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Barrera S, Vázquez-Flores S, Needle D, Rodríguez-Medina N, Iglesias D, Sevigny JL, Gordon LM, Simpson S, Thomas WK, Rodulfo H, De Donato M. Serovars, Virulence and Antimicrobial Resistance Genes of Non-Typhoidal Salmonella Strains from Dairy Systems in Mexico. Antibiotics (Basel) 2023; 12:1662. [PMID: 38136696 PMCID: PMC10740734 DOI: 10.3390/antibiotics12121662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 12/24/2023] Open
Abstract
Salmonella isolated from dairy farms has a significant effect on animal health and productivity. Different serogroups of Salmonella affect both human and bovine cattle causing illness in both reservoirs. Dairy cows and calves can be silent Salmonella shedders, increasing the possibility of dispensing Salmonella within the farm. The aim of this study was to determine the genomic characteristics of Salmonella isolates from dairy farms and to detect the presence of virulence and antimicrobial resistance genes. A total of 377 samples were collected in a cross-sectional study from calves, periparturient cow feces, and maternity beds in 55 dairy farms from the states of Aguascalientes, Baja California, Chihuahua, Coahuila, Durango, Mexico, Guanajuato, Hidalgo, Jalisco, Queretaro, San Luis Potosi, Tlaxcala, and Zacatecas. Twenty Salmonella isolates were selected as representative strains for whole genome sequencing. The serological classification of the strains was able to assign groups to only 12 isolates, but with only 5 of those being consistent with the genomic serotyping. The most prevalent serovar was Salmonella Montevideo followed by Salmonella Meleagridis. All isolates presented the chromosomal aac(6')-Iaa gene that confers resistance to aminoglycosides. The antibiotic resistance genes qnrB19, qnrA1, sul2, aph(6)-Id, aph(3)-ld, dfrA1, tetA, tetC, flor2, sul1_15, mph(A), aadA2, blaCARB, and qacE were identified. Ten pathogenicity islands were identified, and the most prevalent plasmid was Col(pHAD28). The main source of Salmonella enterica is the maternity areas, where periparturient shedders are contaminants and perpetuate the pathogen within the dairy in manure, sand, and concrete surfaces. This study demonstrated the necessity of implementing One Health control actions to diminish the prevalence of antimicrobial resistant and virulent pathogens including Salmonella.
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Affiliation(s)
- Stephany Barrera
- Tecnologico de Monterrey, School of Engineering and Sciences, Querétaro 76130, CP, Mexico; (S.B.); (D.I.); (H.R.)
| | - Sonia Vázquez-Flores
- Tecnologico de Monterrey, School of Engineering and Sciences, Querétaro 76130, CP, Mexico; (S.B.); (D.I.); (H.R.)
| | - David Needle
- Veterinary Diagnostic Lab, University of New Hampshire, Durham, NH 03824, USA;
| | - Nadia Rodríguez-Medina
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Cuernavaca 62100, MR, Mexico;
| | - Dianella Iglesias
- Tecnologico de Monterrey, School of Engineering and Sciences, Querétaro 76130, CP, Mexico; (S.B.); (D.I.); (H.R.)
| | - Joseph L. Sevigny
- Department Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (J.L.S.); (L.M.G.); (S.S.); (W.K.T.)
| | - Lawrence M. Gordon
- Department Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (J.L.S.); (L.M.G.); (S.S.); (W.K.T.)
| | - Stephen Simpson
- Department Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (J.L.S.); (L.M.G.); (S.S.); (W.K.T.)
| | - W. Kelley Thomas
- Department Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (J.L.S.); (L.M.G.); (S.S.); (W.K.T.)
| | - Hectorina Rodulfo
- Tecnologico de Monterrey, School of Engineering and Sciences, Querétaro 76130, CP, Mexico; (S.B.); (D.I.); (H.R.)
| | - Marcos De Donato
- Tecnologico de Monterrey, School of Engineering and Sciences, Querétaro 76130, CP, Mexico; (S.B.); (D.I.); (H.R.)
- The Center for Aquaculture Technologies, San Diego, CA 92121, USA
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Diaz-Lara A, Stevens K, Aguilar-Molina VH, Fernández-Cortés JM, Chabacano León VM, De Donato M, Sharma A, Erickson TM, Al Rwahnih M. High-Throughput Sequencing of Grapevine in Mexico Reveals a High Incidence of Viruses including a New Member of the Genus Enamovirus. Viruses 2023; 15:1561. [PMID: 37515247 PMCID: PMC10386000 DOI: 10.3390/v15071561] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/08/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
This is the first viral metagenomic analysis of grapevine conducted in Mexico. During the summer of 2021, 48 plants displaying virus-like symptoms were sampled in Queretaro, an important grapevine-producing area of Mexico, and analyzed for the presence of viruses via high-throughput sequencing (HTS). The results of HTS were verified by real-time RT-PCR following a standardized testing scheme (Protocol 2010). Fourteen different viruses were identified, including grapevine asteroid mosaic-associated virus (GAMaV), grapevine Cabernet Sauvignon reovirus (GCSV), grapevine fanleaf virus (GFLV), grapevine fleck virus (GFkV), grapevine Pinot gris virus (GPGV), grapevine red globe virus (GRGV), grapevine rupestris stem pitting-associated virus (GRSPaV), grapevine rupestris vein feathering virus (GRVFV), grapevine Syrah virus 1 (GSyV-1), grapevine virus B (GVB), and grapevine leafroll-associated viruses 1, 2, 3, 4 (GLRaV1, 2, 3, 4). Additionally, divergent variants of GLRaV4 and GFkV, and a novel Enamovirus-like virus were discovered. This is the first report of GAMaV, GCSV, GLRaV4, GPGV, GRGV, GRVFV, and GSyV-1 infecting grapevines in Mexico; the impact of these pathogens on production is unknown.
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Affiliation(s)
- Alfredo Diaz-Lara
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico
| | - Kristian Stevens
- Departments of Computer Science and Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA
| | | | | | | | - Marcos De Donato
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico
| | - Ashutosh Sharma
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico
| | - Teresa M Erickson
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA
| | - Maher Al Rwahnih
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA
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Ahmad SM, De Donato M, Bhat BA, Diallo AB, Peters SO. Editorial: Omics technologies in livestock improvement: From selection to breeding decisions. Front Genet 2023; 13:1113417. [PMID: 36685948 PMCID: PMC9846562 DOI: 10.3389/fgene.2022.1113417] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023] Open
Affiliation(s)
- Syed Mudasir Ahmad
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST, Kashmir, India,*Correspondence: Syed Mudasir Ahmad,
| | - Marcos De Donato
- Escuela de Ingeniería y Ciencias, Instituto de Tecnología y Educación Superior de Monterrey (ITESM), Monterrey, Mexico,The Center for Aquaculture Technologies, San Diego, CA, United States
| | | | | | - Sunday O. Peters
- Department of Animal Science, Berry College, Mount Berry, GA, United States
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Hasankhani A, Bahrami A, Mackie S, Maghsoodi S, Alawamleh HSK, Sheybani N, Safarpoor Dehkordi F, Rajabi F, Javanmard G, Khadem H, Barkema HW, De Donato M. In-depth systems biological evaluation of bovine alveolar macrophages suggests novel insights into molecular mechanisms underlying Mycobacterium bovis infection. Front Microbiol 2022; 13:1041314. [PMID: 36532492 PMCID: PMC9748370 DOI: 10.3389/fmicb.2022.1041314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/04/2022] [Indexed: 08/26/2023] Open
Abstract
OBJECTIVE Bovine tuberculosis (bTB) is a chronic respiratory infectious disease of domestic livestock caused by intracellular Mycobacterium bovis infection, which causes ~$3 billion in annual losses to global agriculture. Providing novel tools for bTB managements requires a comprehensive understanding of the molecular regulatory mechanisms underlying the M. bovis infection. Nevertheless, a combination of different bioinformatics and systems biology methods was used in this study in order to clearly understand the molecular regulatory mechanisms of bTB, especially the immunomodulatory mechanisms of M. bovis infection. METHODS RNA-seq data were retrieved and processed from 78 (39 non-infected control vs. 39 M. bovis-infected samples) bovine alveolar macrophages (bAMs). Next, weighted gene co-expression network analysis (WGCNA) was performed to identify the co-expression modules in non-infected control bAMs as reference set. The WGCNA module preservation approach was then used to identify non-preserved modules between non-infected controls and M. bovis-infected samples (test set). Additionally, functional enrichment analysis was used to investigate the biological behavior of the non-preserved modules and to identify bTB-specific non-preserved modules. Co-expressed hub genes were identified based on module membership (MM) criteria of WGCNA in the non-preserved modules and then integrated with protein-protein interaction (PPI) networks to identify co-expressed hub genes/transcription factors (TFs) with the highest maximal clique centrality (MCC) score (hub-central genes). RESULTS As result, WGCNA analysis led to the identification of 21 modules in the non-infected control bAMs (reference set), among which the topological properties of 14 modules were altered in the M. bovis-infected bAMs (test set). Interestingly, 7 of the 14 non-preserved modules were directly related to the molecular mechanisms underlying the host immune response, immunosuppressive mechanisms of M. bovis, and bTB development. Moreover, among the co-expressed hub genes and TFs of the bTB-specific non-preserved modules, 260 genes/TFs had double centrality in both co-expression and PPI networks and played a crucial role in bAMs-M. bovis interactions. Some of these hub-central genes/TFs, including PSMC4, SRC, BCL2L1, VPS11, MDM2, IRF1, CDKN1A, NLRP3, TLR2, MMP9, ZAP70, LCK, TNF, CCL4, MMP1, CTLA4, ITK, IL6, IL1A, IL1B, CCL20, CD3E, NFKB1, EDN1, STAT1, TIMP1, PTGS2, TNFAIP3, BIRC3, MAPK8, VEGFA, VPS18, ICAM1, TBK1, CTSS, IL10, ACAA1, VPS33B, and HIF1A, had potential targets for inducing immunomodulatory mechanisms by M. bovis to evade the host defense response. CONCLUSION The present study provides an in-depth insight into the molecular regulatory mechanisms behind M. bovis infection through biological investigation of the candidate non-preserved modules directly related to bTB development. Furthermore, several hub-central genes/TFs were identified that were significant in determining the fate of M. bovis infection and could be promising targets for developing novel anti-bTB therapies and diagnosis strategies.
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Affiliation(s)
- Aliakbar Hasankhani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
- Biomedical Center for Systems Biology Science Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Shayan Mackie
- Faculty of Science, Earth Sciences Building, University of British Columbia, Vancouver, BC, Canada
| | - Sairan Maghsoodi
- Faculty of Paramedical Sciences, Kurdistan University of Medical Sciences, Kurdistan, Iran
| | - Heba Saed Kariem Alawamleh
- Department of Basic Scientific Sciences, AL-Balqa Applied University, AL-Huson University College, AL-Huson, Jordan
| | - Negin Sheybani
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Farhad Safarpoor Dehkordi
- Halal Research Center of IRI, FDA, Tehran, Iran
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Fatemeh Rajabi
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Ghazaleh Javanmard
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Hosein Khadem
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Herman W. Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Marcos De Donato
- Regional Department of Bioengineering, Tecnológico de Monterrey, Monterrey, Mexico
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Tapia-Arreola AK, Ruiz-Garcia DA, Rodulfo H, Sharma A, De Donato M. High Frequency of Antibiotic Resistance Genes (ARGs) in the Lerma River Basin, Mexico. Int J Environ Res Public Health 2022; 19:ijerph192113988. [PMID: 36360888 PMCID: PMC9657182 DOI: 10.3390/ijerph192113988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 05/31/2023]
Abstract
The spread of beta-lactamase-producing bacteria is of great concern and the environment has been found to be a main source of contamination. Herein, it was proposed to determine the frequency of antimicrobial-resistant-Gram-negative bacteria throughout the Lerma River basin using phenotypic and molecular methods. Resistant bacteria were isolated with chromogenic media and antimicrobial susceptibility tests were used to characterize their resistance. ARGs for beta-lactams, aminoglycosides, and quinolones were detected by PCR. Species were identified by Sanger sequencing the 16S rRNA gene and the representative genomes of MDR strains were sequenced by NGS. A high variation in the number of isolates was observed in the 20 sampled sites, while observing a low diversity among the resistant bacteria. Of the 12 identified bacterial groups, C. freundii, E. coli, and S. marcescens were more predominant. A high frequency of resistance to beta-lactams, quinolones, and aminoglycosides was evidenced, where the blaCTX,qnrB, qnrS y, and aac(6')lb-cr genes were the most prevalent. C. freundii showed the highest frequency of MDR strains. Whole genome sequencing revealed that S. marcescens and K. pneumoniae showed a high number of shared virulence and antimicrobial resistance genes, while E. coli showed the highest number of unique genes. The contamination of the Lerma River with MDR strains carrying various ARGs should raise awareness among environmental authorities to assess the risks and regulations regarding the optimal hygienic and sanitary conditions for this important river that supports economic activities in the different communities in Mexico.
