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Article ; Online: Copper signaling in the brain and beyond.

Ackerman, Cheri M / Chang, Christopher J

2017 Volume 293, Issue 13, Page(s) 4628–4635

Abstract: Transition metals have been recognized and studied primarily in the context of their essential roles as structural and metabolic cofactors for biomolecules that compose living systems. More recently, an emerging paradigm of transition-metal signaling, ... ...

Abstract	Transition metals have been recognized and studied primarily in the context of their essential roles as structural and metabolic cofactors for biomolecules that compose living systems. More recently, an emerging paradigm of transition-metal signaling, where dynamic changes in transitional metal pools can modulate protein function, cell fate, and organism health and disease, has broadened our view of the potential contributions of these essential nutrients in biology. Using copper as a canonical example of transition-metal signaling, we highlight key experiments where direct measurement and/or visualization of dynamic copper pools, in combination with biochemical, physiological, and behavioral studies, have deciphered sources, targets, and physiological effects of copper signals.
MeSH term(s)	Animals ; Brain/metabolism ; Copper/metabolism ; Humans ; Signal Transduction/physiology
Chemical Substances	Copper (789U1901C5)
Language	English
Publishing date	2017-10-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.R117.000176
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Article ; Online: Random access DNA memory using Boolean search in an archival file storage system.

Banal, James L / Shepherd, Tyson R / Berleant, Joseph / Huang, Hellen / Reyes, Miguel / Ackerman, Cheri M / Blainey, Paul C / Bathe, Mark

Nature materials

2021 Volume 20, Issue 9, Page(s) 1272–1280

Abstract: DNA is an ultrahigh-density storage medium that could meet exponentially growing worldwide demand for archival data storage if DNA synthesis costs declined sufficiently and if random access of files within exabyte-to-yottabyte-scale DNA data pools were ... ...

Abstract	DNA is an ultrahigh-density storage medium that could meet exponentially growing worldwide demand for archival data storage if DNA synthesis costs declined sufficiently and if random access of files within exabyte-to-yottabyte-scale DNA data pools were feasible. Here, we demonstrate a path to overcome the second barrier by encapsulating data-encoding DNA file sequences within impervious silica capsules that are surface labelled with single-stranded DNA barcodes. Barcodes are chosen to represent file metadata, enabling selection of sets of files with Boolean logic directly, without use of amplification. We demonstrate random access of image files from a prototypical 2-kilobyte image database using fluorescence sorting with selection sensitivity of one in 10
MeSH term(s)	Archives ; DNA/chemistry ; Fluorescence ; Information Storage and Retrieval ; Plasmids ; Polymerase Chain Reaction ; Silicon Dioxide/chemistry ; Synthetic Biology
Chemical Substances	Silicon Dioxide (7631-86-9) ; DNA (9007-49-2)
Language	English
Publishing date	2021-06-10
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2088679-2
ISSN	1476-4660 ; 1476-1122
ISSN (online)	1476-4660
ISSN	1476-1122
DOI	10.1038/s41563-021-01021-3
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Article ; Online: Analytical Methods for Imaging Metals in Biology: From Transition Metal Metabolism to Transition Metal Signaling.

Ackerman, Cheri M / Lee, Sumin / Chang, Christopher J

Analytical chemistry

2016 Volume 89, Issue 1, Page(s) 22–41

MeSH term(s)	Animals ; Humans ; Molecular Imaging/methods ; Signal Transduction ; Transition Elements/metabolism
Chemical Substances	Transition Elements
Language	English
Publishing date	2016-12-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.6b04631
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Article ; Online: Multiplexed detection of bacterial nucleic acids using Cas13 in droplet microarrays.

Thakku, Sri Gowtham / Ackerman, Cheri M / Myhrvold, Cameron / Bhattacharyya, Roby P / Livny, Jonathan / Ma, Peijun / Gomez, Giselle Isabella / Sabeti, Pardis C / Blainey, Paul C / Hung, Deborah T

PNAS nexus

2022 Volume 1, Issue 1, Page(s) pgac021

Abstract: Rapid and accurate diagnosis of infections is fundamental to individual patient care and public health management. Nucleic acid detection methods are critical to this effort, but are limited either in the breadth of pathogens targeted or by the expertise ...

