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Esmaeili M, Gholizadeh M, Hafezian H, Farhadi A. Sex-specific genetic parameter estimates of body weight in Mazandaran indigenous chickens. J Anim Breed Genet 2024. [PMID: 38308514 DOI: 10.1111/jbg.12855] [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: 08/28/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024]
Abstract
Body weight is an economically important trait in poultry that shows sexual dimorphism (SD). In the present study, variation in SD in Mazandaran native chickens was investigated in terms of the (Co) variance components and genetic parameters of body weight between males and females. Studied traits were body weights at hatch (BW1), 8 weeks (BW8) and 12 weeks of age (BW12). Also, for weight at sexual maturity (WSM) covariance components were only estimated in females. Cross-sex direct and maternal correlations were also estimated for studied traits except for WSM. For this purpose, a deep 21-generation pedigree and body weight data (57,576 BW1, 72,925 BW8, 62,727 BW12 and, 42,496 WSM) were used. Evaluation of SD of body weight was performed using six bivariate animal models with and without considering the genetic and permanent maternal environmental effects under the restricted maximum likelihood method in WOMBAT software. Model with direct additive genetic effects and maternal genetic effects without covariance between them was identified as the best model for BW1 and BW8. The Model including direct additive genetic effects and permanent maternal environmental effects was the best model for BW12 and WSM. Direct heritability (h2 ) estimates for BW1, BW8 and, BW12 were, respectively, 0.05 ± 0.013, 0.17 ± 0.02 and, 0.25 ± 0.03 in males and, 0.05 ± 0.012, 0.15 ± 0.01 and 0.21 ± 0.01 in females. Also, the direct heritability of WSM based on univariate analysis in females was estimated to be 0.40 ± 0.01. Maternal heritability (h m 2 $$ {h}_m^2 $$ ) varied from 0.39 ± 0.01 (BW1) to 0.04 ± 0.009 (BW8) in males, and 0.36 ± 0.10 (BW1) to 0.04 ± 0.006 (BW8) in females. The correlation between direct genetic effects between males and females for BW1 was not significantly different from one. The direct genetic correlation between the two sexes for BW8 and BW12 was significantly different from 1 concluding that these traits are dimorphic in terms of direct genetic effects and therefore independent selection in both sexes is possible.
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Affiliation(s)
- Mohammad Esmaeili
- Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Mohsen Gholizadeh
- Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Hasan Hafezian
- Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Ayoub Farhadi
- Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
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Dadkhah K, Mianji GR, Barzegar A, Farhadi A. Characterization of the mitochondrial Huso huso genome and new aspects of its organization in the presence of tandem repeats in 12S rRNA. BMC Ecol Evol 2023; 23:55. [PMID: 37749487 PMCID: PMC10521412 DOI: 10.1186/s12862-023-02166-2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 09/08/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND The sturgeon group has been economically significant worldwide due to caviar production. Sturgeons consist of 27 species in the world. Mitogenome data could be used to infer genetic diversity and investigate the evolutionary history of sturgeons. A limited number of complete mitogenomes in this family were sequenced. Here, we annotated the mitochondrial Huso huso genome, which revealed new aspects of this species. RESULTS In this species, the mitochondrial genome consisted of 13 genes encoding proteins, 22tRNA and 2rRNA, and two non-coding regions that followed other vertebrates. In addition, H. huso had a pseudo-tRNA-Glu between ND6 and Cytb and a 52-nucleotide tandem repeat with two replications in 12S rRNA. This duplication event is probably related to the slipped strand during replication, which could remain in the strand due to mispairing during replication. Furthermore, an 82 bp repeat sequence with three replications was observed in the D-loop control region, which is usually visible in different species. Regulatory elements were also seen in the control region of the mitochondrial genome, which included termination sequences and conserved regulatory blocks. Genomic compounds showed the highest conservation in rRNA and tRNA, while protein-encoded genes and nonencoded regions had the highest divergence. The mitochondrial genome was phylogenetically assayed using 12 protein-encoding genes. CONCLUSIONS In H. huso sequencing, we identified a distinct genome organization relative to other species that have never been reported. In recent years, along with the advancement in sequencing identified more genome rearrangements. However, it is an essential aspect of researching the evolution of the mitochondrial genome that needs to be recognized.
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Affiliation(s)
- Khadijeh Dadkhah
- Laboratory for Molecular Genetics and Animal Biotechnology, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran.
| | - Ghodrat Rahimi Mianji
- Laboratory for Molecular Genetics and Animal Biotechnology, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Ali Barzegar
- Department of Basic Sciences, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Ayoub Farhadi
- Laboratory for Molecular Genetics and Animal Biotechnology, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
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Alei A, Moradian F, Farhadi A, Rostami M. Identification, Isolation, Cloning, and Expression of a New Alkaline Serine Protease Gene from Native Iranian Bacillus sp. RAM 53 for Use in the Industry. Appl Biochem Biotechnol 2023; 195:5730-5746. [PMID: 37289418 DOI: 10.1007/s12010-023-04585-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2023] [Indexed: 06/09/2023]
Abstract
Proteases are one of the most important and widely applicable proteolytic enzymes that are used in various industries. The aim of this study was to identify, isolate, characterize, and clone the new extracellular alkaline protease from the native bacterium Bacillus sp. RAM53 that was isolated from rice fields in Iran. In this study, first, the primary assay of protease production was performed. The bacteria were cultured in a nutrient broth culture medium at 37° C for 48 h, and then, the enzyme extraction was performed. Enzyme activity was measured by standard methods in the range of 20 to 60 °C and the range of pH 6.0 to 12. Degenerate primers were designed to alkaline protease gene sequences. The isolated gene was cloned into the pET28a+ vector, the positive clones were transferred to Escherichia coli BL21, and the expression of the recombinant enzyme was optimized. The results showed that the optimum temperature and pH of the alkaline protease were 40° C and 9.0, respectively, and were stable at 60° C for 3 h. The molecular weight of the recombinant enzyme was 40 kDa in SDS-PAGE. The recombinant alkaline protease was inhibited by the PMSF inhibitor, indicating that the enzyme was serine protease. The results showed that the sequence alignment of the enzyme gene with the other alkaline protease gene sequences related to Bacillus was 94% identity. The result of Blastx showed about 86% identity to the S8 peptidase family in Bacillus cereus and Bacillus thuringiensis and other Bacillus species. The enzyme may be useful for various industries.
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Affiliation(s)
- Aliakbar Alei
- Department of Basic Sciences, Sari Agricultural Sciences and Natural Resources University, P.O. Box 578, Mazandaran, Iran
| | - Fatemeh Moradian
- Department of Basic Sciences, Sari Agricultural Sciences and Natural Resources University, P.O. Box 578, Mazandaran, Iran.
| | - Ayoub Farhadi
- Department of Animal Sciences, Sari Agricultural Sciences and Natural Resources University, Mazandaran, Iran
| | - Mehdi Rostami
- Rice Research Institute of Iran, Mazandaran Branch, Agricultural Research, Education and Extension Organization, P.O. Box 145, Amol, Tehran, Iran
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Aliabadi S, Zarghami F, Farhadi A, Sharifi F, Moodi M. Effect of Physical Activity on Sleep Outcomes among Iranian Older Adults: A Cross-Sectional Study. Adv Gerontol 2022. [DOI: 10.1134/s2079057022040038] [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: 12/24/2022]
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Zadeh MMA, Rostami E, Farhadi A. An Extremely Productive and Sustainable Procedure for the Synthesis of 2,4,5-Trisubstituted Imidazoles Using Graphene Oxide-Substituted Sulfoacetic Acid Amide. Russ J Org Chem 2022. [DOI: 10.1134/s1070428022100153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Zarabi O, Ahmadi M, Hedayatifard M, Golestan L, Farhadi A. Preservation Effect of Ice-Glazing Using Pullulan and Bay Laurel Extract on the Quality Characteristics of Caspian Trout ( Salmo trutta caspius) during Frozen Storage. Journal of Aquatic Food Product Technology 2022. [DOI: 10.1080/10498850.2022.2109088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Oriana Zarabi
- Department of Food Science and Technology, Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran
| | - Mohammad Ahmadi
- Department of Food Science and Technology, Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran
| | - Masoud Hedayatifard
- Fisheries Department, College of Agriculture and Natural Resources, Qaemshahr branch, Islamic Azad University, Amol, Iran
| | - Leila Golestan
- Department of Food Science and Technology, Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran
| | - Ayoub Farhadi
- Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
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Farhadi A, Mohammadi-Shahboulaghi F, Rassouli M, Sadeghmoghadam L, Nazari S, Froughan M. Perceptions of Caregiving by Family Caregivers of Older Adults with Dementia in Iran: A Qualitative Study. Adv Gerontol 2022. [DOI: 10.1134/s2079057022020060] [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: 11/23/2022]
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Vahedparast H, Nazarian R, Bagherzadeh R, Farhadi A. The Predictor Role of Perceived Social Support and Aging Perception in Treatment Adherence of Older Adults with Chronic Diseases. Adv Gerontol 2021. [DOI: 10.1134/s2079057021020168] [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: 11/23/2022]
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9
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Faryadi S, Sheikhahmadi A, Farhadi A, Nourbakhsh H. Effects of silymarin and nano-silymarin on performance, egg quality, nutrient digestibility, and intestinal morphology of laying hens during storage. Italian Journal of Animal Science 2021. [DOI: 10.1080/1828051x.2021.1975503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Samira Faryadi
- Department of Animal Science, Faculty of Agricultural, University of Kurdistan, Sanandaj, Iran
| | - Ardashir Sheikhahmadi
- Department of Animal Science, Faculty of Agricultural, University of Kurdistan, Sanandaj, Iran
| | - Ayoub Farhadi
- Department of Animal Science, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Himan Nourbakhsh
- Department of Food Science and Engineering, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
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Alizadeh F, Moradian F, Farhadi A. Association of allelic polymorphisms of IGFALS gene with growth traits in Makouei and Ghezel sheep breeds. Trop Anim Health Prod 2020; 52:3027-3034. [PMID: 32588362 DOI: 10.1007/s11250-020-02321-7] [Citation(s) in RCA: 2] [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: 09/21/2019] [Accepted: 06/09/2020] [Indexed: 11/28/2022]
Abstract
Insulin-like growth factor-binding protein acid-labile subunit (IGFALS) encodes a protein which binds to IGF1 and IGFBP-3 to regulate the growth, differentiation, and other physiological processes. The aim of this study was the identification of allelic polymorphisms of the IGFALS gene using the PCR-RFLP technique and evaluation of their association with growth traits. For this end, 120 blood samples were randomly collected from each breed. Following amplification of an 1113-bp fragment of exon 1 and a part of intron 1 of the IGFLAS gene, genotyping was conducted by three restriction enzymes including HinfI, MscI, and PvuII. The results showed that only one allele was observed in IGFALS-PvuII site, while in IGFLAS-MscI site, three AA, AB, and BB genotypes with the frequencies of 17.5%, 32%, and 50.5% and 11%, 37.5%, and 51.5% were observed in Makouei and Ghezel sheep breeds, respectively. Additionally, in the IGFLAS-HinfI site, two AB and BB genotypes with the frequency of 34.2% and 65.8% were observed in Makouei sheep and AA, AB, and BB genotypes with the frequency of 9%, 21%, and 70% were observed in Ghezel sheep. So that, Makouei sheep with AB genotype had more chest girth (CG) compared with other genotypes. Furthermore, a significant association was observed between the genotypes of IGFLAS-HinfI with birth weight (BW) in Ghezel and BW, weaning weight (BW3), and CG in Makouei sheep. Haplotype analysis revealed an association between paternal haplotypes and BW in both Ghezel and Makouei breeds. So that, AAB and ABB haplotypes showed more BW than others in Makouei and Ghezel sheep, respectively.
