Claudio Garibay-Orijel

National Polytechnic Institute, Villa Gustavo A. Madero, The Federal District, Mexico

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Publications (13)28.61 Total impact

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    ABSTRACT: Most Trichloroethylene (TCE) biodegradation reports refer to methanogenic conditions, however, in this work, enhanced sulfidogenesis and TCE biodegradation were achieved in an upflow anaerobic sludge blanket (UASB) reactor in which a completely sulfidogenic sludge, from hydrothermal vents sediments, was developed. The work was divided in three stages, (i) sludge development and sulfate reducing activity (SRA) evaluation, (ii) TCE biodegradation and (iii) SRA evaluation after TCE biodegradation. For (i) SR was 98 ± 0.1%, 84% as sulfide (H2S, 1200 ± 28 mg/L), sulfate reducing activity (SRA) was 188 ± 50 mg COD H2S/g VSS*d. For (ii) The reactor reached 74% of TCE removal, concentrations of vinyl chloride of 16 ± 0.3 μM (5% of the TCE added) and ethene 202 ± 81 μM (67% of the TCE added), SRA of 161 ± 7 mg COD H2S/g VSS*d, 68% of sulfide (H2S) production and 93% of COD removal. For (iii) SRA was of 248 ± 22 mg COD H2S/g VSS*d demonstrating no adverse effects due to TCE. Among the genera of the microorganisms identified in the sludge during TCE biodegradation were: Dehalobacter, Desulfotomaculum, Sulfospirillum, Desulfitobacterium, Desulfovibrio and Clostridium. To the best of our knowledge, this is the first report using a sulfidogenic UASB reactor to biodegrade TCE. The overall conclusions of this work are that the reactor is efficient on both, sulfate and TCE biodegradation and it could be used to decontaminate wastewater containing organic solvents and relatively high concentrations of sulfate.
    International Biodeterioration & Biodegradation 01/2014; 94:182–191. · 2.06 Impact Factor
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    ABSTRACT: BACKGROUND: β-(1,3)(1,6)-D-glucans are fungal cell wall components that have demonstrated immunomodulatory and anti-cancer effects. The (1,3)-β-glucan synthase is one of the main enzymes involved in their biosynthesis. AIMS: To design primers to partially amplify and characterize the (1,3)-β-glucan synthase gene and to determine them in Ganoderma lucidum (G. Lucidum) strain CP-132. METHODS: The primers were designed on the basis of homologous genes in other fungi. Then, with the application of PCR, primers were tested using DNA extracted from the G. lucidum strain CP-382. Amplified sequences were compared with those from the GenBank. RESULTS: Three primer pairs were designed, with all of them amplified products of the expected size. The sequences obtained with primer pairs BGS2113UmF and BGS3097UmR, and BGS547UmF and BGS2113UmR matched with 2 sections of the (1,3)-β-glucan synthase gene. The deduced amino acid sequences showed high similarity with homologous genes from other fungi, particularly Agaricomycetes. CONCLUSIONS: The primer design to partially amplify the (1,3)-β-glucan synthase gene of G. lucidum using sequences from homologous genes was successful. These primers will allow characterizing this important enzyme in a wide range of fungi.
    Revista iberoamericana de micologia. 02/2013;
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    ABSTRACT: Background β-(1,3)(1,6)-D-glucan is fungal cell wall component that has demonstrated immunomodulatory and anti-cancer effects. The (1,3)-β-glucan synthase is one of the main enzymes involved in its biosynthesis. Aims To design primers to partially amplify and characterize the (1,3)-β-glucan synthase gene and to determine them in Ganoderma lucidum (G. Lucidum) strain CP-132. Methods The primers were designed on the basis of homologous genes in other fungi. Then, using the PCR technique, primers were tested using DNA extracted from the G. lucidum strain CP-382. Amplified sequences were compared with those from the GenBank. Results Three primer pairs were designed; all of them produced amplicons of the expected size. The sequences obtained with primer pairs BGS2113UmF and BGS3097UmR, and BGS547UmF and BGS2113UmR matched with 2 sections of the (1,3)-β-glucan synthase gene. The deduced amino acid sequences showed high similarity with homologous genes from other fungi, particularly with those of the Agaricomycetes class. Conclusions The primer design to partially amplify the (1,3)-β-glucan synthase gene of G. lucidum using sequences from homologous genes was successful. These primers will allow to characterize this important enzyme in a wide group of fungi.