Abstract	Rapid and accurate diagnosis of infections is fundamental to individual patient care and public health management. Nucleic acid detection methods are critical to this effort, but are limited either in the breadth of pathogens targeted or by the expertise and infrastructure required. We present here a high-throughput system that enables rapid identification of bacterial pathogens, bCARMEN, which utilizes: (1) modular CRISPR-Cas13-based nucleic acid detection with enhanced sensitivity and specificity; and (2) a droplet microfluidic system that enables thousands of simultaneous, spatially multiplexed detection reactions at nanoliter volumes; and (3) a novel preamplification strategy that further enhances sensitivity and specificity. We demonstrate bCARMEN is capable of detecting and discriminating 52 clinically relevant bacterial species and several key antibiotic resistance genes. We further develop a simple proof of principle workflow using stabilized reagents and cell phone camera optical readout, opening up the possibility of a rapid point-of-care multiplexed bacterial pathogen identification and antibiotic susceptibility testing.
Language	English
Publishing date	2022-04-15
Publishing country	England
Document type	Journal Article
ISSN	2752-6542
ISSN (online)	2752-6542
DOI	10.1093/pnasnexus/pgac021
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Article ; Online: Nucleocytoplasmic shuttling of galectin-3.

Arnoys, Eric J / Ackerman, Cheri M / Wang, John L

Methods in molecular biology (Clifton, N.J.)

2015 Volume 1207, Page(s) 465–483

Abstract: A large number of observations on the nuclear versus cytoplasmic distribution of galectin-3 have been reported, correlating the presence or absence of the protein in a particular compartment of the cell to various parameters such as source of the cells ... ...

Abstract	A large number of observations on the nuclear versus cytoplasmic distribution of galectin-3 have been reported, correlating the presence or absence of the protein in a particular compartment of the cell to various parameters such as source of the cells under study, specific cell type, culture conditions, proliferation status of the cell/culture, or neoplastic transformation. In fact, galectin-3 exhibits the phenomenon of nucleocytoplasmic shuttling, defined as the repeated bidirectional movement of a protein across the nuclear pore complex. Nevertheless, the finding that galectin-3 can show a predominantly nuclear localization under one set of conditions and a prominent cytoplasmic localization under other conditions suggests specific and regulated mechanisms of balance between cytoplasmic anchorage, nuclear import, nuclear retention, and nuclear export. One key consideration in the understanding of these processes is the definition of the signals and receptors that mediate the transport. In this chapter, we describe the experimental procedures that have allowed us to document the phenomenon of nucleocytoplasmic shuttling and the identification of the nuclear localization signal as well as the nuclear export signal.
MeSH term(s)	Active Transport, Cell Nucleus ; Animals ; Cell Fusion ; Cell Nucleus/metabolism ; Cytoplasm/metabolism ; Galectin 3/genetics ; Galectin 3/metabolism ; Humans ; Mice ; Microscopy, Fluorescence ; NIH 3T3 Cells ; Polyethylene Glycols/pharmacology ; Transfection
Chemical Substances	Galectin 3 ; Polyethylene Glycols (30IQX730WE)
Language	English
Publishing date	2015
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-1396-1_30
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Article ; Online: Designing sensitive viral diagnostics with machine learning.

Metsky, Hayden C / Welch, Nicole L / Pillai, Priya P / Haradhvala, Nicholas J / Rumker, Laurie / Mantena, Sreekar / Zhang, Yibin B / Yang, David K / Ackerman, Cheri M / Weller, Juliane / Blainey, Paul C / Myhrvold, Cameron / Mitzenmacher, Michael / Sabeti, Pardis C

Nature biotechnology

2022 Volume 40, Issue 7, Page(s) 1123–1131

Abstract: Design of nucleic acid-based viral diagnostics typically follows heuristic rules and, to contend with viral variation, focuses on a genome's conserved regions. A design process could, instead, directly optimize diagnostic effectiveness using a learned ... ...

