Rafael Rojas-Herrera

Universidad Autónoma de Yucatán, Ciudad de Mérida, Yucatán, Mexico

Are you Rafael Rojas-Herrera?

Claim your profile

Publications (24)36.13 Total impact

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Chemotaxis is a mechanism which involves bacterial mobilization to find nutrients or escape from harmful environments. Although ruminal fermentation processes and it's by products are well-known, the rumen bacterial chemotaxis has received no attention. Daidzein is one of common metabolites in plants and has chemotactic effects on soil bacteria that colonize the plants. There are several tests to assess bacterial chemotaxis, but none focused on anaerobic microorganisms as rumen bacteria. We standardized a chemotaxis assay for rumen bacteria by modifying a well-known aerobic capillary method by combining it with technology commonly used for measuring in vitro gas production Parallel assays were included for studying the daidzein isoflavone as a possible attractant and the effect of different chemoattractants (sterile rumen fluid, cellulose and daidzein) on ruminal bacterial consortium was tested. Daidzein showed 3 phylotypes (phylotype 1, 3 and 4), phylotype 3 was also present in the rumen fluid and cellulose, the phylotype 1 (present only in daidzein) was identified as a microorganism closely related to R. albus 7. A better understanding of the mechanisms underlying rumen microbial fermentation can lead to a proper manipulation in order to create probiotic cultures for cattle, which could act beneficially on the intestinal flora of the individual.
    Livestock Science 06/2014; · 1.10 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Chemotaxis is a mechanism which involves bacterial mobilization to find nutrients or escape from harmful environments. Although ruminal fermentation processes and it's by products are well-known, the rumen bacterial chemotaxis has received no attention. Daidzein is one of common metabolites in plants and has chemotactic effects on soil bacteria that colonize the plants. There are several tests to assess bacterial chemotaxis, but none focused on anaerobic microorganisms as rumen bacteria. We standardized a chemotaxis assay for rumen bacteria by modifying a well-known aerobic capillary method by combining it with technology commonly used for measuring in vitro gas production Parallel assays were included for studying the daidzein isoflavone as a possible attractant and the effect of different chemoattractants (sterile rumen fluid, cellulose and daidzein) on ruminal bacterial consortium was tested. Daidzein showed 3 phylotypes (phylotype 1, 3 and 4), phylotype 3 was also present in the rumen fluid and cellulose, the phylotype 1 (present only in daidzein) was identified as a microorganism closely related to R. albus 7. A better understanding of the mechanisms underlying rumen microbial fermentation can lead to a proper manipulation in order to create probiotic cultures for cattle, which could act beneficially on the intestinal flora of the individual.
    Livestock Science 06/2014; 167:121-125. · 1.10 Impact Factor
  • Animal Production Science 01/2014; 54:1486-1489. · 1.03 Impact Factor
  • Source
    Tropical and Subtropical Agroecosystems. 01/2014;
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Plant cells have the capacity to generate a new plant without egg fertilization by a process known as somatic embryogenesis (SE), in which differentiated somatic cells can form somatic embryos able to generate a functional plant. Although there have been advances in understanding the genetic basis of SE, the epigenetic mechanism that regulates this process is still unknown. Here, we show that the embryogenic development of Coffea canephora proceeds through a crosstalk between DNA methylation and histone modifications during the earliest embryogenic stages of SE. We found that low levels of DNA methylation, histone H3 lysine 9 dimethylation (H3K9me2) and H3K27me3 change according to embryo development. Moreover, the expression of LEAFY COTYLEDON1 (LEC1) and BABY BOOM1 (BBM1) are only observed after SE induction, whereas WUSCHEL-RELATED HOMEOBOX4 (WOX4) decreases its expression during embryo maturation. Using a pharmacological approach, it was found that 5-Azacytidine strongly inhibits the embryogenic response by decreasing both DNA methylation and gene expression of LEC1 and BBM1. Therefore, in order to know whether these genes were epigenetically regulated, we used Chromatin Immunoprecipitation (ChIP) assays. It was found that WOX4 is regulated by the repressive mark H3K9me2, while LEC1 and BBM1 are epigenetically regulated by H3K27me3. We conclude that epigenetic regulation plays an important role during somatic embryogenic development, and a molecular mechanism for SE is proposed.