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Affiliation(s)
- Fatemeh Alizadeh
- Department of Basic Sciences, Sari Agricultural Sciences and Natural Resources University, Sari, Mazandaran, Iran
| | - Fatemeh Moradian
- Department of Basic Sciences, Sari Agricultural Sciences and Natural Resources University, Sari, Mazandaran, Iran.
| | - Ayoub Farhadi
- Laboratory for Molecular Cytogenetic, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Mazandaran, Iran
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Asadpour R, Farhadi A, Jafari Jozani R, Hajibemani A, Tolouei Kaleibar M. Changes in peripheral blood mononuclear cells' mRNA expression of TLRs and CD14 during puerperal metritis in dairy cattle. Iran J Vet Res 2020; 21:120-125. [PMID: 32849891 PMCID: PMC7430367] [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] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 01/05/2020] [Accepted: 01/26/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Peripheral blood mononuclear cells (PBMCs), commonly referred to as lymphocytes and monocytes, representing cells of the innate and adaptive immune systems. AIMS To find out whether changes in PBMCs' mRNA expression of pattern recognition receptors (PRRs) are associated with puerperal metritis in Holstein cows. METHODS Peripheral blood mononuclear cells were collected from 20 cows with puerperal metritis and 20 cows without metritis at 10 days postpartum. Expression of toll-like receptors 2 and 4 (TLR2 and TLR4), and cluster of differentiation 14 (CD14) genes were assessed in PBMCs using a quantitative real time-polymerase chain reaction (qRT-PCR) technique. The data was normalized to glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as a reference gene, and 2-∆∆Ct methodology was used for relative quantification. RESULTS The results of the present study demonstrated that the expression of TLR4 (P=0.04) and CD14 (P=0.008) was significantly greater in cows with puerperal metritis compared to the control group. However, the expression of TLR2 (P=0.06) was not significantly different between cows with puerperal metritis and healthy cows. CONCLUSION This study suggests that puerperal metritis significantly increases the expression of TLR4 and CD14 genes in the PBMCs which contributes to the proper stimulation of inflammation and uterine clearance of bacteria soon after calving.
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Affiliation(s)
- R. Asadpour
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - A. Farhadi
- Graduated from Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - R. Jafari Jozani
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - A. Hajibemani
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - M. Tolouei Kaleibar
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
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Sahebalam H, Gholizadeh M, Hafezian H, Farhadi A. Comparison of parametric, semiparametric and nonparametric methods in genomic evaluation. J Genet 2019. [DOI: 10.1007/s12041-019-1149-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Sahebalam H, Gholizadeh M, Hafezian H, Farhadi A. Comparison of parametric, semiparametric and nonparametric methods in genomic evaluation. J Genet 2019; 98:102. [PMID: 31767821] [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: 06/10/2023]
Abstract
Access to dense panels of molecular markers has facilitated genomic selection in animal breeding. The purpose of this study was to compare the nonparametric (random forest and support vector machine), semiparametric reproducing kernel Hilbert spaces (RKHS), and parametric methods (ridge regression and Bayes A) in prediction of genomic breeding values for traits with different genetic architecture. The predictive performance of different methods was compared in different combinations of distribution of QTL effects (normal and uniform), two levels of QTL numbers (50 and 200), three levels of heritability (0.1, 0.3 and 0.5), and two levels of training set individuals (1000 and 2000). To do this, a genome containing four chromosomes each 100-cM long was simulated on which 500, 1000 and 2000 evenly spaced single-nucleotide markers were distributed. With an increase in heritability and the number of markers, all the methods showed an increase in prediction accuracy (P<0.05). By increasing the number of QTLs from 50 to 200, we found a significant decrease in the prediction accuracy of breeding value in all methods (P<0.05). Also, with the increase in the number of training set individuals, the prediction accuracy increased significantly in all statistical methods (P<0.05). In all the various simulation scenarios, parametric methods showed higher prediction accuracy than semiparametric and nonparametric methods. This superior mean value of prediction accuracy for parametric methods was not statistically significant compared to the semiparametric method, but it was statistically significant compared to the nonparametric method. Bayes A had the highest accuracy of prediction among all the tested methods and, is therefore, recommended for genomic evaluation.
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Affiliation(s)
- Hamid Sahebalam
- Faculty of Animal and Aquatic Science, Department of Animal Science, Sari Agricultural Sciences and Natural Resources University, P.O. Box -578, Sari, Iran.
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Philippi-Kobs A, Farhadi A, Matheis L, Lott D, Chuvilin A, Oepen HP. Impact of Symmetry on Anisotropic Magnetoresistance in Textured Ferromagnetic Thin Films. Phys Rev Lett 2019; 123:137201. [PMID: 31697508 DOI: 10.1103/physrevlett.123.137201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Indexed: 06/10/2023]
Abstract
We report on the magnetoresistance of textured films consisting of 3d-ferromagnetic layers sandwiched by Pt. While the conventional cos^{2}φ behavior of the anisotropic magnetoresistance (AMR) is found when the magnetization M is varied in the film plane, cos^{2n}θ contributions (2n≤6) exist for rotating M in the plane perpendicular to the current. This finding is explained by the symmetry-adapted modeling of AMR of textured films demonstrating that the cos^{2}θ behavior cannot be used as a fingerprint for the presence of spin Hall magnetoresistance (SMR). Further, the interfacial MR contributions for Pt/Ni/Pt contradict the SMR behavior confirming the dominant role of AMR in all-metallic systems.
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Affiliation(s)
- A Philippi-Kobs
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Institut für Nanostruktur- und Festkörperphysik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - A Farhadi
- Institut für Nanostruktur- und Festkörperphysik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - L Matheis
- Institut für Nanostruktur- und Festkörperphysik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - D Lott
- Institute for Materials Research, Helmholtz-Zentrum Geesthacht, Max-Planck-Straße 1, 21502 Geesthacht, Germany
| | - A Chuvilin
- Centro de Investigación Cooperativa nanoGUNE, Av. de Tolosa 76, E-20018 San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, E-480013 Bilbao, Spain
| | - H P Oepen
- Institut für Nanostruktur- und Festkörperphysik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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Khalkhali-Evrigh R, Hedayat-Evrigh N, Hafezian SH, Farhadi A, Bakhtiarizadeh MR. Genome-Wide Identification of Microsatellites and Transposable Elements in the Dromedary Camel Genome Using Whole-Genome Sequencing Data. Front Genet 2019; 10:692. [PMID: 31404266 PMCID: PMC6675863 DOI: 10.3389/fgene.2019.00692] [Citation(s) in RCA: 5] [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: 01/04/2019] [Accepted: 07/02/2019] [Indexed: 01/09/2023] Open
Abstract
Transposable elements (TEs) along with simple sequence repeats (SSRs) are prevalent in eukaryotic genome, especially in mammals. Repetitive sequences form approximately one-third of the camelid genomes, so study on this part of genome can be helpful in providing deeper information from the genome and its evolutionary path. Here, in order to improve our understanding regarding the camel genome architecture, the whole genome of the two dromedaries (Yazdi and Trodi camels) was sequenced. Totally, 92- and 84.3-Gb sequence data were obtained and assembled to 137,772 and 149,997 contigs with a N50 length of 54,626 and 54,031 bp in Yazdi and Trodi camels, respectively. Results showed that 30.58% of Yazdi camel genome and 30.50% of Trodi camel genome were covered by TEs. Contrary to the observed results in the genomes of cattle, sheep, horse, and pig, no endogenous retrovirus-K (ERVK) elements were found in the camel genome. Distribution pattern of DNA transposons in the genomes of dromedary, Bactrian, and cattle was similar in contrast with LINE, SINE, and long terminal repeat (LTR) families. Elements like RTE-BovB belonging to LINEs family in cattle and sheep genomes are dramatically higher than genome of dromedary. However, LINE1 (L1) and LINE2 (L2) elements cover higher percentage of LINE family in dromedary genome compared to genome of cattle. Also, 540,133 and 539,409 microsatellites were identified from the assembled contigs of Yazdi and Trodi dromedary camels, respectively. In both samples, di-(393,196) and tri-(65,313) nucleotide repeats contributed to about 42.5% of the microsatellites. The findings of the present study revealed that non-repetitive content of mammalian genomes is approximately similar. Results showed that 9.1 Mb (0.47% of whole assembled genome) of Iranian dromedary's genome length is made up of SSRs. Annotation of repetitive content of Iranian dromedary camel genome revealed that 9,068 and 11,544 genes contain different types of TEs and SSRs, respectively. SSR markers identified in the present study can be used as a valuable resource for genetic diversity investigations and marker-assisted selection (MAS) in camel-breeding programs.
