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Pandarangga P, Doan PTK, Tearle R, Low WY, Ren Y, Nguyen HTH, Dharmayanti NI, Hemmatzadeh F. mRNA Profiling and Transcriptomics Analysis of Chickens Received Newcastle Disease Virus Genotype II and Genotype VII Vaccines. Pathogens 2024; 13:638. [PMID: 39204239 PMCID: PMC11357267 DOI: 10.3390/pathogens13080638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 07/17/2024] [Accepted: 07/23/2024] [Indexed: 09/03/2024] Open
Abstract
Newcastle Disease Virus (NDV) genotype VII (GVII) is becoming the predominant strain of NDV in the poultry industry. It causes high mortality even in vaccinated chickens with a common NDV genotype II vaccine (GII-vacc). To overcome this, the killed GVII vaccine has been used to prevent NDV outbreaks. However, the debate about vaccine differences remains ongoing. Hence, this study investigated the difference in chickens' responses to the two vaccines at the molecular level. The spleen transcriptomes from vaccinated chickens reveal that GVII-vacc affected the immune response by downregulating neuroinflammation. It also enhanced a synaptogenesis pathway that operates typically in the nervous system, suggesting a mechanism for the neurotrophic effect of this strain. We speculated that the down-regulated immune system regulation correlated with protecting the nervous system from excess leukocytes and cytokine activity. In contrast, GII-vacc inhibited apoptosis by downregulating PERK/ATF4/CHOP as part of the unfolded protein response pathway but did not affect the expression of the same synaptogenesis pathway. Thus, the application of GVII-vacc needs to be considered in countries where GVII is the leading cause of NDV outbreaks. The predicted molecular signatures may also be used in developing new vaccines that trigger specific genes in the immune system in combating NDV outbreaks.
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Affiliation(s)
- Putri Pandarangga
- Departemen Klinik, Reproduksi, dan Patologi, Fakultas Kedokteran dan Kedokteran Hewan, Universitas Nusa Cendana, Kupang 85001, Indonesia;
- School of Animal and Veterinary Sciences, University of Adelaide, Adelaide 5371, Australia; (P.T.K.D.); (H.T.H.N.)
| | - Phuong Thi Kim Doan
- School of Animal and Veterinary Sciences, University of Adelaide, Adelaide 5371, Australia; (P.T.K.D.); (H.T.H.N.)
- Department of Veterinary Medicine, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam
| | - Rick Tearle
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide 5371, Australia; (R.T.); (W.Y.L.); (Y.R.)
| | - Wai Yee Low
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide 5371, Australia; (R.T.); (W.Y.L.); (Y.R.)
| | - Yan Ren
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide 5371, Australia; (R.T.); (W.Y.L.); (Y.R.)
| | - Hanh Thi Hong Nguyen
- School of Animal and Veterinary Sciences, University of Adelaide, Adelaide 5371, Australia; (P.T.K.D.); (H.T.H.N.)
| | | | - Farhid Hemmatzadeh
- School of Animal and Veterinary Sciences, University of Adelaide, Adelaide 5371, Australia; (P.T.K.D.); (H.T.H.N.)
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Zhao K, Ebrahimie E, Mohammadi-Dehcheshmeh M, Lewsey MG, Zheng L, Hoogenraad NJ. Transcriptomic signature of cancer cachexia by integration of machine learning, literature mining and meta-analysis. Comput Biol Med 2024; 172:108233. [PMID: 38452471 DOI: 10.1016/j.compbiomed.2024.108233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 01/23/2024] [Accepted: 02/25/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND Cancer cachexia is a severe metabolic syndrome marked by skeletal muscle atrophy. A successful clinical intervention for cancer cachexia is currently lacking. The study of cachexia mechanisms is largely based on preclinical animal models and the availability of high-throughput transcriptomic datasets of cachectic mouse muscles is increasing through the extensive use of next generation sequencing technologies. METHODS Cachectic mouse muscle transcriptomic datasets of ten different studies were combined and mined by seven attribute weighting models, which analysed both categorical variables and numerical variables. The transcriptomic signature of cancer cachexia was identified by attribute weighting algorithms and was used to evaluate the performance of eleven pattern discovery models. The signature was employed to find the best combination of drugs (drug repurposing) for developing cancer cachexia treatment strategies, as well as to evaluate currently used cachexia drugs by literature mining. RESULTS Attribute weighting algorithms ranked 26 genes as the transcriptomic signature of muscle from mice with cancer cachexia. Deep Learning and Random Forest models performed better in differentiating cancer cachexia cases based on muscle transcriptomic data. Literature mining revealed that a combination of melatonin and infliximab has negative interactions with 2 key genes (Rorc and Fbxo32) upregulated in the transcriptomic signature of cancer cachexia in muscle. CONCLUSIONS The integration of machine learning, meta-analysis and literature mining was found to be an efficient approach to identifying a robust transcriptomic signature for cancer cachexia, with implications for improving clinical diagnosis and management of this condition.
