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Mazaherifar S, Erfanian S, Solhjoo K, Roustazadeh A, Darayesh M, Taghipour A, Falahi S, Kenarkoohi A, Badri M, Heidarnejadi SM, Rasti S, Abdoli A. Detection of Leishmania RNA Virus 2 (LRV2) among Clinical Isolates of Leishmania Major in Four Endemic Regions of Iran. Acta Parasitol 2024:10.1007/s11686-024-00915-x. [PMID: 39190281 DOI: 10.1007/s11686-024-00915-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 08/13/2024] [Indexed: 08/28/2024]
Abstract
PURPOSE Leishmania RNA viruses (LRV) are double-stranded RNA viruses (dsRNA viruses) that play a role in the pathogenesis of Leishmania parasites. Cutaneous leishmaniasis (CL) is endemic in various parts of Iran. Our aimed was to investigate presence of LRV among the Leishmania major isolates in four endemic regions of Iran. METHODS In a cross-sectional study, we assessed the presence of LRV1 and LRV2 in 181 clinical isolates of L. major from four endemic cities in Iran using reverse transcription polymerase chain reaction (RT-PCR). After RNA extraction and cDNA synthesis, RT-PCR tests were conducted with LRV1 and LRV2 specific primers. Human beta-actin and kmp genes served as internal and external controls, respectively, and the Allele ID software was used to optimize melting curves. RESULTS LRV2 was detected in 27.6% (50 out of 181) of L. major isolates, while no LRV1 was found. We did not observe a statistically significant difference in the presence of LRV2 based on age group, number, or location of lesions. CONCLUSION This study confirms the presence of LRV2 in clinical isolates of L. major from endemic regions of Iran. Further researches with larger sample sizes is recommended to explore the association between LRV and clinical symptoms as well as treatment response.
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Affiliation(s)
- Samaneh Mazaherifar
- Zoonoses Research Center, Jahrom University of Medical Sciences, Jahrom, Iran
- Department of Parasitology and Mycology, Jahrom University of Medical Sciences, Jahrom, Iran
| | - Saiedeh Erfanian
- Research Center for NonCommunicable Diseases, Jahrom University of Medical Sciences, Jahrom, Iran
- Department of Advanced Medical Sciences and Technologies, Jahrom University of Medical Sciences, Jahrom, Iran
| | - Kavous Solhjoo
- Zoonoses Research Center, Jahrom University of Medical Sciences, Jahrom, Iran
- Department of Parasitology and Mycology, Jahrom University of Medical Sciences, Jahrom, Iran
| | - Abazar Roustazadeh
- Research Center for NonCommunicable Diseases, Jahrom University of Medical Sciences, Jahrom, Iran
- Department of Advanced Medical Sciences and Technologies, Jahrom University of Medical Sciences, Jahrom, Iran
- Department of Biochemistry and Nutrition, Jahrom University of Medical Sciences, Jahrom, Iran
| | - Mohammad Darayesh
- Research Center for NonCommunicable Diseases, Jahrom University of Medical Sciences, Jahrom, Iran
- Department of Dermatology, Jahrom University of Medical Sciences, Jahrom, Iran
| | - Ali Taghipour
- Zoonoses Research Center, Jahrom University of Medical Sciences, Jahrom, Iran
- Department of Parasitology and Mycology, Jahrom University of Medical Sciences, Jahrom, Iran
| | - Shahab Falahi
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Azra Kenarkoohi
- Department of Microbiology, Ilam University of Medical Sciences, Ilam, Iran
| | - Milad Badri
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | | | - Sima Rasti
- Department of Parasitology and Mycology and Infectious Diseases Research Center, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, IR, Iran
| | - Amir Abdoli
- Zoonoses Research Center, Jahrom University of Medical Sciences, Jahrom, Iran.
- Department of Parasitology and Mycology, Jahrom University of Medical Sciences, Jahrom, Iran.
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Edalat F, Khakpour N, Heli H, Letafati A, Ramezani A, Hosseini SY, Moattari A. Immunological mechanisms of the nucleocapsid protein in COVID-19. Sci Rep 2024; 14:3711. [PMID: 38355695 PMCID: PMC10867304 DOI: 10.1038/s41598-024-53906-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
The emergence of corona virus disease 2019 (COVID-19), resulting from Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has left an indelible mark on a global scale, causing countless infections and fatalities. This investigation delves into the role of the SARS-CoV-2 nucleocapsid (N) protein within the HEK293 cells, shedding light on its influence over apoptosis, interferon signaling, and cytokines production. The N gene was amplified, inserted into the pAdTrack-CMV vector, and then transfected to the HEK293 cells. Changes in the expression of IRF3, IRF7, IFN-β, BAK, BAX, and BCL-2 genes were evaluated. The levels of proinflammatory cytokines of IL-6, IL-12, IL-1β, and TNF-α were also determined. The N protein exhibited an anti-apoptotic effect by modulating critical genes associated with apoptosis, including BAK, BAX, and BCL-2. This effect potentially prolonged the survival of infected cells. The N protein also played a role in immune evasion by suppressing the interferon pathway, evidenced by the downregulation of essential interferon regulatory factors of IRF3 and IRF7, and IFN-β expression. The N protein expression led to a substantial increase in the production of proinflammatory cytokines of IL-6, IL-12, IL-1β, and TNF-α. The N protein emerged as a versatile factor and was exerted over apoptosis, interferon signaling, and cytokine production. These findings carry potential implications for the development of targeted therapies to combat COVID-19 and mitigate its global health impact.
