Papers by sergio alfonso gonzalez hernandez
Energies, 2021
Air classification (AC) is a cost-effective technology that separates the energy-dense light ash ... more Air classification (AC) is a cost-effective technology that separates the energy-dense light ash fraction (LAF) from the inorganic-rich high ash fraction (HAF) of corn stover. HAF could be upgraded into energy-dense solid fuel by hydrothermal carbonization (HTC). However, HTC is a high-temperature, high-pressure process, which requires additional energy to operate. In this study, three different scenarios (i.e., AC only, HTC only, and integrated AC–HTC) were investigated for the energy recovery of corn stover. AC was performed on corn stover at an 8 Hz fan speed, which yielded 84.4 wt. % LAF, 12.8 wt. % HAF, and 2.8 wt. % below screen particles. About 27 wt. % ash was reduced from LAF by the AC process. Furthermore, HTC was performed on raw corn stover and the HAF of corn stover at 200, 230, and 260 °C for 30 min. To evaluate energy recovery, solid products were characterized in terms of mass yield, ash yield, ultimate analysis, proximate analyses, and higher heating value (HHV). Th...
Frontiers in Energy Research, 2018
Preprocessing with air classification, followed by a hybrid biochemical/thermochemical conversion... more Preprocessing with air classification, followed by a hybrid biochemical/thermochemical conversion scheme, was utilized to improve the quality of short rotation woody coppice (SRWC) for biofuels production. Air classification improved sugar release during enzymatic hydrolysis by 6-12% for poplar and willow coppice respectively. Total theoretical sugar release for these hardwood coppices was ∼70%, which suggests that they could be utilized for biochemical conversion. Improved sugar yields after air classification were tied to compositional changes of reduced ash and extractives which can neutralize dilute acid pretreatment and inhibit fermentation. However, air classification was shown to have little to no effect on pyrolytic thermochemical conversion as it removed material without returning a significant improvement in liquid yield. It was also shown that pyrolysis of biochemical conversion lignin rich residue gives liquid yields comparable to whole tree (without any fractionation) pyrolysis, with a higher quality oil that has ∼60% reduced total acid number. Using this combined biochemical/thermochemical conversion strategy can improve yields of fermentable sugars and pyrolysis liquid above 80%, instead of the 60% yield of sugars or bio-oil when using a single conversion strategy. Overall, it has been shown that preprocessing and hybrid conversion pathways are a viable strategy for maximizing biorefinery viability.
Biomass and Bioenergy, 2017
We report here on an experimental study to produce refinery-ready fuel blendstocks via catalytic ... more We report here on an experimental study to produce refinery-ready fuel blendstocks via catalytic hydrodeoxygenation (upgrading) of pyrolysis oil using several biomass feedstocks and various blends. Blends were tested along with the pure materials to determine the effect of blending on product yields and qualities. Within experimental error, oil yields from fast pyrolysis and upgrading are shown to be linear functions of the blend components. Switchgrass exhibited lower fast pyrolysis and upgrading yields than the woody samples, which included clean pine, oriented strand board (OSB), and a mix of piñon and juniper (PJ). The notable exception was PJ, for which the poor upgrading yield of 18% was likely associated with the very high viscosity of the PJ fast pyrolysis oil (947 cp). The highest fast pyrolysis yield (54% dry basis) was obtained from clean pine, while the highest upgrading yield (50%) was obtained from a blend of 80% clean pine and 20% OSB (CP 8 OSB 2). For switchgrass, reducing the fast pyrolysis temperature to 450 °C resulted in a significant increase to the pyrolysis oil yield and reduced hydrogen consumption during hydrotreating, but did not directly affect the hydrotreating oil yield. The water content of fast pyrolysis oils was also observed to increase linearly with the summed content of potassium and sodium, ranging from 21% for clean pine to 37% for switchgrass. Multiple linear regression models demonstrate that fast pyrolysis is strongly dependent upon the contents lignin and volatile matter as well as the sum of potassium and sodium.
Nucleic Acids Research, 2013
We have compiled MultitaskProtDB, available online at http://wallace.uab.es/multitask, to provide... more We have compiled MultitaskProtDB, available online at http://wallace.uab.es/multitask, to provide a repository where the many multitasking proteins found in the literature can be stored. Multitasking or moonlighting is the capability of some proteins to execute two or more biological functions. Usually, multitasking proteins are experimentally revealed by serendipity. This ability of proteins to perform multitasking functions helps us to understand one of the ways used by cells to perform many complex functions with a limited number of genes. Even so, the study of this phenomenon is complex because, among other things, there is no database of moonlighting proteins. The existence of such a tool facilitates the collection and dissemination of these important data. This work reports the database, MultitaskProtDB, which is designed as a friendly user web page containing >288 multitasking proteins with their NCBI and UniProt accession numbers, canonical and additional biological functions, monomeric/oligomeric states, PDB codes when available and bibliographic references. This database also serves to gain insight into some characteristics of multitasking proteins such as frequencies of the different pairs of functions, phylogenetic conservation and so forth.
