1
|
Imae R, Manya H, Tsumoto H, Umezawa K, Miura Y, Endo T. Changes in the amount of nucleotide sugars in aged mouse tissues. Glycobiology 2024; 34:cwae032. [PMID: 38598324 DOI: 10.1093/glycob/cwae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/03/2024] [Accepted: 04/08/2024] [Indexed: 04/12/2024] Open
Abstract
Aging affects tissue glycan profiles, which may alter cellular functions and increase the risk of age-related diseases. Glycans are biosynthesized by glycosyltransferases using the corresponding nucleotide sugar, and the availability of nucleotide sugars affects glycosylation efficiency. However, the effects of aging on nucleotide sugar profiles and contents are yet to be elucidated. Therefore, this study aimed to investigate the effects of aging on nucleotide sugars using a new LC-MS/MS method. Specifically, the new method was used to determine the nucleotide sugar contents of various tissues (brain, liver, heart, skeletal muscle, kidney, lung, and colon) of male C57BL/6NCr mice (7- or 26-month-old). Characteristic age-associated nucleotide sugar changes were observed in each tissue sample. Particularly, there was a significant decrease in UDP-glucuronic acid content in the kidney of aged mice and a decrease in the contents of several nucleotide sugars, including UDP-N-acetylgalactosamine, in the brain of aged mice. Additionally, there were variations in nucleotide sugar profiles among the tissues examined regardless of the age. The kidneys had the highest concentration of UDP-glucuronic acid among the seven tissues. In contrast, the skeletal muscle had the lowest concentration of total nucleotide sugars among the tissues; however, CMP-N-acetylneuraminic acid and CDP-ribitol were relatively enriched. Conclusively, these findings may contribute to the understanding of the roles of glycans in tissue aging.
Collapse
Affiliation(s)
- Rieko Imae
- Molecular Glycobiology, Research Team for Mechanism of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Hiroshi Manya
- Molecular Glycobiology, Research Team for Mechanism of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Hiroki Tsumoto
- Proteome Research, Research Team for Mechanism of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Keitaro Umezawa
- Proteome Research, Research Team for Mechanism of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Yuri Miura
- Proteome Research, Research Team for Mechanism of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Tamao Endo
- Molecular Glycobiology, Research Team for Mechanism of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan
| |
Collapse
|
2
|
Lai L, Zhang M, Liu C, Qu J, Xu D, Jiang Z. A comprehensive evaluation of a polymeric zwitterionic hydrophilic monolith for nucleotide separation. ANAL SCI 2024; 40:85-91. [PMID: 37843729 DOI: 10.1007/s44211-023-00430-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023]
Abstract
Rapid and effective separation of nucleotides (NTs) and their derivatives is crucial for studying their physiological functions. In this work, we comprehensively evaluated the separation ability of a zwitterionic hydrophilic monolith, i.e., poly(N,N-dimethyl-N-(3-methacrylamidopropyl)-N-(3-sulfopropyl)ammonium betaine-co-N,N'-methylenebisacrylamide) (poly(SPP-co-MBA)) for NTs analysis, including its selectivity, chemical stability under extremely basic condition and compatibility with hydrophilic interaction liquid chromatography (HILIC) coupled with mass spectrometry (HILIC-MS). The poly(SPP-co-MBA) monolith exhibited excellent chemical stability, as evidenced by the low relative standard deviation of retention time (0.16-1.05%) after 4000 consecutive injections over one month under strong alkaline elution condition (pH 10). After optimizing the separation conditions, including buffer pH and concentration, organic solvent content and column temperature, four nucleoside triphosphates, five nucleoside diphosphates and five nucleoside monophosphates were baseline separated within 7 min. Additionally, the mixtures containing one nucleoside and its corresponding mono-, di-, and triphosphates were baseline separated within only 3 min, respectively. It is good HILIC-MS compatibility was also confirmed by the satisfactory peak shape and high response of nine NTs. Overall, the proposed poly(SPP-co-MBA) monolith exhibited good mechanical stability and compatibility of HILIC-MS, making it a promising technique for NTs analysis.
Collapse
Affiliation(s)
- Liang Lai
- Institute of Pharmaceutical Analysis, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou, 510632, China
| | - Mengyun Zhang
- Institute of Pharmaceutical Analysis, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou, 510632, China
| | - Chusheng Liu
- Institute of Pharmaceutical Analysis, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou, 510632, China
- Department of Clinical Laboratory, The Third People's Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, National Clinical Research Center for Infectious Diseases, Shenzhen, 518114, China
| | - Jiahuan Qu
- Institute of Pharmaceutical Analysis, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou, 510632, China
| | - Dongsheng Xu
- Institute of Pharmaceutical Analysis, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou, 510632, China.
| | - Zhengjin Jiang
- Institute of Pharmaceutical Analysis, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou, 510632, China.
| |
Collapse
|
3
|
Vignon M, Bastide A, Attina A, David A, Bousquet P, Orti V, Vialaret J, Lehmann S, Periere DD, Hirtz C. Multiplexed LC-MS/MS quantification of salivary RNA modifications in periodontitis. J Periodontal Res 2023; 58:959-967. [PMID: 37349891 DOI: 10.1111/jre.13155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/24/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023]
Abstract
OBJECTIVE To analyse the salivary epitranscriptomic profiles as periodontitis biomarkers using multiplexed mass spectrometry (MS). BACKGROUND The field of epitranscriptomics, which relates to RNA chemical modifications, opens new perspectives in the discovery of diagnostic biomarkers, especially in periodontitis. Recently, the modified ribonucleoside N6-methyladenosine (m6A) was revealed as a crucial player in the etiopathogenesis of periodontitis. However, no epitranscriptomic biomarker has been identified in saliva to date. MATERIALS AND METHODS Twenty-four saliva samples were collected from periodontitis patients (n = 16) and from control subjects (n = 8). Periodontitis patients were stratified according to stage and grade. Salivary nucleosides were directly extracted and, in parallel, salivary RNA was digested into its constituent nucleosides. Nucleoside samples were then quantified by multiplexed MS. RESULTS Twenty-seven free nucleosides were detected and an overlapping set of 12 nucleotides were detected in digested RNA. Among the free nucleosides, cytidine and three other modified nucleosides (inosine, queuosine and m6Am) were significantly altered in periodontitis patients. In digested RNA, only uridine was significantly higher in periodontitis patients. Importantly there was no correlation between free salivary nucleoside levels and the levels of those same nucleotides in digested salivary RNA, except for cytidine, m5C and uridine. This statement implies that the two detection methods are complementary. CONCLUSION The high specificity and sensitivity of MS allowed the detection and quantification of multiple nucleosides from RNA and free nucleosides in saliva. Some ribonucleosides appear to be promising biomarkers of periodontitis. Our analytic pipeline opens new perspectives for diagnostic periodontitis biomarkers.