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Affiliation(s)
- Reza Khalkhali-Evrigh
- Department of Animal Breeding and Genetics, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | | | - Seyed Hasan Hafezian
- Department of Animal Breeding and Genetics, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Ayoub Farhadi
- Department of Animal Breeding and Genetics, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
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Bandi N, Gholizadeh M, Rahimi-Mianji G, Farhadi A. Comparative study of gene structure in the upstream regulatory region of CDC10 and MYBPC1 genes in Iranian fat-tailed and nonfat-tailed sheep breeds. Livest Sci 2019. [DOI: 10.1016/j.livsci.2017.06.014] [Citation(s) in RCA: 1] [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: 11/26/2022]
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Ariyaei A, Farhadi A, Moradian F, Rahimi Mianji G. Cloning, expression and characterization of a novel alkaline serine protease gene from native Iranian Bacillus sp.; a producer of protease for use in livestock. Gene 2019; 693:10-15. [PMID: 30690180 DOI: 10.1016/j.gene.2019.01.020] [Citation(s) in RCA: 5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 01/06/2019] [Accepted: 01/22/2019] [Indexed: 11/26/2022]
Abstract
The use of proteases in the last decade has been welcomed in livestock and poultry industries and has led to significant results such as improved feed conversion ratio, weight gain and increased growth performance. In the present study, isolation and identification of a novel alkaline protease from Iranian Bacillus species was performed in order to use in livestock feed. After primary isolation of bacteria from soil samples of rice fields and early detection of bacterial genus, the zymogram plate was performed for evaluation of production extracellular proteases. Of the 11 strains producing protease, one strain that produced more enzymes was selected to continue the work. Characterization of alkaline protease was done using specific enzyme assays. To confirm the genus of isolates as well as to identify the species close to, molecular analysis of 16S rRNA gene sequence was done. After that, bioinformatics analysis carried out in NCBI database for searching bacterial alkaline proteases gene sequences. The primer designed based on gene homology of close species for extraction of alkaline protease gene. The results showed that the enzyme extract had the highest activity at pH 9.0 and 50 °C. The 16S rRNA gene sequence was submitted for the strain called Bacillus sp. RAM on the NCBI site. According to the results of the phylogenetic tree, the bacterium was belonged to Bacillus genus and Bacillus sp. RAM was close to Thuringiensis C405. The isolated alkaline protease gene successfully cloned in pET28a and transferred to the expression host E.coli BL21. The expression of the protease gene was evaluated by SDS-PAGE electrophoresis. The induced recombinant cells expressed the protease and revealed molecular weight band of about 38 kDa. According to the enzyme properties, this alkaline protease can useful for application in animal industry.
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Affiliation(s)
- Ahmadreza Ariyaei
- Laboratory for Molecular Cytogenetics, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Ayoub Farhadi
- Laboratory for Molecular Cytogenetics, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran.
| | - Fatemeh Moradian
- Department of Basic Sciences, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Ghodrat Rahimi Mianji
- Laboratory for Molecular Cytogenetics, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
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Khalkhali-Evrigh R, Hafezian SH, Hedayat-Evrigh N, Farhadi A, Bakhtiarizadeh MR. Genetic variants analysis of three dromedary camels using whole genome sequencing data. PLoS One 2018; 13:e0204028. [PMID: 30235280 PMCID: PMC6147446 DOI: 10.1371/journal.pone.0204028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 08/31/2018] [Indexed: 12/27/2022] Open
Abstract
Whole genome wide identification and annotation of genetic variations in camels is in its first steps. The aim of this study was the identification of genome wide variants, functional annotations of them and enrichment analysis of affected genes using whole genome sequencing data of three dromedary camels. The genomes of two Iranian female dromedary camels that mostly used to produce meat and milk were sequenced to 41.9-fold and 38.6-fold coverage. A total of 4,727,238 single-nucleotide polymorphisms (SNPs) and 692,908 indels (insertions and deletions) were found by mapping raw reads to the dromedary reference assembly (GenBank Accession: GCA_000767585.1). In-silico functional annotation of the discovered variants in under study samples revealed that most SNPs (2,305,738; 48.78%) and indels (339,756; 49.03%) were located in intergenic regions. A comparison of the identified SNPs with those of the African camel (BioProject Accession: PRJNA269274) indicated that they had 993,474 SNPs in common. We found 15,168 non-synonymous SNPs in the shared variants of the three camels that could affect gene function and protein structure. Obtained results revealed that there were 7085, 6271 and 4688 non-synonymous SNPs among the 3436, 3058 and 2882 genes in the specific gene sets of Yazd dromedary, Trod dromedary and African dromedary, respectively. The list of genes predicted to be affected by non-synonymous variants in different individuals was subjected to gene ontology (GO) enrichment analysis.
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Affiliation(s)
- Reza Khalkhali-Evrigh
- Department of Animal Breeding and Genetics, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Seyed Hasan Hafezian
- Department of Animal Breeding and Genetics, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Nemat Hedayat-Evrigh
- Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
- * E-mail:
| | - Ayoub Farhadi
- Department of Animal Breeding and Genetics, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
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Khani AH, Jazayeri SMM, Ebrahimi E, Younesi-Melerdi E, Farhadi A. The Bifidobacterim bifidum (BIB2) Probiotic Increased Immune System Factors in Men Sprint Athletes. CNF 2018. [DOI: 10.2174/1573401313666170725114130] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Ali Hossein Khani
- Department of Cellular and Molecular Biology, Young Researchers and Elite Club, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | | | - Elahe Ebrahimi
- Department of Microbiology, Pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Elham Younesi-Melerdi
- Genetics & Agricultural Biotechnology Institute of Tabarestan, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Ayoub Farhadi
- Laboratory for Molecular Cytogenetic, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
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Ebrahimi F, Gholizadeh M, Rahimi-Mianji G, Farhadi A. Detection of QTL for greasy fleece weight in sheep using a 50 K single nucleotide polymorphism chip. Trop Anim Health Prod 2017; 49:1657-1662. [PMID: 28801813 DOI: 10.1007/s11250-017-1373-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 03/11/2017] [Accepted: 08/02/2017] [Indexed: 12/27/2022]
Abstract
Genome-wide association studies (GWAS) have introduced an influential tool in the search for quantitative trait loci (QTL) influencing economically important traits in sheep. To identify QTL associated with greasy fleece weight, a GWAS with 50 K single nucleotide polymorphisms (SNPs) was performed in a Baluchi sheep population. Association with greasy fleece weights was tested using the software Plink. The results of our GWAS provided three novel SNP markers and candidate genes associated with greasy fleece weight. A total of three chromosome-wide significant associations were detected for SNP on chromosomes 17 and 20 affecting greasy fleece weight across the four shearing. One of the significant SNP markers was located within ovine known genes namely FAM101A. Further investigation of these identified regions in validation studies will facilitate the identification of strong candidate genes for wool production in sheep.
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Affiliation(s)
- Fatemeh Ebrahimi
- Department of Animal Science, Faculty of Animal and Aquatic Science, Sari Agricultural Sciences and Natural Resources University, P.O. Box -578, Sari, Iran
| | - Mohsen Gholizadeh
- Department of Animal Science, Faculty of Animal and Aquatic Science, Sari Agricultural Sciences and Natural Resources University, P.O. Box -578, Sari, Iran.
| | - Ghodrat Rahimi-Mianji
- Department of Animal Science, Faculty of Animal and Aquatic Science, Sari Agricultural Sciences and Natural Resources University, P.O. Box -578, Sari, Iran
| | - Ayoub Farhadi
- Department of Animal Science, Faculty of Animal and Aquatic Science, Sari Agricultural Sciences and Natural Resources University, P.O. Box -578, Sari, Iran
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Farhadi A, Mohammadi M, Ghorbani M. On the assessment of photocatalytic activity and charge carrier mechanism of TiO 2 @SnO 2 core-shell nanoparticles for water decontamination. J Photochem Photobiol A Chem 2017. [DOI: 10.1016/j.jphotochem.2017.02.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Ghorban Hosseini N, Tebianian M, Farhadi A, Hossein khani A, Rahimi A, Mortazavi M, Hosseini SY, Taghizadeh M, Rezaei M, Mahdavi M. In Silico Analysis of L1/L2 Sequences of Human Papillomaviruses: Implication for Universal Vaccine Design. Viral Immunol 2017; 30:210-223. [DOI: 10.1089/vim.2016.0142] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Nazila Ghorban Hosseini
- Department of Microbiology, Pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Majid Tebianian
- Department of Biotechnology, Razi Vaccine and Serum Research Institute, Karaj, Iran
| | - Ayoub Farhadi
- Laboratory for Molecular Cytogenetic, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Ali Hossein khani
- Department of Cellular and Molecular Biology, Young Researchers and Elite Club, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Arian Rahimi
- Department of Microbiology, Urmia Branch, Islamic Azad University, Urmia, Iran
| | - Mojtaba Mortazavi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Iran
| | - Seyed Younes Hosseini
- GastroenteroHepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Morteza Taghizadeh
- Department of Medical Virology, Iran University of Medical Science, Tehran, Iran
| | - Mahsa Rezaei
- Department of Microbiology, Pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Mehdi Mahdavi
- Department of Immunology, Pasteur Institute of Iran, Tehran, Iran
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Moosavi SA, Ghanbari Z, Farhadi A, Heshmati F, Shabani S, Mofid-Nakhaei MA. Prompt cytomolecular identification of chromosome aberration in irradiated blood cells. Res Mol Med (RMM) 2017. [DOI: 10.29252/rmm.5.1.34] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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Gholami M, Hafezian SH, Rahimi G, Farhadi A, Rahimi Z, Kahrizi D, Kiani S, Karim H, Vaziri S, Muhammadi S, Veisi F, Ghadiri K, Shetabi H, Zargooshi J. Allele specific-PCR and melting curve analysis showed relatively high frequency of β-casein gene A1 allele in Iranian Holstein, Simmental and native cows. Cell Mol Biol (Noisy-le-grand) 2016; 62:138-143. [PMID: 27894411 DOI: 10.14715/cmb/2016.62.12.23] [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] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 11/26/2016] [Indexed: 11/18/2022]
Abstract
There are two allelic forms of A1 and A2 of β-casein gene in dairy cattle. Proteolytic digestion of bovine β-casein A1 type produces bioactive peptide of β-casomorphin-7 known as milk devil. β-casomorphin-7 causes many diseases, including type 1 diabetes, cardiovascular disease syndrome, sudden death and madness. The aim of the present study was to determine the different allelic forms of β-casein gene in Iranian Holstein, Simmental and native cattle in order to identify A1 and A2 variants. The blood samples were collected randomly and DNA was extracted using modified salting out method. An 854 bp fragment including part of exon 7 and part of intron 6 of β-casein gene was amplified by allele specific polymerase chain reaction (AS-PCR). Also, the accuracy of AS-PCR genotyping has been confirmed by melting temperature curve analysis using Real-time PCR machinery. The comparison of observed allele and genotype frequency among the studied breeds was performed using the Fisher exact and Chi-squared test, respectively by SAS program. Obtained results showed the A1 allele frequencies of 50, 51.57, 54.5, 49.4 and 46.6% in Holstein, Simmental, Sistani, Taleshi and Mazandarani cattle populations, respectively. The chi-square test was shown that no any populations were in Hardy-Weinberg equilibrium for studied marker locus. Comparison and analysis of the test results for allelic frequency showed no any significant differences between breeds (P>0.05). The frequency of observed genotypes only differs significantly between Holstein and Taleshi breeds but no any statistically significant differences were found for other breeds (P>0.05). A relatively high frequency of β-casein A1 allele was observed in Iranian native cattle. Therefore, determine the genotypes and preference alleles A2 in these native and commercial cattle is recommended.