Frontiers in Bioengineering and Biotechnology, 2015
Multitasking or moonlighting is the capability of some proteins to execute two or more biochemica... more Multitasking or moonlighting is the capability of some proteins to execute two or more biochemical functions. Usually, moonlighting proteins are experimentally revealed by serendipity. For this reason, it would be helpful that Bioinformatics could predict this multifunctionality, especially because of the large amounts of sequences from genome projects. In the present work, we analyze and describe several approaches that use sequences, structures, interactomics, and current bioinformatics algorithms and programs to try to overcome this problem. Among these approaches are (a) remote homology searches using Psi-Blast, (b) detection of functional motifs and domains, (c) analysis of data from protein-protein interaction databases (PPIs), (d) match the query protein sequence to 3D databases (i.e., algorithms as PISITE), and (e) mutation correlation analysis between amino acids by algorithms as MISTIC. Programs designed to identify functional motif/domains detect mainly the canonical function but usually fail in the detection of the moonlighting one, Pfam and ProDom being the best methods. Remote homology search by Psi-Blast combined with data from interactomics databases (PPIs) has the best performance. Structural information and mutation correlation analysis can help us to map the functional sites. Mutation correlation analysis can only be used in very specific situationsit requires the existence of multialigned family protein sequences-but can suggest how the evolutionary process of second function acquisition took place. The multitasking protein database MultitaskProtDB (http://wallace.uab.es/multitask/), previously published by our group, has been used as a benchmark for the all of the analyses.
Journal of Environmental Science and Health, Part A, 2012
This article may be used for research, teaching, and private study purposes. Any substantial or s... more This article may be used for research, teaching, and private study purposes. Any substantial or systematic reproduction, redistribution, reselling, loan, sub-licensing, systematic supply, or distribution in any form to anyone is expressly forbidden. The publisher does not give any warranty express or implied or make any representation that the contents will be complete or accurate or up to date. The accuracy of any instructions, formulae, and drug doses should be independently verified with primary sources. The publisher shall not be liable for any loss, actions, claims, proceedings, demand, or costs or damages whatsoever or howsoever caused arising directly or indirectly in connection with or arising out of the use of this material.
International Biodeterioration & Biodegradation, 2008
Benzene, toluene, ethyl benzene and xylenes, known collectively as BTEX, are widespread contamina... more Benzene, toluene, ethyl benzene and xylenes, known collectively as BTEX, are widespread contaminants, commonly found in soil, aquifers, and the atmosphere. BTEX degradation was evaluated as separate substrates and in mixtures, in liquid culture, and in packed biofilters with the filamentous fungus Paecilomyces variotii CBS115145. BTEX were differentially utilized by P. variotii: toluene was completely degraded, followed by ethyl benzene; benzene was partially assimilated (45%), similarly to m-and p-xylenes, while o-xylene was only 30% metabolized in liquid culture. Carbon recoveries as CO 2 were 48, 40, and 53% for toluene, benzene, and ethyl benzene, respectively. Initial toluene addition allowed complete elimination of m-xylene in 12 days. In mixtures of toluene-benzene and ethyl benzenebenzene, the toluene degradation rate (0.27 mg l À3 h À1) was lower than the rate obtained with only toluene (0.37 mg l À3 h À1), while for ethyl benzene the rate was 0.15 mg l À3 h À1 as single substrate and 0.10 mg l À3 h À1 in the ethyl benzene-benzene mixture. Benzene degradation was also negatively affected by both toluene and ethyl benzene. Enzymatic analyses showed benzene oxidation activity. In biofiltration experiments average total carbon elimination capacities (TCECs) of 70 gC m À3 h À1 and a maximum of around 110 gC m À3 h À1 for the BTEX mixture were attained. Toluene, ethyl benzene, and benzene ECs were around 70 gC m À3 h À1 , 40 gC m À3 h À1 , and 10 gC m À3 h À1 , respectively.
Infectious Agents and Cancer, 2012
Background Hepatitis B virus (HBV) encodes an oncogenic factor, HBx, which is a multifunctional p... more Background Hepatitis B virus (HBV) encodes an oncogenic factor, HBx, which is a multifunctional protein that can induce dysfunctional regulation of signaling pathways, transcription, and cell cycle progression, among other processes, through interactions with target host factors. The subcellular localization of HBx is both cytoplasmic and nuclear. This dynamic distribution of HBx could be essential to the multiple roles of the protein at different stages during HBV infection. Transactivational functions of HBx may be exerted both in the nucleus, via interaction with host DNA-binding proteins, and in the cytoplasm, via signaling pathways. Although there have been many studies describing different pathways altered by HBx, and its innumerable binding partners, the molecular mechanism that regulates its different roles has been difficult to elucidate. Methods In the current study, we took a bioinformatics approach to investigate whether the viral protein HBx might be regulated via phosp...