Collapse
Affiliation(s)
- Margaux Vignon
- Department of Periodontology, Dental Faculty, University of Montpellier, Montpellier, France
- INM, University of Montpellier, INSERM, Montpellier, France
- LBPC-PPC, University of Montpellier, CHU Montpellier, INM INSERM, Montpellier, France
| | | | - Aurore Attina
- LBPC-PPC, University of Montpellier, CHU Montpellier, INM INSERM, Montpellier, France
| | | | - Philippe Bousquet
- Department of Periodontology, Dental Faculty, University of Montpellier, Montpellier, France
| | - Valérie Orti
- Department of Periodontology, Dental Faculty, University of Montpellier, Montpellier, France
| | - Jérôme Vialaret
- INM, University of Montpellier, INSERM, Montpellier, France
- LBPC-PPC, University of Montpellier, CHU Montpellier, INM INSERM, Montpellier, France
| | - Sylvain Lehmann
- INM, University of Montpellier, INSERM, Montpellier, France
- LBPC-PPC, University of Montpellier, CHU Montpellier, INM INSERM, Montpellier, France
| | | | - Christophe Hirtz
- INM, University of Montpellier, INSERM, Montpellier, France
- LBPC-PPC, University of Montpellier, CHU Montpellier, INM INSERM, Montpellier, France
| |
Collapse
|
4
|
Jena MK, Pathak B. Development of an Artificially Intelligent Nanopore for High-Throughput DNA Sequencing with a Machine-Learning-Aided Quantum-Tunneling Approach. Nano Lett 2023; 23:2511-2521. [PMID: 36799480 DOI: 10.1021/acs.nanolett.2c04062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Solid-state nanopore-based single-molecule DNA sequencing with quantum tunneling technology poses formidable challenges to achieve long-read sequencing and high-throughput analysis. Here, we propose a method for developing an artificially intelligent (AI) nanopore that does not require extraction of the signature transmission function for each nucleotide of the whole DNA strand by integrating supervised machine learning (ML) and transverse quantum transport technology with a graphene nanopore. The optimized ML model can predict the transmission function of all other nucleotides after training with data sets of all the orientations of any nucleotide inside the nanopore with a root-mean-square error (RMSE) of as low as 0.062. Further, up to 96.01% accuracy is achieved in classifying the unlabeled nucleotides with their transmission readouts. We envision that an AI nanopore can alleviate the experimental challenges of the quantum-tunneling method and pave the way for rapid and high-precision DNA sequencing by predicting their signature transmission functions.
Collapse
Affiliation(s)
- Milan Kumar Jena
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh 453552, India
| | - Biswarup Pathak
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh 453552, India
| |
Collapse
|
5
|
Farmer VJ, Zanic M. Beyond the GTP-cap: Elucidating the molecular mechanisms of microtubule catastrophe. Bioessays 2023; 45:e2200081. [PMID: 36398561 PMCID: PMC10648283 DOI: 10.1002/bies.202200081] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022]
Abstract
Almost 40 years since the discovery of microtubule dynamic instability, the molecular mechanisms underlying microtubule dynamics remain an area of intense research interest. The "standard model" of microtubule dynamics implicates a "cap" of GTP-bound tubulin dimers at the growing microtubule end as the main determinant of microtubule stability. Loss of the GTP-cap leads to microtubule "catastrophe," a switch-like transition from microtubule growth to shrinkage. However, recent studies, using biochemical in vitro reconstitution, cryo-EM, and computational modeling approaches, challenge the simple GTP-cap model. Instead, a new perspective on the mechanisms of microtubule dynamics is emerging. In this view, highly dynamic transitions between different structural conformations of the growing microtubule end - which may or may not be directly linked to the nucleotide content at the microtubule end - ultimately drive microtubule catastrophe.
Collapse
Affiliation(s)
- Veronica J. Farmer
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Marija Zanic
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biomolecular and Chemical Engineering, Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| |
Collapse
|
6
|
Shen B, Zhang Z, Shi Q, Du J, Xue Q, Li X. Active compound analysis of Ziziphus jujuba cv. Jinsixiaozao in different developmental stages using metabolomic and transcriptomic approaches. Plant Physiol Biochem 2022; 189:14-23. [PMID: 36030619 DOI: 10.1016/j.plaphy.2022.08.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/22/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Jujube (Ziziphus jujuba Mill.) is a popular fruit with health benefits ascribed to its various metabolites. These metabolites determine the flavors and bioactivities of the fruit, as well as their desirability. However, the dynamics of the metabolite composition and the underlying gene expression that modulate the overall flavor and accumulation of active ingredients during fruit development remain largely unknown. Therefore, we conducted an integrated metabolomic and transcriptomic investigation covering various developmental stages in the jujube cultivar Z. jujuba cv. Jinsixiaozao, which is famous for its nutritional and bioactive properties. A total of 407 metabolites were detected by non-targeted metabolomics. Metabolite accumulation during different jujube developmental stages was examined. Most nucleotides and amino acids and their derivatives accumulated during development, with cAMP increasing notably during ripening. Triterpenes gradually accumulated and were maintained at high concentrations during ripening. Many flavonoids were maintained at relatively high levels in early development, but then rapidly decreased later. Transcriptomic and metabolomic analyses revealed that chalcone synthase (CHS), chalcone isomerase (CHI), flavonol synthase (FLS), and dihydroflavonol 4-reductase (DFR) were mainly responsible for regulating the accumulation of flavonoids. Therefore, the extensive downregulation of these genes was probably responsible for the decreases in flavonoid content during fruit ripening. This study provide an overview of changes of active components in 'Jinsixiaozao' during development and ripening. These findings enhance our understanding of flavor formation and will facilitate jujube breeding for improving both nutrition and function.
Collapse
Affiliation(s)
- Bingqi Shen
- College of Forestry, Northwest A&F University, Yangling, 712100, China; Research Center for Jujube Engineering and Technology National Forestry and Grassland Administration, Yangling, 712100, China; Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhong Zhang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116, Guangdong, China
| | - Qianqian Shi
- College of Forestry, Northwest A&F University, Yangling, 712100, China; Research Center for Jujube Engineering and Technology National Forestry and Grassland Administration, Yangling, 712100, China; Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jiangtao Du
- College of Forestry, Northwest A&F University, Yangling, 712100, China; Research Center for Jujube Engineering and Technology National Forestry and Grassland Administration, Yangling, 712100, China; Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qingtun Xue
- Forestry WorkStation of Weinan City, Weinan, 714000, Shaanxi, China
| | - Xingang Li
- College of Forestry, Northwest A&F University, Yangling, 712100, China; Research Center for Jujube Engineering and Technology National Forestry and Grassland Administration, Yangling, 712100, China; Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
7
|
Fan Y, Sun G, Kaw HY, Zhu L, Wang W. Analytical characterization of nucleotides and their concentration variation in drinking water treatment process. Sci Total Environ 2022; 817:152510. [PMID: 34968603 DOI: 10.1016/j.scitotenv.2021.152510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Nucleotides, as the basic building blocks of nucleic acids, widely exist in aqueous environment. In this study, we developed a solid phase extraction-high performance liquid chromatography-tandem mass spectrometry (SPE-UPLC-MS/MS) method for the analysis of 5'-adenosine monophosphate (AMP), 5'-uridine monophosphate (UMP), 5'-cytidine monophosphate (CMP) and 5'-guanosine monophosphate (GMP). The method achieved limits of detection (LODs) of 0.1-1.0 ng/L, and recoveries of 85-95% for the four tested nucleotides. The occurrence and concentrations of the four nucleotides in water from eight representative drinking water treatment and distribution systems in China were determined using this method. All four nucleotides were detectable in water treatment plant (WTP) influent and effluent, at concentrations of up to 30 ng/L and with occurrence frequency of around 90%. The concentrations of identified nucleotides increased 3-10 times after 10 km of water age in the water distribution system. Biological filters and coagulation increased the concentrations of nucleotides, conversely, active carbon, ozonation, and ultrafiltration membrane removed nucleotides in water. The effects of active carbon and coagulation were further confirmed using laboratory-controlled experiment. In addition, monochlorinated nucleotides were identified as the chlorination products of nucleotides.