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Affiliation(s)
- M Gholami
- Laboratory for Molecular Genetics and Cytogenetics, Department of Animal Sciences, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - S H Hafezian
- Laboratory for Molecular Genetics and Cytogenetics, Department of Animal Sciences, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - G Rahimi
- Laboratory for Molecular Genetics and Cytogenetics, Department of Animal Sciences, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - A Farhadi
- Laboratory for Molecular Genetics and Cytogenetics, Department of Animal Sciences, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Z Rahimi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - D Kahrizi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - S Kiani
- Research Institute of Applied Physics and Astronomy, University of Tabriz, Tabriz, Iran
| | - H Karim
- Department of Cardiology, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - S Vaziri
- Department of Infectious Diseases. Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - S Muhammadi
- Department of Cardiology, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - F Veisi
- Department of Obstetrics and gynecology. Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - K Ghadiri
- Nosocomial Infections Research Center. Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - H Shetabi
- Department of Anesthesiology. Isfahan University of Medical Sciences, Isfahan, Iran
| | - J Zargooshi
- Department of Sexual Medicine, The Rhazes Center for Research in Family Health and Sexual Medicine; Kermanshah University of Medical Sciences, Kermanshah, Iran.
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Miri M, Behzad-Behbahani A, Fardaei M, Farhadi A, Talebkhan Y, Mohammadi M, Tayebinia M, Farokhinejad F, Alavi P, Fanian M, Zare F, Saberzade J, Nikouyan N, Okhovat M, Ranjbaran R, Rafiei Dehbidi G, Naderi S. Construction of bacterial ghosts for transfer and expression of a chimeric hepatitis C virus gene in macrophages. J Microbiol Methods 2015; 119:228-32. [DOI: 10.1016/j.mimet.2015.11.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 11/10/2015] [Accepted: 11/10/2015] [Indexed: 01/06/2023]
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Rahimi-Mianji G, Nejati-Javaremi A, Farhadi A. Genetic diversity, parentage verification, and genetic bottlenecks evaluation in iranian turkmen horse1. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415090082] [Citation(s) in RCA: 2] [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: 11/23/2022]
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Rahimi-Mianji G, Nejati-Javaremi A, Farhadi A. GENETIC DIVERSITY, PARENTAGE VERIFICATION AND GENETIC BOTTLENECKS EVALUATION IN IRANIAN TURKMEN HORSE BREED. Genetika 2015; 51:1066-1074. [PMID: 26606803 DOI: 10.7868/s0016675815090088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The present study was undertaken to genetically evaluate Turkmen horses for genetic diversity and to evaluate whether they have experienced any recent genetic bottlenecks. A total of 565 individuals from Turkmen horses were characterized for within breed diversity using 12 microsatellite markers. The estimated mean allelic diversity was (9.42 ± 1.78) per locus, with a total of 131 alleles in genotyped samples. A high level of genetic variability within this breed was observed in terms of high values of effective number of alleles (4.70 ± 1.36), observed heterozygosity (0.757 ± 0.19), expected Nei's heterozygosity (0.765 ± 0.13), and polymorphism information content (0.776 ± 0.17). The estimated cumulative probability of exclusion of wrongly named parents (PE) was high, with an average value of 99.96% that indicates the effectiveness of applied markers in resolving of parentage typing in Turkmen horse population. The paternity testing results did not show any misidentification and all selected animals were qualified based on genotypic information using a likelihood-based method. Low values of Wright's fixation index, F(IS) (0.012) indicated low levels of inbreeding. A significant heterozygote excess on the basis of different models, as revealed from Sign and Wilcoxon sign rank test suggested that Turkmen horse population is not in mutation-drift equilibrium. But, the Mode-shift indicator test showed a normal 'L' shaped distribution for allelic class and proportion of alleles, thus indicating the absence of bottleneck events in the recent past history of this breed. Further research work should be carrying out to clarify the cause of discrepancy observed forbottleneck results in this breed. In conclusion, despite unplanned breeding in Turkmen horse population, this breed still has sufficient genetic variability and could provide a valuable source of genetic material that may use for meeting the demands of future breeding programs.
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Abstract
1. The objective was to investigate inbreeding depression for some economic traits of Mazandaran native fowls using data collected from 1992 to 2012 (21 generations) using a REML 2. The mean inbreeding coefficient (F) for the whole population and dams was 4.67% and 4.12%, respectively, and most of the inbred birds (75.79%) and inbred dams (72.58%) had F < 12.5%. 3. Individual and dam inbreeding trends were 0.55% and 0.53% per year. 4. Inbreeding depression for body weight at hatch, at 8 weeks and 12 weeks of age, age at sexual maturity, weight at sexual maturity, egg weight at 1st d of laying and average egg weight at 28, 30 and 32 weeks of laying due to a 1% increase in individual inbreeding were -0.11 g, -3.1 g, -1.3 g, 0.15 d, 0.59 g, -0.05 g and -0.03 g, respectively. 5. A 1% increase in maternal inbreeding resulted in a reduction of 0.06, 0.6 and 3.6 g in body weight at hatch, 8 weeks and 12 weeks of age.
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Affiliation(s)
- A Rahmanian
- a Department of Animal Science , Sari University of Agriculture and Natural Resources (SANRU) , Sari , Iran
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Farhadi A, Genualdo V, Perucatti A, Hafezian SH, Rahimi-Mianji G, De Lorenzi L, Parma P, Iannuzzi L, Iannuzzi A. Comparative FISH mapping of BMPR1B, BMP15 and GDF9 fecundity genes on cattle, river buffalo, sheep and goat chromosomes. J Genet 2013; 92:595-7. [PMID: 24371182 DOI: 10.1007/s12041-013-0301-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A Farhadi
- Laboratory for Molecular Genetics and Animal Biotechnology, Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran.
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Papari E, Bastami M, Farhadi A, Abedini SS, Hosseini M, Bahman I, Mohseni M, Garshasbi M, Moheb LA, Behjati F, Kahrizi K, Ropers HH, Najmabadi H. Investigation of primary microcephaly in Bushehr province of Iran: novel STIL and ASPM mutations. Clin Genet 2012; 83:488-90. [PMID: 22989186 DOI: 10.1111/j.1399-0004.2012.01949.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 06/09/2012] [Accepted: 08/07/2012] [Indexed: 11/27/2022]
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Memarian HR, Farhadi A. Potassium peroxydisulfate as an efficient oxidizing agent for conversion of ethyl 3,4-dihydropyrimidin-2(1H)-one-5-carboxylates to their corresponding ethyl pyrimidin-2(1H)-one-5-carboxylates. JICS 2009. [DOI: 10.1007/bf03246543] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Behzad-Behbahani A, Entezam M, Mojiri A, Pouransari R, Rahsaz M, Banihashemi M, Heidari T, Farhadi A, Azarpira N, Yaghobi R, Jowkar Z, Ramzi M, Robati M. INCIDENCE OF HUMAN HERPES VIRUS-6 AND HUMAN CYTOMEGALOVIRUS INFECTIONS IN DONATED BONE MARROW AND UMBILICAL CORD BLOOD HEMATOPOIETIC STEM CELLS. Indian J Med Microbiol 2008. [DOI: 10.1016/s0255-0857(21)01874-0] [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: 11/28/2022]
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Behzad-Behbahani A, Entezam M, Mojiri A, Pouransari R, Rahsaz M, Banihashemi M, Heidari T, Farhadi A, Azarpira N, Yaghobi R, Jowkar Z, Ramzi M, Robati M. Incidence of human herpes virus-6 and human cytomegalovirus infections in donated bone marrow and umbilical cord blood hematopoietic stem cells. Indian J Med Microbiol 2008; 26:252-5. [DOI: 10.4103/0255-0857.42038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Ranjbaran Z, Keefer L, Stepanski E, Farhadi A, Keshavarzian A. The relevance of sleep abnormalities to chronic inflammatory conditions. Inflamm Res 2007. [PMID: 17431741 DOI: 10.1007/s00011-006-] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Sleep is vital to health and quality of life while sleep abnormalities are associated with adverse health consequences. Nevertheless, sleep problems are not generally considered by clinicians in the management of chronic inflammatory conditions (CIC) such as asthma, RA, SLE and IBD. To determine whether this practice is justified, we reviewed the literature on sleep and chronic inflammatory diseases, including effects of sleep on immune system and inflammation. We found that a change in the sleep-wake cycle is often one of the first responses to acute inflammation and infection and that the reciprocal effect of sleep on the immune system in acute states is often protective and restorative. For example, slow wave sleep can attenuate proinflammatory immune responses while sleep deprivation can aggravate those responses. The role of sleep in CIC is not well explored. We found a substantial body of published evidence that sleep disturbances can worsen the course of CIC, aggravate disease symptoms such as pain and fatigue, and increase disease activity and lower quality of life. The mechanism underlying these effects probably involves dysregulation of the immune system. All this suggests that managing sleep disturbances should be considered as an important factor in the overall management of CIC.