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Affiliation(s)
- Kening Zhao
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China; La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
| | - Esmaeil Ebrahimie
- Genomics Research Platform, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC, 3086, Australia; School of Animal and Veterinary Science, The University of Adelaide, Adelaide, SA 5371, Australia; School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Manijeh Mohammadi-Dehcheshmeh
- Genomics Research Platform, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC, 3086, Australia; School of Animal and Veterinary Science, The University of Adelaide, Adelaide, SA 5371, Australia.
| | - Mathew G Lewsey
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia; La Trobe Institute for Sustainable Agriculture and Food, Department of Plant, Animal and Soil Sciences, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia; Australian Research Council Centre of Excellence in Plants for Space, AgriBio Building, La Trobe University, Bundoora, VIC, 3086, Australia.
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Nick J Hoogenraad
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia; Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, School of Cancer Medicine, La Trobe University, Melbourne, VIC, 3084, Australia.
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Feng D, Wu S, Jiang B, He S, Luo Y, Li F, Song B, Song R. Discovery of Novel Isoxazoline Derivatives Containing Diaryl Ether against Fall Armyworms. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:6859-6870. [PMID: 37126004 DOI: 10.1021/acs.jafc.3c00824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
With the continuous evolution of insect resistance, it is a tremendous challenge to control the fall armyworm (Spodoptera frugiperda) with traditional insecticides. To solve this pending issue, a series of novel isoxazoline derivatives containing diaryl ether structures were designed and synthesized, and most of the target compounds exhibited excellent insecticidal activity. Based on the three-dimensional quantitative structure-activity relationship (3D-QSAR) model analysis, we further optimized the molecular structure with compound L35 obtained and tested for its activity. Compound L35 (LC50 = 1.69 mg/L) exhibited excellent insecticidal activity against S. frugiperda, which was better than those of commercial fipronil (LC50 = 70.78 mg/L) and indoxacarb (LC50 = 5.37 mg/L). The enzyme-linked immunosorbent assay showed that L35 could upregulate the levels of GABA in insects. In addition, molecular docking and transcriptomic results also indicated that compound L35 may affect the nervous system of S. frugiperda by acting on GABA receptors. Notably, through high-performance liquid chromatography (HPLC), we were able to obtain the two enantiomers of compound L35, and the insecticidal activity test revealed that S-(+)-L35 was 44 times more active than R-(-)-L35 against S. frugiperda. This study established the chemistry basis and mechanistic foundations for the future development of pesticide candidates against fall armyworms.