    PLoS ONE 08/2013; 8(8):e72160. · 3.53 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Several comparative genomic tools were used to determine the existence of chemiotaxis in ruminal bacteria. Comparative analysis of microbial genomes (database comprehensive microbial resource (CMR)) was used to search for a specific chemiotaxis gene. Then, short sequences of Ruminococcus albus were searched in the database of the National Center for Biotechnology Information, and compared them in the and Concise Microbial Protein. To predict the number of trans-membrane helices of the putative protein, the methyl-accepting chemotaxis proteins (MCP)program was used (TMpred and TopPred). For comparisons of putative protein structures in the MCP and chemotaxis protein, Simple Modular Architecture Research Tool and protein families database were used. Short sequences of the genome of R. albus revealed the presence of chemotaxis genes that could encode a chemoreceptor (MCP)and chemotaxis proteins. Groups of R. albus chemotaxis genes may be responsible for a diverse set of signalling functions, such as the formation of biofilm, adhesion and gene regulation.
    Journal of Applied Animal Research 12/2011; 39(3-39):189-191. · 0.48 Impact Factor
  • Phyton (Buenos Aires). 12/2011; 80(2):231-240.
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Colletotrichum capsici is an important fungal species that causes anthracnose in many genera of plants causing severe economic losses worldwide. A primer set was designed based on the sequences of the ribosomal internal transcribed spacer (ITS1 and ITS2) regions for use in a conventional PCR assay. The primer set (CcapF/CcapR) amplified a single product of 394 bp with DNA extracted from 20 Mexican isolates of C. capsici. The specificity of primers was confirmed by the absence of amplified product with DNA of four other Colletotrichum species and eleven different fungal genera. This primer set is capable of amplifying only C. capsici from different contaminated tissues or fungal structures, thereby facilitating rapid diagnoses as there is no need to isolate and cultivate the fungus in order to identify it. The sensitivity of detection with this PCR method was 10 pg of genomic DNA from the pathogen. This is the first report of a C. capsici-specific primer set. It allows rapid pathogen detection and provides growers with a powerful tool for a rational selection of fungicides to control anthracnose in different crops and in the post-harvest stage.
    Molecular Biotechnology 09/2011; 49(1):48-55. · 2.28 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Development of a method for the isolation and purification of metagenomic RNA (mgRNA) from the ectopic bacterial flora of octopus. Modifications were made to the methods of Valenzuela-Avendaño et al. (Plant Mol Biol Rep, 2005, 23, 199a) and Chomczynski and Sacchi (Anal Biochem, 1987, 162, 156) to develop a protocol based on chemical lysis with Trizol. This proposed protocol effectively isolated mgRNA. The resulting bacterial RNA transcripts were amplified with universal primers directed to the hypervariable regions of the 16S rRNA gene by complementary DNA synthesis. Protocol efficacy in the study of metabolically active bacterial flora was proven using DGGE, which produced a banding pattern that recovered sequences mainly related to the Vibrionaceae family. The analysed samples were clearly complex, and the proposed protocol was proven to effectively isolate mgRNA from the metabolically active bacterial flora associated with octopus. This is the first protocol proposed for the isolation of bacterial mgRNA that allows identification and study of metabolically active bacterial flora associated with octopus. This is an important step forward in understanding and controlling the microbial community of this economically important fishery resource, aimed at detecting its potentially pathogenic bacteria.
    Letters in Applied Microbiology 07/2011; 53(1):8-13. · 1.63 Impact Factor
  • Source
    Biotechnology Letters 03/2011; · 1.74 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: An isolate of Dunaliella salina (DUNS-1) and other two isolates (DUNS-2 and DUNS-3), collected from coastal lagoons with 14 and 30% (w/v) of NaCl, respectively, were analyzed under different saline conditions. Glycerol (380 mg l(-1)) and carotene (5.9 mg l(-1)) contents for DUNS-2 were 0.3 and 10 times higher than DUNS-3, even though both isolates were collected from the same lagoon and share a similar ribosomal DNA sequence.