    Revista Iberoamericana de Micología 01/2013; 30(4):267–270. · 1.31 Impact Factor
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    ABSTRACT: Two-phase partitioning bioreactors (TPPBs) are based on the addition of an organic phase, often called vector, to a bioreactor in order to increase mass transfer of oxygen or gaseous substrates from the gaseous phase to the aqueous phase. In TPPBs, like in any other reactor design, the characterization of the bioprocess is often required for design, control, and operation purposes. Pulse respirometry is a method that allows for microbial processes characterization through the determination of several stoichiometric and kinetic parameters with relatively little experimental effort. Despite its interest and its previous application in countless applications, pulse respirometry has never been applied in TPPBs. In this work, pulse respirometry was assessed in a model TPPB degrading terephthalic acid and using Elvax™ as solid vector to enhance oxygen transfer. The results indicated that the addition of 10 to 20 % Elvax increased oxygen transfer by up to 97 %, compared to control with no vector. Pulse respirometry was successfully applied and allowed for the determination of the growth yield, the substrate affinity constant, and the maximum growth rate, within other. It is concluded that pulse respirometry is a useful method, not only for the characterization of processes in TPPBs but also for the selection of a vector within several brands commercially available.
    Applied biochemistry and biotechnology 12/2012; · 1.94 Impact Factor
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    ABSTRACT: The purpose of our research was to evaluate the effect of eliminating supplementation of sucrose to the reactor influent on the performance of a lab scale partially-aerated methanogenic fluidized bed bioreactor (PAM-FBBR). Two operational stages were distinguished: in the first stage the influent contained a mixture of 120/30/1000 mg/L of 2,4,6-trichlorophenol/phenol/COD-sucrose (TCP/Phe/COD-sucrose); in the second stage only the xenobiotic concentrations were the same 120/30 mg/L of TCP/Phe whereas sucrose addition was discontinued. Removal efficiencies of TCP, Phe, and COD were very high and close for both stages; i.e., η(TCP): 99.9 and 99.9%; η(Phe): 99.9 and 99.9%; η(COD) = 96.46 and 97.48% for stage 1 and stage 2, respectively. Traces of 2,4,6 dichlorophenol (0.05 mg/L) and 4-chlorophenol (0.07-0.26 mg/L) were found during the first 15 days of operation of the second stage, probably due to the adaptation to no co-substrate conditions. Net increase of chloride anion Cl(-) in effluent ranged between 59.5 and 61.5 mg Cl(-)/L that was very close to the maximum theoretical concentration of 62.8 mg Cl(-)/L. PCR-DGGE analysis revealed a richness decrease of eubacterial domain posterior to sucrose elimination from the influent whereas archaeal richness remained almost the same. However, the bioreactor performance was not negatively affected by discontinuing the addition of co-substrate sucrose. Our results indicate that the application of PAM-FBBR to the treatment of groundwaters polluted with chlorophenols and characterized by the lack of easily degradable co-substrates, is a promising alternative for on site bioremediation.