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Affiliation(s)
- Fahime Edalat
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Niloofar Khakpour
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hossein Heli
- Nanomedicine and Nanobiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Arash Letafati
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Amin Ramezani
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Science, Shiraz, Iran
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Younes Hosseini
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Afagh Moattari
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran.
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3
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Akbarabadi A, Ismaili A, Nazarian Firouzabadi F, Ercisli S, Kahrizi D. Assessment of ACC and P450 Genes Expression in Wild Oat (Avena ludoviciana) in Different Tissues Under Herbicide Application. Biochem Genet 2023; 61:1867-1879. [PMID: 36877417 DOI: 10.1007/s10528-023-10357-1] [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: 04/22/2021] [Accepted: 02/15/2023] [Indexed: 03/07/2023]
Abstract
Target-site resistance (TSR) and non-target-site resistance (NTSR) to herbicides in arable weeds are increasing rapidly all over the world and threatening universal food safety. Resistance to herbicides that inhibit ACCase activity has been identified in wild oat. In this study, expression of ACC1, ACC2, CYP71R4 and CYP81B1 genes under herbicide stress conditions were studied in two TSR (resistant in the residue Ile1781-Leu and Ile2041-Asn of ACCase) biotypes, two NTSR biotypes and one susceptible biotype of A. ludoviciana for the first time. Treated and untreated biotypes with ACCase-inhibitor clodinafop propargyl herbicide were sampled from the stem and leaf tissues at 24 h after treatment. Our results showed an increase in gene expression levels in different tissues of both types of resistance biotypes that occurred under herbicide treatment compared with non-herbicide treatment. In all samples, the expression levels of leaf tissue in all studied genes were higher than in stem tissue. The results of ACC gene expression showed that the expression level of ACC1 was significantly higher than that of ACC2. Also, expression levels of TSR biotypes were higher than NTSR biotypes for the ACC1 gene. For both CYP71R4 and CYP81B1 genes, the expression ratio increased significantly in TSR and NTSR biotypes in different tissues after herbicide treatment. In contrast, the expression levels of CYP genes in NTSR biotypes were higher than in TSR biotypes. Our results support the hypothesis that the reaction of plants to herbicide is carried out through a different regulation of genes, which can be the result of the interaction of resistance type in the target or non-target-site.
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Affiliation(s)
- Ali Akbarabadi
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Ahmad Ismaili
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Farhad Nazarian Firouzabadi
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, 25240, Erzurum, Turkey
| | - Danial Kahrizi
- Department of Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
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Panji A, Ismaili A, Sohrabi SM. Genome-wide identification and expression profiling of snakin/GASA genes under drought stress in barley ( Hordeum vulgare L.). 3 Biotech 2023; 13:126. [PMID: 37064004 PMCID: PMC10090255 DOI: 10.1007/s13205-023-03545-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 03/28/2023] [Indexed: 04/18/2023] Open
Abstract
Gibberellic Acid-Stimulated Arabidopsis (GASA) proteins are present in various plants and have a role in plant growth, stress responses, and hormone crosstalk. GASA coding sequences in barley were discovered in this study. We then investigated gene and protein structure, physicochemical characteristics, evolutionary and phylogenetic relationships, promoter region, post-translational modification, and in silico gene expression. Finally, real-time quantitative PCR (RT-qPCR) was used to examine the expression of GASA genes in root and shoot tissues under drought stress. We found 11 GASA genes spread across six of seven chromosomes in the barley genome. A conserved GASA domain and 12-cysteine residues at the C-terminus were included in the proteins. All GASA genes contained secretory signal peptides. The GASA genes in Hordeum vulgare (HvGASA) have been classified into three subfamilies based on evolutionary analysis. According to synteny analyses, segmental duplications are significant in forming the GASA gene family. According to the cis-elements analyses, GASA genes may be induced by a variety of phytohormones and stresses. Tissue-specific expression analysis indicated that GASA genes had varied expression patterns in different tissues. Contrary to common perception, the expression study of GASA genes under biotic and abiotic stresses revealed that GASA genes are more induced by abiotic stresses than biotic stresses. The qPCR confirmed the response of GASA genes to abiotic stresses and showed different expression patterns of these genes under drought stress. Overall, these results can improve our knowledge about the function of GASA genes and provide data for future researches. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03545-8.
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Affiliation(s)
- Anahita Panji
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Ahmad Ismaili
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Seyyed Mohsen Sohrabi
- Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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Arab M, Najafi Zarrini H, Nematzadeh G, Heidari P, Hashemipetroudi SH, Kuhlmann M. Comprehensive Analysis of Calcium Sensor Families, CBL and CIPK, in Aeluropus littoralis and Their Expression Profile in Response to Salinity. Genes (Basel) 2023; 14:genes14030753. [PMID: 36981024 PMCID: PMC10048465 DOI: 10.3390/genes14030753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/11/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Plants have acquired sets of highly regulated and complex signaling pathways to respond to unfavorable environmental conditions during evolution. Calcium signaling, as a vital mechanism, enables plants to respond to external stimuli, including abiotic and biotic stresses, and coordinate the basic processes of growth and development. In the present study, two calcium sensor families, CBL and CIPK, were investigated in a halophyte plant, Aeluropus littoralis, with a comprehensive analysis. Here, six AlCBL genes, and twenty AlCIPK genes were studied. The analysis of the gene structure and conserved motifs, as well as physicochemical properties, showed that these genes are highly conserved during evolution. The expression levels of AlCBL genes and AlCIPK genes were evaluated under salt stress in leaf and root tissue. Based on the real-time RT-PCR results, the AlCIPK gene family had a higher variation in mRNA abundance than the AlCBL gene family. AlCIPK genes were found to have a higher abundance in leaves than in roots. The results suggest that the correlation between AlCBL genes and AlCIPK is tissue-specific, and different correlations can be expected in leaves and roots. Based on these correlations, AlCIPK3.1-AlCBL4.1 and AlCIPK1.2-AlCBL4.4 can be co-expressed in the root tissue, while AlCBL10 has the potential to be co-expressed with AlCIPK5, AlCIPK26, and AlCIPK12.3 in the leaf tissue. Our findings reveal valuable information on the structure and function of calcium sensor families in A. littoralis, a halophyte plant, that can be used in future research on the biological function of CBLs and CIPKs on salt stress resistance.
