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Serem EK, Mburu DM, Abdullahi OA, Bargul JL. A scoping review on tsetse fly blood meal sources and its assay methods since 1956 to 2022. Parasit Vectors 2024; 17:52. [PMID: 38308365 PMCID: PMC10837921 DOI: 10.1186/s13071-023-06114-3] [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: 06/20/2023] [Accepted: 12/27/2023] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND Tsetse flies (Glossina spp.) are the definitive biological vectors of African trypanosomes in humans and animals. Controlling this vector is the most promising method of preventing trypanosome transmission. This requires a comprehensive understanding of tsetse biology and host preference to inform targeted design and management strategies, such as the use of olfaction and visual cues in tsetse traps. No current review exists on host preference and blood meal analyses of tsetse flies. METHODS This review presents a meta-analysis of tsetse fly blood meal sources and the methodologies used to identify animal hosts from 1956 to August 2022. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRIMA-ScR) was applied. This focused on tsetse-endemic countries, blood meal analysis methodologies and the blood meal hosts identified. The articles were retrieved and screened from databases using predetermined eligibility criteria. RESULTS Only 49/393 of the articles retrieved matched the inclusion criteria. Glossina's main hosts in the wild included the bushbuck, buffalo, elephant, warthog, bushpig and hippopotamus. Pigs, livestock and humans were key hosts at the domestic interface. The least studied species included Glossina fuscipleuris, G. fusca, G. medicorum, G. tabaniformis and G. austeni. In the absence of preferred hosts, Glossina fed opportunistically on a variety of hosts. Precipitin, haemagglutination, disc diffusion, complement fixation, ELISA and PCR-based assays were used to evaluate blood meals. Cytochrome b (Cyt b) was the main target gene in PCR to identify the vertebrate hosts. CONCLUSIONS Tsetse blood meal sources have likely expanded because of ecological changes that could have rendered preferred hosts unavailable. The major approaches for analysing tsetse fly blood meal hosts targeted Cyt b gene for species identification by Sanger sequencing. However, small-fragment DNAs, such as the mammalian 12S and 16S rRNA genes, along with second- and third-generation sequencing techniques, could increase sensitivity for host identification in multiple host feeders that Sanger sequencing may misidentify as "noise". This review of tsetse fly blood meal sources and approaches to host identification could inform strategies for tsetse control.
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Affiliation(s)
- Erick Kibichiy Serem
- Department of Anatomy and Physiology, School of Health and Human Sciences, Pwani University, P.O. Box 195-80108, Kilifi, Kenya.
- Pwani University Bioscience Research Centre (PUBReC), Pwani University, P.O. Box 195-80108, Kilifi, Kenya.
| | - David Mwangi Mburu
- Pwani University Bioscience Research Centre (PUBReC), Pwani University, P.O. Box 195-80108, Kilifi, Kenya
- Department of Biological Sciences, School of Pure and Applied Sciences, Pwani University, P.O. Box 195-80108, Kilifi, Kenya
| | - Osman Abdikarim Abdullahi
- Pwani University Bioscience Research Centre (PUBReC), Pwani University, P.O. Box 195-80108, Kilifi, Kenya
- Department of Public Health, School of Health and Human Sciences, Pwani University, P.O. Box 195-80108, Kilifi, Kenya
| | - Joel Ltilitan Bargul
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology (JKUAT), P.O. Box 62000-00200, Nairobi, Kenya
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2
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Stokes T, Cen HH, Kapranov P, Gallagher IJ, Pitsillides AA, Volmar C, Kraus WE, Johnson JD, Phillips SM, Wahlestedt C, Timmons JA. Transcriptomics for Clinical and Experimental Biology Research: Hang on a Seq. ADVANCED GENETICS (HOBOKEN, N.J.) 2023; 4:2200024. [PMID: 37288167 PMCID: PMC10242409 DOI: 10.1002/ggn2.202200024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Indexed: 06/09/2023]
Abstract
Sequencing the human genome empowers translational medicine, facilitating transcriptome-wide molecular diagnosis, pathway biology, and drug repositioning. Initially, microarrays are used to study the bulk transcriptome; but now short-read RNA sequencing (RNA-seq) predominates. Positioned as a superior technology, that makes the discovery of novel transcripts routine, most RNA-seq analyses are in fact modeled on the known transcriptome. Limitations of the RNA-seq methodology have emerged, while the design of, and the analysis strategies applied to, arrays have matured. An equitable comparison between these technologies is provided, highlighting advantages that modern arrays hold over RNA-seq. Array protocols more accurately quantify constitutively expressed protein coding genes across tissue replicates, and are more reliable for studying lower expressed genes. Arrays reveal long noncoding RNAs (lncRNA) are neither sparsely nor lower expressed than protein coding genes. Heterogeneous coverage of constitutively expressed genes observed with RNA-seq, undermines the validity and reproducibility of pathway analyses. The factors driving these observations, many of which are relevant to long-read or single-cell sequencing are discussed. As proposed herein, a reappreciation of bulk transcriptomic methods is required, including wider use of the modern high-density array data-to urgently revise existing anatomical RNA reference atlases and assist with more accurate study of lncRNAs.
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Affiliation(s)
- Tanner Stokes
- Faculty of ScienceMcMaster UniversityHamiltonL8S 4L8Canada
| | - Haoning Howard Cen
- Life Sciences InstituteUniversity of British ColumbiaVancouverV6T 1Z3Canada
| | | | - Iain J Gallagher
- School of Applied SciencesEdinburgh Napier UniversityEdinburghEH11 4BNUK
| | | | | | | | - James D. Johnson
- Life Sciences InstituteUniversity of British ColumbiaVancouverV6T 1Z3Canada
| | | | | | - James A. Timmons
- Miller School of MedicineUniversity of MiamiMiamiFL33136USA
- William Harvey Research InstituteQueen Mary University LondonLondonEC1M 6BQUK
- Augur Precision Medicine LTDStirlingFK9 5NFUK
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3
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Maduraiveeran G. Nanomaterials-based portable electrochemical sensing and biosensing systems for clinical and biomedical applications. J Anal Sci Technol 2022. [DOI: 10.1186/s40543-022-00344-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractMiniaturized electrochemical sensing systems are employed in day-to-day uses in the several area from public health to scientific applications. A variety of electrochemical sensor and biosensor systems may not be effectively employed in real-world diagnostic laboratories and biomedical industries due to their limitation of portability, cost, analytical period, and need of skilled trainer for operating devices. The design of smart and portable sensors with high sensitivity, good selectivity, rapid measurement, and reusable platforms is the driving strength for sensing glucose, lactate, hydrogen peroxide, nitric oxide, mRNA, etc. The enhancement of sensing abilities of such sensor devices through the incorporation of both novel sensitive nanomaterials and design of sensor strategies are evidenced. Miniaturization, cost and energy efficient, online and quantitative detection and multiple sensing ability are the beneficial of the nanostructured-material-based electrochemical sensor and biosensor systems. Owing to the discriminating catalytic action, solidity and biocompatibility for designing sensing system, nanoscale materials empowered electrochemical detection systems are accomplished of being entrenched into/combined with portable or miniaturized devices for specific applications. In this review, the advance development of portable and smart sensing/biosensing systems derived from nanoscale materials for clinical and biomedical applications is described.
Graphical Abstract
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4
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Hephzibah Cathryn R, Udhaya Kumar S, Younes S, Zayed H, George Priya Doss C. A review of bioinformatics tools and web servers in different microarray platforms used in cancer research. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 131:85-164. [PMID: 35871897 DOI: 10.1016/bs.apcsb.2022.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Over the past decade, conventional lab work strategies have gradually shifted from being limited to a laboratory setting towards a bioinformatics era to help manage and process the vast amounts of data generated by omics technologies. The present work outlines the latest contributions of bioinformatics in analyzing microarray data and their application to cancer. We dissect different microarray platforms and their use in gene expression in cancer models. We highlight how computational advances empowered the microarray technology in gene expression analysis. The study on protein-protein interaction databases classified into primary, derived, meta-database, and prediction databases describes the strategies to curate and predict novel interaction networks in silico. In addition, we summarize the areas of bioinformatics where neural graph networks are currently being used, such as protein functions, protein interaction prediction, and in silico drug discovery and development. We also discuss the role of deep learning as a potential tool in the prognosis, diagnosis, and treatment of cancer. Integrating these resources efficiently, practically, and ethically is likely to be the most challenging task for the healthcare industry over the next decade; however, we believe that it is achievable in the long term.
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Affiliation(s)
- R Hephzibah Cathryn
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - S Udhaya Kumar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Salma Younes
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, QU Health, Doha, Qatar
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, QU Health, Doha, Qatar
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India.