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Affiliation(s)
- Z Ranjbaran
- Section of Gastroenterology and Nutrition, Rush University Medical Center, 1725 W. Harrison, Suite 206, Chicago, IL 60612, USA.
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Abstract
Sleep is vital to health and quality of life while sleep abnormalities are associated with adverse health consequences. Nevertheless, sleep problems are not generally considered by clinicians in the management of chronic inflammatory conditions (CIC) such as asthma, RA, SLE and IBD. To determine whether this practice is justified, we reviewed the literature on sleep and chronic inflammatory diseases, including effects of sleep on immune system and inflammation. We found that a change in the sleep-wake cycle is often one of the first responses to acute inflammation and infection and that the reciprocal effect of sleep on the immune system in acute states is often protective and restorative. For example, slow wave sleep can attenuate proinflammatory immune responses while sleep deprivation can aggravate those responses. The role of sleep in CIC is not well explored. We found a substantial body of published evidence that sleep disturbances can worsen the course of CIC, aggravate disease symptoms such as pain and fatigue, and increase disease activity and lower quality of life. The mechanism underlying these effects probably involves dysregulation of the immune system. All this suggests that managing sleep disturbances should be considered as an important factor in the overall management of CIC.
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Affiliation(s)
- Z Ranjbaran
- Section of Gastroenterology and Nutrition, Rush University Medical Center, 1725 W. Harrison, Suite 206, Chicago, IL 60612, USA.
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Forsyth CB, Banan A, Farhadi A, Fields JZ, Tang Y, Shaikh M, Zhang LJ, Engen PA, Keshavarzian A. Regulation of oxidant-induced intestinal permeability by metalloprotease-dependent epidermal growth factor receptor signaling. J Pharmacol Exp Ther 2007; 321:84-97. [PMID: 17220428 DOI: 10.1124/jpet.106.113019] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Inflammatory bowel disease (IBD) affects more than 1 million Americans with more than 30,000 new cases diagnosed each year. IBD increases patient morbidity and susceptibility to colorectal cancer, yet its etiology remains unknown. Current models identify two key determinants of IBD pathogenesis: hyperpermeability of the gut epithelial barrier to bacterial products and an abnormal immune response to these products. Two factors seem critical for hyperpermeability: oxidant-induced stress and proinflammatory cytokines (e.g., tumor necrosis factor-alpha). The aim of this study was to investigate the role of oxidant stress-mediated transactivation of the epidermal growth factor receptor (EGFR) in intestinal hyperpermeability. This study used the Caco-2 human colonic epithelial cell in vitro model of intestinal epithelium. Cells were grown on inserts for permeability and signaling studies and glass coverslips for microscopy studies. show that oxidant-induced intestinal hyperpermeability can be blocked by specific inhibitors of the EGFR, tumor necrosis factor convertase (TACE) metalloprotease, transforming growth factor (TGF)-alpha, and mitogen-activated protein kinases, especially extracellular signal-regulated kinase 1/2. We also show that oxidant initiates these signaling events, in part by causing translocation of TACE to cell-cell contact zones. In this study, our data identify a novel mechanism for oxidant-induced intestinal hyperpermeability relevant to IBD. We propose a new intestinal permeability model in which oxidant transactivates EGFR signaling by activation of TACE and cleavage of precursor TGF-alpha. These data could have a significant effect on our view of IBD pathogenesis and provide new therapeutic targets for IBD treatment.
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Affiliation(s)
- C B Forsyth
- Department of Internal Medicine, Section of Gastroenterology, Rush University Medical Center, 1725 W. Harrison, Suite 206, Chicago, IL 60612, USA.
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Banan A, Zhang LJ, Shaikh M, Fields JZ, Choudhary S, Forsyth CB, Farhadi A, Keshavarzian A. theta Isoform of protein kinase C alters barrier function in intestinal epithelium through modulation of distinct claudin isotypes: a novel mechanism for regulation of permeability. J Pharmacol Exp Ther 2005; 313:962-82. [PMID: 15900076 DOI: 10.1124/jpet.104.083428] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Using monolayers of intestinal Caco-2 cells, we discovered that the isoform of protein kinase C (PKC), a member of the "novel" subfamily of PKC isoforms, is required for monolayer barrier function. However, the mechanisms underlying this novel effect remain largely unknown. Here, we sought to determine whether the mechanism by which PKC- disrupts monolayer permeability and dynamics in intestinal epithelium involves PKC--induced alterations in claudin isotypes. We used cell clones that we recently developed, clones that were transfected with varying levels of plasmid to either stably suppress endogenous PKC- activity (antisense, dominant-negative constructs) or to ectopically express PKC- activity (sense constructs). We then determined barrier function, claudin isotype integrity, PKC- subcellular activity, claudin isotype subcellular pools, and claudin phosphorylation. Antisense transfection to underexpress the PKC- led to monolayer instability as shown by reduced 1) endogenous PKC- activity, 2) claudin isotypes in the membrane and cytoskeletal pools ( downward arrowclaud-1, downward arrowclaud-4 assembly), 3) claudin isotype phosphorylation ( downward arrow phospho-serine, downward arrow phospho-threonine), 4) architectural stability of the claudin-1 and claudin-4 rings, and 5) monolayer barrier function. In these antisense clones, PKC- activity was also substantially reduced in the membrane and cytoskeletal cell fractions. In wild-type (WT) cells, PKC- (82 kDa) was both constitutively active and coassociated with claudin-1 (22 kDa) and claudin-4 (25 kDa), forming endogenous PKC-/claudin complexes. In a second series of studies, dominant-negative inhibition of the endogenous PKC- caused similar destabilizing effects on monolayer barrier dynamics, including claudin-1 and -4 hypophosphorylation, disassembly, and architectural instability as well as monolayer disruption. In a third series of studies, sense overexpression of the PKC- caused not only a mostly cytosolic distribution of this isoform (i.e., <12% in the membrane + cytoskeletal fractions, indicating PKC- inactivity) but also led to disruption of claudin assembly and barrier function of the monolayer. The conclusions of this study are that PKC- activity is required for normal claudin assembly and the integrity of the intestinal epithelial barrier. These effects of PKC- are mediated at the molecular level by changes in phosphorylation, membrane assembly, and/or organization of the subunit components of two barrier function proteins: claudin-1 and claudin-4 isotypes. The ability of PKC- to alter the dynamics of permeability protein claudins is a new function not previously ascribed to the novel subfamily of PKC isoforms.
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Affiliation(s)
- A Banan
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA.
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Banan A, Zhang LJ, Shaikh M, Fields JZ, Choudhary S, Forsyth CB, Farhadi A, Keshavarzian A. theta Isoform of protein kinase C alters barrier function in intestinal epithelium through modulation of distinct claudin isotypes: a novel mechanism for regulation of permeability. J Pharmacol Exp Ther 2005. [PMID: 15900076 DOI: 10.1124/jpet.105.083428] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Using monolayers of intestinal Caco-2 cells, we discovered that the isoform of protein kinase C (PKC), a member of the "novel" subfamily of PKC isoforms, is required for monolayer barrier function. However, the mechanisms underlying this novel effect remain largely unknown. Here, we sought to determine whether the mechanism by which PKC- disrupts monolayer permeability and dynamics in intestinal epithelium involves PKC--induced alterations in claudin isotypes. We used cell clones that we recently developed, clones that were transfected with varying levels of plasmid to either stably suppress endogenous PKC- activity (antisense, dominant-negative constructs) or to ectopically express PKC- activity (sense constructs). We then determined barrier function, claudin isotype integrity, PKC- subcellular activity, claudin isotype subcellular pools, and claudin phosphorylation. Antisense transfection to underexpress the PKC- led to monolayer instability as shown by reduced 1) endogenous PKC- activity, 2) claudin isotypes in the membrane and cytoskeletal pools ( downward arrowclaud-1, downward arrowclaud-4 assembly), 3) claudin isotype phosphorylation ( downward arrow phospho-serine, downward arrow phospho-threonine), 4) architectural stability of the claudin-1 and claudin-4 rings, and 5) monolayer barrier function. In these antisense clones, PKC- activity was also substantially reduced in the membrane and cytoskeletal cell fractions. In wild-type (WT) cells, PKC- (82 kDa) was both constitutively active and coassociated with claudin-1 (22 kDa) and claudin-4 (25 kDa), forming endogenous PKC-/claudin complexes. In a second series of studies, dominant-negative inhibition of the endogenous PKC- caused similar destabilizing effects on monolayer barrier dynamics, including claudin-1 and -4 hypophosphorylation, disassembly, and architectural instability as well as monolayer disruption. In a third series of studies, sense overexpression of the PKC- caused not only a mostly cytosolic distribution of this isoform (i.e., <12% in the membrane + cytoskeletal fractions, indicating PKC- inactivity) but also led to disruption of claudin assembly and barrier function of the monolayer. The conclusions of this study are that PKC- activity is required for normal claudin assembly and the integrity of the intestinal epithelial barrier. These effects of PKC- are mediated at the molecular level by changes in phosphorylation, membrane assembly, and/or organization of the subunit components of two barrier function proteins: claudin-1 and claudin-4 isotypes. The ability of PKC- to alter the dynamics of permeability protein claudins is a new function not previously ascribed to the novel subfamily of PKC isoforms.
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Affiliation(s)
- A Banan
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA.
