Publications by authors named "Claudia Villicaña"

9 Publications

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Optimization of PCR-based TYLCV molecular markers by response surface methodology.

Gene 2021 Jun 23;785:145606. Epub 2021 Mar 23.

Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C., Culiacán, Sinaloa, Mexico. Electronic address:

Tomato (Solanum lycopersicum L.) is one of the most economically important vegetables worldwide. However, its production is affected by the tomato yellow leaf curl virus (TYLCV), causing the greatest devastation in the crop. One strategy to cope with TYLCV implies the use of resistant varieties, whose development can be accelerated by molecular markers. The aim of this study was to optimize endpoint PCR protocols for the detection of the molecular markers TG178, TG105A and P6-25, linked to Ty-1, Ty-2 and Ty-3 resistance genes, respectively, through a response surface methodology (RSM) using a central composite design (CCD) for four factors (temperature of annealing (Ta), DNA amount, MgCl and primer concentrations). Applicability, the limit of detection and dynamic range were also analyzed. The optimized PCR conditions were: for TG178: Ta = 60 °C, 90 ng DNA, 3.36 mM MgCl and 0.13 µM primers; for TG105A: Ta = 54.4 °C, 10 ng DNA, 1.5 mM MgCl and 0.9 µM primers; for P6-25, Ta = 52.5 °C, 50 ng DNA, 2.5 mM MgCl and 0.5 µM primers. Dynamic ranges varied from 0.42 to 103.3 ng of DNA, while the limit of detection was 3.82, 0.42 and 11.47 ng of DNA for the TG178, TG105A and P6-25 molecular makers respectively and was 100% positive in replicates. CCD allowed the optimization of PCR protocols for molecular markers, which may further apply in identifying TYLCV resistant tomato lines.
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http://dx.doi.org/10.1016/j.gene.2021.145606DOI Listing
June 2021

The complete genome and comparative analysis of the phage phiC120 infecting multidrug-resistant Escherichia coli and Salmonella strains.

G3 (Bethesda) 2021 Feb;11(2)

Laboratorio de Biología Molecular y Genómica Funcional, Centro de Investigación en Alimentación y Desarrollo, Sinaloa 80110, México.

Phages infecting Salmonella and Escherichia coli are promising agents for therapeutics and biological control of these foodborne pathogens, in particular those strains with resistance to several antibiotics. In an effort to assess the potential of the phage phiC120, a virulent phage isolated from horse feces in Mexico, we characterized its morphology, host range and complete genome. Herein, we showed that phiC120 possesses strong lytic activity against several multidrug-resistant E. coli O157: H7 and Salmonella strains, and its morphology indicated that is a member of Myoviridae family. The phiC120 genome is double-stranded DNA and consists of 186,570 bp in length with a 37.6% G + C content. A total of 281 putative open reading frames (ORFs) and two tRNAs were found, where 150 ORFs encoded hypothetical proteins with unknown function. Comparative analysis showed that phiC120 shared high similarity at nucleotide and protein levels with coliphages RB69 and phiE142. Detailed phiC120 analysis revealed that ORF 94 encodes a putative depolymerase, meanwhile genes encoding factors associated with lysogeny, toxins, and antibiotic resistance were absent; however, ORF 95 encodes a putative protein with potential allergenic and pro-inflammatory properties, making needed further studies to guarantee the safety of phiC120 for human use. The characterization of phiC120 expands our knowledge about the biology of coliphages and provides novel insights supporting its potential for the development of phage-based applications to control unwanted bacteria.
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http://dx.doi.org/10.1093/g3journal/jkab014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8022965PMC
February 2021

The impact of quorum sensing on the modulation of phage-host interactions.

J Bacteriol 2021 Jan 19. Epub 2021 Jan 19.

CONACYT-Centro de Investigación en Alimentación y Desarrollo A.C. Carretera Culiacán-Eldorado Km 5.5 Col. Campo el Diez, C.P. 80110. Culiacán, Sinaloa, México.

Bacteriophages are the most diverse and abundant biological entities on the Earth and require host bacteria to replicate. Because of this obligate relationship, in addition to the challenging conditions of surrounding environments, phages must integrate information about extrinsic and intrinsic factors when infecting their host. This integration helps to determine whether the infection becomes lytic or lysogenic, which likely influences phage spreading and long-term survival. Although a variety of environmental and physiological clues are known to modulate lysis-lysogeny decisions, the social interplay among phages and host populations has been overlooked until recently. A growing body of evidence indicates that cell-cell communication in bacteria and, more recently, peptide-based communication among phage-phage populations, affect phage-host interactions by controlling phage lysis-lysogeny decisions and phage counter-defensive strategies in bacteria. Here, we explore and discuss the role of signal molecules as well as quorum sensing and quenching factors that mediate phage-host interactions. Our aim is to provide an overview of population-dependent mechanisms that influence phage replication, and how social communication may affect the dynamics and evolution of microbial communities, including their implications in phage therapy.
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http://dx.doi.org/10.1128/JB.00687-20DOI Listing
January 2021

Occurrence and Abundance of Pathogenic Species in Raw Oysters at Retail Seafood Markets in Northwestern Mexico.