    Journal of Environmental Management 04/2012; · 3.06 Impact Factor
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    ABSTRACT: Cysteine proteases (CPs) from the C1 family, which are similar to papain, can be found in animals and plants, as well as some viruses and prokaryotes. These enzymes have diverse physiological functions and are thus very attractive for science and industry. Jacaratia mexicana, a member of the Caricaceae plant family, contains several CPs, the principal being mexicain, found to favorably compete against papain for many industrial applications due to its high stability and specific activity. In this study, leaves of J. mexicana were used to isolate a CP-coding gene, similar to those that code for mexicain and chymomexicain. By using rapid amplification of cDNA ends (RACE) as well as oligonucleotide design from papain-like conserved amino acids (aa), a sequence of 1404 bp consisting of a 5' terminal untranslated region (UTR) of 153 bp, a 3' terminal UTR of 131 bp, with a polyadenylation (poly(A)) signal sequence and a poly(A) tail, and an open reading frame (ORF) of 1046 bp, was obtained by overlapping three partial sequences. Two full-length cDNA sequences that encode for mexicain-like proteases were cloned from mRNA (JmCP4 and JmCP5). JmCP4 is predicted to have an ORF of 1044 bp, which codifies for polypeptides that have a 26 aa signal peptide region, a 108 aa propeptide region and a mature enzyme of 214 aa. A 969 bp fragment (JmCP5) encodes for a partial sequence of a CP gene, without the signal peptide region but with a full-length propeptide region. The sequence analysis showed that this protease presented a high similarity to other plant CPs from J. mexicana, Vasconcellea cundinamarcensis, Vasconcellea stipulata, and Carica papaya, among others, mainly at the conserved catalytic site. Obtaining the sequence of this CP gene from J. mexicana provides an alternative for production in a standard system and could be an initial step towards the commercialization of this enzyme.
    Gene 04/2012; 502(1):60-8. · 2.20 Impact Factor
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    ABSTRACT: Sulfate reduction (SR) and trichloroethylene (TCE) biodegradation at two different temperatures (37 and 70 °C) were investigated in enrichment cultures prepared with two different samples of sediments collected from hydrothermal vents. The unadapted sediments were incubated with sulfate (4 g L−1) as the electron acceptor before TCE addition to enrich them in biomass and to establish a constant sulfate reduction (SR, 87% sulfate conversion and specific H2S concentration of 90.81 ± 8.19 mg H2S g VSS−1), afterwards TCE was added at an initial concentration of 300 μmol L−1. The best results for TCE biodegradation were obtained at 37 °C. At this temperature, SR was up to 92%, whereas TCE biodegradation reached 75% and ethane was detected as the main degradation product. Under thermophilic conditions (70 °C) TCE biodegradation reached up to approximately 60% and the SR was 30% in 30 days of incubation with the chlorinated solvent. Along with these results, the 16S rDNA analysis from samples at 37 °C showed the presence of bacteria belonging to the genera: Clostridium, Bacillus and Desulfuromonas. The overall results on TCE degradation and SR suggest that cometabolic TCE degradation is carried out by sulfate or sulfur reducers and fermentative bacteria at mesophilic conditions.
    International Biodeterioration & Biodegradation 01/2011; 65(1):116-123. · 2.06 Impact Factor
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    ABSTRACT: In March 2009, public health surveillance detected increased numbers of influenza-like illness presenting to hospitals in Mexico City. The aetiological agent was subsequently determined to be a novel influenza A (H1N1) triple reassortant, which has spread worldwide. As a consequence the World Health Organisation has declared the first Influenza pandemic of the 21st century. To describe clinically and molecularly the first outbreak of influenza A pH1N1 (2009) during 1-5 May to establish a baseline of epidemiological data for pH1N1. Also, to monitor for the emergence of antiviral resistance, and mutations affecting virulence and transmissibility. Samples were collected from 751 patients with influenza-like symptoms throughout Mexico City and were tested for influenza A pH1N1 (2009) using real-time PCR. In the samples that were positive for influenza A pH1N1 (2009) fragments from the haemagglutinin (H1) and neuraminidase (N1) genes were sequenced. A total of 203/751 (27%) patients were positive for the pandemic H1N1 (2009) virus (53% male and 47% female). The 0-12-year-old group was the most affected 85/751 (42%). Sequence analysis showed five new variants of the pandemic H1N1 (2009) virus for NA: G249E (GQ292900), M269I (GQ292892), Y274H (GQ292913), T332A (GQ292933), N344K (GQ292882), and four variants for HA: N461K (GQ293006), K505R (GQ292989), I435V (GQ292995), I527N (GQ292997). We have provided a baseline of epidemiological data from the first outbreak of influenza A pH1N1 (2009) during 1-5 May in Mexico City. The sequencing of partial fragments of the HA and NA genes did not show the presence of previously described mutations affecting known sites of antiviral resistance in seasonal influenza A such as the H275Y (oseltamivir resistance), R293 or N295 etc.
