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Narayanaswamy N, Chakraborty K, Saminathan A, Zeichner E, Leung K, Devany J, Krishnan Y. A pH-correctable, DNA-based fluorescent reporter for organellar calcium. Nat Methods 2018; 16:95-102. [PMID: 30532082 DOI: 10.1038/s41592-018-0232-7] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/30/2018] [Indexed: 01/01/2023]
Abstract
It is extremely challenging to quantitate lumenal Ca2+ in acidic Ca2+ stores of the cell because all Ca2+ indicators are pH sensitive, and Ca2+ transport is coupled to pH in acidic organelles. We have developed a fluorescent DNA-based reporter, CalipHluor, that is targetable to specific organelles. By ratiometrically reporting lumenal pH and Ca2+ simultaneously, CalipHluor functions as a pH-correctable Ca2+ reporter. By targeting CalipHluor to the endolysosomal pathway, we mapped lumenal Ca2+ changes during endosomal maturation and found a surge in lumenal Ca2+ specifically in lysosomes. Using lysosomal proteomics and genetic analysis, we found that catp-6, a Caenorhabditis elegans homolog of ATP13A2, was responsible for lysosomal Ca2+ accumulation-an example of a lysosome-specific Ca2+ importer in animals. By enabling the facile quantification of compartmentalized Ca2+, CalipHluor can expand the understanding of subcellular Ca2+ importers.
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Affiliation(s)
- Nagarjun Narayanaswamy
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA
| | - Kasturi Chakraborty
- Department of Chemistry, The University of Chicago, Chicago, IL, USA. .,Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA.
| | - Anand Saminathan
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA
| | | | - KaHo Leung
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA
| | - John Devany
- Department of Physics, The University of Chicago, Chicago, IL, USA
| | - Yamuna Krishnan
- Department of Chemistry, The University of Chicago, Chicago, IL, USA. .,Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA.
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KIKUCHI T, KARIM N, MASUYA H, OTA Y, KUBONO T. An inexpensive high-throughput method to extract high yields of good quality DNA from fungi. Mol Ecol Resour 2009; 9:41-5. [DOI: 10.1111/j.1755-0998.2008.02184.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Reddy PS, Nair S, Mallikarjuna G, Kaul T, Markandeya G, Sopory SK, Reddy MK. A high-throughput, low-cost method for the preparation of "sequencing-ready" phage DNA template. Anal Biochem 2008; 376:258-61. [PMID: 18334224 DOI: 10.1016/j.ab.2008.02.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2008] [Revised: 02/16/2008] [Accepted: 02/19/2008] [Indexed: 10/22/2022]
Abstract
We have developed a simple and efficient protocol for the isolation of good-quality recombinant phage DNA useful for all downstream processing, including automated sequencing. The overnight-grown phage particles were effectively precipitated (without any contaminating Escherichia coli DNA and other culture media components) by adjusting the pH of the culture medium to 5.2 with sodium acetate, followed by addition of ethanol to 25%. The phage DNA was selectively precipitated with ethanol in the presence of guanidinium thiocyanate under alkaline pH, resulting in uniform quality and quantity of phage DNA. The quality of the phage DNA preparation was demonstrated by DNA sequencing that provided an average read length of >700 bases (PHRED20 quality). This protocol for plating, picking, growing, and subsequent DNA purification of individual phage clones can be completely automated using any standard robotic platform. This protocol does not require any commercial kits and can be completed within 2h.
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Affiliation(s)
- Palakolanu Sudhakar Reddy
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110 067, India
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Kessler MM, Willins DA, Zeng Q, Del Mastro RG, Cook R, Doucette-Stamm L, Lee H, Caron A, McClanahan TK, Wang L, Greene J, Hare RS, Cottarel G, Shimer GH. The use of direct cDNA selection to rapidly and effectively identify genes in the fungus Aspergillus fumigatus. Fungal Genet Biol 2002; 36:59-70. [PMID: 12051895 DOI: 10.1016/s1087-1845(02)00002-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Aspergillus fumigatus is one of the causes of invasive lung disease in immunocompromised individuals. To rapidly identify genes in this fungus, including potential targets for chemotherapy, diagnostics, and vaccine development, we constructed cDNA libraries. We began with non-normalized libraries, then to improve this approach we constructed a normalized cDNA library using direct cDNA selection. Normalization resulted in a reduction of the frequency of clones with highly expressed genes and an enrichment of underrepresented cDNAs. Expressed sequence tags generated from both the original and the normalized libraries were compared with the genomes of Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Candida albicans, indicating that a large proportion of A. fumigatus genes do not have orthologs in these fungal species. This method allowed the expeditious identification of genes in a fungal pathogen. The same approach can be applied to other human or plant pathogens to rapidly identify genes without the need for genomic sequence information.
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Dederich DA, Okwuonu G, Garner T, Denn A, Sutton A, Escotto M, Martindale A, Delgado O, Muzny DM, Gibbs RA, Metzker ML. Glass bead purification of plasmid template DNA for high throughput sequencing of mammalian genomes. Nucleic Acids Res 2002; 30:e32. [PMID: 11917038 PMCID: PMC101856 DOI: 10.1093/nar/30.7.e32] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To meet the new challenge of generating the draft sequences of mammalian genomes, we describe the development of a novel high throughput 96-well method for the purification of plasmid DNA template using size-fractionated, acid-washed glass beads. Unlike most previously described approaches, the current method has been designed and optimized to facilitate the direct binding of alcohol-precipitated plasmid DNA to glass beads from alkaline lysed bacterial cells containing the insoluble cellular aggregate material. Eliminating the tedious step of separating the cleared lysate significantly simplifies the method and improves throughput and reliability. During a 4 month period of 96-capillary DNA sequencing of the Rattus norvegicus genome at the Baylor College of Medicine Human Genome Sequencing Center, the average success rate and read length derived from >1 800 000 plasmid DNA templates prepared by the direct lysis/glass bead method were 82.2% and 516 bases, respectively. The cost of this direct lysis/glass bead method in September 2001 was approximately 10 cents per clone, which is a significant cost saving in high throughput genomic sequencing efforts.
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Affiliation(s)
- Debra A Dederich
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Alkek Building, N1409, Houston, TX 77030, USA
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Mitnik L, Novotny M, Felten C, Buonocore S, Koutny L, Schmalzing D. Recent advances in DNA sequencing by capillary and microdevice electrophoresis. Electrophoresis 2001; 22:4104-17. [PMID: 11824631 DOI: 10.1002/1522-2683(200111)22:19<4104::aid-elps4104>3.0.co;2-f] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A number of significant improvements in the electrophoretic performance and design of DNA sequencing devices have culminated in the introduction of truly industrial grade production scale instruments. These instruments have been the workhorses behind the massive increase in genomic sequencing data available in public and private databases. We highlight the recent progress in aspects of capillary electrophoresis (CE) that has enabled these achievements. In addition, we summarize recent developments in the use of microfabricated devices for DNA sequencing that promise to bring the next leap in productivity.
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Affiliation(s)
- L Mitnik
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
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Smith JH, Madan D, Salhaney J, Engelstein M. Automation and robotics for genetic analysis. CURRENT PROTOCOLS IN HUMAN GENETICS 2001; Appendix 2:Appendix 2E. [PMID: 18428218 DOI: 10.1002/0471142905.hga02es21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
This guide to laboratory robotics covers a wide variety of methods amenable to automation including mapping, genotyping, barcoding and data handling, template preparation, reaction setup, colony and plaque picking, and more.
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Affiliation(s)
- J H Smith
- Genomic Profiling Systems, Cambridge, Massachusetts, USA
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