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Affiliation(s)
- Di Feng
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, P.R. China
| | - Shang Wu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, P.R. China
| | - Biaobiao Jiang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, P.R. China
| | - Siqi He
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, P.R. China
| | - Yuqin Luo
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, P.R. China
| | - Fangyi Li
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, P.R. China
| | - Baoan Song
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, P.R. China
| | - Runjiang Song
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, P.R. China
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Govic A, Nasser H, Levay EA, Zelko M, Ebrahimie E, Mohammadi Dehcheshmeh M, Kent S, Penman J, Hazi A. Long-Term Calorie Restriction Alters Anxiety-like Behaviour and the Brain and Adrenal Gland Transcriptomes of the Ageing Male Rat. Nutrients 2022; 14:nu14214670. [PMID: 36364936 PMCID: PMC9654051 DOI: 10.3390/nu14214670] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Further examination of the molecular regulators of long-term calorie restriction (CR), reported to have an anxiolytic effect, may highlight novel therapeutic targets for anxiety disorders. Here, adult male Hooded Wistar rats were exposed to a 25% CR whilst anxiety-like behaviour was assessed at 6-, 12-, and 18-months of age via the elevated plus maze, open field, and acoustic startle tests. Next-generation sequencing was then used to measure transcriptome-wide gene expression in the hypothalamus, amygdala, pituitary, and adrenal glands. Results showed an anxiolytic behavioural profile across early, middle, and late adulthood by CR, with the strongest effects noted at 6-months. Transcriptomic analysis by seven attribute weighting algorithms, including Info Gain Ratio, Rule, Chi Squared, Gini Index, Uncertainty, Relief, and Info Gain, led to the development of a signature of long-term CR, independent of region. Complement C1q A chain (C1qa), an extracellular protein, expression was significantly decreased by CR in most regions examined. Furthermore, text mining highlighted the positive involvement of C1qa in anxiety, depression, neurodegeneration, stress, and ageing, collectively identifying a suitable biomarker candidate for CR. Overall, the current study identified anxiety-related phenotypic changes and a novel transcriptome signature of long-term CR, indicating potential therapeutic targets for anxiety, depression, and neurodegeneration.
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Affiliation(s)
- Antonina Govic
- School of Psychology and Public Health, La Trobe University, Melbourne, VIC 3010, Australia
- Epigenes Australia Pty Ltd., Melbourne, VIC 3010, Australia
- Correspondence: or ; Tel.: +61-3-9780-9996
| | - Helen Nasser
- School of Psychology and Public Health, La Trobe University, Melbourne, VIC 3010, Australia
- Epigenes Australia Pty Ltd., Melbourne, VIC 3010, Australia
| | - Elizabeth A. Levay
- School of Psychology and Public Health, La Trobe University, Melbourne, VIC 3010, Australia
- Epigenes Australia Pty Ltd., Melbourne, VIC 3010, Australia
| | - Matt Zelko
- School of Psychology and Public Health, La Trobe University, Melbourne, VIC 3010, Australia
- Epigenes Australia Pty Ltd., Melbourne, VIC 3010, Australia
| | - Esmaeil Ebrahimie
- Genomics Research Platform, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3000, Australia
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, SA 5371, Australia
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Manijeh Mohammadi Dehcheshmeh
- Genomics Research Platform, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3000, Australia
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, SA 5371, Australia
| | - Stephen Kent
- School of Psychology and Public Health, La Trobe University, Melbourne, VIC 3010, Australia
| | - Jim Penman
- Epigenes Australia Pty Ltd., Melbourne, VIC 3010, Australia
| | - Agnes Hazi
- School of Psychology and Public Health, La Trobe University, Melbourne, VIC 3010, Australia
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Gu L, Zhou Y, Wang G, Deng H, Song X, He X, Wang T, Chen X, Dai J, Li R. Spatial learning and memory impaired after infection of non-neurotropic influenza virus in BALB/c male mice. Biochem Biophys Res Commun 2021; 540:29-36. [PMID: 33429197 DOI: 10.1016/j.bbrc.2020.12.092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 12/25/2020] [Indexed: 02/05/2023]
Abstract
During the influenza pandemic or seasonal influenza outbreak, influenza infection can cause acute influenza-associated encephalopathy/encephalitis (IAE), even death. Patients with severe IAE will also have severe neurological sequelae. Neurologic disorders have been demonstrated in the mice treated with peripheral influenza viruses infection, whether neurotropic or non-neurotropic viruses. However, previous studies focused on the acute phase of infection, and rarely paid attention to a longer range of observations. Therefore, the long-term effect of non-neurotropic virus infection on the host is not very clear. In this study, adult mice were infected with influenza virus H1N1/PR8. Then, spontaneous behavior, body weight, expression of cytokines in brain, spatial learning ability and spatial memory ability were observed, until the complete recovery period. The results showed that cytokines in the brain were highly expressed in the convalescent phase (14 day post inoculation, dpi), especially BDNF, IBA1, CX3CL1 and CD200 were still highly expressed in the recovery phase (28 dpi). Otherwise the emotional and spatial memory ability of mice were impacted in the convalescent phase (14 dpi) and the recovery phase (28 dpi). In brief, BALB/c mice infected with non-neurotropic influenza virus H1N1, the weight and motor ability decreased in acute stage. During the recovery period, the body weight and activity ability were completely restored, whereas the emotion disordered, and the ability of spatial learning and memory were impacted in the infected mice. This long-term behavior impact may be the lag injury caused by non-neurotropic influenza infection.