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Farhadi A, Keshavarzian A, Ranjbaran Z, Fields JZ, Banan A. The role of protein kinase C isoforms in modulating injury and repair of the intestinal barrier. J Pharmacol Exp Ther 2005; 316:1-7. [PMID: 16002462 DOI: 10.1124/jpet.105.085449] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Gastrointestinal cells express a diverse group of protein kinase C (PKC) isoforms that play critical roles in a number of cell functions, including intracellular signaling and barrier integrity. PKC isoforms expressed by gastrointestinal epithelial cells consist of three major PKC subfamilies: conventional isoforms (alpha, beta1, beta2, and gamma), novel isoforms (delta, epsilon, theta, eta, and mu), and atypical isoforms (lambda, tau, and zeta). This review highlights recent discoveries, including our own, that some PKC isoforms in gastrointestinal epithelia monolayer cell culture are involved in injury to, whereas others are involved in protection of, intestinal barrier integrity. For example, certain PKC isoforms aggravate oxidative damage, whereas others protect against it. These findings suggest that the development of agents that selectively activate or inhibit specific PKC isoforms may lead to new therapeutic modalities for important gastrointestinal disorders such as cancer and inflammatory bowel disease.
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Affiliation(s)
- A Farhadi
- Section of Gastroenterology and Nutrition, Division of Digestive Diseases, Rush University Medical Center, 1725 W. Harrison, Suite 206, Chicago, IL 60612, USA.
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Banan A, Zhang LJ, Farhadi A, Fields JZ, Shaikh M, Forsyth CB, Choudhary S, Keshavarzian A. Critical role of the atypical {lambda} isoform of protein kinase C (PKC-{lambda}) in oxidant-induced disruption of the microtubule cytoskeleton and barrier function of intestinal epithelium. J Pharmacol Exp Ther 2004; 312:458-71. [PMID: 15347733 DOI: 10.1124/jpet.104.074591] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Oxidant injury to epithelial cells and gut barrier disruption are key factors in the pathogenesis of inflammatory bowel disease. Studying monolayers of intestinal (Caco-2) cells, we reported that oxidants disrupt the cytoskeleton and cause barrier dysfunction (hyperpermeability). Because the lambda isoform of protein kinase C (PKC-lambda), an atypical diacylglycerol-independent isozyme, is abundant in parental (wild type) Caco-2 cells and is translocated to the particulate fractions upon oxidant exposure, we hypothesized that PKC-lambda is critical to oxidative injury to the assembly and architecture of cytoskeleton and the intestinal barrier function. To this end, Caco-2 cells were transfected with an inducible plasmid, a tetracycline-responsive system, to create novel clones stably overexpressing native PKC-lambda. Other cells were transfected with a dominant-negative plasmid to stably inhibit the activity of native PKC-lambda. Cells were exposed to oxidant (H(2)O(2)) +/- modulators. Parental Caco-2 cells were treated similarly. We then monitored barrier function (fluorescein sulfonic acid clearance), microtubule cytoskeletal stability (confocal microscopy, immunoblotting), subcellular distribution of PKC-lambda (immunofluorescence, immunoblotting, immunoprecipitation), and PKC-lambda isoform activity (in vitro kinase assay). Monolayers were also processed to assess alterations in tubulin assembly, polymerized tubulin (S2, an index of cytoskeletal integrity), and monomeric tubulin (S1, an index of cytoskeletal disassembly) (polyacrylamide gel electrophoresis fractionation and immunoblotting. In parental cells, oxidant caused: 1) translocation of PKC-lambda from the cytosol to the particulate (membrane + cytoskeletal) fractions, 2) activation of native PKC-lambda, 3) tubulin pool instability (increased monomeric S1 and decreased polymerized S2), 4) disruption of cytoskeletal architecture, and 5) barrier dysfunction (hyperpermeability). In transfected clones, overexpression of the atypical (74 kDa) PKC-lambda isoform by itself ( approximately 3.2-fold increase) led to oxidant-like disruptive effects, including cytoskeletal and barrier hyperpermeability. Overexpressed PKC-lambda was mostly found in particulate cell fractions (with a smaller cytosolic distribution) indicating its activation. Disruption by PKC-lambda overexpression was also potentiated by oxidant challenge. Stable inactivation of endogenous PKC-lambda ( approximately 99.6%) by a dominant-negative protected against all measures of oxidant-induced disruption. We conclude that: 1) oxidant induces disruption of epithelial barrier integrity by disassembling the cytoskeleton, in large part, through the activation of PKC-lambda isoform; and 2) activation of PKC-lambda by itself appears to be sufficient for disruption of cellular cytoskeleton and monolayer barrier permeability. The unique ability to mediate an oxidant-like injury and cytoskeletal depolymerization and instability is a novel mechanism not previously attributed to the atypical subfamily of PKC isoforms.
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Affiliation(s)
- A Banan
- Section of Gastroenterology and Nutrition, Rush University of Chicago, College of Medicine, Division of Digestive Diseases, 1725 W. Harrison, Suite 206, Chicago, IL 60612, USA.
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Banan A, Zhang LJ, Shaikh M, Fields JZ, Farhadi A, Keshavarzian A. Novel effect of NF-kappaB activation: carbonylation and nitration injury to cytoskeleton and disruption of monolayer barrier in intestinal epithelium. Am J Physiol Cell Physiol 2004; 287:C1139-51. [PMID: 15175222 DOI: 10.1152/ajpcell.00146.2004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Using monolayers of intestinal cells, we reported that upregulation of inducible nitric oxide synthase (iNOS) is required for oxidative injury and that activation of NF-kappaB is key to cytoskeletal instability. In the present study, we hypothesized that NF-kappaB activation is crucial to oxidant-induced iNOS upregulation and its injurious consequences: cytoskeletal oxidation and nitration and monolayer dysfunction. Wild-type (WT) cells were pretreated with inhibitors of NF-kappaB, with or without exposure to oxidant (H(2)O(2)). Other cells were transfected with an IkappaBalpha mutant (an inhibitor of NF-kappaB). Relative to WT cells exposed to vehicle, oxidant exposure caused increases in IkappaBalpha instability, NF-kappaB subunit activation, iNOS-related activity (NO, oxidative stress, tubulin nitration), microtubule disassembly and instability (increased monomeric and decreased polymeric tubulin), and monolayer disruption. Monolayers pretreated with NF-kappaB inhibitors (MG-132, lactacystin) were protected against oxidation, showing decreases in all measures of the NF-kappaB --> iNOS --> NO pathway. Dominant mutant stabilization of IkappaBalpha to inactivate NF-kappaB suppressed all measures of the iNOS/NO upregulation while protecting monolayers against oxidant insult. In these mutants, we found prevention of tubulin nitration and oxidation and enhancement of cytoskeletal and monolayer stability. We concluded that 1) NF-kappaB is required for oxidant-induced iNOS upregulation and for the consequent nitration and oxidation of cytoskeleton; 2) NF-kappaB activation causes cytoskeletal injury following upregulation of NO-driven processes; and 3) the molecular event underlying the destabilizing effects of NF-kappaB appears to be increases in carbonylation and nitrotyrosination of the subunit components of cytoskeleton. The ability to promote NO overproduction and cytoskeletal nitration/oxidation is a novel mechanism not previously attributed to NF-kappaB in cells.
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Affiliation(s)
- A Banan
- Rush University Medical Center, Department of Internal Medicine, Section of Gastroenterology and Nutrition, 1725 W. Harrison, Suite 206, Chicago, IL 60612, USA.
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Banan A, Zhang LJ, Shaikh M, Fields JZ, Farhadi A, Keshavarzian A. Theta-isoform of PKC is required for alterations in cytoskeletal dynamics and barrier permeability in intestinal epithelium: a novel function for PKC-theta. Am J Physiol Cell Physiol 2004; 287:C218-34. [PMID: 14985240 DOI: 10.1152/ajpcell.00575.2003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Using intestinal Caco-2 cells, we previously showed that assembly of cytoskeleton is required for monolayer barrier function, but the underlying mechanisms remain poorly understood. Because the theta-isoform of PKC is present in wild-type (WT) intestinal cells, we hypothesized that PKC-theta is crucial for changes in cytoskeletal and barrier dynamics. We have created the first multiple sets of gastrointestinal cell clones transfected with varying levels of cDNA to stably inhibit native PKC-theta (antisense, AS; dominant negative, DN) or to express its activity (sense). We studied transfected and WT Caco-2 cells. First, relative to WT cells, AS clones underexpressing PKC-theta showed monolayer injury as indicated by decreased native PKC-theta activity, reduced tubulin phosphorylation, increased tubulin disassembly (decreased polymerized and increased monomeric pools), reduced architectural integrity of microtubules, reduced stability of occludin, and increased barrier hyperpermeability. In these AS clones, PKC-theta was substantially reduced in the particulate fractions, indicating its inactivation. In WT cells, 82-kDa PKC-theta was constitutively active and coassociated with 50-kDa tubulin, forming an endogenous PKC-theta/tubulin complex. Second, DN transfection to inhibit the endogenous PKC-theta led to similar destabilizing effects on monolayers, including cytoskeletal hypophosphorylation, depolymerization, and instability as well as barrier disruption. Third, stable overexpression of PKC-theta led to a mostly cytosolic distribution of theta-isoform (<10% in particulate fractions), indicating its inactivation. In these sense clones, we also found disruption of occludin and microtubule assembly and increased barrier dysfunction. In conclusion, 1). PKC-theta isoform is required for changes in the cytoskeletal assembly and barrier permeability in intestinal monolayers, and 2). the molecular event underlying this novel biological effect of PKC-theta involves changes in phosphorylation and/or assembly of the subunit components of the cytoskeleton. The ability to alter the cytoskeletal and barrier dynamics is a unique function not previously attributed to PKC-theta.
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Affiliation(s)
- A Banan
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA.
