% as palmitic acid) were mainly adsorbed and
entrapped in the sludge that became ‘‘encapsulated’’ by an LCFA layer. However, when palmitic acid was fed, the
biomass-associated LCFA (the totality as palmitic acid) was mainly precipitated in white spots like precipitates in between the sludge, which remained ‘‘non-encapsulated.’’
The two sludges were compared in terms of the specific methanogenic activity (SMA) in the presence of acetate, propionate, butyrate, and H2CO2, before and after the mineralization of similar amounts of biomassassociated LCFA (4.6 and 5.2 g COD-LCFA/g of volatile suspended solids (VSS), for the oleic and palmitic acid fed sludge, respectively). The ‘‘non-encapsulated,’’
sludge exhibited a considerable initial methanogenic activity on all the tested substrates, with the single exception
of butyrate. However, with the ‘‘encapsulated’’ sludge only methane production from ethanol andH2/CO2
was detected, after a lag phase of about 50 h. After mineralization of the biomass-associated LCFA, both sludges exhibited activities of similar order of magnitude
in the presence of the same individual substrates and significantly higher than before. The results evidenced that LCFA accumulation onto the sludge can create a
physical barrier and hinder the transfer of substrates and products, inducing a delay on the initial methane production.
Whatever the mechanism, metabolic or physical, that is behind this inhibition, it is reversible, being eliminated after the depletion of the biomass-associated LCFA.Fundação para a Ciência e Tecnologia (FCT) Fundo Social Europeu (FSE
Laser-guided direct writing for three-dimensional tissue engineering

One of the principal limitations to the size of an engineered tissue is oxygen and nutrient transport. Lacking a vascular bed, cells embedded in an engineered tissue will consume all available oxygen within hours while out branching blood vessels will take days to vascularize the implanted tissue. One possible solution is to directly write vascular structures within the engineered tissue prior to implantation, reconstructing the tissue according to its native architecture. The cell patterning technique, laser-guided direct writing (LGDW), can pattern multiple cells types with micrometer resolution on arbitrary surfaces, including biological gels. Here we show that LGDW can pattern human umbilical vein endothelial cells (HUVEC) in two- and three-dimensions with micrometer accuracy. By patterning HUVEC on Matrigel, we can direct their self-assembly into vascular structures along the desired pattern. Finally, co-culturing the vascular structures with hepatocytes resulted in an aggregated tubular structure similar in organization to a hepatic sinusoid. This capability can facilitate studies of tissue architecture at the single cell level, and of heterotypic interactions underlying processes such as liver and pancreas morphogenesis, differentiation, and angiogenesis.status: publishe
Effects of pH, CO2, and flow pattern on the autotrophic degradation of hydrogen sulfide in a biotrickling filter

In this study, the effects of pH, CO2, and flow pattern on the performance of a biotrickling filter (BTF) packed with plastic Pall rings and treating a H2S-polluted waste gas were investigated to establish the optimum operating conditions and design criteria. The CO2 concentration had no effect on the biodegradation at H2S concentrations below 50 ppm. In the range of 50–127 ppm H2S, CO2 concentrations between 865 and 1,087 ppm enhanced H2S removal, while higher concentrations of 1,309–4,009 ppm CO2 slightly inhibited H2S removal. The co-current flow BTF presented the advantage of a more uniform H2S removal and biomass growth in each section than the counter-current flow BTF. Examination of the pH-effect in the range of pH 2.00–7.00 revealed optimal activity for autotrophs at pH 6.00. Under optimal conditions, the elimination capacity reached 31.12 g H2S/m3/h with a removal efficiency exceeding 97%. In the present research, autotrophic biomass was developed in the BTF, performing both a partial oxidization of H2S to elemental sulfur and a complete oxidization to sulfate, which is favorable from an environmental point of view. Results showed that around 60% of the sulfide concentration fed to the reactor was transformed into sulfate. Such autotrophic trickling filters may present other advantages, including the fact that they do not release any CO2 to the atmosphere. Besides, the limited growth of autotrophs avoids potential clogging problems. Experimental performance data were compared with data from a mathematical model. Comparisons showed that the theoretical model was successful in predicting the performance of the biotrickling filter
In Silico Genome-Scale Reconstruction and Validation of the Staphylococcus aureus Metabolic Network