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5
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Tan HT, Yusoff FM, Khaw YS, Ahmad SA, Shaharuddin NA. Uncovering Research Trends of Phycobiliproteins Using Bibliometric Approach. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112358. [PMID: 34834721 PMCID: PMC8622606 DOI: 10.3390/plants10112358] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Phycobiliproteins are gaining popularity as long-term, high-value natural products which can be alternatives to synthetic products. This study analyzed research trends of phycobiliproteins from 1909 to 2020 using a bibliometric approach based on the Scopus database. The current findings showed that phycobiliprotein is a burgeoning field in terms of publications outputs with "biochemistry, genetics, and molecular biology" as the most related and focused subject. The Journal of Applied Phycology was the most productive journal in publishing articles on phycobiliproteins. Although the United States of America (U.S.A.) contributed the most publications on phycobiliproteins, the Chinese Academy of Sciences (China) is the institution with the largest number of publications. The most productive author on phycobiliproteins was Glazer, Alexander N. (U.S.A.). The U.S.A. and Germany were at the forefront of international collaboration in this field. According to the keyword analysis, the most explored theme was the optimization of microalgae culture parameters and phycobiliproteins extraction methods. The bioactivity properties and extraction of phycobiliproteins were identified as future research priorities. Synechococcus and Arthrospira were the most cited genera. This study serves as an initial step in fortifying the phycobiliproteins market, which is expected to exponentially expand in the future. Moreover, further research and global collaboration are necessary to commercialize phycobiliproteins and increase the consumer acceptability of the pigments and their products.
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Affiliation(s)
- Hui Teng Tan
- Aquatic Animal Health and Therapeutics Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (H.T.T.); (Y.S.K.)
| | - Fatimah Md. Yusoff
- International Institute of Aquaculture and Aquatic Sciences, Universiti Putra Malaysia, Port Dickson 71050, Negeri Sembilan, Malaysia
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Yam Sim Khaw
- Aquatic Animal Health and Therapeutics Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (H.T.T.); (Y.S.K.)
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (S.A.A.); (N.A.S.)
| | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (S.A.A.); (N.A.S.)
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6
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Burian AN, Zhao W, Lo T, Thurtle‐Schmidt DM. Genome sequencing guide: An introductory toolbox to whole-genome analysis methods. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 49:815-825. [PMID: 34378845 PMCID: PMC9291972 DOI: 10.1002/bmb.21561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 06/17/2021] [Accepted: 07/09/2021] [Indexed: 05/05/2023]
Abstract
To fully appreciate genetics, one must understand the link between genotype (DNA sequence) and phenotype (observable characteristics). Advances in high-throughput genomic sequencing technologies and applications, so-called "-omics," have made genetic sequencing readily available across fields in biology from applications in non-traditional study organisms to precision medicine. Thus, understanding these tools is critical for any biologist, especially those early in their career. This comprehensive review discusses the chronological development of different sequencing methods, the bioinformatics steps to analyzing this data, and social and ethical issues raised by these techniques that must be discussed and evaluated, including anticipatory guides and discussion questions for active engagement in the classroom. Additionally, the Supporting Information includes a case study to apply technical and ethical concepts from the text.
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Affiliation(s)
| | - Wufan Zhao
- Department of BiologyDavidson CollegeDavidsonNorth CarolinaUSA
| | - Te‐Wen Lo
- Department of BiologyIthaca CollegeIthacaNew YorkUSA
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7
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Ragab SS. Synthesis and UV-irradiation of photocaged nitrobenzyl-BODIPY derivatives. J PORPHYR PHTHALOCYA 2021. [DOI: 10.1142/s1088424621500735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Two different photocaged 2-nitrobenzyl-BODIPY derivatives were designed and synthesized, where the 2-nitrobenzyl phototrigger is either directly attached to the meso position of BODIPY or through a phenoxy linker. The photochemical and photophysical properties of the two constructs were studied and their fluorescence quantum yields were determined. The ultraviolet irradiation of the two photocaged BODIPYs demonstrated a twofold fluorescence enhancement accompanying the uncaging of the BODIPY with the directly attached phototrigger, while the second switchable dyad with the phenoxy linker retains its essentially unaltered emissive behavior.
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Affiliation(s)
- Sherif Shaban Ragab
- Photochemistry Department, Chemical Industries Research Division, National Research Centre (NRC), El behouth Street, Dokki, Giza, 12622, Egypt
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8
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Orbán L, Shen X, Phua N, Varga L. Toward Genome-Based Selection in Asian Seabass: What Can We Learn From Other Food Fishes and Farm Animals? Front Genet 2021; 12:506754. [PMID: 33968125 PMCID: PMC8097054 DOI: 10.3389/fgene.2021.506754] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/15/2021] [Indexed: 01/08/2023] Open
Abstract
Due to the steadily increasing need for seafood and the plateauing output of fisheries, more fish need to be produced by aquaculture production. In parallel with the improvement of farming methods, elite food fish lines with superior traits for production must be generated by selection programs that utilize cutting-edge tools of genomics. The purpose of this review is to provide a historical overview and status report of a selection program performed on a catadromous predator, the Asian seabass (Lates calcarifer, Bloch 1790) that can change its sex during its lifetime. We describe the practices of wet lab, farm and lab in detail by focusing onto the foundations and achievements of the program. In addition to the approaches used for selection, our review also provides an inventory of genetic/genomic platforms and technologies developed to (i) provide current and future support for the selection process; and (ii) improve our understanding of the biology of the species. Approaches used for the improvement of terrestrial farm animals are used as examples and references, as those processes are far ahead of the ones used in aquaculture and thus they might help those working on fish to select the best possible options and avoid potential pitfalls.
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Affiliation(s)
- László Orbán
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.,Frontline Fish Genomics Research Group, Department of Applied Fish Biology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Keszthely, Hungary
| | - Xueyan Shen
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.,Tropical Futures Institute, James Cook University, Singapore, Singapore
| | - Norman Phua
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - László Varga
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllõ, Hungary.,Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, Gödöllõ, Hungary
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9
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Michiyuki S, Tomita N, Mori Y, Kanda H, Tashiro K, Notomi T. Discrimination of a single nucleotide polymorphism in the haptoglobin promoter region, rs5472, using a competitive fluorophore-labeled probe hybridization assay following loop-mediated isothermal amplification. Biosci Biotechnol Biochem 2021; 85:359-368. [PMID: 33604636 DOI: 10.1093/bbb/zbaa012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/15/2020] [Indexed: 12/22/2022]
Abstract
Personalized peptide vaccination, which involves activation of the host immune system against cancer cells using personalized peptide vaccines (PPVs), can improve overall survival in multiple cancer types. However, the clinical efficacies of PPVs vary for unknown reasons. Recently, a single nucleotide polymorphism (NG_012651.1:g.4461_5460[4960A>G]) in the haptoglobin promoter region, rs5472, was significantly associated with clinical response of PPV. Therefore, rs5472 is expected to be a predictive biomarker for PPV therapy. Here, we described a single nucleotide discrimination method for rs5472 analysis by combining the loop-mediated isothermal amplification and quenching probe methods. In evaluation of saliva samples, this method showed high concordance with the results of Sanger sequencing (100%, n = 36). Importantly, this method did not require calculation of melting temperature for single nucleotide discrimination and could therefore be carried out on a simple instrument. Accordingly, this method may be more robust and applicable to near-patient testing.
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Affiliation(s)
- Satoru Michiyuki
- Biochemical Research Laboratory, Eiken Chemical Co., Ltd., Otawara, Tochigi, Japan
| | - Norihiro Tomita
- Biochemical Research Laboratory, Eiken Chemical Co., Ltd., Otawara, Tochigi, Japan
| | - Yasuyoshi Mori
- Biochemical Research Laboratory, Eiken Chemical Co., Ltd., Otawara, Tochigi, Japan
| | - Hidetoshi Kanda
- Biochemical Research Laboratory, Eiken Chemical Co., Ltd., Otawara, Tochigi, Japan
| | - Kosuke Tashiro
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Nishi-Ku, Fukuoka, Japan
| | - Tsugunori Notomi
- Biochemical Research Laboratory, Eiken Chemical Co., Ltd., Otawara, Tochigi, Japan
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10
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Qin X, Chen J, Zhou T. 22q11.2 deletion syndrome and schizophrenia. Acta Biochim Biophys Sin (Shanghai) 2020; 52:1181-1190. [PMID: 33098288 DOI: 10.1093/abbs/gmaa113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 12/22/2022] Open
Abstract
22q11.2 deletion is a common microdeletion that causes an array of developmental defects including 22q11.2 deletion syndrome (22q11DS) or DiGeorge syndrome and velocardiofacial syndrome. About 30% of patients with 22q11.2 deletion develop schizophrenia. Mice with deletion of the ortholog region in mouse chromosome 16qA13 exhibit schizophrenia-like abnormal behaviors. It is suggested that the genes deleted in 22q11DS are involved in the pathogenesis of schizophrenia. Among these genes, COMT, ZDHHC8, DGCR8, and PRODH have been identified as schizophrenia susceptibility genes. And DGCR2 is also found to be associated with schizophrenia. In this review, we focused on these five genes and reviewed their functions in the brain and the potential pathophysiological mechanisms in schizophrenia, which will give us a deeper understanding of the pathology of schizophrenia.