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Affiliation(s)
- Liming Gu
- Department of Microbiology and Immunology, Shantou University Medical College, Shantou, 515041, Guangdong, China; Center of Pathogen Biology and Immunology, Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Yanlin Zhou
- Department of Microbiology and Immunology, Shantou University Medical College, Shantou, 515041, Guangdong, China; Department of Pathogenic Biology and Immunology, Sanquan College of Xinxiang Medical University, Xinxiang, 453003, Henan, China
| | - Gefei Wang
- Department of Microbiology and Immunology, Shantou University Medical College, Shantou, 515041, Guangdong, China; Center of Pathogen Biology and Immunology, Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Huixiong Deng
- Department of Microbiology and Immunology, Shantou University Medical College, Shantou, 515041, Guangdong, China; Center of Pathogen Biology and Immunology, Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Xinli Song
- Department of Microbiology and Immunology, Shantou University Medical College, Shantou, 515041, Guangdong, China; Center of Pathogen Biology and Immunology, Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Xuanting He
- Department of Microbiology and Immunology, Shantou University Medical College, Shantou, 515041, Guangdong, China; Center of Pathogen Biology and Immunology, Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Tingting Wang
- Department of Microbiology and Immunology, Shantou University Medical College, Shantou, 515041, Guangdong, China; Center of Pathogen Biology and Immunology, Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Xiaoxuan Chen
- Department of Microbiology and Immunology, Shantou University Medical College, Shantou, 515041, Guangdong, China; Center of Pathogen Biology and Immunology, Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Jianping Dai
- Department of Microbiology and Immunology, Shantou University Medical College, Shantou, 515041, Guangdong, China; Center of Pathogen Biology and Immunology, Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Rui Li
- Department of Microbiology and Immunology, Shantou University Medical College, Shantou, 515041, Guangdong, China; Center of Pathogen Biology and Immunology, Shantou University Medical College, Shantou, 515041, Guangdong, China.
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Zhang Y, Xu C, Zhang H, Liu GD, Xue C, Cao Y. Targeting Hemagglutinin: Approaches for Broad Protection against the Influenza A Virus. Viruses 2019; 11:v11050405. [PMID: 31052339 PMCID: PMC6563292 DOI: 10.3390/v11050405] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 04/26/2019] [Accepted: 04/27/2019] [Indexed: 12/13/2022] Open
Abstract
Influenza A viruses are dynamically epidemic and genetically diverse. Due to the antigenic drift and shift of the virus, seasonal vaccines are required to be reformulated annually to match with current circulating strains. However, the mismatch between vaccinal strains and circulating strains occurs frequently, resulting in the low efficacy of seasonal vaccines. Therefore, several “universal” vaccine candidates based on the structure and function of the hemagglutinin (HA) protein have been developed to meet the requirement of a broad protection against homo-/heterosubtypic challenges. Here, we review recent novel constructs and discuss several important findings regarding the broad protective efficacy of HA-based universal vaccines.
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Affiliation(s)
- Yun Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.
| | - Cong Xu
- Research Center of Agricultural of Dongguan City, Dongguan 523086, China.
| | - Hao Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.
| | - George Dacai Liu
- Firstline Biopharmaceuticals Corporation, 12,050 167th PL NE, Redmond, WA 98052, USA.
| | - Chunyi Xue
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.
| | - Yongchang Cao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.