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Estrada-Meza C, Torres-Copado A, Loreti González-Melgoza L, Ruiz-Manriquez LM, De Donato M, Sharma A, Pathak S, Banerjee A, Paul S. Recent insights into the microRNA and long non-coding RNA-mediated regulation of stem cell populations. 3 Biotech 2022; 12:270. [PMID: 36101546 PMCID: PMC9464284 DOI: 10.1007/s13205-022-03343-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 08/29/2022] [Indexed: 12/19/2022] Open
Abstract
Stem cells are undifferentiated cells that have multi-lineage differentiation. The transition from self-renewal to differentiation requires rapid and extensive gene expression alterations. Since different stem cells exhibit diverse non-coding RNAs (ncRNAs) expression profiles, the critical roles of ncRNAs in stem cell reprogramming, pluripotency maintenance, and differentiation have been widely investigated over the past few years. Hence, in this current review, the two main categories of ncRNAs, microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are discussed. While the primary way by which miRNAs restrict mRNA transcription is through miRNA-mRNA interaction, lncRNAs have a wide range of effects on mRNA functioning, including interactions with miRNAs. Both of these ncRNAs participate in the post-transcriptional regulation of crucial biological mechanisms, such as cell cycle regulation, apoptosis, aging, and cell fate decisions. These findings shed light on a previously unknown aspect of gene regulation in stem cell fate determination and behavior. Overall, we summarized the key roles of miRNAs (including exosomal miRNAs) and lncRNAs in the regulation of stem cell populations, such as cardiac, hematopoietic, mesenchymal, neural, and spermatogonial, as well ncRNAs' influence on malignancy through modulating cancer stem cells, which might significantly contribute to clinical stem cell therapy and in regenerative medicine.
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Affiliation(s)
- Carolina Estrada-Meza
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130 Queretaro, Mexico
| | - Andrea Torres-Copado
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130 Queretaro, Mexico
| | - Luisa Loreti González-Melgoza
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130 Queretaro, Mexico
| | - Luis M. Ruiz-Manriquez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130 Queretaro, Mexico
| | - Marcos De Donato
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130 Queretaro, Mexico
| | - Ashutosh Sharma
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130 Queretaro, Mexico
| | - Surajit Pathak
- Chettinad Academy of Research and Education (CARE), Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chennai, India
| | - Antara Banerjee
- Chettinad Academy of Research and Education (CARE), Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chennai, India
| | - Sujay Paul
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130 Queretaro, Mexico
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Paul S, Ruiz-Manriquez LM, Ledesma-Pacheco SJ, Benavides-Aguilar JA, Torres-Copado A, Morales-Rodríguez JI, De Donato M, Srivastava A. Roles of microRNAs in chronic pediatric diseases and their use as potential biomarkers: A review. Arch Biochem Biophys 2021; 699:108763. [PMID: 33460581 DOI: 10.1016/j.abb.2021.108763] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/22/2020] [Accepted: 01/10/2021] [Indexed: 02/09/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding highly conserved RNA molecules that can act as master regulators of gene expression in a sequence-specific manner either by translation repression or mRNA degradation, influencing a wide range of biologic processes that are essential for the maintenance of cellular homeostasis. Chronic pediatric diseases are the leading cause of death worldwide among children and the recent evidence indicates that aberrant miRNA expression significantly contributes to the development of chronic pediatric diseases. This review focuses on the role of miRNAs in five major chronic pediatric diseases including bronchial asthma, congenital heart diseases, cystic fibrosis, type 1 diabetes mellitus, and epilepsy, and their potential use as novel biomarkers for the diagnosis and prognosis of these disorders.
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Affiliation(s)
- Sujay Paul
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130, Queretaro, Mexico.
| | - Luis M Ruiz-Manriquez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130, Queretaro, Mexico
| | - S Janin Ledesma-Pacheco
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130, Queretaro, Mexico
| | - Javier A Benavides-Aguilar
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130, Queretaro, Mexico
| | - Andrea Torres-Copado
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130, Queretaro, Mexico
| | - Jonathan I Morales-Rodríguez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130, Queretaro, Mexico
| | - Marcos De Donato
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130, Queretaro, Mexico
| | - Aashish Srivastava
- Section of Bioinformatics, Clinical Laboratory, Haukeland University Hospital, Bergen, 5021, Norway; Department of Clinical Science, University of Bergen, Bergen, 5021, Norway
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Peters SO, Hussain T, Adenaike AS, Hazzard J, Morenikeji OB, De Donato M, Paul S, Babar M, Yakubu A, Imumorin IG. Evolutionary Pattern of Interferon Alpha Genes in Bovidae and Genetic Diversity of IFNAA in the Bovine Genome. Front Immunol 2020; 11:580412. [PMID: 33117386 PMCID: PMC7561390 DOI: 10.3389/fimmu.2020.580412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/24/2020] [Indexed: 11/13/2022] Open
Abstract
Interferons are secretory proteins induced in response to specific extracellular stimuli which stimulate intra- and intercellular networks for regulating innate and acquired immunity, resistance to viral infections, and normal and tumor cell survival and death. Type 1 interferons plays a major role in the CD8 T-cell response to viral infection. The genomic analysis carried out here for type I interferons within Bovidae family shows that cattle, bison, water buffalo, goat, and sheep (all Bovidae), have different number of genes of the different subtypes, with a large increase in the numbers, compared to human and mouse genomes. A phylogenetic analysis of the interferon alpha (IFNA) proteins in this group shows that the genes do not follow the evolutionary pattern of the species, but rather a cycle of duplications and deletions in the different species. In this study we also studied the genetic diversity of the bovine interferon alpha A (IFNAA), as an example of the IFNA genes in cattle, sequencing a fragment of the coding sequence in 18 breeds of cattle from Pakistan, Nigeria and USA. Similarity analysis allowed the allocation of sequences into 22 haplotypes. Bhagnari, Brangus, Sokoto Gudali, and White Fulani, had the highest number of haplotypes, while Angus, Hereford and Nari Master had the least. However, when analyzed by the average haplotype count, Angus, Bhagnari, Hereford, Holstein, Muturu showed the highest values, while Cholistani, Lohani, and Nari Master showed the lowest values. Haplotype 4 was found in the highest number of individuals (74), and in 15 breeds. Sequences for yak, bison, and water buffalo, were included within the bovine haplotypes. Medium Joining network showed that the sequences could be divided into 4 groups: one with highly similar haplotypes containing mostly Asian and African breeds, one with almost all of the Bos taurus American breeds, one mid-diverse group with mostly Asian and African sequences, and one group with highly divergent haplotypes with five N'Dama sequences and one from each of White Fulani, Dhanni, Tharparkar, and Bhagnari. The large genetic diversity found in IFNAA could be a very good indication of the genetic variation among the different genes of IFNA and could be an adaptation for these species in response to viral challenges they face.
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Affiliation(s)
- Sunday O. Peters
- Department of Animal Science, Berry College, Mount Berry, GA, United States
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Tanveer Hussain
- Department of Molecular Biology, Virtual University of Pakistan, Lahore, Pakistan
| | - Adeyemi S. Adenaike
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
| | - Jordan Hazzard
- Department of Animal Science, Berry College, Mount Berry, GA, United States
| | - Olanrewaju B. Morenikeji
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, United States
- Department of Biology, Hamilton College, Clinton, NY, United States
| | - Marcos De Donato
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Queretaro, Mexico
| | - Sujay Paul
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Queretaro, Mexico
| | - Masroor Babar
- Department of Molecular Biology, Virtual University of Pakistan, Lahore, Pakistan
| | | | - Ikhide G. Imumorin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
- Department of Biological Sciences, First Technical University, Ibadan, Nigeria
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Martínez D, Caña L, Rodulfo H, García J, González D, Rodríguez L, Donato MD. Characteristics of dual carbapenemase-producing Klebsiella pneumoniae strains from an outbreak in Venezuela: a retrospective study. Rev Panam Salud Publica 2020; 44:e50. [PMID: 32973902 PMCID: PMC7498284 DOI: 10.26633/rpsp.2020.50] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 03/12/2020] [Indexed: 12/16/2022] Open
Abstract
Objective. To characterize carbapenemase-producing Klebsiella pneumoniae isolated from patients treated at a hospital in Cumaná, Sucre, Venezuela. Methods. This was a retrospective study conducted at the general hospital in Cumaná where 58 K. pneumoniae strains were analyzed for resistance to antimicrobials, specifically carbapenems, in January – June 2015. Production of metallo-β-lactamases and serine carbapenemases was determined by the double-disc synergy test, using EDTA-sodium mercaptoacetic acid and 3-aminophenyl boronic acid discs, respectively. Multiplex-PCR was used to detect genes coding for carbapenemases. Molecular typing using ERIC-PCR determined the presence of clones. Results. Four strains of K. pneumoniae resistant to carbapenems were identified. Phenotypic methods for detection of metallo-β-lactamases and serine carbapenemases were positive, and PCR demonstrated the co-presence of blaNDM and blaKPC genes in all four strains. ERIC-PCR identified two clones circulating in the hospital. Conclusions. Infection control strategies are needed at the central hospital in Cumaná and its surrounding areas to prevent the spread of these pathogens, especially given the high levels of migration from Venezuela to other countries in South America.
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Affiliation(s)
- Dianny Martínez
- Clinical Bacteriology Laboratory, Antonio Patricio de Alcalá University Hospital Cumaná Venezuela Clinical Bacteriology Laboratory, Antonio Patricio de Alcalá University Hospital, Cumaná, Venezuela
| | - Luisa Caña
- Clinical Bacteriology Laboratory, Antonio Patricio de Alcalá University Hospital Cumaná Venezuela Clinical Bacteriology Laboratory, Antonio Patricio de Alcalá University Hospital, Cumaná, Venezuela
| | - Hectorina Rodulfo
- Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias Querétaro Mexico Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias, Querétaro, Mexico
| | - José García
- Clinical Bacteriology Laboratory, Antonio Patricio de Alcalá University Hospital Cumaná Venezuela Clinical Bacteriology Laboratory, Antonio Patricio de Alcalá University Hospital, Cumaná, Venezuela
| | - Diorelis González
- Clinical Bacteriology Laboratory, Antonio Patricio de Alcalá University Hospital Cumaná Venezuela Clinical Bacteriology Laboratory, Antonio Patricio de Alcalá University Hospital, Cumaná, Venezuela
| | - Lucy Rodríguez
- Clinical Bacteriology Laboratory, Antonio Patricio de Alcalá University Hospital Cumaná Venezuela Clinical Bacteriology Laboratory, Antonio Patricio de Alcalá University Hospital, Cumaná, Venezuela
| | - Marcos De Donato
- Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias Querétaro Mexico Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias, Querétaro, Mexico
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10
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Morenikeji OB, Ajayi OO, Peters SO, Mujibi FD, De Donato M, Thomas BN, Imumorin IG. RNA-seq profiling of skin in temperate and tropical cattle. J Anim Sci Technol 2020; 62:141-158. [PMID: 32292922 PMCID: PMC7142279 DOI: 10.5187/jast.2020.62.2.141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 12/09/2019] [Accepted: 01/03/2020] [Indexed: 11/20/2022]
Abstract
Skin is a major thermoregulatory organ in the body controlling homeothermy, a critical function for climate adaptation. We compared genes expressed between tropical- and temperate-adapted cattle to better understand genes involved in climate adaptation and hence thermoregulation. We profiled the skin of representative tropical and temperate cattle using RNA-seq. A total of 214,754,759 reads were generated and assembled into 72,993,478 reads and were mapped to unique regions in the bovine genome. Gene coverage of unique regions of the reference genome showed that of 24,616 genes, only 13,130 genes (53.34%) displayed more than one count per million reads for at least two libraries and were considered suitable for downstream analyses. Our results revealed that of 255 genes expressed differentially, 98 genes were upregulated in tropically-adapted White Fulani (WF; Bos indicus) and 157 genes were down regulated in WF compared to Angus, AG (Bos taurus). Fifteen pathways were identified from the differential gene sets through gene ontology and pathway analyses. These include the significantly enriched melanin metabolic process, proteinaceous extracellular matrix, inflammatory response, defense response, calcium ion binding and response to wounding. Quantitative PCR was used to validate six representative genes which are associated with skin thermoregulation and epithelia dysfunction (mean correlation 0.92; p < 0.001). Our results contribute to identifying genes and understanding molecular mechanisms of skin thermoregulation that may influence strategic genomic selection in cattle to withstand climate adaptation, microbial invasion and mechanical damage.