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Affiliation(s)
- Mozhdeh Arab
- Department of Plant Biotechnology, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari 4818166996, Iran
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965161, Iran
| | - Hamid Najafi Zarrini
- Department of Plant Biotechnology, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari 4818166996, Iran
| | - Ghorbanali Nematzadeh
- Department of Plant Biotechnology, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari 4818166996, Iran
- Department of Genetic Engineering and Biology, Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University (SANRU), Sari 4818166996, Iran
| | - Parviz Heidari
- Faculty of Agriculture, Shahrood University of Technology, Shahrood 3619995161, Iran
| | - Seyyed Hamidreza Hashemipetroudi
- Department of Genetic Engineering and Biology, Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University (SANRU), Sari 4818166996, Iran
- RG Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 306466 Gatersleben, Germany
| | - Markus Kuhlmann
- RG Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 306466 Gatersleben, Germany
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Olfactory receptors contribute to progression of kidney fibrosis. NPJ Syst Biol Appl 2022; 8:8. [PMID: 35181660 PMCID: PMC8857310 DOI: 10.1038/s41540-022-00217-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 01/21/2022] [Indexed: 11/08/2022] Open
Abstract
Olfactory receptors (ORs) which are mainly known as odor-sensors in the olfactory epithelium are shown to be expressed in several non-sensory tissues. Despite the specified role of some of these receptors in normal physiology of the kidney, little is known about their potential effect in renal disorders. In this study, using the holistic view of systems biology, it was determined that ORs are significantly changed during the progression of kidney fibrosis. For further validation, common differentially expressed ORs resulted from reanalysis of two time-course microarray datasets were selected for experimental evaluation in a validated murine model of unilateral ureteral obstruction (UUO). Transcriptional analysis by real-time quantitative polymerase chain reaction demonstrated considerable changes in the expression pattern of Olfr433, Olfr129, Olfr1393, Olfr161, and Olfr622 during the progression of kidney fibrosis. For localization of these ORs, single-cell RNA-sequencing datasets of normal and UUO mice were reanalyzed. Results showed that Olfr433 is highly expressed in macrophages in day-2 and 7 post-injury in UUO mice and not in normal subgroups. Besides, like previous findings, Olfr1393 was shown to be expressed prominently in the proximal tubular cells of the kidney. In conclusion, our combinatorial temporal approach to the underlying mechanisms of chronic kidney disease highlighted the potential role of ORs in progression of fibrosis. The expression of Olfr433 in the macrophages provides some clue about its relation to molecular mechanisms promoted in the fibrotic kidney. The proposed ORs in this study could be the subject of further functional assessments in the future.
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7
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Paula DP, Andow DA. Melting curve analysis for detection and identification of ghost parasitoids in host carcasses a month after host death. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Débora P. Paula
- Embrapa Recursos Genéticos e BiotecnologiaParque Estação Biológica Brasília Brazil
| | - David A. Andow
- Department of Entomology University of Minnesota St. Paul MN USA
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Kiyanpour F, Abedi M, Gheisari Y. A systematic integrative approach reveals novel microRNAs in diabetic nephropathy. JOURNAL OF RESEARCH IN MEDICAL SCIENCES 2020; 25:1. [PMID: 32055241 PMCID: PMC7003547 DOI: 10.4103/jrms.jrms_289_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 06/19/2019] [Accepted: 09/08/2019] [Indexed: 12/22/2022]
Abstract
Background: Despite huge efforts, the underlying molecular mechanisms of diabetic nephropathy (DN) are yet elusive, and holistic views have rarely been generated. Considering the complexity of DN pathogenesis, the integration of datasets from different molecular types to construct a multilayer map of DN can provide a comprehensive insight toward the disease mechanisms and also can generate new knowledge. Here, we have re-analyzed two mRNA microarray datasets related to glomerular and tubulointerstitial compartments of human diabetic kidneys. Materials and Methods: The quality of the datasets was confirmed by unsupervised hierarchical clustering and principal component analysis. For each dataset, differentially expressed (DE) genes were identified, and transcription factors (TFs) regulating these genes and kinases phosphorylating the TFs were enriched. Furthermore, microRNAs (miRNAs) targeting the DE genes, TFs, and kinases were detected. Based on the harvested genes for glomeruli and tubulointerstitium, key signaling pathways and biological processes involved in diseases pathogenesis were recognized. In addition, the interaction of different elements in each kidney compartment was depicted in multilayer networks, and topology analysis was performed to identify key nodes. Central miRNAs whose target genes were most likely to be related to DN were selected, and their expressions were quantitatively measured in a streptozotocin-induced DN mouse model. Results: Among the examined miRNAs, miR-208a-3p and miR-496a-3p are, for the first time, found to be significantly overexpressed in the cortex of diabetic kidneys compared to controls. Conclusion: We predict that miR-208 is involved in oxygen metabolism and regulation of cellular energy balance. Furthermore, miR-496 potentially regulates protein metabolism and ion transport. However, their exact functions remain to be investigated in future studies. Taken together, starting from transcriptomics data, we have generated multilayer interaction networks and introduced novel players in DN.