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Affiliation(s)
- Xianzheng Qin
- Queen Mary School of Nanchang University, Nanchang University, Nanchang 330031, China
| | - Jiang Chen
- Laboratory of Synaptic Development and Plasticity, Institute of Life Science, Nanchang University, Nanchang 330031, China
| | - Tian Zhou
- School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China
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11
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Bagyinszky E, Giau VV, An SA. Transcriptomics in Alzheimer's Disease: Aspects and Challenges. Int J Mol Sci 2020; 21:E3517. [PMID: 32429229 PMCID: PMC7278930 DOI: 10.3390/ijms21103517] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023] Open
Abstract
Alzheimer's disease (AD) is the most common cause of dementia. Although the heritability of AD is high, the knowledge of the disease-associated genes, their expression, and their disease-related pathways remain limited. Hence, finding the association between gene dysfunctions and pathological mechanisms, such as neuronal transports, APP processing, calcium homeostasis, and impairment in mitochondria, should be crucial. Emerging studies have revealed that changes in gene expression and gene regulation may have a strong impact on neurodegeneration. The mRNA-transcription factor interactions, non-coding RNAs, alternative splicing, or copy number variants could also play a role in disease onset. These facts suggest that understanding the impact of transcriptomes in AD may improve the disease diagnosis and also the therapies. In this review, we highlight recent transcriptome investigations in multifactorial AD, with emphasis on the insights emerging at their interface.
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Affiliation(s)
- Eva Bagyinszky
- Department of Industrial and Environmental Engineering, Graduate School of Environment, Gachon University, Seongnam 13120, Korea;
- Department of Bionano Technology, Gachon University, Seongnam 13120, Korea
| | - Vo Van Giau
- Department of Industrial and Environmental Engineering, Graduate School of Environment, Gachon University, Seongnam 13120, Korea;
- Department of Bionano Technology, Gachon University, Seongnam 13120, Korea
| | - SeongSoo A. An
- Department of Bionano Technology, Gachon University, Seongnam 13120, Korea
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Abstract
In this work we show how DNA microarrays can be produced batch wise on standard microscope slides in a fast, easy, reliable and cost-efficient way. Contrary to classical microarray generation, the microarrays are generated via digital solid phase PCR. We have developed a cavity-chip system made of a PDMS/aluminum composite which allows such a solid phase PCR in a scalable and easy to handle manner. For the proof of concept, a DNA pool composed of two different DNA species was used to show that digital PCR is possible in our chips. In addition, we demonstrate that DNA microarray generation can be realized with different laboratory equipment (slide cycler, manually in water baths and with an automated cartridge system). We generated multiple microarrays and analyzed over 13,000 different monoclonal DNA spots to show that there is no significant difference between the used equipment. To show the scalability of our system we also varied the size and number of the cavities located in the array region up to more than 30,000 cavities with a volume of less than 60 pL per cavity. With this method, we present a revolutionary tool for novel DNA microarrays. Together with new established label-free measurement systems, our technology has the potential to give DNA microarray applications a new boost.
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Sarengaowa, Hu W, Feng K, Jiang A, Xiu Z, Lao Y, Li Y, Long Y. An in situ-Synthesized Gene Chip for the Detection of Food-Borne Pathogens on Fresh-Cut Cantaloupe and Lettuce. Front Microbiol 2020; 10:3089. [PMID: 32117079 PMCID: PMC7012807 DOI: 10.3389/fmicb.2019.03089] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/20/2019] [Indexed: 02/04/2023] Open
Abstract
Fresh foods are vulnerable to foodborne pathogens which cause foodborne illness and endanger people's life and safety. The rapid detection of foodborne pathogens is crucial for food safety surveillance. An in situ-synthesized gene chip for the detection of foodborne pathogens on fresh-cut fruits and vegetables was developed. The target genes were identified and screened by comparing the specific sequences of Salmonella Typhimurium, Vibrio parahemolyticus, Staphylococcus aureus, Listeria monocytogenes, and Escherichia coli O157:H7 from the National Center for Biotechnology Information database. Tiling array probes were designed to target selected genes in an optimized hybridization system. A total of 141 specific probes were selected from 3,227 hybridization probes, comprising 26 L. monocytogenes, 24 S. aureus, 25 E. coli O157:H7, 20 Salmonella Typhimurium, and 46 V. parahemolyticus probes that are unique to this study. The optimized assay had strong amplification signals and high accuracy. The detection limit for the five target pathogens on fresh-cut cantaloupe and lettuce was approximately 3 log cfu/g without culturing and with a detection time of 24 h. The detection technology established in this study can rapidly detect and monitor the foodborne pathogens on fresh-cut fruits and vegetables throughout the logistical distribution chain, i.e., processing, cleaning, fresh-cutting, packaging, storage, transport, and sale, and represents a valuable technology that support the safety of fresh agricultural products.
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Affiliation(s)
- Sarengaowa
- School of Bioengineering, Dalian University of Technology, Dalian, China
- College of Life Science, Dalian Minzu University, Dalian, China
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Dalian, China
| | - Wenzhong Hu
- College of Life Science, Dalian Minzu University, Dalian, China
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Dalian, China
| | - Ke Feng
- College of Life Science, Dalian Minzu University, Dalian, China
| | - Aili Jiang
- College of Life Science, Dalian Minzu University, Dalian, China
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Dalian, China
| | - Zhilong Xiu
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Ying Lao
- College of Life Science, Dalian Minzu University, Dalian, China
| | - Yuanzheng Li
- College of Life Science, Dalian Minzu University, Dalian, China
| | - Ya Long
- College of Life Science, Dalian Minzu University, Dalian, China
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14
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Zhang ZW, Feng LY, Wang JH, Fu YF, Cai X, Wang CQ, Du JB, Yuan M, Chen YE, Xu PZ, Lan T, Chen GD, Wu LT, Li Y, Hu JY, Yuan S. Two-factor ANOVA of SSH and RNA-seq analysis reveal development-associated Pi-starvation genes in oilseed rape. PLANTA 2019; 250:1073-1088. [PMID: 31165231 DOI: 10.1007/s00425-019-03201-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 05/27/2019] [Indexed: 06/09/2023]
Abstract
The 5-leaf-stage rape seedlings were more insensitive to Pi starvation than that of the 3-leaf-stage plants, which may be attributed to the higher expression levels of ethylene signaling and sugar-metabolism genes in more mature seedlings. Traditional suppression subtractive hybridization (SSH) and RNA-Seq usually screen out thousands of differentially expressed genes. However, identification of the most important regulators has not been performed to date. Here, we employed two methods, namely, a two-round SSH and two-factor transcriptome analysis derived from the two-factor ANOVA that is commonly used in the statistics, to identify development-associated inorganic phosphate (Pi) starvation-induced genes in Brassica napus. Several of these genes are related to ethylene signaling (such as EIN3, ACO3, ACS8, ERF1A, and ERF2) or sugar metabolism (such as ACC2, GH3, LHCB1.4, XTH4, and SUS2). Although sucrose and ethylene may counteract each other at the biosynthetic level, they may also work synergistically on Pi-starvation-induced gene expression (such as PT1, PT2, RNS1, ACP5, AT4, and IPS1) and root acid phosphatase activation. Furthermore, three new transcription factors that are responsive to Pi starvation were identified: the zinc-finger MYND domain-containing protein 15 (MYND), a Magonashi family protein (MAGO), and a B-box zinc-finger family salt-tolerance protein. This study indicates that the two methods are highly efficient for functional gene screening in non-model organisms.
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Affiliation(s)
- Zhong-Wei Zhang
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ling-Yang Feng
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jian-Hui Wang
- Horticulture Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Yu-Fan Fu
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xin Cai
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Chang-Quan Wang
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jun-Bo Du
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ming Yuan
- College of Life Sciences, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Yang-Er Chen
- College of Life Sciences, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Pei-Zhou Xu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ting Lan
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Guang-Deng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lin-Tao Wu
- Rape Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, 550008, Guizhou, China
| | - Yun Li
- Rape Research Institute, Chengdu Academy of Agriculture and Forestry, Chengdu, 611130, Sichuan, China
| | - Jin-Yao Hu
- Research Center for Eco-Environmental Engineering, Mianyang Normal University, Mianyang, 621000, Sichuan, China.
| | - Shu Yuan
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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15
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Hata H, Kitajima T, Suyama A. Influence of thermodynamically unfavorable secondary structures on DNA hybridization kinetics. Nucleic Acids Res 2019; 46:782-791. [PMID: 29220504 PMCID: PMC5778496 DOI: 10.1093/nar/gkx1171] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 12/04/2017] [Indexed: 12/11/2022] Open
Abstract
Nucleic acid secondary structure plays an important role in nucleic acid–nucleic acid recognition/hybridization processes, and is also a vital consideration in DNA nanotechnology. Although the influence of stable secondary structures on hybridization kinetics has been characterized, unstable secondary structures, which show positive ΔG° with self-folding, can also form, and their effects have not been systematically investigated. Such thermodynamically unfavorable secondary structures should not be ignored in DNA hybridization kinetics, especially under isothermal conditions. Here, we report that positive ΔG° secondary structures can change the hybridization rate by two-orders of magnitude, despite the fact that their hybridization obeyed second-order reaction kinetics. The temperature dependence of hybridization rates showed non-Arrhenius behavior; thus, their hybridization is considered to be nucleation limited. We derived a model describing how ΔG° positive secondary structures affect hybridization kinetics in stopped-flow experiments with 47 pairs of oligonucleotides. The calculated hybridization rates, which were based on the model, quantitatively agreed with the experimental rate constant.