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Affiliation(s)
- Olanrewaju B Morenikeji
- Department of Animal Production and Health, Federal University of Technology, Akure, Nigeria.,Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, USA.,Animal Genetics and Genomics Laboratory, Office of International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Oyeyemi O Ajayi
- Animal Genetics and Genomics Laboratory, Office of International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853, USA.,Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
| | - Sunday O Peters
- Department of Animal Science, Berry College, Mount Berry, GA 30149, USA
| | | | - Marcos De Donato
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Queretaro 76130, Mexico
| | - Bolaji N Thomas
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Ikhide G Imumorin
- Animal Genetics and Genomics Laboratory, Office of International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853, USA.,African Institute of Bioscience Research and Training, Ibadan, Nigeria.,Department of Biological Sciences, First Technical University, Ibadan, Nigeria.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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11
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Fajardo C, De Donato M, Rodulfo H, Martinez-Rodriguez G, Costas B, Mancera JM, Fernandez-Acero FJ. New Perspectives Related to the Bioluminescent System in Dinoflagellates: Pyrocystis lunula, a Case Study. Int J Mol Sci 2020; 21:ijms21051784. [PMID: 32150894 PMCID: PMC7084563 DOI: 10.3390/ijms21051784] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/19/2020] [Accepted: 03/03/2020] [Indexed: 11/22/2022] Open
Abstract
Pyrocystis lunula is considered a model organism due to its bioluminescence capacity linked to circadian rhythms. The mechanisms underlying the bioluminescent phenomenon have been well characterized in dinoflagellates; however, there are still some aspects that remain an enigma. Such is the case of the presence and diversity of the luciferin-binding protein (LBP), as well as the synthesis process of luciferin. Here we carry out a review of the literature in relation to the molecular players responsible for bioluminescence in dinoflagellates, with particular interest in P. lunula. We also carried out a phylogenetic analysis of the conservation of protein sequence, structure and evolutionary pattern of these key players. The basic structure of the luciferase (LCF) is quite conserved among the sequences reported to date for dinoflagellate species, but not in the case of the LBP, which has proven to be more variable in terms of sequence and structure. In the case of luciferin, its synthesis has been shown to be complex process with more than one metabolic pathway involved. The glutathione S-transferase (GST) and the P630 or blue compound, seem to be involved in this process. In the same way, various hypotheses regarding the role of bioluminescence in dinoflagellates are exposed.
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Affiliation(s)
- Carlos Fajardo
- Microbiology Laboratory, Institute of Viticulture and Agri-food Research (IVAGRO), Environmental and Marine Sciences Faculty. University of Cadiz (UCA), 11510 Puerto Real, Spain;
| | - Marcos De Donato
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, 76130 Queretaro, Mexico; (M.D.D.); (H.R.)
| | - Hectorina Rodulfo
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, 76130 Queretaro, Mexico; (M.D.D.); (H.R.)
| | - Gonzalo Martinez-Rodriguez
- Institute of Marine Sciences of Andalusia (ICMAN), Department of Marine Biology and Aquaculture, Spanish National Research Council (CSIC), 11519 Puerto Real, Spain;
| | - Benjamin Costas
- Interdisciplinary Centre of Marine and Environmental Research of the University of Porto (CIIMAR), 4450-208 Matosinhos, Portugal;
- Institute of Biomedical Sciences Abel Salazar (ICBAS-UP), University of Porto, 4050-313 Porto, Portugal
| | - Juan Miguel Mancera
- Faculty of Marine and Environmental Sciences, Biology Department, University of Cadiz (UCA), 11510 Puerto Real, Spain;
| | - Francisco Javier Fernandez-Acero
- Microbiology Laboratory, Institute of Viticulture and Agri-food Research (IVAGRO), Environmental and Marine Sciences Faculty. University of Cadiz (UCA), 11510 Puerto Real, Spain;
- Correspondence:
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12
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Adeyemi JA, Peters SO, De Donato M, Cervantes AP, Ogunade IM. Effects of a blend of Saccharomyces cerevisiae-based direct-fed microbial and fermentation products on plasma carbonyl-metabolome and fecal bacterial community of beef steers. J Anim Sci Biotechnol 2020; 11:14. [PMID: 32095237 PMCID: PMC7025411 DOI: 10.1186/s40104-019-0419-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/22/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Previous studies have evaluated the metabolic status of animals fed direct-fed microbial (DFM) using enzyme-based assays which are time-consuming and limited to a few metabolites. In addition, little emphasis has been placed on investigating the effects of DFM on hindgut microbiota. We examined the effects of dietary supplementation of a blend of Saccharomyces cerevisiae-based DFM and fermentation products on the plasma concentrations of carbonyl-containing metabolites via a metabolomics approach, and fecal bacterial community, via 16S rRNA gene sequencing, of beef steers during a 42-day receiving period. Forty newly weaned steers were randomly assigned to receive a basal diet with no additive (CON; n = 20) or a basal diet supplemented with 19 g of Commence™ (PROB; n = 20) for a 42-day period. Commence™ (PMI, Arden Hills, MN) is a blend of 6.2 × 1011 cfu/g of S. cerevisiae, 3.5 × 1010 cfu/g of a mixture of Enterococcus lactis, Bacillus subtilis, Enterococcus faecium, and Lactobacillus casei, and the fermentation products of these aforementioned microorganisms and those of Aspergillus oryzae and Aspergillus niger. On d 0 and 40, rectal fecal samples were collected randomly from 10 steers from each treatment group. On d 42, blood was collected for plasma preparation. RESULTS A total number of 812 plasma metabolites were detected. Up to 305 metabolites [fold change (FC) ≥ 1.5, FDR ≤ 0.01] including glucose, hippuric acid, and 5-hydroxykynurenamine were increased by PROB supplementation, whereas 199 metabolites (FC ≤ 0.63, FDR ≤ 0.01) including acetoacetate were reduced. Supplementation of PROB increased (P ≤ 0.05) the relative abundance of Prevotellaceae UCG-003, Megasphaera, Dorea, Acetitomaculum, and Blautia. In contrast, the relative abundance of Elusimicrobium, Moheibacter, Stenotrophomonas, Comamonas, and uncultured bacterium belonging to family p-2534-18B5 gut group (phylum Bacteroidetes) were reduced (P ≤ 0.05). CONCLUSIONS The results of this study demonstrated that supplementation of PROB altered both the plasma carbonyl metabolome towards increased glucose concentration suggesting an improved energy status, and fecal bacterial community, suggesting an increased hindgut fermentation of the beef steers.
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Affiliation(s)
- James A. Adeyemi
- College of Agriculture, Communities, and the Environment, Kentucky State University, Frankfort, KY 40601 USA
| | - Sunday O. Peters
- Department of Animal Science, Berry College, Mount Berry, GA 30149 USA
| | - Marcos De Donato
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Queretaro, Mexico
| | - Andres Pech Cervantes
- Agricultural Research Station, Fort Valley State University, Fort Valley, GA 31030 USA
| | - Ibukun M. Ogunade
- College of Agriculture, Communities, and the Environment, Kentucky State University, Frankfort, KY 40601 USA
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13
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Fajardo C, Amil-Ruiz F, Fuentes-Almagro C, De Donato M, Martinez-Rodriguez G, Escobar-Niño A, Carrasco R, Mancera JM, Fernandez-Acero FJ. An “omic” approach to Pyrocystis lunula: New insights related with this bioluminescent dinoflagellate. J Proteomics 2019; 209:103502. [DOI: 10.1016/j.jprot.2019.103502] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/14/2019] [Accepted: 08/19/2019] [Indexed: 01/10/2023]
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14
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Rodulfo H, Arcia A, Hernández A, Michelli E, Martinez DDV, Guzman M, Sharma A, Donato MD. Virulence factors and integrons are associated with MDR and XDR phenotypes in nosocomial strains of Pseudomonas aeruginosa in a Venezuelan university hospital. Rev Inst Med Trop Sao Paulo 2019; 61:e20. [PMID: 30970111 PMCID: PMC6453424 DOI: 10.1590/s1678-9946201961020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/05/2019] [Indexed: 11/04/2022] Open
Abstract
Multidrug resistance (MDR), virulence and transferable elements potentiate
Pseudomonas aeruginosa's role as an opportunistic pathogen
creating a high risk for public health. In this study, we evaluated the possible
association of multidrug resistance, virulence factors and integrons with
intrahospital P. aeruginosa strains isolated from patients at
Cumana hospital, Venezuela. Relevant clinical-epidemiological data were
collected to study 176 strains (2009-2016) isolated from different hospital
units. Bacterial resistance was classified as susceptible, low-level resistant
(LDR), multidrug resistant (MDR) and extensively drug-resistant (XDR). Most
strains produced pyoverdine, DNase, gelatinase and hemolysin. Around 73% of the
strains showed some type of movement. MDR and XDR strains increased from 2009
(24.2% and 4.8%, respectively) to 2016 (53.1% and 18.8%); while LDR decreased
from 64.5% to 6.3%. The exoU and exoS genes
were found in a significant number of strains (38.1 and 7.4%, respectively).
Class I integrons were detected in 35.8% of the strains and the frequency was
associated with resistance (42.9, 22.4, 41.4 and 61.9%, for susceptible, LDR,
MDR and XDR, respectively). The MDR/XDR strains were positively associated with
hemolysins and exoU, but negatively associated with bacterial
twitching. MDR/XDR phenotypes were also associated with the Intensive Care Unit
(ICU), septicemia, bronchial infection and diabetic foot ulcers, as well as long
hospital stay (≥10 days) and previous antimicrobial treatment. High frequency of
MDR/XDR strains and their association with class I integrons and virulence
factors can increase the infection potential, as well as morbidity and mortality
of patients attending this hospital and could spread infection to the community,
creating a health risk for the region.