    Journal of clinical virology: the official publication of the Pan American Society for Clinical Virology 03/2010; 48(1):36-9. · 3.12 Impact Factor
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    ABSTRACT: In the biological production of xylitol from xylose it has been demonstrated that a low-level supply of oxygen to the culture (∼0.1 volume of air per volume of culture medium per minute) yields an increase of extracellular accumulated xylitol up to 0.65 gxylitol gxylose−1 in our experiments. In spite of the abundant experimental evidence regarding xylitol production, the advances in the mathematical description of the process are relatively scarce. In this work, a stoichiometric model considering the main biochemical reactions (metabolic fluxes) involved in microaerobic xylitol production is proposed. The main metabolic reactions in xylitol production by Candida parapsilosis were incorporated in order to establish a stoichiometric reaction rate analysis of the network. The reaction rates in the metabolic network were calculated both for determined and underdetermined systems. A comparison between predicted and experimentally measured or reported yields has shown that the proposed stoichiometric model correctly depicts the xylitol yield within a 12.8% average error for several xylose-assimilating yeasts. The expected xylitol concentrations for a production process were also estimated after a sensitivity analysis of the metabolic network. An analysis of the estimated metabolic fluxes provided insight into some physiological events involved in the production of xylitol by yeasts.
    Biochemical Engineering Journal. 01/2010;
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    ABSTRACT: A fluidized bed bioreactor (FBBR) was operated for more than 1000 days under two regimes, Methanogenic (M) and Methanogenic-Aerobic (M-A), to remove 2,4,6-trichlorophenol (TCP) and phenol (Phe) from a synthetic wastewater, containing different amounts of TCP and Phe, using different aeration flow-rates (0, 2.13, and 1.06 NL O(2)/L.day). M conditions (80:20 mg/L of TCP:Phe, 0 NL O(2)/L.day) showed similar TCP and Phe removal (>95%). Nevertheless accumulation of 4-chlorophenol (4CP) up to 16 mg/L and Phe up to 4 mg/L was observed, while in M-A conditions (80:20 mg/L of TCP:Phe, 2.13 NL O(2)/L.day) TCP and Phe removal achieved 99.9(+)% and after 70 days no accumulation of intermediates were detected. The increase of TCP and Phe in the influent under M-A conditions from 80:20 to 120:30 mg/L of TCP:Phe did not negatively affect the removal of TCP, intermediates and Phe; in fact, they were similar to those in previous M-A conditions. The decrease in the oxygen flow rate from 2.13 to 1.06 NL O(2)/L.day had no negative effect on pollutant removals, which were as high as in previous two M-A conditions. The specific methanogenic activity of bioparticles of the fluidized bed decreased with long-term partial aeration, starting from 1.097 mmol CH(4)/h.g(TKN) in the M regime (day 60) to <0.02 mmolCH(4)/h.g(TKN) at day 1050, suggesting aerobic regime in the bioreactor rather than an M-A regime. In conclusion, complete removal of TCP and less chlorinated intermediates could be achieved in an initially methanogenic FBBR under conditions of partial aeration, although long-term operation seemed to negatively affect the methanogenic activity of biomass. It is also likely that after extended aeration the microbial community was finally enriched with strains with the ability to attack 2,4,6-TCP under aerobic conditions. This report represents the first evidence of a long exposure to oxygen of an anaerobic microbial consortium that efficiently remove TCP.