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Kargarfard F, Sami A, Hemmatzadeh F, Ebrahimie E. Identifying mutation positions in all segments of influenza genome enables better differentiation between pandemic and seasonal strains. Gene 2019; 697:78-85. [PMID: 30769139 DOI: 10.1016/j.gene.2019.01.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 12/29/2018] [Accepted: 01/17/2019] [Indexed: 01/08/2023]
Abstract
Influenza has a negative sense, single-stranded, and segmented RNA. In the context of pandemic influenza research, most studies have focused on variations in the surface proteins (Hemagglutinin and Neuraminidase). However, new findings suggest that all internal and external proteins of influenza viruses can contribute in pandemic emergence, pathogenicity and increasing host range. The occurrence of the 2009 influenza pandemic and the availability of many external and internal segments of pandemic and non-pandemic sequences offer a unique opportunity to evaluate the performance of machine learning models in discrimination of pandemic from seasonal sequences using mutation positions in all segments. In this study, we hypothesized that identifying mutation positions in all segments (proteins) encoded by the influenza genome would enable pandemic and seasonal strains to be more reliably distinguished. In a large scale study, we applied a range of data mining techniques to all segments of influenza for rule discovery and discrimination of pandemic from seasonal strains. CBA (classification based on association rule mining), Ripper and Decision tree algorithms were utilized to extract association rules among mutations. CBA outperformed the other models. Our approach could discriminate pandemic sequences from seasonal ones with more than 95% accuracy for PA and NP, 99.33% accuracy for NA and 100% accuracy, precision, specificity and sensitivity (recall) for M1, M2, PB1, NS1, and NS2. The values of precision, specificity, and sensitivity were more than 90% for other segments except PB2. If sequences of all segments of one strain were available, the accuracy of discrimination of pandemic strains was 100%. General rules extracted by rule base classification approaches, such as M1-V147I, NP-N334H, NS1-V112I, and PB1-L364I, were able to detect pandemic sequences with high accuracy. We observed that mutations on internal proteins of influenza can contribute in distinguishing the pandemic viruses, similar to the external ones.
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Affiliation(s)
- Fatemeh Kargarfard
- Faculty of Engineering and IT, University of Technology Sydney, New South Wales, Australia; Department of Computer Science and Engineering, School of Electrical Engineering and Computer, Shiraz University, Shiraz, Iran
| | - Ashkan Sami
- Department of Computer Science and Engineering, School of Electrical Engineering and Computer, Shiraz University, Shiraz, Iran
| | - Farhid Hemmatzadeh
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Esmaeil Ebrahimie
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia; Genomics Research Platform, La Trobe University, Melbourne, Victoria 3086, Australia; School of Information Technology and Mathematical Sciences, Division of Information Technology Engineering & Environment, University of South Australia, Adelaide, Australia; School of Biological Sciences, Faculty of Science and Engineering, Flinders University, Adelaide, Australia.
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Zou ZY, Liu J, Chang C, Li JJ, Luo J, Jin Y, Ma Z, Wang TH, Shao JL. Biliverdin administration regulates the microRNA-mRNA expressional network associated with neuroprotection in cerebral ischemia reperfusion injury in rats. Int J Mol Med 2019; 43:1356-1372. [PMID: 30664169 PMCID: PMC6365090 DOI: 10.3892/ijmm.2019.4064] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/18/2018] [Indexed: 12/21/2022] Open
Abstract
Inflammatory response has an important role in the outcome of cerebral ischemia reperfusion injury (CIR). Biliverdin (BV) administration can relieve CIR in rats, but the mechanism remains unknown. The aim of the present study was to explore the expressional network of microRNA (miRNA)-mRNA in CIR rats following BV administration. A rat middle cerebral artery occlusion model with BV treatment was established. After neurobehavior was evaluated by neurological severity scores (NSS), miRNA and mRNA expressional profiles were analyzed by microarray technology from the cerebral cortex subjected to ischemia and BV administration. Then, bioinformatics prediction was used to screen the correlation between miRNA and mRNA, and 20 candidate miRNAs and 33 candidate mRNAs were verified by reverse transcription-quantitative polymerase chain reaction. Furthermore, the regulation relationship between ETS proto-oncogene 1 (Ets1) and miRNA204-5p was examined by luciferase assay. A total of 86 miRNAs were differentially expressed in the BV group compared with the other groups. A total of 10 miRNAs and 26 candidate genes were identified as a core 'microRNA-mRNA' regulatory network that was linked with the functional improvement of BV administration in CIR rats. Lastly, the luciferase assay results confirmed that miRNA204-5p directly targeted Ets1. The present findings suggest that BV administration may regulate multiple miRNAs and mRNAs to improve neurobehavior in CIR rats, by influencing cell proliferation, apoptosis, maintaining ATP homeostasis, and angiogenesis.