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Affiliation(s)
- Hiroaki Hata
- Department of Life Sciences and Institute of Physics, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Tetsuro Kitajima
- Department of Life Sciences and Institute of Physics, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Akira Suyama
- Department of Life Sciences and Institute of Physics, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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16
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Nash T, Huff M, Glen WB, Hardiman G. Pipeline for Integrated Microarray Expression Normalization Tool Kit (PIMENTo) for Tumor Microarray Profiling Experiments. Methods Mol Biol 2019; 1908:153-168. [PMID: 30649727 DOI: 10.1007/978-1-4939-9004-7_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
We have developed a Pipeline for Integrated Microarray Expression & Normalization Tool kit (PIMENTo) with the aim of streamlining the processes necessary for gene expression analysis in tumor tissue using DNA microarrays. Built with the R programming language and leveraging several open-source packages available through CRAN and Bioconductor, PIMENTo enables researchers to perform complex tasks with a minimal number of operations. Here, we describe the pipeline, review necessary data inputs, examine data outputs and quality control assessments and explore the commands to perform such analysis.
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Affiliation(s)
- Thomas Nash
- MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA.,Department of Computer Science, College of Charleston, Charleston, SC, USA
| | - Matthew Huff
- MS in Biomedical Sciences Program, Medical University of South Carolina (MUSC), Charleston, SC, USA
| | - W Bailey Glen
- MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA.,Department of Pathology and Laboratory Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA
| | - Gary Hardiman
- MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA. .,Department of Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA. .,Department of Public Health Sciences, Medical University of South Carolina (MUSC), Charleston, SC, USA. .,School of Biological Sciences & Institute for Global Food Security, Queens University Belfast, Stranmillis Road, Belfast, BT9 5AG, UK.
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17
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Li W, Liu Z, Liang B, Chen S, Zhang X, Tong X, Lou W, Le L, Tang X, Fu F. Identification of core genes in ovarian cancer by an integrative meta-analysis. J Ovarian Res 2018; 11:94. [PMID: 30453999 PMCID: PMC6240943 DOI: 10.1186/s13048-018-0467-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/30/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Epithelial ovarian cancer is one of the most severe public health threats in women. Since it is still challenging to screen in early stages, identification of core genes that play an essential role in epithelial ovarian cancer initiation and progression is of vital importance. RESULTS Seven gene expression datasets (GSE6008, GSE18520, GSE26712, GSE27651, GSE29450, GSE36668, and GSE52037) containing 396 ovarian cancer samples and 54 healthy control samples were analyzed to identify the significant differentially expressed genes (DEGs). We identified 563 DEGs, including 245 upregulated and 318 downregulated genes. Enrichment analysis based on the gene ontology (GO) functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed that the upregulated genes were significantly enriched in cell division, cell cycle, tight junction, and oocyte meiosis, while the downregulated genes were associated with response to endogenous stimuli, complement and coagulation cascades, the cGMP-PKG signaling pathway, and serotonergic synapse. Two significant modules were identified from a protein-protein interaction network by using the Molecular Complex Detection (MCODE) software. Moreover, 12 hub genes with degree centrality more than 29 were selected from the protein-protein interaction network, and module analysis illustrated that these 12 hub genes belong to module 1. Furthermore, Kaplan-Meier analysis for overall survival indicated that 9 of these hub genes was correlated with poor prognosis of epithelial ovarian cancer patients. CONCLUSION The present study systematically validates the results of previous studies and fills the gap regarding a large-scale meta-analysis in the field of epithelial ovarian cancer. Furthermore, hub genes that could be used as a novel biomarkers to facilitate early diagnosis and therapeutic approaches are evaluated, providing compelling evidence for future genomic-based individualized treatment of epithelial ovarian cancer.
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Affiliation(s)
- Wenyu Li
- The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330031, People's Republic of China
| | - Zheran Liu
- Queen Mary School, Medical College of Nanchang University, Nanchang, Jiangxi, 330031, People's Republic of China
| | - Bowen Liang
- School of Public Health, Nanchang University, Nanchang, Jiangxi, 330031, People's Republic of China
| | - Siyang Chen
- School of Public Health, Nanchang University, Nanchang, Jiangxi, 330031, People's Republic of China
| | - Xinping Zhang
- School of Public Health, Nanchang University, Nanchang, Jiangxi, 330031, People's Republic of China
| | - Xiaoqin Tong
- School of Public Health, Nanchang University, Nanchang, Jiangxi, 330031, People's Republic of China
| | - Weiming Lou
- School of Public Health, Nanchang University, Nanchang, Jiangxi, 330031, People's Republic of China
| | - Lulu Le
- The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330031, People's Republic of China
| | - Xiaoli Tang
- School of Basic Medical Science, Nanchang University, Nanchang, Jiangxi, 330031, People's Republic of China.
| | - Fen Fu
- The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330031, People's Republic of China.
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18
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Yi K, Ju YS. Patterns and mechanisms of structural variations in human cancer. Exp Mol Med 2018; 50:1-11. [PMID: 30089796 PMCID: PMC6082854 DOI: 10.1038/s12276-018-0112-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 12/29/2017] [Indexed: 12/16/2022] Open
Abstract
Next-generation sequencing technology has enabled the comprehensive detection of genomic alterations in human somatic cells, including point mutations, chromosomal rearrangements, and structural variations (SVs). Using sophisticated bioinformatics algorithms, unbiased catalogs of SVs are emerging from thousands of human cancer genomes for the first time. Via careful examination of SV breakpoints at single-nucleotide resolution as well as local DNA copy number changes, diverse patterns of genomic rearrangements are being revealed. These "SV signatures" provide deep insight into the mutational processes that have shaped genome changes in human somatic cells. This review summarizes the characteristics of recently identified complex SVs, including chromothripsis, chromoplexy, microhomology-mediated breakage-induced replication (MMBIR), and others, to provide a holistic snapshot of the current knowledge on genomic rearrangements in somatic cells.
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Affiliation(s)
- Kijong Yi
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea.
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19
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Zhuang Q, Cao W, Ni Y, Wang Y. Synthesis-identification integration: One-pot hydrothermal preparation of fluorescent nitrogen-doped carbon nanodots for differentiating nucleobases with the aid of multivariate chemometrics analysis. Talanta 2018; 185:491-498. [DOI: 10.1016/j.talanta.2018.04.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/10/2018] [Accepted: 04/07/2018] [Indexed: 12/31/2022]
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20
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Chen X, Zhang J, Wang Z, Xu X, Zhu B. Combination of Zn2+ and betaine can eliminate the effect of DNA fragments with different GC content on gene chip. Acta Biochim Biophys Sin (Shanghai) 2018; 50:826-827. [PMID: 29897387 DOI: 10.1093/abbs/gmy064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Xiang Chen
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Jiaqi Zhang
- Shanghai BaiO Technology Co., Ltd., Shanghai, China
| | - Ze Wang
- Shanghai BaiO Technology Co., Ltd., Shanghai, China
| | - Xu Xu
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Bin Zhu
- Shanghai BaiO Technology Co., Ltd., Shanghai, China
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21
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De Laet N, Llamas EM, Madder A. Templated DNA Cross-Linking: Towards a Non-Invasive Singlet-Oxygen-Based Triggering Method. CHEMPHOTOCHEM 2018. [DOI: 10.1002/cptc.201700175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Nathalie De Laet
- Organic and Biomimetic Chemistry Research Group Krijgslaan 281, S4; B-9000 Ghent Belgium
| | - Eva M. Llamas
- Organic and Biomimetic Chemistry Research Group Krijgslaan 281, S4; B-9000 Ghent Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group Krijgslaan 281, S4; B-9000 Ghent Belgium
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22
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He X, Zhang C, Shi C, Lu Q. Meta-analysis of mRNA expression profiles to identify differentially expressed genes in lung adenocarcinoma tissue from smokers and non-smokers. Oncol Rep 2018; 39:929-938. [PMID: 29328493 PMCID: PMC5802042 DOI: 10.3892/or.2018.6197] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 12/29/2017] [Indexed: 11/24/2022] Open
Abstract
Compared to other types of lung cancer, lung adenocarcinoma patients with a history of smoking have a poor prognosis during the treatment of lung cancer. How lung adenocarcinoma-related genes are differentially expressed between smoker and non-smoker patients has yet to be fully elucidated. We performed a meta-analysis of four publicly available microarray datasets related to lung adenocarcinoma tissue in patients with a history of smoking using R statistical software. The top 50 differentially expressed genes (DEGs) in smoking vs. non‑smoking patients are shown using heat maps. Additionally, we conducted KEGG and GO analyses. In addition, we performed a PPI network analysis for 8 genes that were selected during a previous analysis. We identified a total of 2,932 DEGs (1,806 upregulated, 1,126 downregulated) and five genes (CDC45, CDC20, ANAPC7, CDC6, ESPL1) that may link lung adenocarcinoma to smoking history. Our study may provide new insights into the complex mechanisms of lung adenocarcinoma in smoking patients, and our novel gene expression signatures will be useful for future clinical studies.