    Biotechnology and Bioengineering 09/2006; 94(5):949-60. · 4.16 Impact Factor
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    ABSTRACT: We describe a useful and simple model for studies of simultaneous methanogenic–denitrification (M–D) systems. One equation predicts an inverse relationship between the percentage of electron donor channeled into dissimilatory denitrification and the loading ratio λ given by grams degradable COD per gram nitrate-N in the influent. It allows the determination of the extent of use of organic matter by the denitrification and the methanogenic pathways for a given concentration of nitrate salts in the influent. This equation was validated with experimental data from the literature and good agreement between predicted and experimental percentages was found. The other equation allows the calculation of the N nutrient requirements in the ammonia nitrogen form (that is, with oxidation number −3). Copyright © 2005 Society of Chemical Industry
    Journal of Chemical Technology & Biotechnology 01/2006; 81(2):173 - 181. · 2.50 Impact Factor
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    ABSTRACT: A fluidized bed bioreactor (FBBR) was operated for more than 575 days to remove 2,4,6-trichlorophenol (TCP) and phenol (Phe) from a synthetic toxic wastewater containing 80 mg L−1 of TCP and 20 mg L−1 of Phe under two regimes: Methanogenic (M) and Partially-Aerated Methanogenic (PAM). The mesophilic, laboratory-scale FBBR consisted of a glass column (3 L capacity) loaded with 1 L of 1 mm diameter granular activated carbon colonized by an anaerobic consortium. Sucrose (1 g COD L−1) was used as co-substrate in the two conditions. The hydraulic residence time was kept constant at 1 day. Both conditions showed similar TCP and Phe removal (99.9 + %); nevertheless, in the Methanogenic regime, the accumulation of 4-chlorophenol (4CP) up to 16 mg L−1 and phenol up to 4 mg L−1 was observed, whereas in PAM conditions 4CP and other intermediates were not detected. The specific methanogenic activity of biomass decreased from 1.01 ± 0.14 in M conditions to 0.19 ± 0.06 mmolCH4 h−1 gTKN−1 in PAM conditions whereas the specific oxygen uptake rate increased from 0.039 ± 0.008 in M conditions to 0.054 ± 0.012 mmolO2 h−1 gTKN−1, which suggested the co-existence of both methanogenic archaea and aerobic bacteria in the undefined consortium. The advantage of the PAM condition over the M regime is that it provides for the thorough removal of less-substituted chlorophenols produced by the reductive dehalogenation of TCP rather than the removal of the parent compound itself. Copyright © 2005 Society of Chemical Industry
    Journal of Chemical Technology & Biotechnology 09/2005; 80(10):1180 - 1187. · 2.50 Impact Factor
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    ABSTRACT: A PCR-based method for the quantitative detection of Lentinus edodes and Trametes versicolor, two ligninolytic fungi applied for wastewater treatment and bioremediation, was developed. Genomic DNA was used to optimize a PCR method targeting the conserved copper-binding sequence of laccase genes. The method allowed the quantitative detection and differentiation of these fungi in single and defined-mixed cultures after fractionation of the PCR products by electrophoresis in agarose gels. Amplified products of about 150 bp for L. edodes, and about 200 bp for T. versicolor were purified and cloned. The PCR method showed a linear detection response in the 1.0 microg-1 ng range. The same method was tested with genomic DNA from a third fungus (Phanerochaete chrysosporium), yielding a fragment of about 400 bp. Southern-blot and DNA sequence analysis indicated that a specific PCR product was amplified from each genome, and that these corresponded to sequences of laccase genes. This PCR protocol permits the detection and differentiation of three ligninolytic fungi by amplifying DNA fragments of different sizes using a single pair of primers, without further enzymatic restriction of the PCR products. This method has potential use in the monitoring, evaluation, and improvement of fungal cultures used in wastewater treatment processes.
    Applied Microbiology and Biotechnology 07/2005; 67(4):524-31. · 3.69 Impact Factor