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Affiliation(s)
- Zhi-Yao Zou
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650000, P.R. China
| | - Jia Liu
- Experimental Animal Center, Kunming Medical University, Kunming, Yunnan 650000, P.R. China
| | - Cheng Chang
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650000, P.R. China
| | - Jun-Jie Li
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650000, P.R. China
| | - Jing Luo
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650000, P.R. China
| | - Yuan Jin
- Experimental Animal Center, Kunming Medical University, Kunming, Yunnan 650000, P.R. China
| | - Zheng Ma
- Experimental Animal Center, Kunming Medical University, Kunming, Yunnan 650000, P.R. China
| | - Ting-Hua Wang
- Experimental Animal Center, Kunming Medical University, Kunming, Yunnan 650000, P.R. China
| | - Jian-Lin Shao
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650000, P.R. China
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Farhadian M, Rafat SA, Hasanpur K, Ebrahimi M, Ebrahimie E. Cross-Species Meta-Analysis of Transcriptomic Data in Combination With Supervised Machine Learning Models Identifies the Common Gene Signature of Lactation Process. Front Genet 2018; 9:235. [PMID: 30050559 PMCID: PMC6052129 DOI: 10.3389/fgene.2018.00235] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 06/13/2018] [Indexed: 01/13/2023] Open
Abstract
Lactation, a physiologically complex process, takes place in mammary gland after parturition. The expression profile of the effective genes in lactation has not comprehensively been elucidated. Herein, meta-analysis, using publicly available microarray data, was conducted identify the differentially expressed genes (DEGs) between pre- and post-peak milk production. Three microarray datasets of Rat, Bos Taurus, and Tammar wallaby were used. Samples related to pre-peak (n = 85) and post-peak (n = 24) milk production were selected. Meta-analysis revealed 31 DEGs across the studied species. Interestingly, 10 genes, including MRPS18B, SF1, UQCRC1, NUCB1, RNF126, ADSL, TNNC1, FIS1, HES5 and THTPA, were not detected in original studies that highlights meta-analysis power in biosignature discovery. Common target and regulator analysis highlighted the high connectivity of CTNNB1, CDD4 and LPL as gene network hubs. As data originally came from three different species, to check the effects of heterogeneous data sources on DEGs, 10 attribute weighting (machine learning) algorithms were applied. Attribute weighting results showed that the type of organism had no or little effect on the selected gene list. Systems biology analysis suggested that these DEGs affect the milk production by improving the immune system performance and mammary cell growth. This is the first study employing both meta-analysis and machine learning approaches for comparative analysis of gene expression pattern of mammary glands in two important time points of lactation process. The finding may pave the way to use of publically available to elucidate the underlying molecular mechanisms of physiologically complex traits such as lactation in mammals.