Applied and Environmental Microbiology, 2005
A biofiltration system inoculated with the mold Paecilomyces variotii CBS115145 showed a toluene ... more A biofiltration system inoculated with the mold Paecilomyces variotii CBS115145 showed a toluene elimination capacity (EC) of around 250 g/m 3 of biofilter/h, which was higher than the values usually reported for bacteria. P. variotii assimilated m - and p -cresols but not the o isomer. Initial toluene hydroxylation occurred both on the methyl group and through the p -cresol pathway. These results were corroborated by detecting benzyl alcohol, benzaldehyde, and p -cresol as volatile intermediates. In liquid cultures with toluene as a substrate, the activity of toluene oxygenase (TO) was 5.6 nmol of O 2 /min/mg of biomass, and that of benzyl alcohol dehydrogenase was 16.2 nmol of NADH/min/mg of protein. Toluene biodegradation determined from the TO activity in the biofilter depended on the biomass distribution and the substrate concentration. The specific enzymatic activity decreased from 6.3 to 1.9 nmol of O 2 /min/mg of biomass along the reactor. Good agreement was found between th...
The treatment of hydrophobic volatile pollutants is limited by the poor transfer of the compounds... more The treatment of hydrophobic volatile pollutants is limited by the poor transfer of the compounds from the gaseous to the liquid biotic phase, where biodegradation occurs. Fungi have shown high Elimination Capacities (EC) with hydrophobic compounds through their increased transfer surface and more favorable partition. This study evaluates silicone oil for enhancing hexane transport and biodegradation by the fungus Fusarium solani in various bioreactor configurations. Silicone oil was first selected among various solvents for its biocompatibility, non-biodegradability and good partitioning properties. Biodegradation experiments were conducted in 1.5 L stirred tank or in 2.5 L packed bed biofilters fed with an hexane load of 180 g.m-3 reactor .h-1 (EBRT: 1 min). Hexane EC of 120 g.m-3 reactor .h-1 was obtained in the stirred tank bioreactor inoculated with Fusarium solani. The addition of 5% of silicone oil to a fungal biofilter improves hexane degradation to 180 g.m-3 reactor .hwith a maximum of 360 g.m-3 reactor .h-1. Control experiments without oil were around 40% lower. These results confirm that the use of an adequate organic phase enhances the transport and subsequently biodegradation of hydrophobic compounds such as hexane.
Journal of Computer Science & Systems Biology, 2009
The advent of genomics should have facilitated the identification of microbial virulence factors,... more The advent of genomics should have facilitated the identification of microbial virulence factors, a key objective for vaccine design, especially for live attenuated vaccines. It is generally assumed than when the bacterial pathogen infects the host it expresses a set of genes, a number of them being virulence factors. However, up to now, although several Omics methods have been applied to identify virulence genes, i.e., DNA microarrays, In Vivo Expression Technology (IVET), Signature-Tagged Mutagenesis (STM), Differential Fluorescence Induction (DFI), etc., the results are quite meager. Among the genes identified by these techniques there are many related to cellular stress, basal metabolism, etc., which cannot be directly involved in virulence, or at least cannot be considered useful candidates to be deleted for designing a vaccine. Among the genes disclosed by these methodologies there are a number annotated as being hypothetical or unknown proteins. As these ORFs can hide some true virulence factors, we have selected all of these hypothetical proteins from several respiratory diseases and predicted their biological functions by a careful and in-depth analysis of each one. Although some of the re-annotations match with functions that can be related to microbial virulence, it can be concluded that identification of virulence factors remains elusive.
Genome announcements, Jan 23, 2014
The hepatitis B virus (HBV) is a DNA virus belonging to the Hepadnaviridae family. Viral isolates... more The hepatitis B virus (HBV) is a DNA virus belonging to the Hepadnaviridae family. Viral isolates have been classified into 10 genotypes, named from A to J, and several subtypes. We report the full-genome sequence from a single molecular clone of HBV genotype F1b, amplified from a chronically infected Chilean patient.