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Banan A, Zhang LJ, Shaikh M, Fields JZ, Farhadi A, Keshavarzian A. Inhibition of oxidant-induced nuclear factor-kappaB activation and inhibitory-kappaBalpha degradation and instability of F-actin cytoskeletal dynamics and barrier function by epidermal growth factor: key role of phospholipase-gamma isoform. J Pharmacol Exp Ther 2004; 309:356-68. [PMID: 14724221 DOI: 10.1124/jpet.103.062232] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Using monolayers of intestinal (Caco-2) cells as a model for studying inflammatory bowel disease (IBD), we previously showed that nuclear factor-kappaB (NF-kappaB) activation is required for oxidant-induced disruption of cytoskeletal and barrier integrity. Epidermal growth factor (EGF) stabilizes the F-actin cytoskeleton and protects against oxidant damage, but the mechanism remains unclear. We hypothesized that the mechanism involves activation of phospholipase C-gamma (PLC-gamma), which prevents NF-kappaB activation and the consequences of this activation, namely, cytoskeletal and barrier disruption. We studied wild-type and transfected cells. The latter were transfected with varying levels (1-5 microg) of cDNA to either stably overexpress PLC-gamma or to inhibit its activation. Cells were pretreated with EGF before exposure to oxidant (H(2)O(2)). Stably overexpressing PLC-gamma (+2.0-fold) or preincubating with EGF protected against oxidant injury as indicated by 1) decreases in several NF-kappaB-related variables [NF-kappaB (p50/p65 subunit) nuclear translocation, NF-kappaB subunit activity, inhibitory-kappaBalpha (I-kappaBalpha) phosphorylation and degradation]; 2) increases in F-actin and decreases in G-actin; 3) stabilization of the actin cytoskeletal architecture; and 4) enhancement of barrier function. Overexpression induced inactivation of NF-kappaB was potentiated by EGF. PLC-gamma was found mostly in membrane and cytoskeletal fractions (<9% in the cytosolic fractions), indicating its activation. Dominant negative inhibition of endogenous PLC-gamma (-99%) substantially prevented all measures of EGF protection against NF-kappaB activation. We concluded 1) EGF protects against oxidant-induced barrier disruption through PLC-gamma activation, which inactivates NF-kappaB; 2) Activation of PLC-gamma by itself is protective against NF-kappaB activation; 3) the ability to modulate the dynamics of NF-kappaB/I-kappa Balpha is a novel mechanism not previously attributed to the PLC family of isoforms in cells; and 4) development of PLC-gamma mimetics represents a possible new therapeutic strategy for IBD.
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Affiliation(s)
- A Banan
- Division of Digestive Diseases, Department of Internal Medicine, Section of Gastroenterology and Nutrition, Rush University of Chicago School of Medicine, 1725 W. Harrison, Suite 206, Chicago, IL 60612, USA.
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Banan A, Zhang LJ, Farhadi A, Fields JZ, Shaikh M, Keshavarzian A. PKC-beta1 isoform activation is required for EGF-induced NF-kappaB inactivation and IkappaBalpha stabilization and protection of F-actin assembly and barrier function in enterocyte monolayers. Am J Physiol Cell Physiol 2003; 286:C723-38. [PMID: 14602581 DOI: 10.1152/ajpcell.00329.2003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Using monolayers of intestinal Caco-2 cells, we reported that activation of NF-kappaB is required for oxidative disruption and that EGF protects against this injury but the mechanism remains unclear. Activation of the PKC-beta1 isoform is key to monolayer barrier integrity. We hypothesized that EGF-induced activation of PKC-beta1 prevents oxidant-induced activation of NF-kappaB and the consequences of NF-kappaB activation, F-actin, and barrier dysfunction. We used wild-type (WT) and transfected cells. The latter were transfected with varying levels of cDNA to overexpress or underexpress PKC-beta1. Cells were pretreated with EGF or PKC modulators +/- oxidant. Pretreatment with EGF protected monolayers by increasing native PKC-beta1 activity, decreasing IkappaBalpha phosphorylation/degradation, suppressing NF-kappaB activation (p50/p65 subunit nuclear translocation/activity), enhancing stable actin (increased F-actin-to-G-actin ratio), increasing stability of actin cytoskeleton, and reducing barrier hyperpermeability. Cells stably overexpressing PKC-beta1 were protected by low, previously nonprotective doses of EGF or modulators. In these clones, we found enhanced IkappaBalpha stabilization, NF-kappaB inactivation, actin stability, and barrier function. Low doses of the modulators led to increases in PKC-beta1 in the particulate fractions, indicating activation. Stably inhibiting endogenous PKC-beta1 substantially prevented all measures of EGF's protection against NF-kappaB activation. We conclude that EGF-mediated protection against oxidant disruption of the intestinal barrier function requires PKC-beta1 activation and NF-kappaB suppression. The molecular event underlying this unique effect of PKC-beta1 involves inhibition of phosphorylation and increases in stabilization of IkappaBalpha. The ability to inhibit the dynamics of NF-kappaB/IkappaBalpha and F-actin disassembly is a novel mechanism not previously attributed to the classic subfamily of PKC isoforms.
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Affiliation(s)
- A Banan
- Division of Digestive Diseases, Department of Internal Medicine, Department of Pharmacology, and Department of Molecular Physiology, Rush University Medical Center, Chicago, Illinois 60612, USA.
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Banan A, Zhang LJ, Shaikh M, Fields JZ, Farhadi A, Keshavarzian A. Key role of PLC-gamma in EGF protection of epithelial barrier against iNOS upregulation and F-actin nitration and disassembly. Am J Physiol Cell Physiol 2003; 285:C977-93. [PMID: 12788694 DOI: 10.1152/ajpcell.00121.2003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Upregulation of inducible nitric oxide synthase (iNOS) is key to oxidant-induced disruption of intestinal (Caco-2) monolayer barrier, and EGF protects against this disruption by stabilizing the cytoskeleton. PLC-gamma appears to be essential for monolayer integrity. We thus hypothesized that PLC-gamma activation is essential in EGF protection against iNOS upregulation and the consequent cytoskeletal oxidation and disarray and monolayer disruption. Intestinal cells were transfected to stably overexpress PLC-gamma or to inhibit its activation and were then pretreated with EGF +/- oxidant (H2O2). Wild-type (WT) intestinal cells were treated similarly. Relative to WT monolayers exposed to oxidant, pretreatment with EGF protected monolayers by: increasing native PLC-gamma activity; decreasing six iNOS-related variables (iNOS activity/protein, NO levels, oxidative stress, actin oxidation/nitration); increasing stable F-actin; maintaining actin stability; and enhancing barrier integrity. Relative to WT cells exposed to oxidant, transfected monolayers overexpressing PLC-gamma (+2.3-fold) were protected, as indicated by decreases in all measures of iNOS-driven pathway and enhanced actin and barrier integrity. Overexpression-induced inhibition of iNOS was potentiated by low doses of EGF. Stable inhibition of PLC-gamma prevented all measures of EGF protection against iNOS upregulation. We conclude that 1) EGF protects against oxidative stress disruption of intestinal barrier by stabilizing F-Actin, largely through the activation of PLC-gamma and downregulation of iNOS pathway; 2) activation of PLC-gamma is by itself essential for cellular protection against oxidative stress of iNOS; and 3) the ability to suppress iNOS-driven reactions and cytoskeletal oxidation and disassembly is a novel mechanism not previously attributed to the PLC family of isoforms.
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Affiliation(s)
- A Banan
- Department of Internal Medicine, Section of Gastroenterology and Nutrition, Rush University School of Medicine, 1725 W. Harrison, Suite 206, Chicago, IL 60612, USA.
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Banan A, Fields JZ, Zhang LJ, Shaikh M, Farhadi A, Keshavarzian A. Zeta isoform of protein kinase C prevents oxidant-induced nuclear factor-kappaB activation and I-kappaBalpha degradation: a fundamental mechanism for epidermal growth factor protection of the microtubule cytoskeleton and intestinal barrier integrity. J Pharmacol Exp Ther 2003; 307:53-66. [PMID: 12893839 DOI: 10.1124/jpet.103.053835] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Oxidant damage and gut barrier disruption contribute to the pathogenesis of a variety of inflammatory gastrointestinal disorders, including inflammatory bowel disease (IBD). In our studies using a model of the gastrointestinal (GI) epithelial barrier, monolayers of intestinal (Caco-2) cells, we investigated damage to and protection of the monolayer barrier. We reported that activation of nuclear factor-kappaB (NF-kappaB) via degradation of its endogenous inhibitor I-kappaBalpha is key to oxidant-induced disruption of barrier integrity and that growth factor (epidermal growth factor, EGF) protects against this injury by stabilizing the cytoskeletal filaments. Protein kinase C (PKC) activation seems to be required for monolayer maintenance, especially activation of the atypical zeta isoform of PKC. In an attempt to investigate, at the molecular level, the fundamental events underlying EGF protection against oxidant disruption, we tested the intriguing hypothesis that EGF-induced activation of PKC-zeta prevents oxidant-induced activation of NF-kappaB and the consequences of NF-kappaB activation, namely, cytoskeletal and barrier disruption. Monolayers of wild-type (WT) Caco-2 cells were incubated with oxidant (H2O2) with or without EGF or modulators. In other studies, we used the first gastrointestinal cell clones created by stable transfection of varying levels (1-5 microg) of cDNA to either overexpress PKC-zeta or to inhibit its expression. Transfected cell clones were then pretreated with EGF or a PKC activator (diacylglycerol analog 1-oleoyl-2-acetyl-glycerol, OAG) before oxidant. We monitored the following endpoints: monolayer barrier integrity, stability of the microtubule cytoskeleton, subcellular distribution and activity of the PKC-zeta isoform, intracellular levels and phosphorylation of the NF-kappaB inhibitor I-kappaBalpha, and nuclear translocation and activity of NF-kappaB subunits p65 and p50. Monolayers were also fractionated and processed to assess alterations in the structural protein of the microtubules, polymerized tubulin (S2), and monomeric tubulin (S1). Our data indicated that relative to WT monolayers exposed only to oxidant, pretreatment with EGF protected cell monolayers by 1) increasing native PKC-zeta activity; 2) decreasing several variables related to NF-kappaB activation [NF-kappaB (both p50 and p65 subunits) nuclear translocation, NF-kappaB subunits activity, I-kappaBalpha degradation, and phosphorylation]; 3) increasing stable tubulin (increased polymerized S2 tubulin and decreased monomeric S1 tubulin); 4) maintaining the cytoarchitectural integrity of microtubules; and 5) preventing hyperpermeability (barrier disruption). In addition, relative to WT cells exposed to oxidant, monolayers of transfected cells stably overexpressing PKC-zeta (approximately 3.0-fold increase) were protected as indicated by decreases in all measures of NF-kappaB activation as well as enhanced stability of microtubule cytoarchitecture and barrier function. Overexpression induced stabilization of I-kappaBalpha and inactivation of NF-kappaB was OAG-independent, although EGF potentiated this protection. Approximately 90% of the overexpressed PKC-zeta resided in particulate (membrane + cytoskeletal) fractions (with less than 10% in cytosolic fractions), indicating constitutive activation of the zeta isoform of PKC. Furthermore, antisense transfection to stably inhibit native PKC-zeta expression (-95%) and activation (-99%) prevented all measures of EGF-induced protection against NF-kappaB activation and monolayer disruption. We conclude the following: 1) EGF protects against oxidant disruption of the intestinal barrier integrity, in large part, through the activation of PKC-zeta and inactivation of NF-kappaB (an inflammatory mediator); 2) activation of PKC-zeta is by itself required for monolayer protection against oxidant stress of NF-kappaB activation; 3) the mechanism underlying this novel biological effect of the atypical PKC isoform zeta seems to involve suppression of phosphorylation and enhancement of stabilization of I-kappaBalpha; and 4) development of agents that can mimic or enhance PKC-zeta-induced suppression of NF-kappaB activation may be a useful therapeutic strategy for preventing oxidant damage to GI mucosal epithelium in disorders such as IBD. To our knowledge, this is the first report that PKC-zeta can inhibit the dynamics of NF-kappaB and cytoskeletal disassembly in cells.