Collapse
Affiliation(s)
- Yi Fan
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Guangrong Sun
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Han Yeong Kaw
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Lizhong Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Wei Wang
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China.
| |
Collapse
|
8
|
Straube H, Herde M. Purification and Analysis of Nucleotides and Nucleosides from Plants. Methods Mol Biol 2022; 2466:145-155. [PMID: 35585317 DOI: 10.1007/978-1-0716-2176-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This protocol describes necessary steps to isolate and quantify nucleotides and nucleosides from plant samples. Proper sample preparation in combination with liquid chromatography coupled to mass spectrometry enables the sensitive detection and quantification of metabolites of low abundance. Utilizing a liquid-liquid extraction in combination with a weak anion-exchange solid phase extraction enables the separation of negatively charged molecules from uncharged metabolites or cations.
Collapse
Affiliation(s)
- Henryk Straube
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover, Germany
| | - Marco Herde
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover, Germany.
| |
Collapse
|
9
|
Righini M, Costa J, Zhou W. DNA bridges: A novel platform for single-molecule sequencing and other DNA-protein interaction applications. PLoS One 2021; 16:e0260428. [PMID: 34807931 PMCID: PMC8608331 DOI: 10.1371/journal.pone.0260428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 11/10/2021] [Indexed: 01/22/2023] Open
Abstract
DNA molecular combing is a technique that stretches thousands of long individual DNA molecules (up to 10 Mbp) into a parallel configuration on surface. It has previously been proposed to sequence these molecules by synthesis. However, this approach poses two critical challenges: 1-Combed DNA molecules are overstretched and therefore a nonoptimal substrate for polymerase extension. 2-The combing surface sterically impedes full enzymatic access to the DNA backbone. Here, we introduce a novel approach that attaches thousands of molecules to a removable surface, with a tunable stretching factor. Next, we dissolve portions of the surface, leaving the DNA molecules suspended as 'bridges'. We demonstrate that the suspended molecules are enzymatically accessible, and we have used an enzyme to incorporate labeled nucleotides, as predicted by the specific molecular sequence. Our results suggest that this novel platform is a promising candidate to achieve high-throughput sequencing of Mbp-long molecules, which could have additional genomic applications, such as the study of other protein-DNA interactions.
Collapse
Affiliation(s)
- Maurizio Righini
- Department of Advanced Research and Development, Centrillion Technologies, Palo Alto, California, United States of America
| | - Justin Costa
- Department of Advanced Research and Development, Centrillion Technologies, Palo Alto, California, United States of America
| | - Wei Zhou
- Department of Advanced Research and Development, Centrillion Technologies, Palo Alto, California, United States of America
| |
Collapse
|
10
|
Straube H, Witte CP, Herde M. Analysis of Nucleosides and Nucleotides in Plants: An Update on Sample Preparation and LC-MS Techniques. Cells 2021; 10:689. [PMID: 33804650 PMCID: PMC8003640 DOI: 10.3390/cells10030689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Nucleotides fulfill many essential functions in plants. Compared to non-plant systems, these hydrophilic metabolites have not been adequately investigated in plants, especially the less abundant nucleotide species such as deoxyribonucleotides and modified or damaged nucleotides. Until recently, this was mainly due to a lack of adequate methods for in-depth analysis of nucleotides and nucleosides in plants. In this review, we focus on the current state-of-the-art of nucleotide analysis in plants with liquid chromatography coupled to mass spectrometry and describe recent major advances. Tissue disruption, quenching, liquid-liquid and solid-phase extraction, chromatographic strategies, and peculiarities of nucleotides and nucleosides in mass spectrometry are covered. We describe how the different steps of the analytical workflow influence each other, highlight the specific challenges of nucleotide analysis, and outline promising future developments. The metabolite matrix of plants is particularly complex. Therefore, it is likely that nucleotide analysis methods that work for plants can be applied to other organisms as well. Although this review focuses on plants, we also discuss advances in nucleotide analysis from non-plant systems to provide an overview of the analytical techniques available for this challenging class of metabolites.
Collapse
Affiliation(s)
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, 30419 Hannover, Germany;
| | - Marco Herde
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, 30419 Hannover, Germany;
| |
Collapse
|
11
|
Karikari B, Wang Z, Zhou Y, Yan W, Feng J, Zhao T. Identification of quantitative trait nucleotides and candidate genes for soybean seed weight by multiple models of genome-wide association study. BMC Plant Biol 2020; 20:404. [PMID: 32873245 PMCID: PMC7466808 DOI: 10.1186/s12870-020-02604-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/16/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Seed weight is a complex yield-related trait with a lot of quantitative trait loci (QTL) reported through linkage mapping studies. Integration of QTL from linkage mapping into breeding program is challenging due to numerous limitations, therefore, Genome-wide association study (GWAS) provides more precise location of QTL due to higher resolution and diverse genetic diversity in un-related individuals. RESULTS The present study utilized 573 breeding lines population with 61,166 single nucleotide polymorphisms (SNPs) to identify quantitative trait nucleotides (QTNs) and candidate genes for seed weight in Chinese summer-sowing soybean. GWAS was conducted with two single-locus models (SLMs) and six multi-locus models (MLMs). Thirty-nine SNPs were detected by the two SLMs while 209 SNPs were detected by the six MLMs. In all, two hundred and thirty-one QTNs were found to be associated with seed weight in YHSBLP with various effects. Out of these, seventy SNPs were concurrently detected by both SLMs and MLMs on 8 chromosomes. Ninety-four QTNs co-localized with previously reported QTL/QTN by linkage/association mapping studies. A total of 36 candidate genes were predicted. Out of these candidate genes, four hub genes (Glyma06g44510, Glyma08g06420, Glyma12g33280 and Glyma19g28070) were identified by the integration of co-expression network. Among them, three were relatively expressed higher in the high HSW genotypes at R5 stage compared with low HSW genotypes except Glyma12g33280. Our results show that using more models especially MLMs are effective to find important QTNs, and the identified HSW QTNs/genes could be utilized in molecular breeding work for soybean seed weight and yield. CONCLUSION Application of two single-locus plus six multi-locus models of GWAS identified 231 QTNs. Four hub genes (Glyma06g44510, Glyma08g06420, Glyma12g33280 & Glyma19g28070) detected via integration of co-expression network among the predicted candidate genes.