Molecular BioSystems, 2011
Physical Review E, 2006
We present a mesoscopic hydrodynamic description of the dynamics of colloidal suspensions. We con... more We present a mesoscopic hydrodynamic description of the dynamics of colloidal suspensions. We consider the system as a gas of Brownian particles suspended in a Newtonian heat bath subjected to stationary non-equilibrium conditions imposed by a velocity field. Using results already obtained in previous studies in the field by means of a generalized Fokker-Planck equation, we obtain a set of coupled differential equations for the local diffusion current and the evolution of the total stress tensor. We find that the dynamic shear viscosity of the system contains contributions arising from the finite size of the particles.
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 2012
Pigment patterning in animals generally occurs during early developmental stages and has ecologic... more Pigment patterning in animals generally occurs during early developmental stages and has ecological, physiological, ethological, and evolutionary significance. Despite the relative simplicity of color patterns, their emergence depends upon multilevel complex processes. Thus, theoretical models have become necessary tools to further understand how such patterns emerge. Recent studies have reevaluated the importance of epigenetic, as well as genetic factors in developmental pattern formation. Yet epigenetic phenomena, specially those related to physical constraints that might be involved in the emergence of color patterns, have not been fully studied. In this article, we propose a model of color patterning in which epigenetic aspects such as cell migration, cell-tissue interactions, and physical and mechanical phenomena are central. This model considers that motile cells embedded in a fibrous, viscoelastic matrix-mesenchyme-can deform it in such a way that tension tracks are formed. We postulate that these tracks act, in turn, as guides for subsequent cell migration and establishment, generating long-range phenomenological interactions. We aim to describe some general aspects of this developmental phenomenon with a rather simple mathematical model. Then we discuss our model in the context of available experimental and morphological evidence for reptiles, amphibians, and fishes, and compare it with other patterning models. We also put forward novel testable predictions derived from our model, regarding, for instance, the localization of the postulated tension tracks, and we propose new experiments. Finally, we discuss how the proposed mechanism could constitute a dynamic patterning module accounting for pattern formation in many animal lineages.
Environmental Science & Technology, 2006
Biofiltration of hydrophobic volatile pollutants is intrinsically limited by poor transfer of the... more Biofiltration of hydrophobic volatile pollutants is intrinsically limited by poor transfer of the pollutants from the gaseous to the liquid biotic phase, where biodegradation occurs. This study was conducted to evaluate the potential of silicone oil for enhancing the transport and subsequent biodegradation of hexane by the fungus Fusarium solani in various bioreactor configurations. Silicone oil was first selected among various solvents for its biocompatibility, nonbiodegradability, and good partitioning properties toward hexane. In batch tests, the use of silicone oil improved hexane specific biodegradation by approximately 60%. Subsequent biodegradation experiments were conducted in stirred-tank (1.5 L) and packed-bed (2.5 L) bioreactors fed with a constant gaseous hexane load of 180 g‚m-3 reactor ‚h-1 and operated for 12 and 40 days, respectively. In the stirred reactors, the maximum hexane elimination capacity (EC) increased from 50 g‚m-3 reactor ‚h-1 (removal efficiency, RE of 28%) in the control not supplied with silicone oil to 120 g‚m-3 reactor ‚h-1 in the biphasic system (67% RE). In the packed-bed bioreactors, the maximum EC ranged from 110 (50% RE) to 180 g‚m-3 reactor ‚h-1 (>90% RE) in the control and two-liquid-phase systems, respectively. These results represent, to the best of our knowledge, the first reported case of fungi use in a two-liquid-phase bioreactor and the highest hexane removal capacities so far reported in biofilters.
Chemical Engineering Journal, 2009
The objective of this work was to evaluate different operational strategies for photobioreactors ... more The objective of this work was to evaluate different operational strategies for photobioreactors to remove carbon dioxide using the cyanobacteria, Aphanothece microscopica Nägeli. Two types of reactor configuration, bubble column and airlift were evaluated under three different operational conditions to treat air containing 15% carbon dioxide: simple operation, air recirculation and two sequential reactors. The results obtained showed that the reactor configuration and the operational mode were both determinant criteria for the performance of photobioreactors in the biological conversion of carbon dioxide. Operations with air recirculation showed possibilities for use in small-scale operations, but two-stage sequential photobioreactors (elimination capacity and removal efficiency of 12,217 g carbon /m 3 reactor day and 52.5%, respectively) were shown to be the operational mode with greatest potential for application on an industrial scale by the increased removal efficiency.
Boletín Médico del Hospital Infantil de México, 2014
Conclusiones: Los resultados permiten considerar que la mayoría de los casos con TTRN recibieron ... more Conclusiones: Los resultados permiten considerar que la mayoría de los casos con TTRN recibieron un tratamiento apropiado. Es recomendable desarrollar estrategias efectivas, como reducir la creciente tasa de partos por cesárea, para prevenir la TTRN.
Revista De Investigacion Clinica, 2011
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Papers by sergio alfonso gonzalez hernandez