Abstract	Design of nucleic acid-based viral diagnostics typically follows heuristic rules and, to contend with viral variation, focuses on a genome's conserved regions. A design process could, instead, directly optimize diagnostic effectiveness using a learned model of sensitivity for targets and their variants. Toward that goal, we screen 19,209 diagnostic-target pairs, concentrated on CRISPR-based diagnostics, and train a deep neural network to accurately predict diagnostic readout. We join this model with combinatorial optimization to maximize sensitivity over the full spectrum of a virus's genomic variation. We introduce Activity-informed Design with All-inclusive Patrolling of Targets (ADAPT), a system for automated design, and use it to design diagnostics for 1,933 vertebrate-infecting viral species within 2 hours for most species and within 24 hours for all but three. We experimentally show that ADAPT's designs are sensitive and specific to the lineage level and permit lower limits of detection, across a virus's variation, than the outputs of standard design techniques. Our strategy could facilitate a proactive resource of assays for detecting pathogens.
MeSH term(s)	Machine Learning ; Neural Networks, Computer ; Nucleic Acids
Chemical Substances	Nucleic Acids
Language	English
Publishing date	2022-03-03
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-022-01213-5
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Zs.A 2167: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Tuning the Color Palette of Fluorescent Copper Sensors through Systematic Heteroatom Substitution at Rhodol Cores.

Jia, Shang / Ramos-Torres, Karla M / Kolemen, Safacan / Ackerman, Cheri M / Chang, Christopher J

ACS chemical biology

2017 Volume 13, Issue 7, Page(s) 1844–1852

Abstract: Copper is an essential nutrient for sustaining life, and emerging data have expanded the roles of this metal in biology from its canonical functions as a static enzyme cofactor to dynamic functions as a transition metal signal. At the same time, loosely ... ...

Abstract	Copper is an essential nutrient for sustaining life, and emerging data have expanded the roles of this metal in biology from its canonical functions as a static enzyme cofactor to dynamic functions as a transition metal signal. At the same time, loosely bound, labile copper pools can trigger oxidative stress and damaging events that are detrimental if misregulated. The signal/stress dichotomy of copper motivates the development of new chemical tools to study its spatial and temporal distributions in native biological contexts such as living cells. Here, we report a family of fluorescent copper sensors built upon carbon-, silicon-, and phosphorus-substituted rhodol dyes that enable systematic tuning of excitation/emission colors from orange to near-infrared. These probes can detect changes in labile copper levels in living cells upon copper supplementation and/or depletion. We demonstrate the ability of the carbon-rhodol based congener, Copper Carbo Fluor 1 (CCF1), to identify elevations in labile copper pools in the Atp7a
MeSH term(s)	Animals ; Color ; Copper/metabolism ; Drug Design ; Fluorescence ; Fluorescent Dyes/chemical synthesis ; Fluorescent Dyes/chemistry ; HEK293 Cells ; Heterocyclic Compounds, 3-Ring/chemical synthesis ; Heterocyclic Compounds, 3-Ring/chemistry ; Humans ; Mice ; Microscopy, Confocal/methods ; Microscopy, Fluorescence/methods ; Molecular Structure
Chemical Substances	Fluorescent Dyes ; Heterocyclic Compounds, 3-Ring ; Copper (789U1901C5)
Language	English
Publishing date	2017-11-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1554-8937
ISSN (online)	1554-8937
DOI	10.1021/acschembio.7b00748
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Article ; Online: Multimodal LA-ICP-MS and nanoSIMS imaging enables copper mapping within photoreceptor megamitochondria in a zebrafish model of Menkes disease.

Ackerman, Cheri M / Weber, Peter K / Xiao, Tong / Thai, Bao / Kuo, Tiffani J / Zhang, Emily / Pett-Ridge, Jennifer / Chang, Christopher J

Metallomics : integrated biometal science

2018 Volume 10, Issue 3, Page(s) 474–485

Abstract: Copper is essential for eukaryotic life, and animals must acquire this nutrient through the diet and distribute it to cells and organelles for proper function of biological targets. Indeed, mutations in the central copper exporter ATP7A contribute to a ... ...

Abstract	Copper is essential for eukaryotic life, and animals must acquire this nutrient through the diet and distribute it to cells and organelles for proper function of biological targets. Indeed, mutations in the central copper exporter ATP7A contribute to a spectrum of diseases, including Menkes disease, with symptoms ranging from neurodegeneration to lax connective tissue. As such, a better understanding of the fundamental impacts of ATP7A mutations on in vivo copper distributions is of relevance to those affected by these diseases. Here we combine metal imaging and optical imaging techniques at a variety of spatial resolutions to identify tissues and structures with altered copper levels in the Calamity
MeSH term(s)	Animals ; Copper/metabolism ; Copper-transporting ATPases/genetics ; Copper-transporting ATPases/metabolism ; Disease Models, Animal ; Laser Therapy ; Menkes Kinky Hair Syndrome/metabolism ; Menkes Kinky Hair Syndrome/pathology ; Mitochondria/metabolism ; Multimodal Imaging/methods ; Mutation ; Nanotechnology ; Phenotype ; Photoreceptor Cells, Vertebrate/metabolism ; Photoreceptor Cells, Vertebrate/pathology ; Spectrometry, Mass, Electrospray Ionization ; Spectrometry, Mass, Secondary Ion ; Zebrafish/growth & development ; Zebrafish/metabolism
Chemical Substances	Copper (789U1901C5) ; Copper-transporting ATPases (EC 3.6.3.54)
Language	English
Publishing date	2018-03-06
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2474317-3
ISSN	1756-591X ; 1756-5901
ISSN (online)	1756-591X
ISSN	1756-5901
DOI	10.1039/c7mt00349h
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Article ; Online: Author Correction: Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants.