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Affiliation(s)
- Farnoush Kiyanpour
- Department of Genetics and Molecular Biology, Isfahan University of Medical Sciences, Isfahan, Iran.,Student Research Committee, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Abedi
- Department of Genetics and Molecular Biology, Isfahan University of Medical Sciences, Isfahan, Iran.,Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Yousof Gheisari
- Department of Genetics and Molecular Biology, Isfahan University of Medical Sciences, Isfahan, Iran.,Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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Zhao Q, Zhang R, Xiao Y, Niu Y, Shao F, Li Y, Peng Z. Comparative Transcriptome Profiling of the Loaches Triplophysa bleekeri and Triplophysa rosa Reveals Potential Mechanisms of Eye Degeneration. Front Genet 2020; 10:1334. [PMID: 32010191 PMCID: PMC6977438 DOI: 10.3389/fgene.2019.01334] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 12/06/2019] [Indexed: 12/30/2022] Open
Abstract
Eye degeneration is one of the most obvious characteristics of organisms restricted to subterranean habitats. In cavefish, eye degeneration has evolved independently numerous times and each process is associated with different genetic mechanisms. To gain a better understanding of these mechanisms, we compared the eyes of adult individuals of the cave loach Triplophysa rosa and surface loach Triplophysa bleekeri. Compared with the normal eyes of the surface loach, those of the cave loach were found to possess a small abnormal lens and a defective retina containing photoreceptor cells that lack outer segments. Sequencing of the transcriptomes of both species to identify differentially expressed genes (DEGs) and genes under positive selection revealed 4,802 DEGs and 50 genes under positive selection (dN/dS > 1, FDR < 0.1). For cave loaches, we identified one Gene Ontology category related to vision that was significantly enriched in downregulated genes. Specifically, we found that many of the downregulated genes, including pitx3, lim2, crx, gnat2, rx1, rho, prph2, and β|γ-crystallin are associated with lens/retinal development and maintenance. However, compared with those in the surface loach, the lower dS rates but higher dN rates of the protein-coding sequences in T. rosa indicate that changes in amino acid sequences might be involved in the adaptation and visual degeneration of cave loaches. We also found that genes associated with light perception and light-stimulated vision have evolved at higher rates (some genes dN/dS > 1 but FDR > 0.1). Collectively, the findings of this study indicate that the degradation of cavefish vision is probably associated with both gene expression and amino acid changes and provide new insights into the mechanisms underlying the degeneration of cavefish eyes.
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Affiliation(s)
- Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Renyi Zhang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yingqi Xiao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Yabing Niu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Yanping Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
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Behzadi P, Ranjbar R. DNA microarray technology and bioinformatic web services. Acta Microbiol Immunol Hung 2019; 66:19-30. [PMID: 30010394 DOI: 10.1556/030.65.2018.028] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The pan-genomic microarray technique is used for environmental and/or clinical studies. Although microarray is an accurate and sharp diagnostic tool, the expertized bioinformaticians were able to minimize the outcome biases and maximize the flexibility and accuracy of the technique. The knowledge of bioinformatics plays a key role in association with probe designing and the utilization of correct probe sets and platforms. This technique is divided into two parts as dry lab (in silico studies) and wet lab (in vitro studies). Each part covers the other and are known as complementary divisions. In the case of microarray probe designing, a wide range of software, tools, and databases are necessary. Obviously, the application of right databases, software, and tools decreases the probable biases in the outcomes. Due to the importance of suitable probe designing, this article has focused its look onto a variety of online/offline databases, software, and tools.
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Affiliation(s)
- Payam Behzadi
- 1 Department of Microbiology, College of Basic Sciences, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Reza Ranjbar
- 2 Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Prerostova S, Dobrev PI, Gaudinova A, Knirsch V, Körber N, Pieruschka R, Fiorani F, Brzobohatý B, černý M, Spichal L, Humplik J, Vanek T, Schurr U, Vankova R. Cytokinins: Their Impact on Molecular and Growth Responses to Drought Stress and Recovery in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:655. [PMID: 29872444 PMCID: PMC5972670 DOI: 10.3389/fpls.2018.00655] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/27/2018] [Indexed: 05/02/2023]
Abstract
Our phenotyping and hormonal study has characterized the role of cytokinins (CK) in the drought and recovery responses of Arabidopsis thaliana. CK down-regulation was achieved by overexpression of the gene for CK deactivating enzyme cytokinin oxidase/dehydrogenase (CKX): constitutive (35S:CKX) or at the stress onset using a dexamethasone-inducible pOp/LhGR promoter (DEX:CKX). The 35S:CKX plants exhibited slow ontogenesis and higher expression levels of stress-associated genes, e.g., AtP5CS1, already at well-watered conditions. CK down-regulation resulted during drought in higher stress tolerance (indicated by relatively low up-regulation of the expression of drought stress marker gene AtRD29B) accompanied with lower leaf water loss. Nevertheless, these plants exhibited slow and delayed recovery after re-watering. CK levels were increased at the stress onset by stimulation of the expression of CK biosynthetic gene isopentenyl transferase (ipt) (DEX:IPT) or by application of exogenous CK meta-topolin. After water withdrawal, long-term CK elevation resulted in higher water loss in comparison with CKX transformants as well as with plants overexpressing ipt driven by senescence-inducible SAG12 promoter (SAG:IPT), which gradually enhanced CKs during the stress progression. In all cases, CK up-regulation resulted in fast and more vigorous recovery. All drought-stressed plants exhibited growth suppression associated with elevation of abscisic acid and decrease of auxins and active CKs (with the exception of SAG:IPT plants). Apart from the ipt overexpressers, also increase of jasmonic and salicylic acid was found.