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Affiliation(s)
- Xiaona He
- Department of Biostatistics and Epidemiology, School of Public Health, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Cheng Zhang
- Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Chao Shi
- Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Quqin Lu
- Department of Biostatistics and Epidemiology, School of Public Health, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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23
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Zhang Y, Cheng M, Wang Y, Shi F. Constructing a Multiplexed DNA Pattern by Combining Precise Magnetic Manipulation and DNA-Driven Assembly. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:1100-1108. [PMID: 28903006 DOI: 10.1021/acs.langmuir.7b02608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
There is an urgent demand to construct multiplexed biomolecular patterns to obtain more biological information from a single experiment. However, with only limited reports focusing on defective top-down approaches, challenges remain to develop a bottom-up strategy for multiplexed patterning. To this end, a novel strategy has been proposed to fabricate multiplexed DNA patterns via macroscopic assembly through combined precise magnetic manipulation and DNA hybridization-driven self-assembly. Therefore, a multiplexed DNA pattern composed of glass fibers loaded with multiple specific strands of DNA was constructed, and its potential application in simultaneous detection of multiplex target DNA was demonstrated. Moreover, the fabricated multiplexed DNA pattern shows an erasable behavior because the hybridized DNA can be disassembled by strand displacement.
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Affiliation(s)
- Yingwei Zhang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology , Beijing, 100029, China
| | - Mengjiao Cheng
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology , Beijing, 100029, China
| | - Yue Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology , Beijing, 100029, China
| | - Feng Shi
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology , Beijing, 100029, China
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24
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Affiliation(s)
- Bing Xing Wang
- Department of Statistics, Zhejiang Gongshang University, Hangzhou, China
| | - Fangtao Wu
- Department of Statistics, Zhejiang Gongshang University, Hangzhou, China
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25
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Ott A, Liu S, Schnable JC, Yeh CT‘E, Wang KS, Schnable PS. tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci. Nucleic Acids Res 2017; 45:e178. [PMID: 29036322 PMCID: PMC5716196 DOI: 10.1093/nar/gkx853] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/09/2017] [Accepted: 09/13/2017] [Indexed: 12/20/2022] Open
Abstract
Conventional genotyping-by-sequencing (cGBS) strategies suffer from high rates of missing data and genotyping errors, particularly at heterozygous sites. tGBS® genotyping-by-sequencing is a novel method of genome reduction that employs two restriction enzymes to generate overhangs in opposite orientations to which (single-strand) oligos rather than (double-stranded) adaptors are ligated. This strategy ensures that only double-digested fragments are amplified and sequenced. The use of oligos avoids the necessity of preparing adaptors and the problems associated with inter-adaptor annealing/ligation. Hence, the tGBS protocol simplifies the preparation of high-quality GBS sequencing libraries. During polymerase chain reaction (PCR) amplification, selective nucleotides included at the 3'-end of the PCR primers result in additional genome reduction as compared to cGBS. By adjusting the number of selective bases, different numbers of genomic sites are targeted for sequencing. Therefore, for equivalent amounts of sequencing, more reads per site are available for SNP calling. Hence, as compared to cGBS, tGBS delivers higher SNP calling accuracy (>97-99%), even at heterozygous sites, less missing data per marker across a population of samples, and an enhanced ability to genotype rare alleles. tGBS is particularly well suited for genomic selection, which often requires the ability to genotype populations of individuals that are heterozygous at many loci.
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Affiliation(s)
- Alina Ott
- Department of Agronomy, Iowa State University, Ames, IA 50011-3650, USA
| | - Sanzhen Liu
- Department of Agronomy, Iowa State University, Ames, IA 50011-3650, USA
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
- Data2Bio LLC, Ames, IA 50011-3650, USA
| | - James C. Schnable
- Data2Bio LLC, Ames, IA 50011-3650, USA
- Department of Agriculture and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Cheng-Ting ‘Eddy’ Yeh
- Department of Agronomy, Iowa State University, Ames, IA 50011-3650, USA
- Data2Bio LLC, Ames, IA 50011-3650, USA
| | | | - Patrick S. Schnable
- Department of Agronomy, Iowa State University, Ames, IA 50011-3650, USA
- Data2Bio LLC, Ames, IA 50011-3650, USA
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26
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Abstract
Molecular insights from genome and systems biology are influencing how cancer is diagnosed and treated. We critically evaluate big data challenges in precision medicine. The melanoma research community has identified distinct subtypes involving chronic sun-induced damage and the mitogen-activated protein kinase driver pathway. In addition, despite low mutation burden, non-genomic mitogen-activated protein kinase melanoma drivers are found in membrane receptors, metabolism, or epigenetic signaling with the ability to bypass central mitogen-activated protein kinase molecules and activating a similar program of mitogenic effectors. Mutation hotspots, structural modeling, UV signature, and genomic as well as non-genomic mechanisms of disease initiation and progression are taken into consideration to identify resistance mutations and novel drug targets. A comprehensive precision medicine profile of a malignant melanoma patient illustrates future rational drug targeting strategies. Network analysis emphasizes an important role of epigenetic and metabolic master regulators in oncogenesis. Co-occurrence of driver mutations in signaling, metabolic, and epigenetic factors highlights how cumulative alterations of our genomes and epigenomes progressively lead to uncontrolled cell proliferation. Precision insights have the ability to identify independent molecular pathways suitable for drug targeting. Synergistic treatment combinations of orthogonal modalities including immunotherapy, mitogen-activated protein kinase inhibitors, epigenetic inhibitors, and metabolic inhibitors have the potential to overcome immune evasion, side effects, and drug resistance.
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Affiliation(s)
- Fabian V Filipp
- Systems Biology and Cancer Metabolism, Program for Quantitative Systems Biology, University of California Merced, 2500 North Lake Road, Merced, CA, 95343, USA.
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27
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Furst AL, Smith MJ, Francis MB. Direct Electrochemical Bioconjugation on Metal Surfaces. J Am Chem Soc 2017; 139:12610-12616. [DOI: 10.1021/jacs.7b06385] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ariel L. Furst
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
| | - Matthew J. Smith
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
| | - Matthew B. Francis
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
- Materials
Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720-1460, United States
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28
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Saljooqi A, Shamspur T, Mostafavi A. Ag-4-ATP-MWCNT electrode modified with dsDNA as label-free electrochemical sensor for the detection of daunorubicin anticancer drug. Bioelectrochemistry 2017; 118:161-167. [PMID: 28843934 DOI: 10.1016/j.bioelechem.2017.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/11/2017] [Accepted: 08/15/2017] [Indexed: 10/19/2022]
Abstract
This paper describes the synthesis of Ag-4-ATP-MWCNT nanocomposite and its use as a modifier of working electrode. The surface of the electrochemical Ag-4-ATP-MWCNT electrode was modified with a double-stranded DNA (dsDNA) to detect daunorubicin-DNA interactions. Differential pulse voltammetry was applied to develop an electroanalytical procedure for the determination of daunorubicin and evaluate its interaction with dsDNA immobilized on the electrode surface. After the optimization of operational parameters, the linear dependence of the peak current on the daunorubicin concentration was observed in the range of 0.10×10-8 to 1.00×10-5molL-1, with the detection and quantification limits of 3.00×10-10 and 1.00×10-9molL-1, respectively. The proposed biosensor was successfully applied to validate its capability for the determination of daunorubicin in human serum and urine samples.
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Affiliation(s)
- Asma Saljooqi
- Department of Chemistry, Shahid Bahonar University of Kerman, Kerman, PO Box 76169-133, Iran; Young Research Society, Shahid Bahonar University of Kerman, Kerman, PO Box 76169-133, Iran
| | - Tayebeh Shamspur
- Department of Chemistry, Shahid Bahonar University of Kerman, Kerman, PO Box 76169-133, Iran.
| | - Ali Mostafavi
- Department of Chemistry, Shahid Bahonar University of Kerman, Kerman, PO Box 76169-133, Iran
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29
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Li J, Wang F. Towards Unsupervised Gene Selection: A Matrix Factorization Framework. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017; 14:514-521. [PMID: 28113598 DOI: 10.1109/tcbb.2016.2591545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The recent development of microarray gene expression techniques have made it possible to offer phenotype classification of many diseases. However, in gene expression data analysis, each sample is represented by quite a large number of genes, and many of them are redundant or insignificant to clarify the disease problem. Therefore, how to efficiently select the most useful genes has been becoming one of the most hot research topics in the gene expression data analysis. In this paper, a novel unsupervised two-stage coarse-fine gene selection method is proposed. In the first stage, we apply the kmeans algorithm to over-cluster the genes and discard some redundant genes. In the second stage, we select the most representative genes from the remaining ones based on matrix factorization. Finally the experimental results on several data sets are presented to show the effectiveness of our method.