Collapse
Affiliation(s)
- Benjamin Karikari
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Zili Wang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yilan Zhou
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Wenliang Yan
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Jianying Feng
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| | - Tuanjie Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| |
Collapse
|
12
|
Young F, Rogers S, Robertson DL. Predicting host taxonomic information from viral genomes: A comparison of feature representations. PLoS Comput Biol 2020; 16:e1007894. [PMID: 32453718 PMCID: PMC7307784 DOI: 10.1371/journal.pcbi.1007894] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 06/22/2020] [Accepted: 04/21/2020] [Indexed: 12/13/2022] Open
Abstract
The rise in metagenomics has led to an exponential growth in virus discovery. However, the majority of these new virus sequences have no assigned host. Current machine learning approaches to predicting virus host interactions have a tendency to focus on nucleotide features, ignoring other representations of genomic information. Here we investigate the predictive potential of features generated from four different ‘levels’ of viral genome representation: nucleotide, amino acid, amino acid properties and protein domains. This more fully exploits the biological information present in the virus genomes. Over a hundred and eighty binary datasets for infecting versus non-infecting viruses at all taxonomic ranks of both eukaryote and prokaryote hosts were compiled. The viral genomes were converted into the four different levels of genome representation and twenty feature sets were generated by extracting k-mer compositions and predicted protein domains. We trained and tested Support Vector Machine, SVM, classifiers to compare the predictive capacity of each of these feature sets for each dataset. Our results show that all levels of genome representation are consistently predictive of host taxonomy and that prediction k-mer composition improves with increasing k-mer length for all k-mer based features. Using a phylogenetically aware holdout method, we demonstrate that the predictive feature sets contain signals reflecting both the evolutionary relationship between the viruses infecting related hosts, and host-mimicry. Our results demonstrate that incorporating a range of complementary features, generated purely from virus genome sequences, leads to improved accuracy for a range of virus host prediction tasks enabling computational assignment of host taxonomic information. Elucidating the host of a newly identified virus species is an important challenge, with applications from knowing the source species of a newly emerged pathogen to understanding the bacteriophage-host relationships within the microbiome of any of earth’s ecosystems. Current high throughput methods used to identify viruses within biological or environmental samples have resulted in an unprecedented increase in virus discovery. However, for the majority of these virus genomes the host species/taxonomic classification remains unknown. To address this gap in our knowledge there is a need for fast, accurate computational methods for the assignment of putative host taxonomic information. Machine learning is an ideal approach but to maximise predictive accuracy the viral genomes need to be represented in a format (sets of features) that makes the discriminative information available to the machine learning algorithm. Here, we compare different types of features derived from the same viral genomes for their ability to predict host information. Our results demonstrate that all these feature sets are predictive of host taxonomy and when combined have the potential to improve accuracy over the use of individual feature sets across many virus host prediction applications.
Collapse
Affiliation(s)
- Francesca Young
- MRC-University of Glasgow Centre For Virus Research, Glasgow, United Kingdom
| | - Simon Rogers
- School of Computing Science, University of Glasgow, Glasgow, United Kingdom
| | - David L. Robertson
- MRC-University of Glasgow Centre For Virus Research, Glasgow, United Kingdom
- * E-mail:
| |
Collapse
|
13
|
Ismail I, Hwang YH, Joo ST. Low-temperature and long-time heating regimes on non-volatile compound and taste traits of beef assessed by the electronic tongue system. Food Chem 2020; 320:126656. [PMID: 32224424 DOI: 10.1016/j.foodchem.2020.126656] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 03/10/2020] [Accepted: 03/19/2020] [Indexed: 11/20/2022]
Abstract
The influence of temperature-time combinations on non-volatile compound and taste traits of beef semitendinosus muscles tested by the electronic tongue was studied. Single-stage sous-vide at 60 and 70 °C (6 and 12 h), and two-stage sous-vide that sequentially cooked at 45 °C (3 h) and 60 °C (either 3 or 9 h) were compared with traditional cooking at 70 °C (30 min). Umami was better explained in the given model of partial least squares regression than astringency, sourness, saltiness, bitterness, and richness. Sous-vide at 70 °C for 12 h characterized the most umami, likely adenosine-5'-monophosphate (AMP) and guanosine-5'-monophosphate (GMP) as significant contributors. Two-stage sous-vide projected higher histidine, leucine, inosine, and hypoxanthine with the astringent and sour taste significant after 6 and 12 h cooking, respectively. Equivalent umami concentration (EUC) between umami amino acids and umami nucleotides showed a strong relationship to umami taste assessed by the electronic tongue.
Collapse
Affiliation(s)
- Ishamri Ismail
- Division of Applied Life Science (BK21+), Gyeongsang National University, Jinju 52828, South Korea; Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut Campus, Terengganu 22200, Malaysia
| | - Young-Hwa Hwang
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, South Korea
| | - Seon-Tea Joo
- Division of Applied Life Science (BK21+), Gyeongsang National University, Jinju 52828, South Korea; Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, South Korea.
| |
Collapse
|
14
|
Wiegand T, Schledorn M, Malär AA, Cadalbert R, Däpp A, Terradot L, Meier BH, Böckmann A. Nucleotide Binding Modes in a Motor Protein Revealed by 31 P- and 1 H-Detected MAS Solid-State NMR Spectroscopy. Chembiochem 2020; 21:324-330. [PMID: 31310428 PMCID: PMC7318265 DOI: 10.1002/cbic.201900439] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Indexed: 12/16/2022]
Abstract
Protein-nucleic acid interactions play important roles not only in energy-providing reactions, such as ATP hydrolysis, but also in reading, extending, packaging, or repairing genomes. Although they can often be analyzed in detail with X-ray crystallography, complementary methods are needed to visualize them in complexes, which are not crystalline. Here, we show how solid-state NMR spectroscopy can detect and classify protein-nucleic interactions through site-specific 1 H- and 31 P-detected spectroscopic methods. The sensitivity of 1 H chemical-shift values on noncovalent interactions involved in these molecular recognition processes is exploited allowing us to probe directly the chemical bonding state, an information, which is not directly accessible from an X-ray structure. We show that these methods can characterize interactions in easy-to-prepare sediments of the 708 kDa dodecameric DnaB helicase in complex with ADP:AlF4- :DNA, and this despite the very challenging size of the complex.
Collapse
Affiliation(s)
- Thomas Wiegand
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Maarten Schledorn
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Alexander A. Malär
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Riccardo Cadalbert
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Alexander Däpp
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Laurent Terradot
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Beat H. Meier
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural BiochemistryLabex EcofectUMR 5086 CNRS/Université de Lyon7 Passage du vercors69367LyonFrance
| |
Collapse
|
15
|
Goto Y, Matsui K, Yanagi I, Takeda KI. Silicon nitride nanopore created by dielectric breakdown with a divalent cation: deceleration of translocation speed and identification of single nucleotides. Nanoscale 2019; 11:14426-14433. [PMID: 31334729 DOI: 10.1039/c9nr03563j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nanopore DNA sequencing with a solid-state nanopore requires deceleration of the ultrafast translocation speed of single-stranded DNA (ssDNA). We report an unexpected phenomenon: controlled dielectric breakdown (CBD) with a divalent metal cation, especially Ca2+, provides a silicon nitride nanopore with the ability to decelerate ssDNA speed to 100 μs per base even after solution replacement. This speed is two orders of magnitude slower than that for CBD with a conventional monovalent metal cation. Temperature dependence experiments revealed that the enthalpic barrier for a nanopore created via CBD with Ca2+ is 25-30kBT, comparable to that of a biological nanopore. The slowing effect originates from the strong interaction between ssDNA and divalent cations, which were coated on the sidewall of the nanopore during the CBD process. In addition, we found that the nanopore created via CBD with Ca2+ can decelerate the speed of even single-nucleotide monomers, dNMPs, to 0.1-10 ms per base. The four single nucleotides could be statistically identified according to their blockade currents. Our approach is simple and practical because it simultaneously allows nanopore fabrication, ssDNA deceleration and the identification of nucleotide monomers.