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Affiliation(s)
- Sylva Prerostova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
| | - Petre I. Dobrev
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
| | - Alena Gaudinova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
| | - Vojtech Knirsch
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
| | - Niklas Körber
- IBG-2: Plant Sciences, Institute for Bio-and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Roland Pieruschka
- IBG-2: Plant Sciences, Institute for Bio-and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Fabio Fiorani
- IBG-2: Plant Sciences, Institute for Bio-and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Břetislav Brzobohatý
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS and CR — Central European Institute of Technology, Mendel University in Brno, Brno, Czechia
| | - Martin černý
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS and CR — Central European Institute of Technology, Mendel University in Brno, Brno, Czechia
| | - Lukas Spichal
- Department of Chemical Biology and Genetics, Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany Czech Academy of Sciences and Faculty of Science of Palacky University, Olomouc, Czechia
| | - Jan Humplik
- Laboratory of Growth Regulators, Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany Czech Academy of Sciences, Faculty of Science of Palacky University, Olomouc, Czechia
| | - Tomas Vanek
- Laboratory of Plant Biotechnologies, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
| | - Ulrich Schurr
- IBG-2: Plant Sciences, Institute for Bio-and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Radomira Vankova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
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Rismani E, Fazeli MS, Mahmoodzadeh H, Movassagh A, Azami S, Karimipoor M, Teimoori-Toolabi L. Pattern of LRP6 gene expression in tumoral tissues of colorectal cancer. Cancer Biomark 2018; 19:151-159. [PMID: 28387660 DOI: 10.3233/cbm-160175] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Colorectal cancer (CRC) is known as one of the most leading causes of death from cancer in the world. Wnt signaling pathway is the most important signaling pathway activated in this type of cancer. The low-density lipoprotein (LDL) receptor-related protein-6 (LRP6) functions as a co-receptor in order to trigger this signaling pathway. OBJECTIVE The expression of LRP6 was studied in cell lines, tumoral and normal adjacent tissues from patients affected with colorectal cancer. MATERIALS AND METHODS The expression of LRP6 was assayed by quantitative Real time PCR. RESULTS LRP6 is overexpressed at the transcript and protein level in HCT116 and SW480 in comparison to HUVEC as the non-cancerous cell. Furthermore, LRP6 was significantly up-regulated in 61% of human malignant tissues (p-value = 0.0008). In inherited type of disease, this upregulation was lower than other types of colorectal cancer, while in rectal cancer the overexpression was significantly higher (p-value = 0.039). Gene expression was not correlated with the age, gender and the stage of disease. CONCLUSION Due to the profound overexpression of LRP6 in sporadic and rectal types of cancer compared to normal colonic ones, antagonist related approaches can be promising for targeted therapies of cancer.
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Affiliation(s)
- Elham Rismani
- Molecular Medicine Department, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Sadegh Fazeli
- Department of Surgery, Division of Colo-Rectal Surgery, Imam Khomeini Medical Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Habibollah Mahmoodzadeh
- Cancer Institute of Iran, Imam Khomeini Medical Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Aghdas Movassagh
- Molecular Medicine Department, Pasteur Institute of Iran, Tehran, Iran
| | - Sina Azami
- Molecular Medicine Department, Pasteur Institute of Iran, Tehran, Iran
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13
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Prerostova S, Dobrev PI, Gaudinova A, Hosek P, Soudek P, Knirsch V, Vankova R. Hormonal dynamics during salt stress responses of salt-sensitive Arabidopsis thaliana and salt-tolerant Thellungiella salsuginea. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 264:188-198. [PMID: 28969799 DOI: 10.1016/j.plantsci.2017.07.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 07/26/2017] [Accepted: 07/30/2017] [Indexed: 05/25/2023]
Abstract
Salt stress responses in salt-sensitive Arabidopsis thaliana (2-150mM NaCl) and the closely related salt-tolerant Thellungiella salsuginea (Eutrema halophila, 150-350mM NaCl) were compared to identify hormonal and transcriptomic changes associated with enhanced stress tolerance. Phytohormone levels, expression of selected genes, membrane stability, and Na+ and K+ concentrations were measured in shoot apices, leaves, and roots. Thellungiella exhibited higher salt stress tolerance associated with elevated basal levels of abscisic acid and jasmonic acid, and lower levels of active cytokinins (excluding cis-zeatin) in shoot apices. Analysis of the dynamics of the early salt stress response (15min to 24h) revealed that the halophyte response was faster and stronger. Very mild stress, in our hydropony arrangement 2-25mM NaCl, affected the transcription of genes involved in cytokinin metabolism (AtIPTs, AtCKXs). Mild stress induced in Arabidopsis (50mM) stress responses only in shoot apices, while in Thellungiella (150mM) across the whole plant. Arabidopsis exhibited in hydropony evidence of severe stress above 75mM NaCl and died in 150mM, whereas the halophyte only became severely stressed above 225mM. The responses of individual phytohormones (cytokinins, auxin, abscisic acid, jasmonic acid, salicylic acid and their metabolites) to salinity are discussed.