A genome-scale metabolic model of the Gram-positive, facultative anaerobic opportunistic pathogen Staphylococcus aureus N315 was constructed based on current genomic data, literature, and physiological information. The model comprises 774 metabolic processes representing approximately 23% of all protein-coding regions. The model was extensively validated against experimental observations and it correctly predicted main physiological properties of the wild-type strain, such as aerobic and anaerobic respiration and fermentation. Due to the frequent involvement of S. aureus in hospital-acquired bacterial infections combined with its increasing antibiotic resistance, we also investigated the clinically relevant phenotype of small colony variants and found that the model predictions agreed with recent findings of proteome analyses. This indicates that the model is useful in assisting future experiments to elucidate the interrelationship of bacterial metabolism and resistance. To help directing future studies for novel chemotherapeutic targets, we conducted a large-scale in silico gene deletion study that identified 158 essential intracellular reactions. A more detailed analysis showed that the biosynthesis of glycans and lipids is rather rigid with respect to circumventing gene deletions, which should make these areas particularly interesting for antibiotic development. The combination of this stoichiometric model with transcriptomic and proteomic data should allow a new quality in the analysis of clinically relevant organisms and a more rationalized system-level search for novel drug targets.
Kinetics of lactose fermentation using a recombinant saccharomyces cerevisiae strain

This work presents a multi-route, non-structural kinetic model for interpretation of ethanol fermentation of lactose using a recombinant flocculent Saccharomyces cerevisiae strain expressing both the
LAC4 (coding for β-galactosidase) and LAC12 (coding for lactose permease) genes of Kluyveromyces lactis. In this model, the values of different metabolic pathways are
calculated applying a modified Monod equation rate in which the growth rate is proportional to the concentration of a key enzyme controlling the single metabolic pathway.
In this study, three main metabolic routes for S. cerevisiae are considered: oxidation of lactose, reduction of lactose (producing ethanol), and oxidation of ethanol. The main
bioprocess variables determined experimentally were lactose, ethanol, biomass, and dissolved oxygen concentrations.
Parameters of the proposed kinetic model were established by fitting the experimental data obtained in a small lab-scale fermentor with the initial lactose concentrations ranging from 5 g/dm³ to 50 g/dm³. A very good
agreement between experimental data and simulated profiles of the main variables (lactose, ethanol, biomass, and dissolved oxygen concentrations) was achieved.Slovak Scientific Grant Agency ; Fundação para a Ciência e a Tecnologia (FCT
Proof-of-concept of a novel micro-bioreactor for fast development of industrial bioprocesses

The experimental performance of a novel
micro-bioreactor envisaged for parallel screening and development of industrial bioprocesses has been tested in this work. The micro-bioreactor with an internal volume
of 4.5mL is operated under oscillatory flow mixing (OFM), where a controllable mixing and mass transfer rates are achieved under batch or continuous laminar flow conditions.
Several batch fermentations with a flocculent
Saccharomyces cerevisiae strain were carried out at initial glucose concentrations (S0) range of ~5–20 g/L and compared to yeast growth kinetics in a stirred tank (ST)
bioreactor. Aerobic fermentations were monitored ex situ in terms of pH, DO, glucose consumption, and biomass and ethanol production (wherever applicable). An average
biomass production increase of 83% was obtained in the micro-bioreactor when compared with the ST, with less 93.6% air requirements. It also corresponded to a
214% increase on biomass production when compared with growth in a shaken flask (SF) at S0=20 g/L. Further anaerobic fermentations at the same initial glucose concentration
ranges gave the opportunity to use state-ofthe-art fiber optics technology for on-line and real-time monitoring of this bioprocess. Time profiles of biomass concentration (measured as optical density (OD))were very
similar in the ST bioreactor and in the micro-bioreactor, with a highly reproducible yeast growth in these two scale-down platforms.Fundação para a Ciência e a Tecnologia (FCT