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Affiliation(s)
- Mohammad Farhadian
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Seyed A Rafat
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Karim Hasanpur
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | | | - Esmaeil Ebrahimie
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia.,Institute of Biotechnology, Shiraz University, Shiraz, Iran.,Division of Information Technology, Engineering and the Environment, School of Information Technology & Mathematical Sciences, University of South Australia, Adelaide, SA, Australia.,School of Biological Sciences, Faculty of Science and Engineering, Flinders University, Adelaide, SA, Australia
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Alanazi IO, AlYahya SA, Ebrahimie E, Mohammadi-Dehcheshmeh M. Computational systems biology analysis of biomarkers in lung cancer; unravelling genomic regions which frequently encode biomarkers, enriched pathways, and new candidates. Gene 2018; 659:29-36. [DOI: 10.1016/j.gene.2018.03.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 02/07/2018] [Accepted: 03/15/2018] [Indexed: 12/15/2022]
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11
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A role for viral infections in Parkinson's etiology? Neuronal Signal 2018; 2:NS20170166. [PMID: 32714585 PMCID: PMC7373231 DOI: 10.1042/ns20170166] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/06/2018] [Accepted: 03/19/2018] [Indexed: 02/06/2023] Open
Abstract
Despite over 200 years since its first description by James Parkinson, the cause(s) of most cases of Parkinson's disease (PD) are yet to be elucidated. The disparity between the current understanding of PD symptomology and pathology has led to numerous symptomatic therapies, but no strategy for prevention or disease cure. An association between certain viral infections and neurodegenerative diseases has been recognized, but largely ignored or dismissed as controversial, for decades. Recent epidemiological studies have renewed scientific interest in investigating microbial interactions with the central nervous system (CNS). This review examines past and current clinical findings and overviews the potential molecular implications of viruses in PD pathology.
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Sharifi S, Pakdel A, Ebrahimi M, Reecy JM, Fazeli Farsani S, Ebrahimie E. Integration of machine learning and meta-analysis identifies the transcriptomic bio-signature of mastitis disease in cattle. PLoS One 2018; 13:e0191227. [PMID: 29470489 PMCID: PMC5823400 DOI: 10.1371/journal.pone.0191227] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 12/29/2017] [Indexed: 12/14/2022] Open
Abstract
Gram-negative bacteria such as Escherichia coli (E. coli) are assumed to be among the main agents that cause severe mastitis disease with clinical signs in dairy cattle. Rapid detection of this disease is so important in order to prevent transmission to other cows and helps to reduce inappropriate use of antibiotics. With the rapid progress in high-throughput technologies, and accumulation of various kinds of '-omics' data in public repositories, there is an opportunity to retrieve, integrate, and reanalyze these resources to improve the diagnosis and treatment of different diseases and to provide mechanistic insights into host resistance in an efficient way. Meta-analysis is a relatively inexpensive option with good potential to increase the statistical power and generalizability of single-study analysis. In the current meta-analysis research, six microarray-based studies that investigate the transcriptome profile of mammary gland tissue after induced mastitis by E. coli infection were used. This meta-analysis not only reinforced the findings in individual studies, but also several novel terms including responses to hypoxia, response to drug, anti-apoptosis and positive regulation of transcription from RNA polymerase II promoter enriched by up-regulated genes. Finally, in order to identify the small sets of genes that are sufficiently informative in E. coli mastitis, the differentially expressed gene introduced by meta-analysis were prioritized by using ten different attribute weighting algorithms. Twelve meta-genes were detected by the majority of attribute weighting algorithms (with weight above 0.7) as most informative genes including CXCL8 (IL8), NFKBIZ, HP, ZC3H12A, PDE4B, CASP4, CXCL2, CCL20, GRO1(CXCL1), CFB, S100A9, and S100A8. Interestingly, the results have been demonstrated that all of these genes are the key genes in the immune response, inflammation or mastitis. The Decision tree models efficiently discovered the best combination of the meta-genes as bio-signature and confirmed that some of the top-ranked genes -ZC3H12A, CXCL2, GRO, CFB- as biomarkers for E. coli mastitis (with the accuracy 83% in average). This research properly indicated that by combination of two novel data mining tools, meta-analysis and machine learning, increased power to detect most informative genes that can help to improve the diagnosis and treatment strategies for E. coli associated with mastitis in cattle.