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Affiliation(s)
- Sylva Prerostova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany AS CR, Rozvojova 263, 165 02 Prague 6, Czech Republic; Department of Experimental Plant Biology, Faculty of Science, Charles University, Vinicna 5, 128 44 Prague 2, Czech Republic
| | - Petre I Dobrev
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany AS CR, Rozvojova 263, 165 02 Prague 6, Czech Republic
| | - Alena Gaudinova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany AS CR, Rozvojova 263, 165 02 Prague 6, Czech Republic
| | - Petr Hosek
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany AS CR, Rozvojova 263, 165 02 Prague 6, Czech Republic
| | - Petr Soudek
- Laboratory of Plant Biotechnologies, Institute of Experimental Botany AS CR, Rozvojova 263, 165 02 Prague 6, Czech Republic
| | - Vojtech Knirsch
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany AS CR, Rozvojova 263, 165 02 Prague 6, Czech Republic
| | - Radomira Vankova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany AS CR, Rozvojova 263, 165 02 Prague 6, Czech Republic.
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Landa P, Dytrych P, Prerostova S, Petrova S, Vankova R, Vanek T. Transcriptomic Response of Arabidopsis thaliana Exposed to CuO Nanoparticles, Bulk Material, and Ionic Copper. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:10814-10824. [PMID: 28832134 DOI: 10.1021/acs.est.7b02265] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Engineered nanoparticles (ENPs) exhibit unique properties advantageous in a number of applications, but they also represent potential health and environmental risks. In this study, we investigated the phytotoxic mechanism of CuO ENPs using transcriptomic analysis and compared this response with the response to CuO bulk particles and ionic Cu2+. Ionic Cu2+ at the concentration of 0.16 mg L-1 changed transcription of 2692 genes (p value of <0.001, fold change of ≥2) after 7 days of exposure, whereas CuO ENPs and bulk particles (both in the concentration of 10 mg L-1) altered the expression of 922 and 482 genes in Arabidopsis thaliana roots, respectively. The similarity between transcription profiles of plants exposed to ENPs and ionic Cu2+ indicated that the main factor in phytotoxicity was the release of Cu2+ ions from CuO ENPs after 7 days of exposure. The effect of Cu2+ ions was evident in all treatments, as indicated by the down-regulation of genes involved in metal homeostasis and transport and the up-regulation of oxidative stress response genes. ENPs were more soluble than bulk particles, resulting in the up-regulation of metallochaperone-like genes or the down-regulation of aquaporins and metal transmembrane transporters that was also characteristic for ionic Cu2+ exposure.
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Affiliation(s)
- Premysl Landa
- Laboratory of Plant Biotechnologies, Institute of Experimental Botany of the CAS, v.v.i. , Rozvojova 263, 165 02 Prague 6 - Lysolaje, Czech Republic
| | - Pavel Dytrych
- Department of Catalysis and Reaction Engineering, Institute of Chemical Process Fundamentals of the CAS, v.v.i. , Rozvojova 135/1, 165 02 Prague 6 - Lysolaje, Czech Republic
| | - Sylva Prerostova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany of the CAS, v.v.i. , Rozvojova 263, 165 02 Prague 6 - Lysolaje, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University in Prague , Vinicna 5, 128 44 Prague 2, Czech Republic
| | - Sarka Petrova
- Laboratory of Plant Biotechnologies, Institute of Experimental Botany of the CAS, v.v.i. , Rozvojova 263, 165 02 Prague 6 - Lysolaje, Czech Republic
| | - Radomira Vankova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany of the CAS, v.v.i. , Rozvojova 263, 165 02 Prague 6 - Lysolaje, Czech Republic
| | - Tomas Vanek
- Laboratory of Plant Biotechnologies, Institute of Experimental Botany of the CAS, v.v.i. , Rozvojova 263, 165 02 Prague 6 - Lysolaje, Czech Republic
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Heiniger H, Adlard RD. Relatedness of novel species of Myxidium Bütschli, 1882, Zschokkella Auerbach, 1910 and Ellipsomyxa Køie, 2003 (Myxosporea: Bivalvulida) from the gall bladders of marine fishes (Teleostei) from Australian waters. Syst Parasitol 2014; 87:47-72. [DOI: 10.1007/s11230-013-9454-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 10/24/2013] [Indexed: 10/25/2022]
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Abstract
Although the ferret model has been extensively used to study pathogenesis and transmission of influenza viruses, little has been done to determine whether ferrets are a good surrogate animal model to study influenza virus reassortment. It has been previously shown that the pandemic 2009 H1N1 (H1N1pdm) virus was able to transmit efficiently in ferrets. In coinfection studies with either seasonal H1N1 or H3N2 strains (H1N1s or H3N2s, respectively), the H1N1pdm virus was able to outcompete these strains and become the dominant transmissible virus. However, lack of reassortment could have been the result of differences in the cell or tissue tropism of these viruses in the ferret. To address this issue, we performed coinfection studies with recombinant influenza viruses carrying the surface genes of a seasonal H3N2 strain in the background of an H1N1pdm strain and vice versa. After serial passages in ferrets, a dominant H1N2 virus population was obtained with a constellation of gene segments, most of which, except for the neuraminidase (NA) and PB1 segments, were from the H1N1pdm strain. Our studies suggest that ferrets recapitulate influenza virus reassortment events. The H1N2 virus generated through this process resembles similar viruses that are emerging in nature, particularly in pigs.