Collapse
Affiliation(s)
- Yusuke Goto
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd, 1-280 Higashi-Koigakubo, Kokubunji, Tokyo 185-8601, Japan.
| | | | | | | |
Collapse
|
16
|
He L, Wei X, Ma X, Yin X, Song M, Donninger H, Yaddanapudi K, McClain CJ, Zhang X. Simultaneous Quantification of Nucleosides and Nucleotides from Biological Samples. J Am Soc Mass Spectrom 2019; 30:987-1000. [PMID: 30847833 PMCID: PMC6520184 DOI: 10.1007/s13361-019-02140-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/17/2019] [Accepted: 01/17/2019] [Indexed: 05/16/2023]
Abstract
We report a reverse phase chromatography mass spectrometry (LC-MS) method for simultaneous quantification of nucleosides and nucleotides from biological samples, where compound identification was achieved by a tier-wise approach and compound quantification was achieved via external calibration. A total of 65 authentic standards of nucleosides and nucleotides were used for the platform development. The limit of detection (LOD) of those compounds ranged from 0.05 nmol/L to 1.25 μmol/L, and their limit of quantification (LOQ) ranged from 0.10 nmol/L to 2.50 μmol/L. Using the developed method, nucleosides and nucleotides from human plasma, human urine, and rat liver were quantified. Seventy-nine nucleosides and nucleotides were identified from human urine and 28 of them were quantified with concentrations of 13.0 nmol/L-151 μmol/L. Fifty-five nucleosides and nucleotides were identified from human plasma and 22 of them were quantified with concentrations of 1.21 nmol/L-8.54 μmol/L. Fifty-one nucleosides and nucleotides were identified from rat liver and 23 were quantified with concentrations of 1.03 nmol/L-31.7 μmol/L. These results demonstrate that the developed method can be used to investigate the concentration change of nucleosides and nucleotides in biological samples for the purposes of biomarker discovery or elucidation of disease mechanisms.
Collapse
Affiliation(s)
- Liqing He
- Department of Chemistry, University of Louisville, 2210 South Brook Street, Louisville, KY, 40208, USA.
- Alcohol Research Center, University of Louisville, Louisville, KY, 40208, USA.
- Hepatobiology and Toxicology Program, University of Louisville, Louisville, KY, 40208, USA.
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY, 40208, USA.
| | - Xiaoli Wei
- Department of Chemistry, University of Louisville, 2210 South Brook Street, Louisville, KY, 40208, USA
- Alcohol Research Center, University of Louisville, Louisville, KY, 40208, USA
- Hepatobiology and Toxicology Program, University of Louisville, Louisville, KY, 40208, USA
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY, 40208, USA
| | - Xipeng Ma
- Department of Chemistry, University of Louisville, 2210 South Brook Street, Louisville, KY, 40208, USA
- Alcohol Research Center, University of Louisville, Louisville, KY, 40208, USA
- Hepatobiology and Toxicology Program, University of Louisville, Louisville, KY, 40208, USA
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY, 40208, USA
| | - Xinmin Yin
- Department of Chemistry, University of Louisville, 2210 South Brook Street, Louisville, KY, 40208, USA
- Alcohol Research Center, University of Louisville, Louisville, KY, 40208, USA
- Hepatobiology and Toxicology Program, University of Louisville, Louisville, KY, 40208, USA
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY, 40208, USA
| | - Ming Song
- Alcohol Research Center, University of Louisville, Louisville, KY, 40208, USA
- Hepatobiology and Toxicology Program, University of Louisville, Louisville, KY, 40208, USA
- Department of Medicine, University of Louisville, Louisville, KY, 40208, USA
| | - Howard Donninger
- Department of Medicine, University of Louisville, Louisville, KY, 40208, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, 40208, USA
| | - Kavitha Yaddanapudi
- Department of Medicine, University of Louisville, Louisville, KY, 40208, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, 40208, USA
| | - Craig J McClain
- Alcohol Research Center, University of Louisville, Louisville, KY, 40208, USA
- Hepatobiology and Toxicology Program, University of Louisville, Louisville, KY, 40208, USA
- Department of Medicine, University of Louisville, Louisville, KY, 40208, USA
- Department of Pharmacology & Toxicology, University of Louisville, Louisville, KY, 40208, USA
- Robley Rex Louisville VAMC, Louisville, KY, 40292, USA
| | - Xiang Zhang
- Department of Chemistry, University of Louisville, 2210 South Brook Street, Louisville, KY, 40208, USA
- Alcohol Research Center, University of Louisville, Louisville, KY, 40208, USA
- Hepatobiology and Toxicology Program, University of Louisville, Louisville, KY, 40208, USA
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY, 40208, USA
- Department of Pharmacology & Toxicology, University of Louisville, Louisville, KY, 40208, USA
| |
Collapse
|
17
|
Abstract
Selenium (Se) is an essential trace element because of its presence in selenoproteins in the form of selenocysteine residue. Both Se deficiency, which compromises selenoprotein functions, and excess Se, which is toxic, have been associated with altered redox homeostasis and adverse health conditions. Surprisingly, we found that, although Se deficiency led to a drastic decline in selenoprotein expression, mice subjected to this dietary regimen for their entire life had normal lifespans. To understand the molecular mechanisms involved, we performed systemic analyses at the level of metabolome, transcriptome, and microRNA profiling. These analyses revealed that Se deficiency reduced amino acid levels, elevated mononucleotides, altered metabolism, and activated signaling pathways linked to longevity-related nutrient sensing. The data show that the metabolic control associated with nutrient sensing coordinately responds to suppressed selenoprotein functions, resulting in normal lifespan under Se deficiency.
Collapse
Affiliation(s)
- Sun Hee Yim
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| |
Collapse
|
18
|
Linscheid MW. Molecules and elements for quantitative bioanalysis: The allure of using electrospray, MALDI, and ICP mass spectrometry side-by-side. Mass Spectrom Rev 2019; 38:169-186. [PMID: 29603315 DOI: 10.1002/mas.21567] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 03/12/2018] [Indexed: 06/08/2023]
Abstract
To understand biological processes, not only reliable identification, but quantification of constituents in biological processes play a pivotal role. This is especially true for the proteome: protein quantification must follow protein identification, since sometimes minute changes in abundance tell the real tale. To obtain quantitative data, many sophisticated strategies using electrospray and MALDI mass spectrometry (MS) have been developed in recent years. All of them have advantages and limitations. Several years ago, we started to work on strategies, which are principally capable to overcome some of these limits. The fundamental idea is to use elemental signals as a measure for quantities. We began by replacing the radioactive 32 P with the "cold" natural 31 P to quantify modified nucleotides and phosphorylated peptides and proteins and later used tagging strategies for quantification of proteins more generally. To do this, we introduced Inductively Coupled Plasma Mass Spectrometry (ICP-MS) into the bioanalytical workflows, allowing not only reliable and sensitive detection but also quantification based on isotope dilution absolute measurements using poly-isotopic elements. The detection capability of ICP-MS becomes particularly attractive with heavy metals. The covalently bound proteins tags developed in our group are based on the well-known DOTA chelate complex (1,4,7,10-tetraazacyclododecane-N,N',N″,N‴-tetraacetic acid) carrying ions of lanthanoides as metal core. In this review, I will outline the development of this mutual assistance between molecular and elemental mass spectrometry and discuss the scope and limitations particularly of peptide and protein quantification. The lanthanoide tags provide low detection limits, but offer multiplexing capabilities due to the number of very similar lanthanoides and their isotopes. With isotope dilution comes previously unknown accuracy. Separation techniques such as electrophoresis and HPLC were used and just slightly adapted workflows, already in use for quantification in bioanalysis. Imaging mass spectrometry (MSI) with MALDI and laser ablation ICP-MS complemented the range of application in recent years.