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Affiliation(s)
- Hectorina Rodulfo
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Queretaro, Mexico.,Universidad de Oriente, Laboratório de Genética Molecular, Cumaná, Venezuela
| | - Anlenys Arcia
- Universidad de Oriente, Laboratório de Genética Molecular, Cumaná, Venezuela
| | - Aldo Hernández
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Queretaro, Mexico
| | - Elvia Michelli
- Universidad de Oriente, Laboratório de Genética Molecular, Cumaná, Venezuela
| | - Dianny Del Valle Martinez
- Hospital Universitario Antonio Patricio de Alcalá, Laboratório de Bacteriología Clínica, Cumaná, Venezuela
| | - Militza Guzman
- Universidad de Oriente, Laboratório de Genética Molecular, Cumaná, Venezuela
| | - Ashutoch Sharma
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Queretaro, Mexico
| | - Marcos De Donato
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Queretaro, Mexico.,Universidad de Oriente, Laboratório de Genética Molecular, Cumaná, Venezuela
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15
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Ajayi OO, Peters SO, De Donato M, Sowande SO, Mujibi FDN, Morenikeji OB, Thomas BN, Adeleke MA, Imumorin IG. Computational genome-wide identification of heat shock protein genes in the bovine genome. F1000Res 2018; 7:1504. [PMID: 30542619 PMCID: PMC6259560 DOI: 10.12688/f1000research.16058.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/12/2018] [Indexed: 11/20/2022] Open
Abstract
Background: Heat shock proteins (HSPs) are molecular chaperones known to bind and sequester client proteins under stress. Methods: To identify and better understand some of these proteins, we carried out a computational genome-wide survey of the bovine genome. For this, HSP sequences from each subfamily (sHSP, HSP40, HSP70 and HSP90) were used to search the Pfam (Protein family) database, for identifying exact HSP domain sequences based on the hidden Markov model. ProtParam tool was used to compute potential physico-chemical parameters detectable from a protein sequence. Evolutionary trace (ET) method was used to extract evolutionarily functional residues of a homologous protein family. Results: We computationally identified 67 genes made up of 10, 43, 10 and 4 genes belonging to small HSP, HSP40, HSP70 and HSP90 families respectively. These genes were widely dispersed across the bovine genome, except in chromosomes 24, 26 and 27, which lack bovine HSP genes. We found an uncharacterized outer dense fiber (
ODF1) gene in cattle with an intact alpha crystallin domain, like other small HSPs. Physico-chemical characteristic of aliphatic index was higher in HSP70 and HSP90 gene families, compared to small HSP and HSP40. Grand average hydropathy showed that small HSP (sHSP), HSP40, HSP70 and HSP90 genes had negative values except for
DNAJC22, a member of HSP40 gene family. The uniqueness of
DNAJA3 and
DNAJB13 among HSP40 members, based on multiple sequence alignment, evolutionary trace analysis and sequence identity dendrograms, suggests evolutionary distinct structural and functional features, with unique roles in substrate recognition and chaperone functions. The monophyletic pattern of the sequence identity dendrograms of cattle, human and mouse HSP sequences suggests functional similarities. Conclusions: Our computational results demonstrate the first-pass
in-silico identification of heat shock proteins and calls for further investigation to better understand their functional roles and mechanisms in Bovidae.
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Affiliation(s)
- Oyeyemi O Ajayi
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria.,International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Sunday O Peters
- Department of Animal Science, Berry College, Mount Berry, GA, 30149, USA
| | - Marcos De Donato
- International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.,Departamento Regional de Bioingenierias, Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Queretaro, Mexico
| | - Sunday O Sowande
- Department of Animal Production and Health, Federal University of Agriculture, Abeokuta, Nigeria
| | | | - Olanrewaju B Morenikeji
- International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.,Department of Animal Production and Health, Federal University of Technology, Akure, Nigeria
| | - Bolaji N Thomas
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, 14623, USA
| | - Matthew A Adeleke
- School of Life Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Ikhide G Imumorin
- International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30032, USA.,African Institute of Bioscience Research and Training, Ibadan, Nigeria
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16
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Hussain T, Babar ME, Donato MD, Wajid A, Nadeem A, Ahmad Z, Khan WA, Peters SO, Imumorin IG. Phylogeny of Pakistani Cattle Breeds using Mitochondrial Cytochrome b Gene. PAK J ZOOL 2018. [DOI: 10.17582/journal.pjz/2018.50.6.2029.2035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Peters SO, Hussain T, Adenaike AS, Adeleke MA, De Donato M, Hazzard J, Babar ME, Imumorin IG. Genetic Diversity of Bovine Major Histocompatibility Complex Class II DRB3 locus in cattle breeds from Asia compared to those from Africa and America. J Genomics 2018; 6:88-97. [PMID: 29928467 PMCID: PMC6004549 DOI: 10.7150/jgen.26491] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/25/2018] [Indexed: 12/31/2022] Open
Abstract
Genetic polymorphisms and diversity of BoLA-DRB3.2 are essential because of DRB3 gene's function in innate immunity and its association with infectious diseases resistance or tolerance in cattle. The present study was aimed at assessing the level of genetic diversity of DRB3 in the exon 2 (BoLA-DRB3.2) region in African, American and Asian cattle breeds. Amplification of exon 2 in 174 cattle revealed 15 haplotypes. The breeds with the highest number of haplotypes were Brangus (10), Sokoto Gudali (10) and Dajal (9), while the lowest number of haplotypes were found in Holstein and Sahiwal with 4 haplotypes each. Medium Joining network obtained from haplotypic data showed that all haplotypes condensed around a centric area and each sequence (except in H-3, H-51 and H-106) representing almost a specific haplotype. The BoLA-DRB3.2 sequence analyses revealed a non-significant higher rate of non-synonymous (dN) compared to synonymous substitutions (dS). The ratio of dN/dS substitution across the breeds were observed to be greater than one suggesting that variation at the antigen-binding sites is under positive selection; thus increasing the chances of these breeds to respond to wide array of pathogenic attacks. An analysis of molecular variance revealed that 94.01 and 5.99% of the genetic variation was attributable to differences within and among populations, respectively. Generally, results obtained suggest that within breed genetic variation across breeds is higher than between breeds. This genetic information will be important for investigating the relationship between BoLADRB3.2 and diseases in various cattle breeds studied with attendant implication on designing breeding programs that will aim at selecting individual cattle that carry resistant alleles.
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Affiliation(s)
- Sunday O Peters
- Department of Animal Science, Berry College, Mount Berry, GA 30149.,Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602
| | - Tanveer Hussain
- Department of Molecular Biology, Virtual University of Pakistan, Lahore, Pakistan
| | - Adeyemi S Adenaike
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
| | - Matthew A Adeleke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal (Westville Campus), P/Bag X54001, Durban 4000, South Africa
| | - Marcos De Donato
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Quretaro, Mexico
| | - Jordan Hazzard
- Department of Animal Science, Berry College, Mount Berry, GA 30149
| | - Masroor E Babar
- Department of Molecular Biology, Virtual University of Pakistan, Lahore, Pakistan
| | - Ikhide G Imumorin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332.,African Institute for Bioscience Research and Training, Ibadan, Nigeria
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18
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García J, Martínez D, Caña L, González D, Rodríguez L, Rodulfo H, Donato MD, Guzmán M. Genes qnr en Enterobacteriaceae aisladas en un hospital de Venezuela. Rev Chilena Infectol 2018; 35:147-154. [DOI: 10.4067/s0716-10182018000200147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 01/30/2018] [Indexed: 11/17/2022] Open
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19
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Ajayi OO, Peters SO, De Donato M, Mujibi FD, Khan WA, Hussain T, Babar ME, Imumorin IG, Thomas BN. Genetic variation in N- and C-terminal regions of bovine DNAJA1 heat shock protein gene in African, Asian and American cattle. J Genomics 2018; 6:1-8. [PMID: 29290829 PMCID: PMC5744232 DOI: 10.7150/jgen.23248] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 11/18/2017] [Indexed: 11/12/2022] Open
Abstract
DNAJA1 or heat shock protein 40 (Hsp40) is associated with heat adaptation in various organisms. We amplified and sequenced a total of 1,142 bp of bovine Hsp40 gene representing the critical N-terminal (NTR) and C-terminal (CTR) regions in representative samples of African, Asian and American cattle breeds. Eleven and 9 different haplotypes were observed in the NTR in Asian and African breeds respectively while in American Brangus, only two mutations were observed resulting in two haplotypes. The CTR appears to be highly conserved between cattle and yak. In-silico functional analysis with PANTHER predicted putative deleterious functional impact of c.161 T>A; p. V54Q while alignment of bovine and human NTR-J domains revealed that p.Q19H, p.E20Q and p. E21X mutations occurred in helix 2 and p.V54Q missense mutation occurred in helix 3 respectively. The 124 bp insertion found in the yak DNAJA1 ortholog may have significant functional relevance warranting further investigation. Our results suggest that these genetic differences may be concomitant with population genetic history and possible functional consequences for climate adaptation in bovidae.
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Affiliation(s)
- Oyeyemi O. Ajayi
- Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853
| | - Sunday O. Peters
- Department of Animal Science, Berry College, Mount Berry, GA 30149
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602
| | - Marcos De Donato
- Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853
- Departamento Regional de Bioingenierias, Instituto Tecnologico y de Estudios Superiores de Monterrey, Queretaro, Mexico
| | - F. Denis Mujibi
- Usomi Ltd., PO Box 105086-00101, Ushirika Road, Karen, Nairobi, Kenya
| | - Waqas A. Khan
- Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Tanveer Hussain
- Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853
- Department of Molecular Biology, Virtual University of Pakistan, Lahore, Pakistan
| | - Masroor E. Babar
- African Institute for Biosciences Research and Training, Ibadan, Nigeria
| | - Ikhide G. Imumorin
- Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
- African Institute for Biosciences Research and Training, Ibadan, Nigeria
| | - Bolaji N. Thomas
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester NY, 14623
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De Donato M, Hussain T, Rodulfo H, Peters SO, Imumorin IG, Thomas BN. Conservation of Repeats at the Mammalian KCNQ1OT1-CDKN1C Region Suggests a Role in Genomic Imprinting. Evol Bioinform Online 2017; 13:1176934317715238. [PMID: 28659711 PMCID: PMC5476424 DOI: 10.1177/1176934317715238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/23/2017] [Indexed: 12/19/2022] Open
Abstract
KCNQ1OT1 is located in the region with the highest number of genes showing genomic imprinting, but the mechanisms controlling the genes under its influence have not been fully elucidated. Therefore, we conducted a comparative analysis of the KCNQ1/KCNQ1OT1-CDKN1C region to study its conservation across the best assembled eutherian mammalian genomes sequenced to date and analyzed potential elements that may be implicated in the control of genomic imprinting in this region. The genomic features in these regions from human, mouse, cattle, and dog show a higher number of genes and CpG islands (detected using cpgplot from EMBOSS), but lower number of repetitive elements (including short interspersed nuclear elements and long interspersed nuclear elements), compared with their whole chromosomes (detected by RepeatMasker). The KCNQ1OT1-CDKN1C region contains the highest number of conserved noncoding sequences (CNS) among mammals, where we found 16 regions containing about 38 different highly conserved repetitive elements (using mVista), such as LINE1 elements: L1M4, L1MB7, HAL1, L1M4a, L1Med, and an LTR element: MLT1H. From these elements, we found 74 CNS showing high sequence identity (>70%) between human, cattle, and mouse, from which we identified 13 motifs (using Multiple Em for Motif Elicitation/Motif Alignment and Search Tool) with a significant probability of occurrence, 3 of which were the most frequent and were used to find transcription factor-binding sites. We detected several transcription factors (using JASPAR suite) from the families SOX, FOX, and GATA. A phylogenetic analysis of these CNS from human, marmoset, mouse, rat, cattle, dog, horse, and elephant shows branches with high levels of support and very similar phylogenetic relationships among these groups, confirming previous reports. Our results suggest that functional DNA elements identified by comparative genomics in a region densely populated with imprinted mammalian genes may be related to the regulation of imprinted gene expression.