J Food Prot 2019 Dec;82(12):2094-2099

Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C.

Seafood has frequently been associated with foodborne illness because pathogens are easily introduced during seafood cultivation, handling, and processing. and are human pathogens that cause gastroenteritis and cholera, respectively, and can cause fatal wound infections and septicemia. However, information about the occurrence of these pathogens in oysters from the Pacific coast of Mexico is limited to . In the present study, we evaluated the presence and abundance of these three species in 68 raw oysters () obtained from retail seafood markets in Sinaloa, Mexico. The most probable number (MPN)-PCR assay was used for amplification of the (thermolabile hemolysin), (outer membrane protein), and (hemolytic cytolysin) genes that are specific to and respectively. All oyster samples were positive for at least one species. and prevalences were 77.9, 8.8, and 32.3% overall, respectively, and most species were present in all sample periods with increased prevalence in period 3. The (thermostable direct hemolysin) gene was detected in 30.1%, (TDH-related hemolysin) was detected in 3.7%, and / was detected in 7.5% of the total -positive samples (53 of 68), whereas the pandemic serotype O3:K6 ( positive) was detected in only 1 sample (1.8%). The total prevalence of and/or was 41.5%. In none of the samples positive for were the cholera toxin () and cholix () toxigenic genes or the gene encoding the O1 and O139 antigens amplified, suggesting the presence of non-O1 non-O139 strains. Our results clearly indicated a high prevalence of pathogenic species in raw oysters from retail seafood markets in Mexico. Consumption of these raw oysters carries the potential risk of foodborne illness, which can be limited by cooking.
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http://dx.doi.org/10.4315/0362-028X.JFP-19-237DOI Listing
December 2019

Involvement of OpsLTP1 from Opuntia streptacantha in abiotic stress adaptation and lipid metabolism.

Funct Plant Biol 2019 08;46(9):816-829

Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Apdo, Postal 128, 23096 La Paz, B.C.S., México; and Corresponding author. Email:

Plant lipid transfer proteins (LTPs) exhibit the ability to transfer lipids between membranes in vitro, and have been implicated in diverse physiological processes associated to plant growth, reproduction, development, biotic and abiotic stress responses. However, their mode of action is not yet fully understood. To explore the functions of the OpsLTP1 gene encoding a LTP from cactus pear Opuntia streptacantha Lem., we generated transgenic Arabidopsis thaliana (L.) Heynh. plants to overexpress OpsLTP1 and contrasted our results with the loss-of-function mutant ltp3 from A. thaliana under abiotic stress conditions. The ltp3 mutant seeds showed impaired germination under salt and osmotic treatments, in contrast to OpsLTP1 overexpressing lines that displayed significant increases in germination rate. Moreover, stress recovery assays showed that ltp3 mutant seedlings were more sensitive to salt and osmotic treatments than wild-type plants suggesting that AtLTP3 is required for stress-induced responses, while the OpsLTP1 overexpressing line showed no significant differences. In addition, OpsLTP1 overexpressing and ltp3 mutant seeds stored lower amount of total lipids compared with wild-type seeds, showing changes primarily on 16C and 18C fatty acids. However, ltp3 mutant also lead changes in lipid profile and no over concrete lipids which may suggest a compensatory activation of other LTPs. Interestingly, linoleic acid (18:2ω6) was consistently increased in neutral, galactoglycerolipids and phosphoglycerolipids of OpsLTP1 overexpressing line indicating a role of OpsLTP1 in the modulation of lipid composition in A. thaliana.
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http://dx.doi.org/10.1071/FP18280DOI Listing
August 2019

Dental Pulp Stem Cells: Current Advances in Isolation, Expansion and Preservation.

Tissue Eng Regen Med 2017 Aug 14;14(4):333-347. Epub 2017 Mar 14.

CONACYT - Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingenierías, Universidad Autónoma de Yucatán (UADY), Periférico Norte Kilómetro 33.5, Tablaje Catastral 13615 Chuburná de Hidalgo Inn, CP 97203 Mérida, Yucatán México.

Dental pulp stem cells (DPSCs) are mesenchymal stem cells with high self-renewal potential that have the ability to differentiate into several cell types. Thus, DPSCs have become a promising source of cells for several applications in regenerative medicine, tissue engineering, and stem cell therapy. Numerous methods have been reported for the isolation, expansion, and preservation of DPSCs. However, methods are diverse and do not follow specific rules or parameters, which can affect stem cell properties, adding more variation to experimental results. In this review, we compare and analyze current experimental evidence to propose some factors that can be useful to establish better methods or improved protocols to prolong the quality of DPSCs. In addition, we highlight other factors related to biological aspects of dental tissue source (e.g., age, genetic background) that should be considered before tooth selection. Although current methods have reached significant advances, optimization is still required to improve culture stability and its maintenance for an extended period without losing stem cell properties. In addition, there is still much that needs to be done toward clinical application due to the fact that most of DPSCs procedures are not currently following good manufacturing practices. The establishment of optimized general or tailored protocols will allow obtaining well-defined DPSCs cultures with specific properties, which enable more reproducible results that will be the basis to develop effective and safe therapies.
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http://dx.doi.org/10.1007/s13770-017-0036-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6171610PMC
August 2017

The basal transcription machinery as a target for cancer therapy.