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Howard C, Socratous E, Williams S, Graham E, Fowler MR, Scott NW, Bremner PD, Slater A. PlantID - DNA-based identification of multiple medicinal plants in complex mixtures. Chin Med 2012; 7:18. [PMID: 22838839 PMCID: PMC3464944 DOI: 10.1186/1749-8546-7-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 07/28/2012] [Indexed: 11/28/2022] Open
Abstract
Background An efficient method for the identification of medicinal plant products is now a priority as the global demand increases. This study aims to develop a DNA-based method for the identification and authentication of plant species that can be implemented in the industry to aid compliance with regulations, based upon the economically important Hypericum perforatum L. (St John’s Wort or Guan ye Lian Qiao). Methods The ITS regions of several Hypericum species were analysed to identify the most divergent regions and PCR primers were designed to anneal specifically to these regions in the different Hypericum species. Candidate primers were selected such that the amplicon produced by each species-specific reaction differed in size. The use of fluorescently labelled primers enabled these products to be resolved by capillary electrophoresis. Results Four closely related Hypericum species were detected simultaneously and independently in one reaction. Each species could be identified individually and in any combination. The introduction of three more closely related species to the test had no effect on the results. Highly processed commercial plant material was identified, despite the potential complications of DNA degradation in such samples. Conclusion This technique can detect the presence of an expected plant material and adulterant materials in one reaction. The method could be simply applied to other medicinal plants and their problem adulterants.
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Affiliation(s)
- Caroline Howard
- Biomolecular Technology Group, Faculty of Health and Life Sciences, De Montfort University, Leicester, LE1 9BH, UK.
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Darling JA, Mahon AR. From molecules to management: adopting DNA-based methods for monitoring biological invasions in aquatic environments. ENVIRONMENTAL RESEARCH 2011; 111:978-988. [PMID: 21353670 DOI: 10.1016/j.envres.2011.02.001] [Citation(s) in RCA: 219] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 01/31/2011] [Accepted: 02/01/2011] [Indexed: 05/30/2023]
Abstract
Recent technological advances have driven rapid development of DNA-based methods designed to facilitate detection and monitoring of invasive species in aquatic environments. These tools promise to improve on traditional monitoring approaches by enhancing detection sensitivity, reducing analytical turnaround times and monitoring costs, and increasing specificity of target identifications. However, despite the promise of DNA-based monitoring methods, the adoption of these tools in decision-making frameworks remains challenging. Here, rather than explore technical aspects of method development, we examine impediments to effective translation of those methods into management contexts. In addition to surveying current use of DNA-based tools for aquatic invasive species monitoring, we explore potential sources of uncertainty associated with molecular technologies and possibilities for limiting that uncertainty and effectively communicating its implications for decision-making. We pay particular attention to the recent adoption of DNA-based methods for detection of invasive Asian carp species in the United States Great Lakes region, as this example illustrates many of the challenges associated with applying molecular tools to achieve desired management outcomes. Our goal is to provide a useful assessment of the obstacles associated with integrating DNA-based methods into aquatic invasive species management, and to offer recommendations for future efforts aimed at overcoming those obstacles.
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Affiliation(s)
- John A Darling
- United States Environmental Protection Agency, National Exposure Research Laboratory, Molecular Ecology Research Branch, Cincinnati, OH 45268, USA.
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Kim H, Bartsch MS, Renzi RF, He J, Van de Vreugde JL, Claudnic MR, Patel KD. Automated digital microfluidic sample preparation for next-generation DNA sequencing. ACTA ACUST UNITED AC 2011; 16:405-14. [PMID: 22093297 DOI: 10.1016/j.jala.2011.07.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Indexed: 10/17/2022]
Abstract
Next-generation sequencing (NGS) technology is a promising tool for identifying and characterizing unknown pathogens, but its usefulness in time-critical biodefense and public health applications is currently limited by the lack of fast, efficient, and reliable automated DNA sample preparation methods. To address this limitation, we are developing a digital microfluidic (DMF) platform to function as a fluid distribution hub, enabling the integration of multiple subsystem modules into an automated NGS library sample preparation system. A novel capillary interface enables highly repeatable transfer of liquid between the DMF device and the external fluidic modules, allowing both continuous-flow and droplet-based sample manipulations to be performed in one integrated system. Here, we highlight the utility of the DMF hub platform and capillary interface for automating two key operations in the NGS sample preparation workflow. Using an in-line contactless conductivity detector in conjunction with the capillary interface, we demonstrate closed-loop automated fraction collection of target analytes from a continuous-flow sample stream into droplets on the DMF device. Buffer exchange and sample cleanup, the most repeated steps in NGS library preparation, are also demonstrated on the DMF platform using a magnetic bead assay and achieving an average DNA recovery efficiency of 80%±4.8%.