    Biotechnology Letters 01/2011; 33(5):1021-6. · 1.74 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The application of different diets have focused on seeking greater production in the ruminant animal feed varies, thus affecting rumen microbial population, however, the production efficiency of ruminants has been reported inconsistently. Furthermore, studies have been conducted secondary metabolites secreted by plants and has been having a function of attractant or repellent in plant-microbe interactions. So our goal is to integrate knowledge of rumen bacteria-particle interactions of forage used for food and flavonoids as stimulants in the flagellar movement. Thus, understanding the signaling pathways used by rumen bacteria to colonize food particles and degradation. Research and implement programs using genomic tools to help us discover chemotactic genes in rumen bacteria that contribute to elucidate principles governing the communication of microbial populations, their interactions and main products of microbial metabolism, and thus could raise the handling of ruminal fermentation, creating the probiotic cultures for cattle.
    Tropical and Subtropical Agroecosystems. 01/2011; 14:891-900.
  • [Show abstract] [Hide abstract]
    ABSTRACT: A new method is described for extraction of metagenomic DNA from soil and sediments which is based on DNA adsorption to silica without the use of phenol, ethanol precipitation or a cesium chloride gradient. High-quality DNA was obtained, and PCR inhibition was overcome by adding bovine serum albumin and adjusting magnesium concentration. By using PCR-DGGE with Firmicutes and lactic acid bacteria-specific primers the extracted metagenomic DNA was shown to contain a mixture of bacterial genomes. This method can be used for screening bacterial diversity in soil and sediment samples.
    Molecular Biotechnology 04/2008; 40(1):13-7. · 2.28 Impact Factor
  • Source
    M Zamudio-Maya, J Narváez-Zapata, R Rojas-Herrera
    [Show abstract] [Hide abstract]
    ABSTRACT: To identify lactic acid bacteria (LAB) colonies isolated from sediments of a coastal marsh by the reduction of 2,3,5-triphenyltetrazolium chloride (TTC) in MRS medium. Single colonies isolated from sediments of a coastal marsh by enrichment in MRS broth were selected from MRS-TTC plates and classified according to colony phenotype based on TTC reduction. A total of 37 colonies grouped in seven different phenotypes were identified by analysis of its 16S ribosomal gene sequence. Most isolates belonged to the Firmicutes phylum, mainly to orders Bacillales and Lactobacillales. LAB were represented by 20 isolates, 15 of which belong to the genus Weissella. Enrichment in MRS was highly selective for the isolation of bacteria belonging to phylum Firmicutes. Several different phenotypes were developed by LAB and must be considered during LAB isolation based on TTC reduction. To our knowledge, this is the first study aimed at determining a relationship between colony phenotype from TTC reduction and a partial identification of isolates based on 16S ribosomal gene sequence similarities. Besides, this is the first report of isolation of W. cibaria from environmental samples.
    Letters in Applied Microbiology 04/2008; 46(3):402-7. · 1.63 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Genetic improvement of coffee, an important commercial crop, through classical breeding is slow and cumbersome. Biotechnology offers alternative strategies for generating new and improved coffee varieties, including those resistances to environmental extremes, pests, and diseases, low in caffeine, and with uniform fruit maturation. Large improvements in somatic embryogenesis, development of haploids, and scale-up of micropropagation have been accomplished in the last 5yr. The recent identification of expressed sequence tags (EST) that are differentially expressed during the infestation of coffee plants by coffee leaf miners and the isolation and cloning of the promoter for the N-methyltransferase gene associated with caffeine production open up the possibility of producing varieties of coffee with new traits. This review provides a summary of in vitro biological advances and directions as to how they could be applied to improve the production and quality of coffee.
    In Vitro Cellular & Developmental Biology - Plant 12/2007; 43(6):507-520. · 1.16 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Somatic embryogenesis is the process by which somatic cells, under induction conditions, generate embryogenic cells, which go through a series of morphological and biochemical changes that result in the formation of a somatic embryo. Somatic embryogenesis differs from zygotic embryogenesis in that it is observable, its various culture conditions can be controlled, and a lack of material is not a limiting factor for experimentation. These characteristics have converted somatic embryogenesis into a model system for the study of morphological, physiological, molecular and biochemical events occurring during the onset and development of embryogenesis in higher plants; it also has potential biotechnological applications. The focus of this review is on embryo development through somatic embryogenesis and especially the factors affecting cell and embryo differentiation.