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30
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Broadgate S, Yu J, Downes SM, Halford S. Unravelling the genetics of inherited retinal dystrophies: Past, present and future. Prog Retin Eye Res 2017; 59:53-96. [PMID: 28363849 DOI: 10.1016/j.preteyeres.2017.03.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 02/07/2023]
Abstract
The identification of the genes underlying monogenic diseases has been of interest to clinicians and scientists for many years. Using inherited retinal dystrophies as an example of monogenic disease we describe the history of molecular genetic techniques that have been pivotal in the discovery of disease causing genes. The methods that were developed in the 1970's and 80's are still in use today but have been refined and improved. These techniques enabled the concept of the Human Genome Project to be envisaged and ultimately realised. When the successful conclusion of the project was announced in 2003 many new tools and, as importantly, many collaborations had been developed that facilitated a rapid identification of disease genes. In the post-human genome project era advances in computing power and the clever use of the properties of DNA replication has allowed the development of next-generation sequencing technologies. These methods have revolutionised the identification of disease genes because for the first time there is no need to define the position of the gene in the genome. The use of next generation sequencing in a diagnostic setting has allowed many more patients with an inherited retinal dystrophy to obtain a molecular diagnosis for their disease. The identification of novel genes that have a role in the development or maintenance of retinal function is opening up avenues of research which will lead to the development of new pharmacological and gene therapy approaches. Neither of which can be used unless the defective gene and protein is known. The continued development of sequencing technologies also holds great promise for the advent of truly personalised medicine.
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Affiliation(s)
- Suzanne Broadgate
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Levels 5 and 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Jing Yu
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Levels 5 and 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Susan M Downes
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, Oxford, OX3 9DU, UK
| | - Stephanie Halford
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Levels 5 and 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK.
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Barrette RW, Rowland JM, Grau FR, McIntosh MT. Development of a Feature and Template-Assisted Assembler and Application to the Analysis of a Foot-and-Mouth Disease Virus Genotyping Microarray. PLoS One 2017; 12:e0166870. [PMID: 28045937 PMCID: PMC5207525 DOI: 10.1371/journal.pone.0166870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 11/05/2016] [Indexed: 12/04/2022] Open
Abstract
Several RT-PCR and genome sequencing strategies exist for the resolution of Foot-and-Mouth Disease virus (FMDV). While these approaches are relatively straightforward, they can be vulnerable to failure due to the unpredictable nature of FMDV genome sequence variations. Sequence independent single primer amplification (SISPA) followed by genotyping microarray offers an attractive unbiased approach to FMDV characterization. Here we describe a custom FMDV microarray and a companion feature and template-assisted assembler software (FAT-assembler) capable of resolving virus genome sequence using a moderate number of conserved microarray features. The results demonstrate that this approach may be used to rapidly characterize naturally occurring FMDV as well as an engineered chimeric strain of FMDV. The FAT-assembler, while applied to resolving FMDV genomes, represents a new bioinformatics approach that should be broadly applicable to interpreting microarray genotyping data for other viruses or target organisms.
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Affiliation(s)
- Roger W. Barrette
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Foreign Animal Disease Diagnostic Laboratory, Plum Island Animal Disease Center, Orient, NY, United States of America
- * E-mail:
| | - Jessica M. Rowland
- Department of Environmental and Global Health, Emerging Pathogens Institute University of Florida, Gainesville, FL, United States of America
| | - Frederic R. Grau
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Foreign Animal Disease Diagnostic Laboratory, Plum Island Animal Disease Center, Orient, NY, United States of America
| | - Michael T. McIntosh
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Foreign Animal Disease Diagnostic Laboratory, Plum Island Animal Disease Center, Orient, NY, United States of America
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Piątek Ł, Grzymała-Busse JW. LEMRG: Decision Rule Generation Algorithm for Mining MicroRNA Expression Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1028:105-137. [DOI: 10.1007/978-981-10-6041-0_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Expanding the Immunology Toolbox: Embracing Public-Data Reuse and Crowdsourcing. Immunity 2016; 45:1191-1204. [DOI: 10.1016/j.immuni.2016.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/30/2016] [Accepted: 12/01/2016] [Indexed: 12/15/2022]
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Cooley P, Wallace D, Antohe B. Applicatons of Ink-Jet Printing Technology to BioMEMS and Microfluidic Systems. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/s1535-5535-04-00214-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Applications of microfluidics and MEMS (micro-electromechanical systems) technology are emerging in many areas of biological and life sciences. Non-contact microdispensing systems for accurate, high-throughput deposition of bioactive fluids can be an enabling technology for these applications. In addition to bioactive fluid dispensing, ink-jet based microdispensing allows integration of features (electronic, photonic, sensing, structural, etc.) that are not possible, or very difficult, with traditional photolithographic-based MEMS fabrication methods. Our single fluid and multifluid (MatrixJet™) piezoelectric microdispensers have been used for spot synthesis of peptides, production of microspheres to deliver drugs/biological materials, microprinting of biodegradable polymers for cell proliferation in tissue engineering applications, and spot deposition for DNA, diagnostic immunoassay, antibody and protein arrays. We have created optical elements, sensors, and electrical interconnects by microdeposition of polymers and metal alloys. We have also demonstrated the integration of a reversed phase microcolumn within a piezoelectric dispenser for use in the fractionation of peptides for mass spectrometer analysis.
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Abstract
The papers published in this Special Issue “SNP arrays” (Single Nucleotide Polymorphism Arrays) focus on several perspectives associated with arrays of this type. The range of papers vary from a case report to reviews, thereby targeting wider audiences working in this field. The research focus of SNP arrays is often human cancers but this Issue expands that focus to include areas such as rare conditions, animal breeding and bioinformatics tools. Given the limited scope, the spectrum of papers is nothing short of remarkable and even from a technical point of view these papers will contribute to the field at a general level. Three of the papers published in this Special Issue focus on the use of various SNP array approaches in the analysis of three different cancer types. Two of the papers concentrate on two very different rare conditions, applying the SNP arrays slightly differently. Finally, two other papers evaluate the use of the SNP arrays in the context of genetic analysis of livestock. The findings reported in these papers help to close gaps in the current literature and also to give guidelines for future applications of SNP arrays.
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Affiliation(s)
- Jari Louhelainen
- Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, UK.
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Giuliano KA, DeBiasio RL, Dunlay RT, Gough A, Volosky JM, Zock J, Pavlakis GN, Taylor DL. High-Content Screening: A New Approach to Easing Key Bottlenecks in the Drug Discovery Process. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/108705719700200410] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Recent improvements in target discovery and high throughput screening (HTS) have increased the pressure at key points along the drug discovery pipeline. High-content screening (HCS) was developed to ease bottlenecks that have formed at target validation and lead optimization points in the pipeline. HCS defines the role of targets in cell functions by combining fluorescence-based reagents with the ArrayScan™ System to automatically extract temporal and spatial information about target activities within cells. The ArrayScan System is a tabletop instrument that includes optics for subcellular resolution of fluorescence signals from many cells in a field within a well of a microtiter plate. One demonstrated application is a high-content screen designed to measure the drug-induced transport of a green fluorescent protein-human glucocorticoid receptor chimeric protein from the cytoplasm to the nucleus of human tumor cells. A high-content screen is also described for the multiparametric measurement of apoptosis. This single screen provides measurements of nuclear size and shape changes, nuclear DNA content, mitochondrial potential, and actin-cytoskeletal rearrangements during drug-induced programmed cell death. The next generation HCS system is a miniaturized screening platform, the CellChip™ System, that will increase the throughput of HCS, while integrating HCS with HTS on the same platform.
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Affiliation(s)
| | | | | | - Albert Gough
- BioDx, Inc., 635 William Pitt Way, Pittsburgh, PA 15238
| | | | - Joseph Zock
- BioDx, Inc., 635 William Pitt Way, Pittsburgh, PA 15238
| | - George N. Pavlakis
- ABL-Basic Research Program, National Cancer Institute-FCRDC, Frederick, MD 21702
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Extended Abstracts. Toxicol Pathol 2016. [DOI: 10.1177/019262339702500633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Abstract
A convergence between molecular biological technique and the technology of miniaturization has produced the "gene chip" or microhybridization array. This device multiplies by several thousand fold the power of the northern blot for studying gene expression. Now, it is possible to survey simultaneously a large fraction of all genes in an experimental organism, and within a few years all of the approximately 140,000 human genes will be within reach of the technique. This capability is not only accelerating the rate of research into gene expression and function, it is changing the perspective of inquiry from single genes in isolation to networks of genes operating as a system. Many neurological diseases, from hydrocephalus to schizophrenia, have a genetic component, and individual responses to therapeutic drugs can vary with the genetic background of patients. In neurology and neurobiology, the ability to obtain "gene expression profiles" from nervous tissue promises to illuminate interactions between neuronal genes and the environment, development, disease, aging, and response to drugs and injury.