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Affiliation(s)
- Marcos De Donato
- Animal Genetics and Genomics Laboratory, Office of International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA.,Escuela de Bioingenierias, Tecnologico de Monterrey, Campus Querétaro, Santiago de Querétaro, Mexico
| | - Tanveer Hussain
- Animal Genetics and Genomics Laboratory, Office of International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA.,Department Molecular Biology, Virtual University of Pakistan, Lahore, Pakistan
| | - Hectorina Rodulfo
- Escuela de Bioingenierias, Tecnologico de Monterrey, Campus Querétaro, Santiago de Querétaro, Mexico
| | - Sunday O Peters
- Department of Animal Science, Berry College, Mount Berry, GA, USA
| | - Ikhide G Imumorin
- Animal Genetics and Genomics Laboratory, Office of International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA.,African Institute for Biosciences Research and Training, Ibadan, Nigeria.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Bolaji N Thomas
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, USA
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Martínez D, Araque Y, Roduifo H, Caña L, García J, Gonzáiez D, Rodríguez L, De Donato M. [Clonal relationship and detection of blaKPC gene in strains of Klebsiella pneumoniae resistant to carbapenems, at a hospital in Venezuela]. Rev Chilena Infectol 2017; 33:524-530. [PMID: 28112335 DOI: 10.4067/s0716-10182016000500006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/06/2016] [Indexed: 11/17/2022] Open
Abstract
In order to study the clonal relationship and blaKPC gene detection in clinical isolates of Klebsiella pneumoniae resistant to carbapenems, we analyzed 22 clinical isolates of K. pneumoniae with resistance to imipenem and/ or meropenem, isolated in the laboratory of bacteriology at the University Hospital "Antonio Patricio de Alcalá" (HUAPA) from the Cumana city, Sucre state, Venezuela, for a period of five consecutive years. Susceptibility to different antimicrobials was determined, and the presence of carbapenemases was detected by modified Hodge method, phenyl boronic acid synergy and combination discs. blaKPC gene detection was conducted by polymerase chain reaction and the clonal relationship was determined by pulsed field electrophoresis. High rates of antimicrobial resistance were found, five strains were negative, at least one phenotypic method, and all carried the blaKPC gene. Clonal spread was observed only in the intensive care unit (ICU), while in other services, polyclonality was found. We concluded that blaKPC gene is present in K. pneumoniae strains resistant to carbapenems isolated in the HUAPA and clonal spread it was only in the ICU.
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Affiliation(s)
- Dianny Martínez
- Laboratorio de Bacteriología, Hospital Universitario Antonio Patricio de Alcalá, Cumaná, Venezuela
| | - Yasmina Araque
- Postgrado en Biología Aplicada, Universidad de Oriente, Cumaná, Venezuela
| | - Hectorina Roduifo
- Laboratorio de Genética Molecular, Instituto de Biomedicina y Ciencias Aplicadas Dra. Susan Tai, Cumaná, Venezuela
| | - Luisa Caña
- Laboratorio de Bacteriología, Hospital Universitario Antonio Patricio de Alcalá, Cumaná, Venezuela
| | - José García
- Laboratorio de Bacteriología, Hospital Universitario Antonio Patricio de Alcalá, Cumaná, Venezuela
| | - Diorelis Gonzáiez
- Laboratorio de Bacteriología, Hospital Universitario Antonio Patricio de Alcalá, Cumaná, Venezuela
| | - Lucy Rodríguez
- Laboratorio de Bacteriología, Hospital Universitario Antonio Patricio de Alcalá, Cumaná, Venezuela
| | - Marcos De Donato
- Laboratorio de Genética Molecular, Instituto de Biomedicina y Ciencias Aplicadas Dra. Susan Tai, Cumaná, Venezuela
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22
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De Donato M, Peters SO, Hussain T, Rodulfo H, Thomas BN, Babar ME, Imumorin IG. Molecular evolution of type II MAGE genes from ancestral MAGED2 gene and their phylogenetic resolution of basal mammalian clades. Mamm Genome 2017; 28:443-454. [DOI: 10.1007/s00335-017-9695-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/06/2017] [Indexed: 01/08/2023]
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23
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Yakubu A, Salako AE, De Donato M, Peters SO, Takeet MI, Wheto M, Okpeku M, Imumorin IG. Association of SNP variants of MHC Class II DRB gene with thermo-physiological traits in tropical goats. Trop Anim Health Prod 2016; 49:323-336. [PMID: 27909914 DOI: 10.1007/s11250-016-1196-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/24/2016] [Indexed: 11/30/2022]
Abstract
Host defense in vertebrates depend on many secreted regulatory proteins such as major histocompatibility complex (MHC) class II which provide important regulatory and effector functions of T cells. Gene polymorphism in the second exon of Capra-DRB gene in three major Nigerian goat breeds [West African Dwarf (WAD), Red Sokoto (RS), and Sahel (SH)] was analyzed by restriction fragment length polymorphisms (RFLP). Four restriction enzymes, BsaHI, AluI, HaeIII, and SacII, were utilized. The association between the polymorphic sites and some heat tolerance traits were also investigated in a total of 70 WAD, 90 RS, and 50 SH goats. Fourteen different types of alleles identified in the Nigerian goats, four of which were found in the peptide coding region (A57G, Q89R, G104D, and T112I), indicate a high degree of polymorphism at the DRB locus in this species. An obvious excess (P < 0.01) of non-synonymous substitutions than synonymous (dN/dS) in this locus is a reflection of adaptive evolution and positive selection. The phylogenetic trees revealed largely species-wise clustering in DRB gene. BsaHI, AluI, HaeIII, and SacII genotype frequencies were in Hardy-Weinberg equilibrium (P > 0.05), except AluI in RS goats and HaeIII in WAD goats (P < 0.05). The expected heterozygosity (H), which is a measure of gene diversity in the goat populations, ranged from 0.16 to 0.50. Genotypes AA (BsaHI), GG, GC and CC (AluI) and GG, GA, AA (HaeIII) appeared better in terms of heat tolerance. The heat-tolerant ability of SH and RS goats to the hot and humid tropical environment of Nigeria seemed better than that of the WAD goats. Sex effect (P < 0.05) was mainly on pulse rate and heat stress index, while there were varying interaction effects on heat tolerance. Variation at the DRB locus may prove to be important in possible selection and breeding for genetic resistance to heat stress in the tropics.
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Affiliation(s)
- Abdulmojeed Yakubu
- Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA. .,Department of Animal Science, Nasarawa State University, Lafia, Nigeria. .,Department of Animal Science, University of Ibadan, Ibadan, Nigeria.
| | | | - Marcos De Donato
- Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.,Laboratorio Genetica Molecular, IBB, Universidad de Oriente, Cumana, Venezuela
| | - Sunday O Peters
- Department of Animal Science, Berry College, Mt Berry, GA, 30249, USA
| | - Michael I Takeet
- Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.,Department of Veterinary Microbiology and Parasitology, Federal University of Agriculture, Abeokuta, Nigeria
| | - Mathew Wheto
- Department of Animal Breeding and Genetics, University of Agriculture, Abeokuta, Nigeria
| | - Moses Okpeku
- Department of Livestock Production, Niger Delta University, Amassoma, Nigeria.,State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Science (CAS), Kunming Institute of Zoology, Kunming, Yunnan Province, China
| | - Ikhide G Imumorin
- Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.
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24
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Rodulfo H, Martínez D, De Donato M. Molecular identification of multidrug resistant Enterobacter hormaechei in Venezuela. Invest Clin 2016; 57:402-408. [PMID: 29938989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Besides the importance of Enterobacter cloacae species complex as a nosocomial pathogen, little is known about the frequency of each species/genotype. Here, we describe a strain of E. hormaechei subsp. hormaechei isolated from a bronchial secretion of a patient, in the Intensive Care Unit at the General Hospital of Cumaná, Venezuela, who died due to complications of his infection. The molecular identification was done by sequencing the 16S rRNA gene and comparing it to sequences from the GenBank. This strain showed resistance to multiple families of antibiotics (MDR), and the genes blaKPC and blaVIM were detected by PCR. This is the first time E. hormaechei has been identified in Venezuela.
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25
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Takeet MI, Peters SO, Fagbemi BO, De Donato M, Takeet VO, Wheto M, Imumorin IG. Phylogeny of Trypanosoma brucei and Trypanosoma evansi in naturally infected cattle in Nigeria by analysis of repetitive and ribosomal DNA sequences. Trop Anim Health Prod 2016; 48:1235-40. [PMID: 27174432 DOI: 10.1007/s11250-016-1081-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/05/2016] [Indexed: 11/28/2022]
Abstract
In continuing efforts to better understand the genetics of bovine trypanosomosis, we assessed genetic diversity of Trypanosoma brucei and Trypanosoma evansi in naturally infected Nigerian cattle using repetitive DNA and internal transcribed spacer 1 of rDNA sequences and compared these sequences to species from other countries. The length of repetitive DNA sequences in both species ranged from 161 to 244 bp and 239 to 240 bp for T. brucei and T. evansi, respectively, while the ITS1 rDNA sequences length range from 299 to 364 bp. The mean GC content of ITS1 rDNA sequences was 33.57 %, and that of repetitive sequences were 39.9 and 31.1 % for T. brucei and T. evansi, respectively. Result from sequence alignment revealed both T. brucei and T. evansi repetitive DNA sequences to be more polymorphic than ITS1 rDNA sequences, with moderate points of deletion and insertions. T. brucei separated into two clades when subjected to phylogenetic analysis. T. evansi repetitive DNA sequences clustered tightly within the T. brucei clade while the ITS1 rDNA sequences of T. brucei were clearly separated from T. theileri and T. vivax individually used as outgroups. This study suggest that ITS1 rDNA sequences may not be suitable for phylogenetic differentiation of the Trypanozoon group and also suggest that T. evansi may be a phenotypic variant of T. brucei which may have potential implications in designing prevention and therapeutic strategies.
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Affiliation(s)
- Michael I Takeet
- Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA. .,Department of Veterinary Microbiology and Parasitology, Federal University of Agriculture, Abeokuta, Nigeria. .,Department of Veterinary Microbiology and Parasitology, University of Ibadan, Ibadan, Nigeria.
| | - Sunday O Peters
- Department of Animal Science, Berry College, Mount Berry, GA, 30149, USA.,Department of Animal and Dairy sciences, University of Georgia, Athens, GA, 30602, USA
| | - Benjamin O Fagbemi
- Department of Veterinary Microbiology and Parasitology, University of Ibadan, Ibadan, Nigeria
| | - Marcos De Donato
- Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.,Department of Biomedicine, Universidad de Oriente, Cumana, Venezuela
| | - Vivian O Takeet
- Department of Veterinary Medicine and Surgery, Federal University of Agriculture, Abeokuta, Nigeria
| | - Mathew Wheto
- Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.,Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
| | - Ikhide G Imumorin
- Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
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Michelli E, Millán A, Rodulfo H, Michelli M, Luiggi J, Carreño N, De Donato M. Identification of enteropathogenic Escherichia coli in children with acute diarrheic syndrome from Sucre State, Venezuela. Biomedica 2016; 36:118-127. [PMID: 27622632 DOI: 10.7705/biomedica.v36i0.2928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 10/11/2015] [Indexed: 06/06/2023]
Abstract
INTRODUCTION Diarrheagenic Escherichia coli is an important causative agent of acute diarrheic syndrome. OBJECTIVE To identify clonal groups of enteropathogenic E. coli (EPEC), in 485 children with acute diarrhea aged 0 to 10 years attending health care centers in Arismendi, Benítez and Sucre municipalities, Sucre state, Venezuela, from March to December, 2011. MATERIALS AND METHODS After obtaining the informed consent, stool samples were collected. Escherichia coli was identified using standard coproculture methods and serology with polyvalent and monovalent antisera. DNA was isolated, and eae (intimin) and bfpA (bundlin) genes were amplified through two multiplex polymerase chain reactions (PCR). RESULTS The presence of bacterial infection was determined in 39.6% of coprocultures. The prevalence of E. coli was 54.7%; 82.9% of these isolates were positive by serology for the evaluated serogroups and serotypes, which were mostly identified in children between 0 and 2 years (37.9%); 48.6% of E. coli strains amplified the eae gene; of these, 58.8% were classified as typical EPEC (eae+ y bfp+). EPEC II was the most common serogroup (38.7%), with predominance of typical EPEC (60%). In positive strains for eae gene, the β intimin allele was the most frequently identified (74.5%). Only four strains with O157:H7 serotype were identified, which showed no PCR amplification of the eae and bfpA genes. CONCLUSION This study showed the importance of molecular tests to identify diarrheagenic E. coli strains causing clinical conditions of varying severity.