    Plant Cell Tissue and Organ Culture 09/2006; 86(3):285-301. · 2.61 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Genetic studies and pathogen detection in plants using molecular methods require the isolation of DNA from a large number of samples in a short time span. A rapid and versatile protocol for extracting high-quality DNA from different plant species is described. This method yields from 1 to 2 mg of DNA per gram of tissue. The absorbance ratios (A260/A280) obtained ranged from 1.6 to 2.0. A minimal presence of contaminating metabolites (as polymerase chain reaction [PCR] inhibitors) in samples and a considerable savings in reagents are characteristics of this protocol, as well as the low cost of the analysis per sample. The quality of the DNA was suitable for PCR amplification.
    Molecular Biotechnology 11/2005; 31(2):137-9. · 2.28 Impact Factor
  • R Rojas-Herrera, V.M Loyola-Vargas
    [Show abstract] [Hide abstract]
    ABSTRACT: A gene fragment, termed AR-52, was cloned by differential display analysis during the induction of somatic embryogenesis in foliar explants of Coffea arabica. It is homologous to several class III chitinases and Northern blot shows that it is up regulated during somatic embryogenesis and scarcely expressed in embryos at any developmental stage. AR-52 is also induced by wounding the leaves of in vitro cultured plantlets but not induced in a non-embryogenic suspension culture. Chitinase zymography revealed the existence of at least three-chitinolitic bands that are also regulated during somatic embryogenesis and wounding.
    Plant Science 10/2002; · 4.11 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Histocytological analysis carried out on leaf explants of Coffea arabica undergoing somatic embryogenesis revealed that, using a culture method involving a single Gelrite-containing semisolid medium, the entire region surrounding the edge of the plant-derived leaf explants showed the differentiation of organized structures with little or no callusing. Histological examination of embryogenesis without callus formation (direct somatic embryogenesis) revealed that at approximately 1 week after the explant had been placed in culture, the development of the embryo began in the form of a small, isodiametric, densely cytoplasmic cell that underwent a series of organized divisions. In embryogenesis from callus (indirect somatic embryogenesis), however, the embryogenic cell was observed within the first week. Our histological observations indicate that both direct and indirect somatic embryos of coffee that form on explanted leaf segments and callus, respectively, have a unicellular origin.
    Plant Cell Reports 05/2002; 20(12):1141-1149. · 2.94 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Somatic embryogenesis (SE) is a very useful system for studying the differentiation process in plants and involves gene regulation at several levels. During SE induction in Coffea arabica cv. Catura Rojo two types of cell clusters, embryogenic (EC) and non-embryogenic (NEC), were observed. The goal of this work was to compare the most relevant characteristics between EC and NEC for a better understanding of the mechanism driving SE. Morphohistological observations indicated a correlation between the morphological features of clusters and their embryogenic competence. On the other hand, no variation at the DNA level, studied by AFLP, were found to explain the disparity in embryogenic competence of clusters, but gene expression, observed by RNA differential display, and SDS-PAGE showed differences that can explain that disparity. Our results lead us to propose that differential gene expression can modulate the embryogenic capacity of coffee cells and that the number of genes turned off in somatic cells to allow for the change from a somatic to an embryogenic state, is higher than those genes that are turned on.
    Journal of Plant Physiology 01/2002; 159(11):1267-1270. · 2.77 Impact Factor

Publication Stats

165 Citations
36.13 Total Impact Points

Institutions

  • 2008–2014
    • Universidad Autónoma de Yucatán
      • Faculty of Chemical Engineering
      Ciudad de Mérida, Yucatán, Mexico
  • 2005–2006
    • Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco
      Guadalajara, Jalisco, Mexico
  • 2002
    • Centro de Investigación Científica de Yucatán
      • Unidad de Bioquimica y Biologia Molecular de Plantas
      Ciudad de Mérida, Yucatán, Mexico
  • 2001–2002
    • Instituto Nacional de Ciencias Agrícolas
      La Habana, Ciudad de La Habana, Cuba