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Affiliation(s)
- R Douglas Fields
- Laboratory of Developmental Neurobiology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Nesrin Ozsarac
- Laboratory of Developmental Neurobiology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
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Zhou Y, Liu Z, Rothschild KJ, Lim MJ. Proteome-wide drug screening using mass spectrometric imaging of bead-arrays. Sci Rep 2016; 6:26125. [PMID: 27194112 PMCID: PMC4872124 DOI: 10.1038/srep26125] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/27/2016] [Indexed: 12/17/2022] Open
Abstract
A fundamental challenge in the drug discovery process is to develop compounds with high efficacy and minimal side-effects. We describe a new approach to proteome-wide drug screening for detection of on- and off-target binding which combines the advantages of mass spectrometry with microarray technology. The method involves matrix-assisted laser desorption/ionization mass spectrometric imaging (MALDI-MSI) of agarose micro-beads randomly arrayed at high-density in custom micro-well plates. Each bead carries a unique protein target and a corresponding photocleavable mass-tag for coding (PC-Mass-Tag). Compounds bound to specific protein beads and a photo-released coding PC-Mass-Tag are detected simultaneously using MALDI-MSI. As an initial demonstration of this approach, two kinase-targeted drugs, Dasatinib and Brigatinib (AP26113), were simultaneously screened against a model 50-member kinase-bead library. A MALDI-MSI scan performed at the equivalent density of 495,000 beads in the footprint of a microscope slide yielded 100% sensitivity for detecting known strong interactions with no false positives.
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Affiliation(s)
- Ying Zhou
- AmberGen, Inc., 313 Pleasant Street, Watertown, MA 02472, United States
| | - Ziying Liu
- AmberGen, Inc., 313 Pleasant Street, Watertown, MA 02472, United States
| | - Kenneth J Rothschild
- AmberGen, Inc., 313 Pleasant Street, Watertown, MA 02472, United States.,Molecular Biophysics Laboratory, Department of Physics and Photonics Center, Boston University, Boston, MA 02215, United States
| | - Mark J Lim
- AmberGen, Inc., 313 Pleasant Street, Watertown, MA 02472, United States
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Khomyakova E, Liquier J, Huynh-Dinh T, Florentiev V, Mirzabekov A, Taillandier E. Targeting of Pu.Py Duplexes by GA and GT Rich Oligonucleotides on Microchip and in Solution. J Biomol Struct Dyn 2016; 17 Suppl 1:227-35. [PMID: 22607429 DOI: 10.1080/07391102.2000.10506626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Abstract Formation of triple helices with GA and GT third strands has been studied. Besides the usual investigation techniques common for characterizing triple helical formation (CD spectroscopy, gel shift mobility assay, chemical probing and S1 nuclease footprinting) we have used a new technique in which targeting of polypurine sequences in duplexes was demonstrated on oligonucleotide microchips. This technique is very successful to quickly test a large number of potential triple helix formation. In this work we used oligonucleotide microairay to study the specificity of DNA duplex recognition by GA and GT strands. Generic 6-mer microchip containing all possible 4(6) = 4,096 single-stranded hexadeoxyribonucleotides immobilized within individual gel pads was applied. To study formation of intermolecular triple helices on the generic microchip, a number of Pu.Py duplexes were formed by hybridization of the mixture of purine octadeoxyribonucleotides on the microchip followed by targeting of the duplexes by GA or GT third strands. Melting behavior of the formed structures was investigated using fluorescence measurements under microscope. In solution we present the results obtained for GT triplexes and discuss the characteristics of the CD spectra. Results obtained by S1 nuclease footprinting, KMnO(4) and DMS chemical probing are consistent with the spectroscopic data reflecting triplex structure formation.
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Affiliation(s)
- E Khomyakova
- a Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , 32 Vavilov St. , 117984 , Moscow , Russia
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41
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Ma DL, Wang W, Mao Z, Kang TS, Han QB, Chan PWH, Leung CH. Utilization of G-Quadruplex-Forming Aptamers for the Construction of Luminescence Sensing Platforms. Chempluschem 2016; 82:8-17. [DOI: 10.1002/cplu.201600036] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/07/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry; Hong Kong Baptist University; 224 Waterloo Road, Kowloon Tong Hong Kong 852 P. R. China
| | - Wanhe Wang
- Department of Chemistry; Hong Kong Baptist University; 224 Waterloo Road, Kowloon Tong Hong Kong 852 P. R. China
| | - Zhifeng Mao
- Department of Chemistry; Hong Kong Baptist University; 224 Waterloo Road, Kowloon Tong Hong Kong 852 P. R. China
| | - Tian-Shu Kang
- State Key Laboratory of Quality Research in Chinese Medicine; Institute of Chinese Medical Sciences; University of Macau; Macao 999078 P. R. China
| | - Quan-Bin Han
- School of Chinese Medicine; Hong Kong Baptist University; Kowloon Hong Kong 852 P. R. China
| | - Philip Wai Hong Chan
- School of Chemistry; Monash University; Clayton VIC 3800 Australia
- Department of Chemistry; University of Warwick; Coventry CV4 7AL United Kingdom
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine; Institute of Chinese Medical Sciences; University of Macau; Macao 999078 P. R. China
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Lu N, Gao A, Zhou H, Wang Y, Yang X, Wang Y, Li T. Progress in Silicon Nanowire-Based Field-Effect Transistor Biosensors for Label-Free Detection of DNA. CHINESE J CHEM 2016. [DOI: 10.1002/cjoc.201500857] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Abstract
INTRODUCTION Peyronie disease (PD) is a progressive fibrotic disorder of the penile tunica albuginea that results in fibrotic penile plaques and can lead to penile deformity. Characterized by aberrant fibrosis resulting in part from the persistence of myofibroblasts and altered gene expression, the molecular factors underpinning PD and other related fibrotic diatheses are just being elucidated. A genetic link to PD was first identified three decades ago using pedigree analyses. However, the specific genetic factors that predispose patients to aberrant fibrosis remain unknown, and the relations between these fibrotic conditions and other heritable diseases, including malignancy, are uncharacterized. AIM To review the current landscape linking molecular and genetic factors to aberrant fibrosis in PD and related fibrotic diatheses, including Dupuytren disease. METHODS Review and evaluation of the literature from 1970 to the present for genetic factors associated with PD were performed. MAIN OUTCOME MEASURES Data describing the genetic factors associated with PD were obtained. RESULTS We describe the known structural chromosomal abnormalities and single-nucleotide polymorphisms associated with fibrotic diatheses and discuss the spectrum of differential gene expression data comparing normal tissues with those derived from men with PD or Dupuytren disease. We discuss epigenetic mechanisms that might regulate gene expression and alter predisposition to fibrosis. CONCLUSION Although the current understanding of the genetic factors associated with PD is limited, significant advances have been made during the past three decades. Further research is necessary to provide a more comprehensive understanding of the landscape of genetic factors responsible for the development of PD.
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Mosinger J, Lang K, Kubát P. Photoactivatable Nanostructured Surfaces for Biomedical Applications. Top Curr Chem (Cham) 2016; 370:135-68. [DOI: 10.1007/978-3-319-22942-3_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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45
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Duncan R, Kourout M, Grigorenko E, Fisher C, Dong M. Advances in multiplex nucleic acid diagnostics for blood-borne pathogens: promises and pitfalls. Expert Rev Mol Diagn 2015; 16:83-95. [PMID: 26581018 DOI: 10.1586/14737159.2016.1112272] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The large number of blood-borne viruses, bacteria and parasites currently of concern, as well as many newly emerging pathogens, presents a daunting challenge to protection of the safety of blood for transfusion and diagnosing infectious diseases. Focusing on nucleic acid diagnostic tests, multiplex devices are coming into use with many more in various developmental stages that promise to offer solutions to the clinical need. The characteristics, advantages and disadvantages of platforms in clinical use and at the research and development stage are examined here. The presence of multiple assays and associated reagents operating simultaneously on one platform, implementation in traditional clinical laboratories and regulatory review will present special challenges. Fortunately, clinical laboratories have made dramatic technical progress in the last two decades and regulatory agencies have publicly expressed support for development of multiplex devices.