Collapse
MESH Headings
- Animals
- Chelating Agents/chemistry
- Chromatography, High Pressure Liquid/instrumentation
- Chromatography, High Pressure Liquid/methods
- Heterocyclic Compounds, 1-Ring/chemistry
- Humans
- Lanthanoid Series Elements/chemistry
- Nucleotides/analysis
- Proteins/analysis
- Spectrometry, Mass, Electrospray Ionization/instrumentation
- Spectrometry, Mass, Electrospray Ionization/methods
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
- Workflow
Collapse
|
19
|
Abstract
Genomics is increasingly considered a global enterprise - the fact that biological information can flow rapidly around the planet is taken to be important to what genomics is and what it can achieve. However, the large-scale international circulation of nucleotide sequence information did not begin with the Human Genome Project. Efforts to formalize and institutionalize the circulation of sequence information emerged concurrently with the development of centralized facilities for collecting that information. That is, the very first databases build for collecting and sharing DNA sequence information were, from their outset, international collaborative enterprises. This paper describes the origins of the International Nucleotide Sequence Database Collaboration between GenBank in the United States, the European Molecular Biology Laboratory Databank, and the DNA Database of Japan. The technical and social groundwork for the international exchange of nucleotide sequences created the conditions of possibility for imagining nucleotide sequences (and subsequently genomes) as a "global" objects. The "transnationalism" of nucleotide sequence was critical to their ontology - what DNA sequences came to be during the Human Genome Project was deeply influenced by international exchange.
Collapse
Affiliation(s)
- Hallam Stevens
- School of Humanities and Social Sciences, Nanyang Technological University, 14 Nanyang Drive #05-07, Singapore, 637332, Singapore.
| |
Collapse
|
20
|
Chen X, Zhan L, Shen S. [Determinnation of nucleosides and nucleotides in milk powder by UPLC-MS/MS]. Wei Sheng Yan Jiu 2018; 47:804-814. [PMID: 30593310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
OBJECTIVE To establish a method for the determination of five nucleosides, including adenosine( A), guanosine( G), cytidine( C), uridine( U), inosine( I), and five nucleotides, including cytidine monophosphate( CMP), uridine monophosphate( UMP), adenosin monophosphate( AMP), inosine monphosphate( IMP), guanosine monophosphate( GMP), from milk powder products by ultra-high performance liquid chromatography-tandem triple quadrupole mass spectrometry( UPLCMS/MS). METHODS After hydrolysis with warm water, the sample was deproteinated by25% acetic acid in water. The analysis was performed on a T3 column( 2. 1 mm × 100 mm, 1. 8 μm) and gradiently eluted using 0. 1% formic acid in both acetonitrile and water as the mobile phase. The samples were determined by mass spectrometry in the positive ion mode with the multiple reaction monitoring mode, quantified by the external standard method. RESULTS Five kinds of nucleosides and five kinds of nucleotides were separated within ten minutes. IMP and GMP were linear in the concentration range of 10-1000 ng/m L, and theother nucleosides and nucleotides were linear in the concentration range of 5-1000 ng/m L. The limits of detection for five nucleasides and nucleatides were in the range of 0. 002-0. 150 mg/kg. Recoveries of five nucleasides and nucleatides at different levels were in ranges of 89%-121%, with the relative standard deviations were in ranges of 0. 91%-8. 84%( n = 6). CONCLUSION This method is fast, accurate and sensitive and the preprocessing is simple, which can be used for determination of five nucleosides and five nuclestides in milk powder products effectively.
Collapse
Affiliation(s)
- Xi Chen
- National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China
| | - Lin Zhan
- National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China
| | - Shi Shen
- National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China
| |
Collapse
|
21
|
Im J, Sen S, Lindsay S, Zhang P. Recognition Tunneling of Canonical and Modified RNA Nucleotides for Their Identification with the Aid of Machine Learning. ACS Nano 2018; 12:7067-7075. [PMID: 29932668 DOI: 10.1021/acsnano.8b02819] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
In the present study, we demonstrate a tunneling nanogap technique to identify individual RNA nucleotides, which can be used as a mechanism to read the nucleobases for direct sequencing of RNA in a solid-state nanopore. The tunneling nanogap is composed of two electrodes separated by a distance of <3 nm and functionalized with a recognition molecule. When a chemical entity is captured in the gap, it generates electron tunneling currents, a process we call recognition tunneling (RT). Using RT nanogaps created in a scanning tunneling microscope (STM), we acquired the electron tunneling signals for the canonical and two modified RNA nucleotides. To call the individual RNA nucleotides from the RT data, we adopted a machine learning algorithm, support vector machine (SVM), for the data analysis. Through the SVM, we were able to identify the individual RNA nucleotides and distinguish them from their DNA counterparts with reasonably high accuracy. Since each RNA nucleoside contains a hydroxyl group at the 2'-position of its sugar ring in an RNA strand, it allows for the formation of a tunneling junction at a larger nanogap compared to the DNA nucleoside in a DNA strand, which lacks the 2' hydroxyl group. It also proves advantageous for the manufacture of RT devices. This study is a proof-of-principle demonstration for the development of an RT nanopore device for directly sequencing single RNA molecules, including those bearing modifications.
Collapse
|
22
|
Palermo A, Forsberg EM, Warth B, Aisporna AE, Billings E, Kuang E, Benton HP, Berry D, Siuzdak G. Fluorinated Gold Nanoparticles for Nanostructure Imaging Mass Spectrometry. ACS Nano 2018; 12:6938-6948. [PMID: 29966083 DOI: 10.1021/acsnano.8b02376] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Nanostructure imaging mass spectrometry (NIMS) with fluorinated gold nanoparticles (f-AuNPs) is a nanoparticle assisted laser desorption/ionization approach that requires low laser energy and has demonstrated high sensitivity. Here we describe NIMS with f-AuNPs for the comprehensive analysis of metabolites in biological tissues. F-AuNPs assist in desorption/ionization by laser-induced release of the fluorocarbon chains with minimal background noise. Since the energy barrier required to release the fluorocarbons from the AuNPs is minimal, the energy of the laser is maintained in the low μJ/pulse range, thus limiting metabolite in-source fragmentation. Electron microscopy analysis of tissue samples after f-AuNP NIMS shows a distinct "raising" of the surface as compared to matrix assisted laser desorption ionization ablation, indicative of a gentle desorption mechanism aiding in the generation of intact molecular ions. Moreover, the use of perfluorohexane to distribute the f-AuNPs on the tissue creates a hydrophobic environment minimizing metabolite solubilization and spatial dislocation. The transfer of the energy from the incident laser to the analytes through the release of the fluorocarbon chains similarly enhances the desorption/ionization of metabolites of different chemical nature, resulting in heterogeneous metabolome coverage. We performed the approach in a comparative study of the colon of mice exposed to three different diets. F-AuNP NIMS allows the direct detection of carbohydrates, lipids, bile acids, sulfur metabolites, amino acids, nucleotide precursors as well as other small molecules of varied biological origins. Ultimately, the diversified molecular coverage obtained provides a broad picture of a tissue's metabolic organization.