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Affiliation(s)
- Elvia Michelli
- Laboratorio de Genética Molecular, Instituto de Investigaciones en Biomedicina y Ciencias Aplicadas "Dra. Susan Tai", Universidad de Oriente, Cumaná, Sucre, Venezuela Laboratorio de Microbiología Clínica, Departamento de Bioanálisis, Universidad de Oriente, Cumaná, Sucre, Venezuela.
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Teixeira B, Rodulfo H, Carreño N, Guzmán M, Salazar E, De Donato M. AMINOGLYCOSIDE RESISTANCE GENES IN Pseudomonas aeruginosa ISOLATES FROM CUMANA, VENEZUELA. Rev Inst Med Trop Sao Paulo 2016; 58:13. [PMID: 27007556 PMCID: PMC4804550 DOI: 10.1590/s1678-9946201658013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 09/14/2015] [Indexed: 11/18/2022] Open
Abstract
The enzymatic modification of aminoglycosides by aminoglycoside-acetyltransferases
(AAC), aminoglycoside-adenyltransferases (AAD), and
aminoglycoside-phosphotransferases (APH), is the most common resistance mechanism in
P. aeruginosa and these enzymes can be coded on
mobile genetic elements that contribute to their dispersion. One hundred and thirty
seven P. aeruginosa isolates from the University Hospital, Cumana,
Venezuela (HUAPA) were evaluated. Antimicrobial susceptibility was determined by the
disk diffusion method and theaac, aadB and
aph genes were detected by PCR. Most of the P.
aeruginosa isolates (33/137) were identified from the Intensive Care Unit
(ICU), mainly from discharges (96/137). The frequency of resistant P.
aeruginosaisolates was found to be higher for the aminoglycosides
tobramycin and amikacin (30.7 and 29.9%, respectively). Phenotype VI, resistant to
these antibiotics, was the most frequent (14/49), followed by phenotype I, resistant
to all the aminoglycosides tested (12/49). The
aac(6´)-Ib,aphA1 and aadB genes
were the most frequently detected, and the simultaneous presence of several
resistance genes in the same isolate was demonstrated. Aminoglycoside resistance in
isolates ofP. aeruginosa at the HUAPA is partly due to the presence
of the aac(6´)-Ib, aphA1 andaadB
genes, but the high rates of antimicrobial resistance suggest the existence of
several mechanisms acting together. This is the first report of aminoglycoside
resistance genes in Venezuela and one of the few in Latin America.
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Affiliation(s)
| | - Hectorina Rodulfo
- Lab. Genética Molecular, Universidad de Oriente, Cumaná, Venezuela, , , ,
| | - Numirin Carreño
- Lab. Genética Molecular, Universidad de Oriente, Cumaná, Venezuela, , , ,
| | - Militza Guzmán
- Lab. de Bacteriología Molecular, Dpto. Bioanálisis, Universidad de Oriente, Cumaná, Venezuela, ,
| | - Elsa Salazar
- Lab. de Bacteriología Molecular, Dpto. Bioanálisis, Universidad de Oriente, Cumaná, Venezuela, ,
| | - Marcos De Donato
- Lab. Genética Molecular, Universidad de Oriente, Cumaná, Venezuela, , , ,
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Cheeseman IH, Miller B, Tan JC, Tan A, Nair S, Nkhoma SC, De Donato M, Rodulfo H, Dondorp A, Branch OH, Mesia LR, Newton P, Mayxay M, Amambua-Ngwa A, Conway DJ, Nosten F, Ferdig MT, Anderson TJC. Population Structure Shapes Copy Number Variation in Malaria Parasites. Mol Biol Evol 2015; 33:603-20. [PMID: 26613787 PMCID: PMC4760083 DOI: 10.1093/molbev/msv282] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in seven countries in Africa, South East Asia and South America using a high-density single-nucleotide polymorphism/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500 bp to 59 kb, as well as 10,107 flanking, biallelic single-nucleotide polymorphisms. Overall, CNVs were rare, small, and skewed toward low frequency variants, consistent with the deleterious model. Relative to African and South East Asian populations, CNVs were significantly more common in South America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g., DNA helicase and three conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen.
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Affiliation(s)
- Ian H Cheeseman
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Becky Miller
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - John C Tan
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - Asako Tan
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - Shalini Nair
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Standwell C Nkhoma
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Marcos De Donato
- Lab. Genetica Molecular, IIBCAUDO, Universidad De Oriente, Cumana, Venezuela
| | - Hectorina Rodulfo
- Lab. Genetica Molecular, IIBCAUDO, Universidad De Oriente, Cumana, Venezuela
| | - Arjen Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Oralee H Branch
- Division of Parasitology, Department of Microbiology, New York University School of Medicine
| | - Lastenia Ruiz Mesia
- Laboratorio De Investigaciones De Productos Naturales Y Antiparasitarios, Universidad Nacional De La Amazonia Peruana, Iquitos, Peru
| | - Paul Newton
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Mayfong Mayxay
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR Faculty of Postgraduate Studies, University of Health Sciences, Vientiane, Lao PDR
| | | | - David J Conway
- Medical Research Council Unit, Fajara, Banjul, The Gambia Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - François Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Michael T Ferdig
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - Tim J C Anderson
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
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Martínez D, Marcano D, Rodulfo H, Salgado N, Cuaical N, Rodriguez L, Caña L, Medina B, Guzman M, De Donato M. KPC and VIM producing Enterobacter cloacae strain from a hospital in northeastern Venezuela. Invest Clin 2015; 56:182-187. [PMID: 26299058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
An 83-year-old male patient is admitted to the central hospital in Cumana, Venezuela with severe urinary infection, history of hospitalizaions and prolonged antimicrobial treatments. A strain of Enterobacter cloacae was isolated showing resistance to multiple types of antibiotics (only sensitive to gentamicin), with phenotype of serine- and metallo-carbapenemases. Both, bla(VIM-2) and bla(KPC) genes were detected in the isolate. This is the first report of an Enterobacteriaceae species producing both KPC carbapenemase and VIM metallo carbapenemase in Venezuela. This finding has a great clinical and epidemiological impact in the region, because of the feasibility of transferring these genes, through mobile elements to other strains of Enterobacter and to other infection-causing species of bacteria.
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30
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Martínez D, Rodulfo HE, Rodríguez L, Caña LE, Medina B, Guzman M, Carreño N, Marcano D, De Donato M. First report of metallo-β-lactamases producing Enterobacter spp. strains from Venezuela. Rev Inst Med Trop Sao Paulo 2014; 56:67-9. [PMID: 24553611 PMCID: PMC4085824 DOI: 10.1590/s0036-46652014000100010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 05/29/2013] [Indexed: 11/21/2022] Open
Abstract
Clinical strains of Enterobacter were isolated from Cumana's Central Hospital in Venezuela, and classified as E. cloacae (21), E. aerogenes (7), E. intermedium (1), E. sakazakii (1) and three unclassified. The strains showed high levels of resistance, especially to SXT (58.1%), CRO (48.8%), CAZ (46.6%), PIP (46.4%), CIP (45.2%) and ATM (43.3%). This is the first report for South America of blaVIM-2 in two E. cloacae and one Enterobacter sp., which also showed multiple mechanisms of resistance. Both E. cloacae showed blaTEM-1, but only one showed blaCTX-M-15 gene, while no blaSHV was detected.
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Affiliation(s)
- Dianny Martínez
- Lab. Genetica Molecular, IIBCAUDO, Universidad de Oriente, Cumana, Venezuela, Lab. Genetica Molecular, IIBCAUDO, Universidad de Oriente, Cumana, Venezuela
| | - Hectorina E Rodulfo
- Lab. Genetica Molecular, IIBCAUDO, Universidad de Oriente, Cumana, Venezuela, Lab. Genetica Molecular, IIBCAUDO, Universidad de Oriente, Cumana, Venezuela
| | - Lucy Rodríguez
- Lab. Bacteriologia, Hospital Universitario Antonio Patricio de Alcalá, Cumaná, Venezuela, Lab. Bacteriologia, Hospital Universitario Antonio Patricio de Alcalá, Cumaná, Venezuela
| | - Luisa E Caña
- Lab. Bacteriologia, Hospital Universitario Antonio Patricio de Alcalá, Cumaná, Venezuela, Lab. Bacteriologia, Hospital Universitario Antonio Patricio de Alcalá, Cumaná, Venezuela
| | - Belkis Medina
- Lab. Bacteriologia, Hospital Universitario Antonio Patricio de Alcalá, Cumaná, Venezuela, Lab. Bacteriologia, Hospital Universitario Antonio Patricio de Alcalá, Cumaná, Venezuela
| | - Militza Guzman
- Lab. de Bacteriologia Molecular, Dpto. Bioanalisis, Universidad de Oriente, Cumaná, Venezuela, Lab. de Bacteriologia Molecular, Dpto. Bioanalisis, Universidad de Oriente, Cumaná, Venezuela
| | - Numirin Carreño
- Lab. Genetica Molecular, IIBCAUDO, Universidad de Oriente, Cumana, Venezuela, Lab. Genetica Molecular, IIBCAUDO, Universidad de Oriente, Cumana, Venezuela
| | - Daniel Marcano
- Instituto Nacional de Higiene Dr Rafael Rangel, Caracas, Venezuela, Instituto Nacional de Higiene Dr Rafael Rangel, Caracas, Venezuela
| | - Marcos De Donato
- Lab. Genetica Molecular, IIBCAUDO, Universidad de Oriente, Cumana, Venezuela, Lab. Genetica Molecular, IIBCAUDO, Universidad de Oriente, Cumana, Venezuela
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Ajayi OO, Adefenwa MA, Agaviezor BO, Ikeobi CON, Wheto M, Okpeku M, Amusan SA, Yakubu A, De Donato M, Peters SO, Imumorin IG. A novel TaqI polymorphism in the coding region of the ovine TNXB gene in the MHC class III region: morphostructural and physiological influences. Biochem Genet 2013; 52:1-14. [PMID: 23877191 DOI: 10.1007/s10528-013-9622-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 03/14/2013] [Indexed: 12/16/2022]
Abstract
The tenascin-XB (TNXB) gene has antiadhesive effects, functions in matrix maturation in connective tissues, and localizes to the major histocompatibility complex class III region. We hypothesized that it may influence adaptive physiological response through an effect on blood vessel function. We identified a novel g.1324 A→G polymorphism at a TaqI recognition site in a 454 bp fragment of ovine TNXB and genotyped it in 150 Nigerian sheep using PCR-RFLP. The missense mutation changes glutamic acid (GAA) to glycine (GGA). Among SNP genotypes, significant differences (P < 0.05) were observed in body weight and fore cannon bone length. Interaction effects of breed, SNP genotype, and geographic location had a significant effect (P < 0.05) on chest girth. The SNP genotype was significantly (P < 0.05) associated with physiological traits of pulse rate and skin temperature. The observed effect of this novel polymorphism may be mediated through its role in connective tissue biology, requiring further association and functional studies.