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Affiliation(s)
- Somayeh Sharifi
- Department of Animal Science, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
| | - Abbas Pakdel
- Department of Animal Science, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | | | - James M. Reecy
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
| | | | - Esmaeil Ebrahimie
- School of Medicine, The University of Adelaide, Adelaide, Australia
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
- Division of Information Technology, Engineering and the Environment, School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, South Australia, Australia
- School of Biological Sciences, Faculty of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
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Isolation, Characterization, Cryopreservation of Human Amniotic Stem Cells and Differentiation to Osteogenic and Adipogenic Cells. PLoS One 2016; 11:e0158281. [PMID: 27434028 PMCID: PMC4951121 DOI: 10.1371/journal.pone.0158281] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 06/13/2016] [Indexed: 01/27/2023] Open
Abstract
Human stem cells and progenitor cells can be used to treat cancer and replace dysfunctional cells within a tissue or organ. The objective of this study was to identify the appropriate cells type in regenerative medicine and targeted therapy. As an alternative to embryonic and bone marrow stem cells, we examined human amniotic fluid stem cells (hAFSCs), one of the potential source of multipotent stem cells isolated from both cell pellet (using single-stage method), and supernatant of human amniotic fluid. Source of isolation and unique property of the cells emphasize that these cells are one of the promising new tools in therapeutic field. Double sources for isolation and availability of the left over samples in diagnostic laboratory at the same time have less legal and ethical concerns compared with embryonic stem cell studies. Cells were isolated, cultured for 18th passage for 6 months and characterized using qPCR and flow cytometry. Cells showed good proliferative ability in culture condition. The cells successfully differentiated into the adipogenic and osteogenic lineages. Based on these findings, amniotic fluid can be considered as an appropriate and convenient source of human amniotic fluid stem cells. These cells provide potential tools for therapeutic applications in the field of regenerative medicine. To get a better understanding of crosstalk between Oct4/NANOG with osteogenesis and adipogenesis, we used network analysis based on Common Targets algorithm and Common Regulators algorithm as well as subnetwork discovery based on gene set enrichment. Network analysis highlighted the possible role of MIR 302A and MIR let-7g. We demonstrated the high expression of MIR 302A and low expression of MIR let7g in hAFSCs by qPCR.
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Pashaiasl M, Ebrahimi M, Ebrahimie E. Identification of the key regulating genes of diminished ovarian reserve (DOR) by network and gene ontology analysis. Mol Biol Rep 2016; 43:923-37. [PMID: 27324248 DOI: 10.1007/s11033-016-4025-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 05/30/2016] [Indexed: 11/30/2022]
Abstract
Diminished ovarian reserve (DOR) is one of the reasons for infertility that not only affects both older and young women. Ovarian reserve assessment can be used as a new prognostic tool for infertility treatment decision making. Here, up- and down-regulated gene expression profiles of granulosa cells were analysed to generate a putative interaction map of the involved genes. In addition, gene ontology (GO) analysis was used to get insight intol the biological processes and molecular functions of involved proteins in DOR. Eleven up-regulated genes and nine down-regulated genes were identified and assessed by constructing interaction networks based on their biological processes. PTGS2, CTGF, LHCGR, CITED, SOCS2, STAR and FSTL3 were the key nodes in the up-regulated networks, while the IGF2, AMH, GREM, and FOXC1 proteins were key in the down-regulated networks. MIRN101-1, MIRN153-1 and MIRN194-1 inhibited the expression of SOCS2, while CSH1 and BMP2 positively regulated IGF1 and IGF2. Ossification, ovarian follicle development, vasculogenesis, sequence-specific DNA binding transcription factor activity, and golgi apparatus are the major differential groups between up-regulated and down-regulated genes in DOR. Meta-analysis of publicly available transcriptomic data highlighted the high coexpression of CTGF, connective tissue growth factor, with the other key regulators of DOR. CTGF is involved in organ senescence and focal adhesion pathway according to GO analysis. These findings provide a comprehensive system biology based insight into the aetiology of DOR through network and gene ontology analyses.
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Affiliation(s)
- Maryam Pashaiasl
- Women's Reproductive Health Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran. .,Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. .,Department of Anatomical Sciences, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mansour Ebrahimi
- Bioinformatics Research Group and Department of Biology, Qom University, Qom, Iran
| | - Esmaeil Ebrahimie
- Division of Information Technology, Engineering and the Environment, School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, Australia.,Institute of Biotechnology, Shiraz University, Shiraz, Iran.,Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, Australia.,School of Biological Sciences, Faculty of Science and Engineering, Flinders University, Adelaide, Australia
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