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Affiliation(s)
- A Banan
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA.
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Banan A, Farhadi A, Fields JZ, Mutlu E, Zhang L, Keshavarzian A. Evidence that nuclear factor-kappa B activation is critical in oxidant-induced disruption of the microtubule cytoskeleton and barrier integrity and that its inactivation is essential in epidermal growth factor-mediated protection of the monolayers of intestinal epithelia. J Pharmacol Exp Ther 2003; 306:13-28. [PMID: 12815011 DOI: 10.1124/jpet.103.047415] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Using monolayers of intestinal (Caco-2) cells, we showed that oxidants disrupt the microtubule cytoskeleton and barrier integrity; epidermal growth factor (EGF) was protective via stabilization of the microtubules. Because proinflammatory conditions activate nuclear factor-kappaB (NF-kappaB), we hypothesized that oxidants disrupt barrier integrity through activation of NF-kappaB and that EGF protects by suppressing NF-kappaB. Parental cells were pretreated with EGF or NF-kappaB or inhibitory kappaBalpha (I-kappaBalpha) modulators. Other cells were stably transfected with varying levels of a dominant negative mutant for the NF-kappaB inhibitor I-kappaBalpha. Both types of cells were grown as monolayers and then exposed to oxidant (H2O2). We then monitored monolayer barrier integrity (permeability), stability of the microtubule cytoskeleton (confocal microscopy, immunoblotting), intracellular levels of the I-kappaBalpha (immunoblotting), translocation, and activity of NF-kappaB (immunoblotting, sensitive enzyme-linked immunosorbent assay). Monolayers were also fractionated and processed to assess alterations in 1) polymerized tubulin (S2; an index of cytoskeletal integrity) and 2) monomeric tubulin (S1; an index of disassembly) (polyacrylamide gel electrophoresis fractionation and immunoblotting). We found the following: 1) Oxidants caused I-kappaBalpha degradation, NF-kappaB translocation, NF-kappaB (p50 and p65 subunits) activation, tubulin disassembly ( upward arrow S1, downward arrow S2), microtubule architectural instability, and barrier disruption. I-kappaBalpha stabilizers and NF-kappaB inhibitors [e.g., carbobenzyloxy-leuleu-leucinol (MG-132), lactacystin] suppressed oxidants injurious effects. 2) EGF (10 ng/ml) stabilized I-kappaBalpha and prevented both NF-kappaB translocation and activation while protecting monolayers against oxidants. 3) In stably transfected cells, transfection-induced stabilization of I-kappaBalpha by itself led to EGF-like protective effects. In these mutant cells, protection was not potentiated by EGF (10 ng/ml). Conclusions are 1) oxidants induce disruption of the cytoskeleton and intestinal barrier integrity, in part, through I-kappaBalpha degradation and subsequent NF-kappaB activation, 2) I-kappaBalpha stabilization is by itself protective, mimicking EGF, and 3) EGF protects cell monolayers through I-kappaBalpha stabilization and NF-kappaB inactivation. To our knowledge, this is the first report that NF-kappaB can affect the dynamics of cytoskeletal assembly and intestinal barrier integrity.
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Affiliation(s)
- A Banan
- Department of Internal Medicine, Section of Gastroenterology and Nutrition, Rush University Medical Center, Chicago, IL 60612, USA.
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Banan A, Farhadi A, Fields JZ, Zhang LJ, Shaikh M, Keshavarzian A. The delta-isoform of protein kinase C causes inducible nitric-oxide synthase and nitric oxide up-regulation: key mechanism for oxidant-induced carbonylation, nitration, and disassembly of the microtubule cytoskeleton and hyperpermeability of barrier of intestinal epithelia. J Pharmacol Exp Ther 2003; 305:482-94. [PMID: 12606598 DOI: 10.1124/jpet.102.047308] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Using intestinal (Caco-2) cells, we found that oxidant-induced disruption of barrier integrity requires microtubule disassembly. Protein kinase C (PKC)-delta isoform seems to be essential for disruption, but the mechanism is unknown. Because inducible nitric-oxide synthase (iNOS) is key to oxidant stress, we hypothesized that PKC-delta activation is essential in oxidant-induced iNOS up-regulation and the consequent cytoskeletal oxidation and disarray and monolayer barrier dysfunction. Cells were transfected with an inducible plasmid to overexpress native PKC-delta or with a dominant-negative to inhibit the activity of native PKC-delta. Clones were then incubated with oxidant (H(2)O(2)) +/- modulators. Parental cells were treated similarly. Exposure to oxidant-disrupted monolayers by increasing native PKC-delta activity, increasing six iNOS-related variables (iNOS activity and protein, nitric oxide, oxidative stress, tubulin oxidation and nitration), decreasing polymerized tubulin, disrupting the cytoarchitecture of microtubules, and causing monolayer dysfunction. Induction of PKC-delta overexpression by itself (3.5-fold) led to oxidant-like disruptive effects, including activation of the iNOS-driven pathway. Overexpression-induced up-regulation of iNOS was potentiated by oxidants. iNOS inhibitors or oxidant scavengers were protective. Dominant inhibition of native PKC-delta activity (99.5%) prevented all measures of oxidant-induced iNOS up-regulation and protected the monolayer barrier. The conclusions are as follows. 1) Oxidants induce loss of epithelial barrier integrity by oxidizing and disassembling the cytoskeleton, in part, through the activation of PKC-delta and up-regulation of iNOS. 2) Overexpression and activation of PKC-delta are by themselves key for cellular injury by oxidative stress of iNOS. 3) We thus report a pathophysiological mechanism, activation of iNOS pathway and its injurious consequences to the cytoskeleton, including oxidation and nitration, among the "novel" subfamily of PKC isoforms.
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Affiliation(s)
- A Banan
- Department of Internal Medicine, Section of Gastroenterology and Nutrition, Pharmacology, and Molecular Physiology, Rush University of Chicago, 1725 W. Harrison, Suite 206, Chicago, IL 60612, USA.
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Keshavarzian A, Banan A, Farhadi A, Komanduri S, Mutlu E, Zhang Y, Fields JZ. Increases in free radicals and cytoskeletal protein oxidation and nitration in the colon of patients with inflammatory bowel disease. Gut 2003; 52:720-8. [PMID: 12692059 PMCID: PMC1773652 DOI: 10.1136/gut.52.5.720] [Citation(s) in RCA: 181] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Overproduction of colonic oxidants contributes to mucosal injury in inflammatory bowel disease (IBD) but the mechanisms are unclear. Our recent findings using monolayers of intestinal cells suggest that the mechanism could be oxidant induced damage to cytoskeletal proteins. However, oxidants and oxidative damage have not been well characterised in IBD mucosa. AIMS To determine whether there are increases in oxidants and in tissue and cytoskeletal protein oxidation in IBD mucosa. METHODS We measured nitric oxide (NO) and markers of oxidative injury (carbonylation and nitrotyrosination) to tissue and cytoskeletal proteins in colonic mucosa from IBD patients (ulcerative colitis, Crohn's disease, specific colitis) and controls. Outcomes were correlated with IBD severity score. RESULTS Inflamed mucosa showed the greatest increases in oxidants and oxidative damage. Smaller but still significant increases were seen in normal appearing mucosa of patients with active and inactive IBD. Tissue NO levels correlated with oxidative damage. Actin was markedly (>50%) carbonylated and nitrated in inflamed tissues of active IBD, less so in normal appearing tissues. Tubulin carbonylation occurred in parallel; tubulin nitration was not observed. NO and all measures of oxidative damage in tissue and cytoskeletal proteins in the mucosa correlated with IBD severity. Disruption of the actin cytoarchitecture was primarily within the epithelial cells and paracellular area. CONCLUSIONS Oxidant levels increase in IBD along with oxidation of tissue and cytoskeletal proteins. Oxidative injury correlated with disease severity but is also present in substantial amounts in normal appearing mucosa of IBD patients, suggesting that oxidative injury does not necessarily lead to tissue injury and is not entirely a consequence of tissue injury. Marked actin oxidation (>50%)-which appears to result from cumulative oxidative damage-was only seen in inflamed mucosa, suggesting that oxidant induced cytoskeletal disruption is required for tissue injury, mucosal disruption, and IBD flare up.
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Affiliation(s)
- A Keshavarzian
- Department of Internal Medicine (Division of Digestive Diseases), Pharmacology, and Molecular Physiology, Rush University Medical Center, Chicago, IL 60612, USA.
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Banan A, Farhadi A, Fields JZ, Mutlu E, Zhang L, Keshavarzian A. Evidence That Nuclear Factor-κB Activation Is Critical in Oxidant-Induced Disruption of the Microtubule Cytoskeleton and Barrier Integrity and That Its Inactivation Is Essential in Epidermal Growth Factor-Mediated Protection of the Monolayers of Intestinal Epithelia. J Pharmacol Exp Ther 2003. [DOI: 10.1124/jpet.102.047415] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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