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Affiliation(s)
- Oyeyemi O Ajayi
- Department of Animal Breeding and Genetics, University of Agriculture, Abeokuta, Nigeria
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Yakubu A, Salako AE, De Donato M, Takeet MI, Peters SO, Adefenwa MA, Okpeku M, Wheto M, Agaviezor BO, Sanni TM, Ajayi OO, Onasanya GO, Ekundayo OJ, Ilori BM, Amusan SA, Imumorin IG. Genetic Diversity in Exon 2 of the Major Histocompatibility Complex Class II DQB1 Locus in Nigerian Goats. Biochem Genet 2013; 51:954-66. [DOI: 10.1007/s10528-013-9620-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 02/13/2013] [Indexed: 10/26/2022]
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Sanni TM, Onasanya GO, Adefenwa MA, Yakubu A, Ikeobi CON, Adebambo OA, Talabi AO, Ozoje MO, Wheto M, Takeet MI, Peters SO, Donato MD, Thomas BN, Imumorin IG. Molecular Diagnosis of Subclinical African Trypanosoma vivax Infection and Association with Physiological Indices and Serum Metabolites in Extensively Managed Goats in the Tropics. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ojvm.2013.31007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Takeet MI, Fagbemi BO, De Donato M, Yakubu A, Rodulfo HE, Peters SO, Wheto M, Imumorin IG. Molecular survey of pathogenic trypanosomes in naturally infected Nigerian cattle. Res Vet Sci 2012; 94:555-61. [PMID: 23245680 DOI: 10.1016/j.rvsc.2012.10.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 10/11/2012] [Accepted: 10/21/2012] [Indexed: 10/27/2022]
Abstract
Microscopy and polymerase chain reaction (PCR) were used to survey pathogenic trypanosome infection in naturally infected Nigerian cattle. In 411 animals sampled, microscopy detected 15.1% positive infection of at least one of Trypanosoma brucei, Trypanosoma congolense or Trypanosoma vivax, while PCR detected 63.7% positive infections of at least one of those species and Trypanosoma evansi. PCR detected 4.4%, 48.7%, 26.0% and 0.5% respectively of T. brucei, T. congolense, T. vivax and T. evansi infections. All of the T. congolense detected were savannah-type, except for two forest-type infections. Prevalence of mixed infections was 13.9%, being primarily co-infection by T. congolense and T. vivax while prevalence of mixed infections by T. evansi, T. vivax and T. congolense was 1.5%. Microscopy showed poor sensitivity but specificity greater than 94%. Infection rates were much higher in Southern than in Northern Nigeria. Infections were lowest in N'dama compared to Muturu, Sokoto Gudali and White Fulani breeds. Animals with T. vivax monoinfection and mixed infections showed significantly lower packed cell volume (PCV) values. Those infected with any Trypanosoma species with <200 parasites/μl showed higher PCV values than those infected with >200 parasites/μl. The new finding of savannah- and forest-type T. congolense in Nigeria and the relatively high abundance of mixed infections are of significant clinical relevance. This study also suggests that T. congolense is the most prevalent species in Nigeria.
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Affiliation(s)
- Michael I Takeet
- Dept. of Animal Science, Cornell University, Ithaca, NY 14853, USA.
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Rodulfo H, Ahmar B, Rodríguez ME, Mora L, De Donato M. Nested PCR reveals elevated over-diagnosis of E. histolytica in Barcelona, Venezuela. Invest Clin 2012; 53:365-377. [PMID: 23513487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The aim of this study was to identify the presence of Entamoeba histolytica and E. dispar by nested PCR in children attending the "Dr. Luis Razetti" Hospital, Barcelona, Anzoátegui State. Of the 1,141 fecal samples coproparasitologically evaluated by conventional microscopy, 150 were diagnosed positive for E. histolytica in 0-10 year-old-children, of both sexes. The signs, symptoms and a full coproparasitological report were obtained from all of these and nested PCR was performed to identify E. histolytica and E. dispar. The conventional microscopy results showed a diagnostic frequency of E. histolytica in 13.2% of the cases, of which 79.3% were positive only for this pathogen. However, nested PCR showed that of these, only 28% (42/150) were actually infected by Entamoeba spp., revealing a high over-diagnosis of E. histolytica. We also identified 9.3% E. histolytica, 4% E. dispar and 4.7% mixed infections. Diarrhea was the most common symptom, followed by abdominal pain and fever. Bloody stools were statistically associated with E. histolytica, but were also found for E. dispar infections. This study demonstrates that molecular techniques complementary to conventional methods enable the correct identification of Entamoeba spp., thus contributing to an improved epidemiological assessment of these parasites and implementation of the appropriate treatment.
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Affiliation(s)
- Hectorina Rodulfo
- Laboratorio de Genética Molecular, Instituto de Investigaciones en Biomedicina y Ciencias Aplicadas "Dra. Susan Tai", Universidad de Oriente, Núcleo de Sucre, Cumaná, Venezuela
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Agaviezor BO, Peters SO, Adefenwa MA, Yakubu A, Adebambo OA, Ozoje MO, Ikeobi CO, Wheto M, Ajayi OO, Amusan SA, Ekundayo OJ, Sanni TM, Okpeku M, Onasanya GO, De Donato M, Ilori BM, Kizilkaya K, Imumorin IG. Morphological and microsatellite DNA diversity of Nigerian indigenous sheep. J Anim Sci Biotechnol 2012; 3:38. [PMID: 23176051 PMCID: PMC3563600 DOI: 10.1186/2049-1891-3-38] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 11/01/2012] [Indexed: 11/10/2022] Open
Abstract
Background Sheep is important in the socio-economic lives of people around the world. It is estimated that more than half of our once common livestock breeds are now endangered. Since genetic characterization of Nigerian sheep is still lacking, we analyzed ten morphological traits on 402 animals and 15 microsatellite DNA markers in 384 animals of the 4 Nigerian sheep breeds to better understand genetic diversity for breeding management and germplasm conservation. Results Morphological traits of Uda and Balami were significantly (P < 0.05) higher than Yankasa, which were both higher than West African Dwarf (WAD) sheep. Stepwise discriminant analysis showed tail length, rump height, chest girth, ear length and chest depth as the most discriminating variables for classification. Mahalanobis distances show the least differentiation between Uda and Balami and the largest between WAD and Balami sheep. While 93.3% of WAD sheep were correctly assigned to their source genetic group, 63.9% of Yankasa, 61.2% of Balami and 45.2% of Uda were classified correctly by nearest neighbour discriminant analysis. The overall high Polymorphism Information Content (PIC) of all microsatellite markers ranged from 0.751 to 0.927 supporting their use in genetic characterization. Expected heterozygosity was high for all loci (0.783 to 0.93). Mean heterozygote deficiency across all populations (0.171 to 0.534) possibly indicate significant inbreeding (P < 0.05). Mean values for FST, FIT and FIS statistics across all loci were 0.088, 0.394 and 0.336 respectively. Yankasa and Balami are the most closely related breeds (DA = 0.184) while WAD and Balami are the farthest apart breeds (DA = 0.665), which is coincident with distance based on morphological analysis and population structure assessed by STRUCTURE. Conclusions These results suggest that within-breed genetic variation in Nigerian sheep is higher than between-breeds and may be a valuable tool for genetic improvement and conservation. The higher genetic variability in Yankasa suggests the presence of unique ancestral alleles reflecting the presence of certain functional genes which may result in better adaptability in more agro-ecological zones of Nigeria. These genetic characteristics are potentially useful in planning improvement and conservation strategies in Nigerian indigenous sheep.
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Rodulfo H, De Donato M, Luiggi J, Michelli E, Millán A, Michelli M. Molecular characterization of Salmonella strains in individuals with acute diarrhea syndrome in the State of Sucre, Venezuela. Rev Soc Bras Med Trop 2012; 45:329-33. [PMID: 22760131 DOI: 10.1590/s0037-86822012000300010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2011] [Accepted: 07/29/2011] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION In Venezuela, acute diarrheic syndrome (ADS) is a primary cause of morbi-mortality, often involving the Salmonella genus. Salmonella infections are associated with acute gastroenteritis, one of the most common alimentary intoxications, and caused by the consumption of contaminated water and food, especially meat. METHODS Conventional and molecular methods were used to detect Salmonella strains from 330 fecal samples from individuals of different ages and both sexes with ADS. Polymerase chain reaction (PCR) was used for the molecular characterization of Salmonella, using invA, sefA, and fliC genes for the identification of this genus and the serotypes Enteritidis and Typhimurium, respectively. RESULTS The highest frequency of individuals with ADS was found in children 0-2 years old (39.4%), and the overall frequency of positive coprocultures was 76.9%. A total of 14 (4.2%) strains were biochemically and immunologically identified as Salmonella enterica subsp. enterica, of which 7 were classified as belonging to the Enteritidis serotype, 4 to the Typhimurium serotype, and 3 to other serotypes. The S. enterica strains were distributed more frequently in the age groups 3-4 and 9-10 years old. CONCLUSIONS The molecular characterization method used proved to be highly specific for the typing of S. enterica strains using DNA extracted from both the isolated colonies and selective enrichment broths directly inoculated with fecal samples, thus representing a complementary tool for the detection and identification of ADS-causing bacteria.
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Affiliation(s)
- Hectorina Rodulfo
- Laboratório de Genética Molecular, Instituto de Investigaciones en Biomedicina y Ciencias Aplicadas Dra. Suzan Tai, Universidade de Oriente, Cumaná, Sucre, Venezuela
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Imumorin IG, Kim EH, Lee YM, De Koning DJ, van Arendonk JA, De Donato M, Taylor JF, Kim JJ. Genome Scan for Parent-of-Origin QTL Effects on Bovine Growth and Carcass Traits. Front Genet 2011; 2:44. [PMID: 22303340 PMCID: PMC3268597 DOI: 10.3389/fgene.2011.00044] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 06/25/2011] [Indexed: 11/13/2022] Open
Abstract
Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents, and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus × Brahman cattle crossbreds. We identified 24 POE–QTL on 15 Bos taurus autosomes (BTAs) of which six were significant at 5% genome-wide (GW) level and 18 at the 5% chromosome-wide (CW) significance level. Six QTL were paternally expressed while 15 were maternally expressed. Three QTL influencing post-weaning growth map to the proximal end of BTA2 (linkage region of 0–9 cM; genomic region of 5.0–10.8 Mb), for which only one imprinted ortholog is known so far in the human and mouse genomes, and therefore may potentially represent a novel imprinted region. The detected QTL individually explained 1.4 ∼ 5.1% of each trait’s phenotypic variance. Comparative in silico analysis of bovine genomic locations show that 32 out of 1,442 known mammalian imprinted genes from human and mouse homologs map to the identified QTL regions. Although several of the 32 genes have been associated with quantitative traits in cattle, only two (GNAS and PEG3) have experimental proof of being imprinted in cattle. These results lend additional support to recent reports that POE on quantitative traits in mammals may be more common than previously thought, and strengthen the need to identify and experimentally validate cattle orthologs of imprinted genes so as to investigate their effects on quantitative traits.
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Mendoza R, De Donato M, de Waard JH, Takiff H, Bello T, Chirinos G. [Susceptibility of M. tuberculosis to antituberculosis drugs as determined by two methods, in Sucre state, Venezuela]. Invest Clin 2010; 51:445-455. [PMID: 21365873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The objective of this study was to evaluate the resistance to isoniazid (INH), rifampicin (RIF), streptomycin (STR) and ethambutol (EMB), with the Canetti's proportions method (PM) and the nitrate reductase assay (NRA) of 59 clinical strains of Mycobacterium tuberculosis, isolated in the period of august 2005 to december 2006, in Sucre state, Venezuela. Primary and acquired drug resistance was 6.3% and 14.3%, respectively. Only one strain was found to be multidrug resistant (MDR). The overall agreement between the NRA and PM was 100% for INH, RIF and EMB, and 96% for STR. The time to obtain results was 10 to 14 days for the NRA, compared to 42 days for the PM. The NRA was easy to perform and therefore represents a useful tool for rapid and accurate determination of drug-resistant M. tuberculosis. The sequence of the rpoB gene of the RIF resistant strain demonstrated a never described mutation (change in the codon 456; TCG > CAG) in the hypervariable region of 81 base pairs where most of the mutations of the RIF resistant strains have been reported. Comparison of our results with those of the last resistance prevalence study carried out in the years 1998-1999, shows a decrease in the studied area.