Collapse
Affiliation(s)
- Amelia Palermo
- Scripps Center for Metabolomics , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Erica M Forsberg
- Department of Chemistry and Biochemistry , San Diego State University , 5500 Campanile Drive , San Diego , California 92182 , United States
| | - Benedikt Warth
- Department of Food Chemistry and Toxicology, Faculty of Chemistry and Vienna Metabolomics Center (VIME) , University of Vienna , Währingerstraße 38 , 1090 Vienna , Austria
| | - Aries E Aisporna
- Scripps Center for Metabolomics , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Elizabeth Billings
- Scripps Center for Metabolomics , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Ellen Kuang
- Department of Chemistry and Biochemistry , San Diego State University , 5500 Campanile Drive , San Diego , California 92182 , United States
| | - H Paul Benton
- Scripps Center for Metabolomics , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - David Berry
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry Meets Microbiology , University of Vienna , Althanstraße 14 , 1090 Vienna , Austria
| | - Gary Siuzdak
- Scripps Center for Metabolomics , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
- Department of Chemistry, Molecular and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| |
Collapse
|
23
|
Frank A, Froese T. The Standard Genetic Code can Evolve from a Two-Letter GC Code Without Information Loss or Costly Reassignments. ORIGINS LIFE EVOL B 2018; 48:259-272. [PMID: 29959584 DOI: 10.1007/s11084-018-9559-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/21/2018] [Indexed: 11/27/2022]
Abstract
It is widely agreed that the standard genetic code must have been preceded by a simpler code that encoded fewer amino acids. How this simpler code could have expanded into the standard genetic code is not well understood because most changes to the code are costly. Taking inspiration from the recently synthesized six-letter code, we propose a novel hypothesis: the initial genetic code consisted of only two letters, G and C, and then expanded the number of available codons via the introduction of an additional pair of letters, A and U. Various lines of evidence, including the relative prebiotic abundance of the earliest assigned amino acids, the balance of their hydrophobicity, and the higher GC content in genome coding regions, indicate that the original two nucleotides were indeed G and C. This process of code expansion probably started with the third base, continued with the second base, and ended up as the standard genetic code when the second pair of letters was introduced into the first base. The proposed process is consistent with the available empirical evidence, and it uniquely avoids the problem of costly code changes by positing instead that the code expanded its capacity via the creation of new codons with extra letters.
Collapse
Affiliation(s)
- Alejandro Frank
- Institute for Nuclear Sciences (ICN), National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- Center for the Sciences of Complexity (C3), National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- El Colegio Nacional, Mexico City, Mexico
| | - Tom Froese
- Center for the Sciences of Complexity (C3), National Autonomous University of Mexico (UNAM), Mexico City, Mexico.
- Institute for Applied Mathematics and Systems Research (IIMAS), National Autonomous University of Mexico (UNAM), Mexico City, Mexico.
| |
Collapse
|
24
|
Abstract
Raman imaging microscopy is a powerful tool for label-free imaging of biological samples. It has the advantage of measuring the spatial distribution of endogenous proteins and lipids in cells, as well as obtaining chemical information on these endogenous molecules, such as hydrogen bonding and electrostatic interactions. However, because Raman intensity is very weak compared with fluorescence intensity, obtaining a reliable Raman image requires fast acquisition of a Raman image and rejection of background fluorescence. In this chapter, we describe the procedure for obtaining images of the Raman band of interest using a multipoint technique, which is the fast acquisition method for obtaining an image.
Collapse
Affiliation(s)
- Shinji Kajimoto
- Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Mizuki Takeuchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Takakazu Nakabayashi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan.
| |
Collapse
|
25
|
Masumoto H, Matsuyama S. The combination of NAD+-dependent deacetylase gene deletion and the interruption of gluconeogenesis causes increased glucose metabolism in budding yeast. PLoS One 2018; 13:e0194942. [PMID: 29579121 PMCID: PMC5868833 DOI: 10.1371/journal.pone.0194942] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 03/13/2018] [Indexed: 01/16/2023] Open
Abstract
Metabolic engineering focuses on rewriting the metabolism of cells to enhance native products or endow cells with the ability to produce new products. This engineering has the potential for wide-range application, including the production of fuels, chemicals, foods and pharmaceuticals. Glycolysis manages the levels of various secondary metabolites by controlling the supply of glycolytic metabolites. Metabolic reprogramming of glycolysis is expected to cause an increase in the secondary metabolites of interest. In this study, we constructed a budding yeast strain harboring the combination of triple sirtuin gene deletion (hst3∆ hst4∆ sir2∆) and interruption of gluconeogenesis by the deletion of the FBP1 gene encoding fructose-1,6-bisphosphatase (fbp1∆). hst3∆ hst4∆ sir2∆ fbp1∆ cells harbored active glycolysis with high glucose consumption and active ethanol productivity. Using capillary electrophoresis–time-of-flight mass spectrometry (CE–TOF/MS) analysis, hst3∆ hst4∆ sir2∆ fbp1∆ cells accumulated not only glycolytic metabolites but also secondary metabolites, including nucleotides that were synthesized throughout the pentose phosphate (PP) pathway, although various amino acids remained at low levels. Using the stable isotope labeling assay for metabolites, we confirmed that hst3∆ hst4∆ sir2∆ fbp1∆ cells directed the metabolic fluxes of glycolytic metabolites into the PP pathway. Thus, the deletion of three sirtuin genes (HST3, HST4 and SIR2) and the FBP1 gene can allow metabolic reprogramming to increase glycolytic metabolites and several secondary metabolites except for several amino acids.
Collapse
Affiliation(s)
- Hiroshi Masumoto
- Transdisciplinary Research Integration Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, Japan
- * E-mail:
| | - Shigeru Matsuyama
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, Japan
| |
Collapse
|
26
|
Kong Y, Yang X, Ding Q, Zhang YY, Sun BG, Chen HT, Sun Y. Comparison of non-volatile umami components in chicken soup and chicken enzymatic hydrolysate. Food Res Int 2017; 102:559-566. [PMID: 29195986 DOI: 10.1016/j.foodres.2017.09.038] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 08/27/2017] [Accepted: 09/12/2017] [Indexed: 11/19/2022]
Abstract
Umami taste is an important part to the taste of chicken. To isolate and identify non-volatile umami compounds, fractions from chicken soup and hydrolysate were prepared and analyzed. Amino acids were analyzed by amino acid analyzer. Organic acids and nucleotides were determined by ultra-performance liquid chromatography. Separation procedures utilizing ultrafiltration, Sephadex G-15 and reversed-phase high-performance liquid chromatography were used to isolate umami taste peptides. Combined with sensory evaluation and LC-Q-TOF-MS, the amino acid sequences of 12 oligopeptides were determined. The amount of taste compounds was higher in chicken enzymatic hydrolysate than that of chicken soup. Eight oligopeptides from chicken enzymatic hydrolysate were identified, including Ala-Asp, Ala-Met, His-Ser, Val-Glu, Ala-Glu, Asp-Ala-Gly, Glu-Asp and Ala-Glu-Ala. Four oligopeptides from chicken soup were identified, including Val-Thr, Ala-His, Ala-Phe and Thr-Glu.
Collapse
Affiliation(s)
- Yan Kong
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Laboratory for Food Quality and Safety, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Xiao Yang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Laboratory for Food Quality and Safety, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Qi Ding
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Laboratory for Food Quality and Safety, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Yu-Yu Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Laboratory for Food Quality and Safety, Beijing Technology & Business University (BTBU), Beijing 100048, China.
| | - Bao-Guo Sun
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Laboratory for Food Quality and Safety, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Hai-Tao Chen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Laboratory for Food Quality and Safety, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Ying Sun
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Laboratory for Food Quality and Safety, Beijing Technology & Business University (BTBU), Beijing 100048, China
| |
Collapse
|
27
|
Tahir M, Hayat M, Kabir M. Sequence based predictor for discrimination of enhancer and their types by applying general form of Chou's trinucleotide composition. Comput Methods Programs Biomed 2017; 146:69-75. [PMID: 28688491 DOI: 10.1016/j.cmpb.2017.05.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 05/05/2017] [Accepted: 05/19/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND AND OBJECTIVES Enhancers are pivotal DNA elements, which are widely used in eukaryotes for activation of transcription genes. On the basis of enhancer strength, they are further classified into two groups; strong enhancers and weak enhancers. Due to high availability of huge amount of DNA sequences, it is needed to develop fast, reliable and robust intelligent computational method, which not only identify enhancers but also determines their strength. Considerable progress has been achieved in this regard; however, timely and precisely identification of enhancers is still a challenging task. METHODS Two-level intelligent computational model for identification of enhancers and their subgroups is proposed. Two different feature extraction techniques including di-nucleotide composition and tri-nucleotide composition were adopted for extraction of numerical descriptors. Four classification methods including probabilistic neural network, support vector machine, k-nearest neighbor and random forest were utilized for classification. RESULTS The proposed method yielded 77.25% of accuracy for dataset S1 contains enhancers and non-enhancers, whereas 64.70% of accuracy for dataset S2 comprises of strong enhancer and weak enhancer sequences using jackknife cross-validation test. CONCLUSION The predictive results validated that the proposed method is better than that of existing approaches so far reported in the literature. It is thus highly observed that the developed method will be useful and expedient for basic research and academia.