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Affiliation(s)
- Robert Duncan
- a Center for Biologics Evaluation and Research , US FDA , Silver Spring , MD , USA
| | - Moussa Kourout
- a Center for Biologics Evaluation and Research , US FDA , Silver Spring , MD , USA
| | | | - Carolyn Fisher
- a Center for Biologics Evaluation and Research , US FDA , Silver Spring , MD , USA
| | - Ming Dong
- a Center for Biologics Evaluation and Research , US FDA , Silver Spring , MD , USA
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Kalidhasan N, Joshi D, Bhatt TK, Gupta AK. Identification of key genes involved in root development of tomato using expressed sequence tag analysis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2015; 21:491-503. [PMID: 26600676 PMCID: PMC4646861 DOI: 10.1007/s12298-015-0304-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 04/19/2015] [Accepted: 06/09/2015] [Indexed: 05/11/2023]
Abstract
Root system of plants are actually fascinating structures, not only critical for plant development, but also important for storage and conduction. Due to its agronomic importance, identification of genes involved in root development has been a subject of intense study. Tomato is the one of the most consumed vegetables in the world. Tomato has been used as model system for dicot plants because of its small genome, well-established transformation techniques and well-constructed physical map. The present study is targeted to identify of root specific genes expressed temporally and also gene(s) involved in lateral root and profuse root development. A total of 890 ESTs were identified from five EST libraries constructed using SSH approach which included temporal gene regulation (early and late) and genes involved in morphogenetic traits (lateral and profuse rooting). One hundred sixty-one unique ESTs identified from various libraries were categorized based on their putative functions and deposited in NCBI-dbEST database. In addition, 36 ESTs were selected for validation of their expression by RT-PCR. The present findings will help in shedding light to the unexplored developmental process of root growth in tomato and plant in general.
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Affiliation(s)
- N. Kalidhasan
- />Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, 625021 India
| | - Deepti Joshi
- />Department of Biotechnology, School of LifeSciences, Central University of Rajasthan, Bandarsindri, 305801 India
| | - Tarun Kumar Bhatt
- />Department of Biotechnology, School of LifeSciences, Central University of Rajasthan, Bandarsindri, 305801 India
| | - Aditya Kumar Gupta
- />Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, 625021 India
- />Department of Biotechnology, School of LifeSciences, Central University of Rajasthan, Bandarsindri, 305801 India
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Rosenberg JM, Utz PJ. Protein microarrays: a new tool for the study of autoantibodies in immunodeficiency. Front Immunol 2015; 6:138. [PMID: 25904912 PMCID: PMC4387933 DOI: 10.3389/fimmu.2015.00138] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/12/2015] [Indexed: 12/19/2022] Open
Abstract
Autoimmunity is highly coincident with immunodeficiency. In a small but growing number of primary immunodeficiencies, autoantibodies are diagnostic of a given disease and implicated in disease pathogenesis. In order to improve our understanding of the role of autoantibodies in immunodeficiencies and to discover novel autoantibodies, new proteomic tools are needed. Protein microarrays have the ability to screen for reactivity to hundreds to many thousands of unique autoantigens simultaneously on a single chip using minimal serum input. Here, we review different types of protein microarrays and how they can be useful in framing the study of primary and secondary immunodeficiencies.
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Affiliation(s)
- Jacob M Rosenberg
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine , Stanford, CA , USA
| | - Paul J Utz
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine , Stanford, CA , USA ; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine , Stanford, CA , USA
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Goswami PP, Syed A, Beck CL, Albright TR, Mahoney KM, Unash R, Smith EA, Winter AH. BODIPY-derived photoremovable protecting groups unmasked with green light. J Am Chem Soc 2015; 137:3783-6. [PMID: 25751156 DOI: 10.1021/jacs.5b01297] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Photoremovable protecting groups derived from meso-substituted BODIPY dyes release acetic acid with green wavelengths >500 nm. Photorelease is demonstrated in cultured S2 cells. The photocaging structures were identified by our previously proposed strategy of computationally searching for carbocations with low-energy diradical states as a possible indicator of a nearby productive conical intersection. The superior optical properties of these photocages make them promising alternatives to the popular o-nitrobenzyl photocage systems.
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Affiliation(s)
- Pratik P Goswami
- Department of Chemistry, Iowa State University, 2101d Hach Hall, Ames, Iowa 50011, United States
| | - Aleem Syed
- Department of Chemistry, Iowa State University, 2101d Hach Hall, Ames, Iowa 50011, United States
| | - Christie L Beck
- Department of Chemistry, Iowa State University, 2101d Hach Hall, Ames, Iowa 50011, United States
| | - Toshia R Albright
- Department of Chemistry, Iowa State University, 2101d Hach Hall, Ames, Iowa 50011, United States
| | - Kaitlyn M Mahoney
- Department of Chemistry, Iowa State University, 2101d Hach Hall, Ames, Iowa 50011, United States
| | - Ryan Unash
- Department of Chemistry, Iowa State University, 2101d Hach Hall, Ames, Iowa 50011, United States
| | - Emily A Smith
- Department of Chemistry, Iowa State University, 2101d Hach Hall, Ames, Iowa 50011, United States
| | - Arthur H Winter
- Department of Chemistry, Iowa State University, 2101d Hach Hall, Ames, Iowa 50011, United States
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Pillai S, Chellappan SP. ChIP on chip and ChIP-Seq assays: genome-wide analysis of transcription factor binding and histone modifications. Methods Mol Biol 2015; 1288:447-72. [PMID: 25827896 DOI: 10.1007/978-1-4939-2474-5_26] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Deregulation of transcriptional activity of many genes has been causatively linked to human diseases including cancer. Altered patterns of gene expression in normal and cancer cells are the result of inappropriate expression of transcription factors and chromatin modifying proteins. Chromatin immunoprecipitation assay is a well-established tool for investigating the interactions between regulatory proteins and DNA at distinct stages of gene activation. ChIP coupled with DNA microarrays, known as ChIP on chip, or sequencing of DNA associated with the factors (ChIP-Seq) allow us to determine the entire spectrum of in vivo DNA binding sites for a given protein. This has been of immense value because ChIP on chip assays and ChIP-Seq experiments can provide a snapshot of the transcriptional regulatory mechanisms on a genome-wide scale. This chapter outlines the general strategies used to carry out ChIP-chip assays to study the differential recruitment of regulatory molecules based on the studies conducted in our lab as well as other published protocols; these can be easily modified to a ChIP-Seq analysis.
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Affiliation(s)
- Smitha Pillai
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
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50
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Hijano AJ, Loscertales IG, Ibáñez SE, Higuera FJ. Periodic emission of droplets from an oscillating electrified meniscus of a low-viscosity, highly conductive liquid. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:013011. [PMID: 25679712 DOI: 10.1103/physreve.91.013011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Indexed: 06/04/2023]
Abstract
The generation of identical droplets of controllable size in the micrometer range is a problem of much interest owing to the numerous technological applications of such droplets. This work reports an investigation of the regime of periodic emission of droplets from an electrified oscillating meniscus of a liquid of low viscosity and high electrical conductivity attached to the end of a capillary tube, which may be used to produce droplets more than ten times smaller than the diameter of the tube. To attain this periodic microdripping regime, termed axial spray mode II by Juraschek and Röllgen [R. Juraschek and F. W. Röllgen, Int. J. Mass Spectrom. 177, 1 (1998)], liquid is continuously supplied through the tube at a given constant flow rate, while a dc voltage is applied between the tube and a nearby counter electrode. The resulting electric field induces a stress at the surface of the liquid that stretches the meniscus until, in certain ranges of voltage and flow rate, it develops a ligament that eventually detaches, forming a single droplet, in a process that repeats itself periodically. While it is being stretched, the ligament develops a conical tip that emits ultrafine droplets, but the total mass emitted is practically contained in the main droplet. In the parametrical domain studied, we find that the process depends on two main dimensionless parameters, the flow rate nondimensionalized with the diameter of the tube and the capillary time, q, and the electric Bond number B(E), which is a nondimensional measure of the square of the applied voltage. The meniscus oscillation frequency made nondimensional with the capillary time, f, is of order unity for very small flow rates and tends to decrease as the inverse of the square root of q for larger values of this parameter. The product of the meniscus mean volume times the oscillation frequency is nearly constant. The characteristic length and width of the liquid ligament immediately before its detachment approximately scale as powers of the flow rate and depend only weakly on the applied voltage. The diameter of the main droplets nondimensionalized with the diameter of the tube satisfies d(d)≈(6/π)(1/3)(q/f)(1/3), from mass conservation, while the electric charge of these droplets is about 1/4 of the Rayleigh charge. At the minimum flow rate compatible with the periodic regimen, the dimensionless diameter of the droplets is smaller than one-tenth, which presents a way to use electrohydrodynamic atomization to generate droplets of highly conducting liquids in the micron-size range, in marked contrast with the cone-jet electrospray whose typical droplet size is in the nanometric regime for these liquids. In contrast with other microdripping regimes where the mass is emitted upon the periodic formation of a narrow capillary jet, the present regime gives one single droplet per oscillation, except for the almost massless fine aerosol emitted in the form of an electrospray.
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Affiliation(s)
- A J Hijano
- Andalucía Tech, Escuela Técnica Superior de Ingeniería Industrial, Universidad de Málaga, 29071 Málaga, Spain
| | - I G Loscertales
- Andalucía Tech, Escuela Técnica Superior de Ingeniería Industrial, Universidad de Málaga, 29071 Málaga, Spain
| | - S E Ibáñez
- Escuela Técnica Superior de Ingenieros Aeronáuticos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - F J Higuera
- Escuela Técnica Superior de Ingenieros Aeronáuticos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
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