Welch, Nicole L / Zhu, Meilin / Hua, Catherine / Weller, Juliane / Mirhashemi, Marzieh Ezzaty / Nguyen, Tien G / Mantena, Sreekar / Bauer, Matthew R / Shaw, Bennett M / Ackerman, Cheri M / Thakku, Sri Gowtham / Tse, Megan W / Kehe, Jared / Uwera, Marie-Martine / Eversley, Jacqueline S / Bielwaski, Derek A / McGrath, Graham / Braidt, Joseph / Johnson, Jeremy /

Cerrato, Felecia / Moreno, Gage K / Krasilnikova, Lydia A / Petros, Brittany A / Gionet, Gabrielle L / King, Ewa / Huard, Richard C / Jalbert, Samantha K / Cleary, Michael L / Fitzgerald, Nicholas A / Gabriel, Stacey B / Gallagher, Glen R / Smole, Sandra C / Madoff, Lawrence C / Brown, Catherine M / Keller, Matthew W / Wilson, Malania M / Kirby, Marie K / Barnes, John R / Park, Daniel J / Siddle, Katherine J / Happi, Christian T / Hung, Deborah T / Springer, Michael / MacInnis, Bronwyn L / Lemieux, Jacob E / Rosenberg, Eric / Branda, John A / Blainey, Paul C / Sabeti, Pardis C / Myhrvold, Cameron

Nature medicine

2023 Volume 30, Issue 1, Page(s) 307

Language	English
Publishing date	2023-11-09
Publishing country	United States
Document type	Published Erratum
ZDB-ID	1220066-9
ISSN	1546-170X ; 1078-8956
ISSN (online)	1546-170X
ISSN	1078-8956
DOI	10.1038/s41591-023-02684-y
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Zs.A 4212: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 39: Show issues

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Article ; Online: Massively parallel screening of synthetic microbial communities.

Kehe, Jared / Kulesa, Anthony / Ortiz, Anthony / Ackerman, Cheri M / Thakku, Sri Gowtham / Sellers, Daniel / Kuehn, Seppe / Gore, Jeff / Friedman, Jonathan / Blainey, Paul C

Proceedings of the National Academy of Sciences of the United States of America

2019 Volume 116, Issue 26, Page(s) 12804–12809

Abstract: Microbial communities have numerous potential applications in biotechnology, agriculture, and medicine. Nevertheless, the limited accuracy with which we can predict interspecies interactions and environmental dependencies hinders efforts to rationally ... ...

Abstract	Microbial communities have numerous potential applications in biotechnology, agriculture, and medicine. Nevertheless, the limited accuracy with which we can predict interspecies interactions and environmental dependencies hinders efforts to rationally engineer beneficial consortia. Empirical screening is a complementary approach wherein synthetic communities are combinatorially constructed and assayed in high throughput. However, assembling many combinations of microbes is logistically complex and difficult to achieve on a timescale commensurate with microbial growth. Here, we introduce the kChip, a droplets-based platform that performs rapid, massively parallel, bottom-up construction and screening of synthetic microbial communities. We first show that the kChip enables phenotypic characterization of microbes across environmental conditions. Next, in a screen of ∼100,000 multispecies communities comprising up to 19 soil isolates, we identified sets that promote the growth of the model plant symbiont
MeSH term(s)	Bacteria/isolation & purification ; Bacteriological Techniques/methods ; High-Throughput Screening Assays/methods ; Microbial Consortia ; Microbial Interactions ; Microfluidics/methods ; Soil Microbiology
Language	English
Publishing date	2019-06-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1900102116
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