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Affiliation(s)
- Rosmy Mendoza
- Laboratorio de Genética Molecular, Instituto de Investigaciones en Biomedicina y Ciencias Aplicadas "Dra. Susan Tai", Universidad de Oriente, Núcleo de Sucre, Cumaná, Venezuela
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González B, Rodulfo H, De Donato M, Berrizbeitia M, Gómez C, González L. [Hematologic variations in patient with malaria caused by Plasmodium vivax before, during and after treatment]. Invest Clin 2009; 50:187-201. [PMID: 19662814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
In order to determine the relationship between hematological parameters, parasitaemia and malaria episodes, we evaluated 59 individuals of both sexes, infected with Plasmodium vivax and 30 controls from Sucre state. Blood samples were obtained by venous puncture and from the earlobe at day of diagnosis, 8 and 30 days post-diagnosis. We carried out hematological analysis, microscopic and molecular (PCR) diagnosis and the parasitaemia was calculated. There were significant differences by sex for hemoglobin, erythrocytes and hematocrit (p < 0.01 in all three analysis). These values in males, decreased by day 8 with respect to day 0 (p < 0.001; p = 0.006 y p = 0.025, respectively). In females, significant differences were only seen in hemoglobin and hematocrit between controls and patients (p < 0.001). The average number of leucocytes at the day of diagnosis was within the reference values, but slightly lower compared to the controls and the samples during and after the treatment. The average proportion of eosinophils was higher than normal for both, controls and patients, during and after the treatment. Thrombocytopenia was observed at diagnosis, but a week after, the values increased significantly (p < 0.001). There was an inverse relationship between parasitaemia and platelet count and a direct relationship between the first and hemoglobin at day 0, as well as with the difference in platelet counts between day 0 and day 8 (p = 0.044 and p = 0.014, respectively). This difference was the only parameter related to the number of malaria episodes (p = 0.040). Thrombocytopenia showed to be an indicator of acute malaria.
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Affiliation(s)
- Brunnell González
- Departamento de Enfermería, Escuela de Ciencias, Universidad de Orientc, Núcleo Suere, Cumaná, Venezuela.
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Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigó R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen HC, Chrast J, Câmara F, Ermolaeva O, Henrichsen CN, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Kokocinski F, Landrum M, Maglott D, Pruitt K, Sapojnikov V, Searle SM, Solovyev V, Souvorov A, Ucla C, Wyss C, Anzola JM, Gerlach D, Elhaik E, Graur D, Reese JT, Edgar RC, McEwan JC, Payne GM, Raison JM, Junier T, Kriventseva EV, Eyras E, Plass M, Donthu R, Larkin DM, Reecy J, Yang MQ, Chen L, Cheng Z, Chitko-McKown CG, Liu GE, Matukumalli LK, Song J, Zhu B, Bradley DG, Brinkman FSL, Lau LPL, Whiteside MD, Walker A, Wheeler TT, Casey T, German JB, Lemay DG, Maqbool NJ, Molenaar AJ, Seo S, Stothard P, Baldwin CL, Baxter R, Brinkmeyer-Langford CL, Brown WC, Childers CP, Connelley T, Ellis SA, Fritz K, Glass EJ, Herzig CTA, Iivanainen A, Lahmers KK, Bennett AK, Dickens CM, Gilbert JGR, Hagen DE, Salih H, Aerts J, Caetano AR, Dalrymple B, Garcia JF, Gill CA, Hiendleder SG, Memili E, Spurlock D, Williams JL, Alexander L, Brownstein MJ, Guan L, Holt RA, Jones SJM, Marra MA, Moore R, Moore SS, Roberts A, Taniguchi M, Waterman RC, Chacko J, Chandrabose MM, Cree A, Dao MD, Dinh HH, Gabisi RA, Hines S, Hume J, Jhangiani SN, Joshi V, Kovar CL, Lewis LR, Liu YS, Lopez J, Morgan MB, Nguyen NB, Okwuonu GO, Ruiz SJ, Santibanez J, Wright RA, Buhay C, Ding Y, Dugan-Rocha S, Herdandez J, Holder M, Sabo A, Egan A, Goodell J, Wilczek-Boney K, Fowler GR, Hitchens ME, Lozado RJ, Moen C, Steffen D, Warren JT, Zhang J, Chiu R, Schein JE, Durbin KJ, Havlak P, Jiang H, Liu Y, Qin X, Ren Y, Shen Y, Song H, Bell SN, Davis C, Johnson AJ, Lee S, Nazareth LV, Patel BM, Pu LL, Vattathil S, Williams RL, Curry S, Hamilton C, Sodergren E, Wheeler DA, Barris W, Bennett GL, Eggen A, Green RD, Harhay GP, Hobbs M, Jann O, Keele JW, Kent MP, Lien S, McKay SD, McWilliam S, Ratnakumar A, Schnabel RD, Smith T, Snelling WM, Sonstegard TS, Stone RT, Sugimoto Y, Takasuga A, Taylor JF, Van Tassell CP, Macneil MD, Abatepaulo ARR, Abbey CA, Ahola V, Almeida IG, Amadio AF, Anatriello E, Bahadue SM, Biase FH, Boldt CR, Carroll JA, Carvalho WA, Cervelatti EP, Chacko E, Chapin JE, Cheng Y, Choi J, Colley AJ, de Campos TA, De Donato M, Santos IKFDM, de Oliveira CJF, Deobald H, Devinoy E, Donohue KE, Dovc P, Eberlein A, Fitzsimmons CJ, Franzin AM, Garcia GR, Genini S, Gladney CJ, Grant JR, Greaser ML, Green JA, Hadsell DL, Hakimov HA, Halgren R, Harrow JL, Hart EA, Hastings N, Hernandez M, Hu ZL, Ingham A, Iso-Touru T, Jamis C, Jensen K, Kapetis D, Kerr T, Khalil SS, Khatib H, Kolbehdari D, Kumar CG, Kumar D, Leach R, Lee JCM, Li C, Logan KM, Malinverni R, Marques E, Martin WF, Martins NF, Maruyama SR, Mazza R, McLean KL, Medrano JF, Moreno BT, Moré DD, Muntean CT, Nandakumar HP, Nogueira MFG, Olsaker I, Pant SD, Panzitta F, Pastor RCP, Poli MA, Poslusny N, Rachagani S, Ranganathan S, Razpet A, Riggs PK, Rincon G, Rodriguez-Osorio N, Rodriguez-Zas SL, Romero NE, Rosenwald A, Sando L, Schmutz SM, Shen L, Sherman L, Southey BR, Lutzow YS, Sweedler JV, Tammen I, Telugu BPVL, Urbanski JM, Utsunomiya YT, Verschoor CP, Waardenberg AJ, Wang Z, Ward R, Weikard R, Welsh TH, White SN, Wilming LG, Wunderlich KR, Yang J, Zhao FQ. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 2009; 324:522-8. [PMID: 19390049 DOI: 10.1126/science.1169588] [Citation(s) in RCA: 806] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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De Donato M, Ramirez R, Howell C, Verginelli R, Orta T, Cabrera S, Mata E, Manrique R. Artificial family selection based on growth rate in cultivated lines of Litopenaeus vannamei (Decapoda, Penaeidae) from Venezuela. Genet Mol Biol 2008. [DOI: 10.1590/s1415-47572008000500009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Mora L, García A, De Donato M, Urdaneta H. [Epidemiologic and molecular study of Entamoeba histolytica and Entamoeba dispar strains in pacients with diarrhea in Cumana, Sucre state, Venezuela]. Invest Clin 2008; 49:225-237. [PMID: 18717268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
An epidemiological and molecular study on E. histolytica and E. dispar was carried out in 428 patients with gastrointestinal symptomatology of diarrhea from different health centers in Cumana, Sucre state. The samples were processed through: direct examination with 0.85% physiological saline solution, temporal lugol staining, trichromic staining and the Ritchie method of concentration; a sucrose gradient was used for cyst isolation. The small subunit of the 16S RNA was amplified by nested, multiplex PCR for the molecular detection. The E. histolytica/E. dispar prevalences according to the direct, Ritchie and trichromic staining methods were 20.09, 13.79 and 12.15%, respectively; while prevalences according to PCR for E. histolytica and E. dispar were 6.31% and 4.44%, respectively, also detecting four cases of mixed infection. Sequencing of the amplified fragments of E. histolytica showed 100% homology with the sequences with strains from Merida (Venezuela), USA, Brazil, Mexico and GenBank. The infections by E. histolytica and E. dispar were statistically associated with age but not with sex. The presence of mucus, blood and abdominal pain were only associated to E. histolytica infection. The moderate prevalence of E. histolytica shows the endemic status of this population and warns about the potential problem as a morbidity and mortality in Sucre state. The frequency of E. dispar in this population suggests the existence of an overestimation problem in the diagnosis of amoebiasis with its clinical and epidemiological implications, and shows the poor knowledge about the true prevalences of this protozoan. The PCR allowed for the differential identification of E. histolytica and E. dispar, as well as the presence of mixed infections, making a great tool for epidemiological amoebiasis studies.
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Affiliation(s)
- Leonor Mora
- Postgrado de Biología Aplicada, Universidad de Oriente. Núcleo de Sucre, Cumaná, Venezuela.
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De Donato M, Gallagher DS, Lehn C, Gill C, Taylor JF. Molecular cytogenetic assignment of genes to bovine chromosome 5. Genet Mol Res 2003; 2:260-70. [PMID: 14966674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Seven genes were assigned by molecular cytogenetic methods to bovine chromosome 5. To accomplish this, specific primers were either publicly available or were designed from highly conserved regions of the publicly available mammalian gene sequences. The identity of the amplified segments was verified by sequencing and alignment with the published sequences. The optimized primers that amplified the desired bovine genes were used for screening a bovine bacterial artificial chromosome library. The positive clones were localized to a specific band of bovine chromosome 5 by fluorescence in situ hybridization. The genes HOXC4, SP1 and IGFBP6 were localized to band q21, COL2A1 was localized to bands q21-q23, IGF1 was localized to band q26, MB to band q31 and the gene CYP2D6 was localized to band q35. The cytogenetic assignment of SP1, IGFBP6, COL2A1, IGF1, MB and CYP2D6 is first reported here and the assignment of HOXC4 refines the previous assignment of this gene. The identification and localization of these genes further support the development of the human to bovine comparative map through characterizing the homologous segments conserved in the evolution of these species. This information will be useful for the future localization of genes that affect economically important traits in bovines.
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Affiliation(s)
- Marcos De Donato
- Department of Animal Science, Texas A and M University, College Station, TX 77843, USA.
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Ji Y, Raska WA, Donato MD, Islam-Faridi MN, Price HJ, Stelly DM. Identification and distinction among segmental duplication-deficiencies by fluorescence in situ hybridization (FISH)-adorned multivalent analysis. Genome 1999. [DOI: 10.1139/g99-012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Most simple reciprocal translocation homozygotes and heterozygotes are euploid, and normal in genotype. However, translocation heterozygotes form six types of numerically balanced meiotic products. The cross of a translocation heterozygote with a normal individual can yield normal progeny, translocation heterozygotes, or any of four segmentally aneuploid duplication-deficient types (dp-dfs). Using metaphase I configuration analysis, most dp-dfs can be distinguished easily from normal and heterozygous translocations. However, identification of the four dp-df types is often impossible unless there is an appreciable karyotypic difference in arm size, relative breakpoint position, or a diagnostic cytological marker. Here we demonstrated the utility and facility of dp-df identification by means of meiotic fluorescence in situ hybridization (FISH) to adorn one chromosome arm with a molecular marker. The rationale is presented diagrammatically, and exemplified by identifying both adjacent-1 and adjacent-2 dp-dfs in Gossypium hirsutum. Polymorphism is not required among marker loci, so analysis of dp-dfs can proceed without requirement of sexual hybridization or sophisticated high-polymorphism marker systems. Besides facilitating the identification of dp-dfs, such an analysis can provide facile means to assign marker loci to chromosomes, arms, and segments. Integrative mapping of chromosomal, physical, and recombination maps will thus be facilitated. An ability to readily distinguish adjacent-1 and adjacent-2 types of dp-dfs should also enhance strategic derivation of other aneuploids, e.g., dp-df related monosomes and trisomes.Key words: Gossypium, cotton, duplication-deficiency, fluorescence in situ hybridization, repetitive DNA.
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