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Affiliation(s)
- Hanyoup Kim
- Sandia National Laboratories, Livermore, CA 94550, USA
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20
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Srivastava GP, Hanumappa M, Kushwaha G, Nguyen HT, Xu D. Homolog-specific PCR primer design for profiling splice variants. Nucleic Acids Res 2011; 39:e69. [PMID: 21415011 PMCID: PMC3105385 DOI: 10.1093/nar/gkr127] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Revised: 02/20/2011] [Accepted: 02/21/2011] [Indexed: 11/13/2022] Open
Abstract
To study functional diversity of proteins encoded from a single gene, it is important to distinguish the expression levels among the alternatively spliced variants. A variant-specific primer pair is required to amplify each alternatively spliced variant individually. For this purpose, we developed a new feature, homolog-specific primer design (HSPD), in our high-throughput primer and probe design software tool, PRIMEGENS-v2. The algorithm uses a de novo approach to design primers without any prior information of splice variants or close homologs for an input query sequence. It not only designs primer pairs but also finds potential isoforms and homologs of the input sequence. Efficiency of this algorithm was tested for several gene families in soybean. A total of 187 primer pairs were tested under five different abiotic stress conditions with three replications at three time points. Results indicate a high success rate of primer design. Some primer pairs designed were able to amplify all splice variants of a gene. Furthermore, by utilizing combinations within the same multiplex pool, we were able to uniquely amplify a specific variant or duplicate gene. Our method can also be used to design PCR primers to specifically amplify homologs in the same gene family. PRIMEGENS-v2 is available at: http://primegens.org.
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Affiliation(s)
- Gyan Prakash Srivastava
- Department of Computer Science, Christopher S. Bond Life Sciences Center, Division of Plant Sciences and National Center for Soybean Biotechnology, Agriculture Building, University of Missouri and Informatics Institute, University of Missouri, Columbia, MO 65211, USA
| | - Mamatha Hanumappa
- Department of Computer Science, Christopher S. Bond Life Sciences Center, Division of Plant Sciences and National Center for Soybean Biotechnology, Agriculture Building, University of Missouri and Informatics Institute, University of Missouri, Columbia, MO 65211, USA
| | - Garima Kushwaha
- Department of Computer Science, Christopher S. Bond Life Sciences Center, Division of Plant Sciences and National Center for Soybean Biotechnology, Agriculture Building, University of Missouri and Informatics Institute, University of Missouri, Columbia, MO 65211, USA
| | - Henry T. Nguyen
- Department of Computer Science, Christopher S. Bond Life Sciences Center, Division of Plant Sciences and National Center for Soybean Biotechnology, Agriculture Building, University of Missouri and Informatics Institute, University of Missouri, Columbia, MO 65211, USA
| | - Dong Xu
- Department of Computer Science, Christopher S. Bond Life Sciences Center, Division of Plant Sciences and National Center for Soybean Biotechnology, Agriculture Building, University of Missouri and Informatics Institute, University of Missouri, Columbia, MO 65211, USA
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Bacterial population genomics and infectious disease diagnostics. Trends Biotechnol 2010; 28:611-8. [PMID: 20961641 DOI: 10.1016/j.tibtech.2010.09.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 09/03/2010] [Accepted: 09/07/2010] [Indexed: 01/14/2023]
Abstract
New sequencing technologies have made the production of bacterial genome sequences increasingly easy, and it can be confidently forecasted that vast genomic databases will be generated in the next few years. Here, we detail how collections of bacterial genomes from a particular species (population genomics libraries) have already been used to improve the design of several diagnostic assays for bacterial pathogens. Genome sequencing itself is also becoming more commonly used for epidemiological, forensic and clinical investigations. There is an opportunity for the further development of bioinformatic tools to bring even further value to bacterial diagnostic genomics.
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Severgnini M, Cremonesi P, Consolandi C, Caredda G, De Bellis G, Castiglioni B. ORMA: a tool for identification of species-specific variations in 16S rRNA gene and oligonucleotides design. Nucleic Acids Res 2009; 37:e109. [PMID: 19531738 PMCID: PMC2760787 DOI: 10.1093/nar/gkp499] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Revised: 04/30/2009] [Accepted: 05/24/2009] [Indexed: 11/24/2022] Open
Abstract
16S rRNA gene is one of the preferred targets for resolving species phylogenesis issues in microbiological-related contexts. However, the identification of single-nucleotide variations capable of distinguishing a sequence among a set of homologous ones can be problematic. Here we present ORMA (Oligonucleotide Retrieving for Molecular Applications), a set of scripts for discriminating positions search and for performing the selection of high-quality oligonucleotide probes to be used in molecular applications. Two assays based on Ligase Detection Reaction (LDR) are presented. First, a new set of probe pairs on cyanobacteria 16S rRNA sequences of 18 different species was compared to that of a previous study. Then, a set of LDR probe pairs for the discrimination of 13 pathogens contaminating bovine milk was evaluated. The software determined more than 100 candidate probe pairs per dataset, from more than 300 16S rRNA sequences, in less than 5 min. Results demonstrated how ORMA improved the performance of the LDR assay on cyanobacteria, correctly identifying 12 out of 14 samples, and allowed the perfect discrimination among the 13 milk pathogenic-related species. ORMA represents a significant improvement from other contexts where enzyme-based techniques have been employed on already known mutations of a single base or on entire subsequences.
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Affiliation(s)
- Marco Severgnini
- Institute of Biomedical Technologies, Italian National Research Council, Segrate, Italy.
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