Cancer Cell Int 2014 Feb 28;14(1):18. Epub 2014 Feb 28.

Departament of Developmental Genetics, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Mexico, Mexico.

General transcription is required for the growth and survival of all living cells. However, tumor cells require extraordinary levels of transcription, including the transcription of ribosomal RNA genes by RNA polymerase I (RNPI) and mRNA by RNA polymerase II (RNPII). In fact, cancer cells have mutations that directly enhance transcription and are frequently required for cancer transformation. For example, the recent discovery that MYC enhances the transcription of the majority genes in the genome correlates with the fact that several transcription interfering drugs preferentially kill cancer cells. In recent years, advances in the mechanistic studies of the basal transcription machinery and the discovery of drugs that interfere with multiple components of transcription are being used to combat cancer. For example, drugs such as triptolide that targets the general transcription factors TFIIH and JQ1 to inhibit BRD4 are administered to target the high proliferative rate of cancer cells. Given the importance of finding new strategies to preferentially sensitize tumor cells, this review primarily focuses on several transcription inhibitory drugs to demonstrate that the basal transcription machinery constitutes a potential target for the design of novel cancer drugs. We highlight the drugs' mechanisms for interfering with tumor cell survival, their importance in cancer treatment and the challenges of clinical application.
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http://dx.doi.org/10.1186/1475-2867-14-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3942515PMC
February 2014

The genetic depletion or the triptolide inhibition of TFIIH in p53-deficient cells induces a JNK-dependent cell death in Drosophila.

J Cell Sci 2013 Jun 2;126(Pt 11):2502-15. Epub 2013 Apr 2.

Departamento de Genética del Desarrollo, Instituto de Biotecnología, Avenida Universidad 2001, Cuernavaca Morelos 62250, México.

Transcription factor IIH (TFIIH) participates in transcription, nucleotide excision repair and the control of the cell cycle. In the present study, we demonstrate that the Dmp52 subunit of TFIIH in Drosophila physically interacts with the fly p53 homologue, Dp53. The depletion of Dmp52 in the wing disc generates chromosome fragility, increases apoptosis and produces wings with a reduced number of cells; cellular proliferation, however, is not affected. Interestingly, instead of suppressing the apoptotic phenotype, the depletion of Dp53 in Dmp52-depleted wing disc cells increases apoptosis and the number of cells that suffer from chromosome fragility. The apoptosis induced by the depletion of Dmp52 alone is partially dependent on the JNK pathway. In contrast, the enhanced apoptosis caused by the simultaneous depletion of Dp53 and Dmp52 is absolutely JNK-dependent. In this study, we also show that the anti-proliferative drug triptolide, which inhibits the ATPase activity of the XPB subunit of TFIIH, phenocopies the JNK-dependent massive apoptotic phenotype of Dp53-depleted wing disc cells; this observation suggests that the mechanism by which triptolide induces apoptosis in p53-deficient cancer cells involves the activation of the JNK death pathway.
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http://dx.doi.org/10.1242/jcs.122721DOI Listing
June 2013

Physical and functional interactions between Drosophila homologue of Swc6/p18Hamlet subunit of the SWR1/SRCAP chromatin-remodeling complex with the DNA repair/transcription factor TFIIH.

J Biol Chem 2012 Sep 3;287(40):33567-80. Epub 2012 Aug 3.

Department of Developmental Genetics, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca Morelos, México.

The multisubunit DNA repair and transcription factor TFIIH maintains an intricate cross-talk with different factors to achieve its functions. The p8 subunit of TFIIH maintains the basal levels of the complex by interacting with the p52 subunit. Here, we report that in Drosophila, the homolog of the p8 subunit (Dmp8) is encoded in a bicistronic transcript with the homolog of the Swc6/p18(Hamlet) subunit (Dmp18) of the SWR1/SRCAP chromatin remodeling complex. The SWR1 and SRCAP complexes catalyze the exchange of the canonical histone H2A with the H2AZ histone variant. In eukaryotic cells, bicistronic transcripts are not common, and in some cases, the two encoded proteins are functionally related. We found that Dmp18 physically interacts with the Dmp52 subunit of TFIIH and co-localizes with TFIIH in the chromatin. We also demonstrated that Dmp18 genetically interacts with Dmp8, suggesting that a cross-talk might exist between TFIIH and a component of a chromatin remodeler complex involved in histone exchange. Interestingly, our results also show that when the level of one of the two proteins is decreased and the other maintained, a specific defect in the fly is observed, suggesting that the organization of these two genes in a bicistronic locus has been selected during evolution to allow co-regulation of both genes.
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http://dx.doi.org/10.1074/jbc.M112.383505DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460457PMC
September 2012