Collapse
Affiliation(s)
- Muhammad Tahir
- Department of Computer Science, Abdul Wali Khan University Mardan, KP Pakistan
| | - Maqsood Hayat
- Department of Computer Science, Abdul Wali Khan University Mardan, KP Pakistan.
| | - Muhammad Kabir
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| |
Collapse
|
28
|
Cybulski TR, Boyden ES, Church GM, Tyo KEJ, Kording KP. Nucleotide-time alignment for molecular recorders. PLoS Comput Biol 2017; 13:e1005483. [PMID: 28459860 PMCID: PMC5432193 DOI: 10.1371/journal.pcbi.1005483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 05/15/2017] [Accepted: 03/24/2017] [Indexed: 11/18/2022] Open
Abstract
Using a DNA polymerase to record intracellular calcium levels has been proposed as a novel neural recording technique, promising massive-scale, single-cell resolution monitoring of large portions of the brain. This technique relies on local storage of neural activity in strands of DNA, followed by offline analysis of that DNA. In simple implementations of this scheme, the time when each nucleotide was written cannot be determined directly by post-hoc DNA sequencing; the timing data must be estimated instead. Here, we use a Dynamic Time Warping-based algorithm to perform this estimation, exploiting correlations between neural activity and observed experimental variables to translate DNA-based signals to an estimate of neural activity over time. This algorithm improves the parallelizability of traditional Dynamic Time Warping, allowing several-fold increases in computation speed. The algorithm also provides a solution to several critical problems with the molecular recording paradigm: determining recording start times and coping with DNA polymerase pausing. The algorithm can generally locate DNA-based records to within <10% of a recording window, allowing for the estimation of unobserved incorporation times and latent neural tunings. We apply our technique to an in silico motor control neuroscience experiment, using the algorithm to estimate both timings of DNA-based data and the directional tuning of motor cortical cells during a center-out reaching task. We also use this algorithm to explore the impact of polymerase characteristics on system performance, determining the precision of a molecular recorder as a function of its kinetic and error-generating properties. We find useful ranges of properties for DNA polymerase-based recorders, providing guidance for future protein engineering attempts. This work demonstrates a useful general extension to dynamic alignment algorithms, as well as direct applications of that extension toward the development of molecular recorders, providing a necessary stepping stone for future biological work.
Collapse
Affiliation(s)
- Thaddeus R. Cybulski
- Department of Physical Medicine and Rehabilitation, Rehabilitation Institute of Chicago, Northwestern University, Chicago, Illinois, United States of America
- * E-mail:
| | - Edward S. Boyden
- Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - George M. Church
- Biophysics Program, Harvard University, Boston, Massachusetts, United States of America
- Wyss Institute, Harvard University, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Harvard University, Boston, Massachusetts, United States of America
| | - Keith E. J. Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, United States of America
| | - Konrad P. Kording
- Department of Physical Medicine and Rehabilitation, Rehabilitation Institute of Chicago, Northwestern University, Chicago, Illinois, United States of America
- Department of Physiology, Northwestern University, Chicago, Illinois, United States of America
- Department of Applied Mathematics, Northwestern University, Evanston, Illinois, United States of America
| |
Collapse
|
29
|
Kip Ç, Demir C, Tuncel A. One pot synthesis of carboxyl functionalized-polyhedral oligomeric siloxane based monolith via photoinitiated thiol-methacrylate polymerization for nano-hydrophilic interaction chromatography. J Chromatogr A 2017; 1502:14-23. [PMID: 28457489 DOI: 10.1016/j.chroma.2017.04.044] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 03/27/2017] [Accepted: 04/23/2017] [Indexed: 01/06/2023]
Abstract
A hybrid monolith exhibiting almost retention independent separation performance in hydrophilic interaction chromatography (HILIC) was obtained by one-pot photoinitiated thiol-methacrylate polymerization. Polyhedral oligomeric silsesquioxane containing methacrylate units (POSS-MA) was used as the main monomer and crosslinking agent, together with a hydrophilic ligand with two carboxyl groups, mercaptosuccinic acid (MSA) as the thiol agent and chromatographic ligand. The isocratic separation of nucleosides, nucleotides and organic acids on MSA attached-poly(POSS-MA) monolith was investigated in HILIC mode. The van-Deemter plots for obtained for nucleosides, nucleotides and benzoic acids clearly showed that there were two regions in each graph with two different slopes in the studied range of linear flow rate (i.e. 0.2-4.3mm/s). The slope of plate height-linear velocity curve was so small in the low linear velocity region between 0.2-2.1mm/s while the slope in high linear velocity region between 2.1-4.3mm/s was so higher with respect to the first region. The van-Deemter plots sketched for all analyte grous used in HILIC mode obeyed this tendency Almost "retention independent plate height behavior" was demonstrated in HILIC, using nucleotides, nucleotides or benzoic acids as the analytes in the linear velocity range of 0.2-2.1mm/s. This behavior was explained by the porous structure of the synthesized monolith facilitating the convective transport of analytes. The variation of plate height was not retention-independent within high linear velocity range (>3.2mm/s) when nucleosides were separated in HILIC mode.
Collapse
Affiliation(s)
- Çiğdem Kip
- Chemical Engineering Department, Hacettepe University, 06800, Ankara, Turkey
| | - Cihan Demir
- Chemical Engineering Department, Hacettepe University, 06800, Ankara, Turkey
| | - Ali Tuncel
- Chemical Engineering Department, Hacettepe University, 06800, Ankara, Turkey; Division of Nanotechnology and Nanomedicine, Hacettepe University, 06800 Ankara, Turkey.
| |
Collapse
|
30
|
Korshoj LE, Afsari S, Khan S, Chatterjee A, Nagpal P. Single Nucleobase Identification Using Biophysical Signatures from Nanoelectronic Quantum Tunneling. Small 2017; 13:1603033. [PMID: 28067976 DOI: 10.1002/smll.201603033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 11/19/2016] [Indexed: 06/06/2023]
Abstract
Nanoelectronic DNA sequencing can provide an important alternative to sequencing-by-synthesis by reducing sample preparation time, cost, and complexity as a high-throughput next-generation technique with accurate single-molecule identification. However, sample noise and signature overlap continue to prevent high-resolution and accurate sequencing results. Probing the molecular orbitals of chemically distinct DNA nucleobases offers a path for facile sequence identification, but molecular entropy (from nucleotide conformations) makes such identification difficult when relying only on the energies of lowest-unoccupied and highest-occupied molecular orbitals (LUMO and HOMO). Here, nine biophysical parameters are developed to better characterize molecular orbitals of individual nucleobases, intended for single-molecule DNA sequencing using quantum tunneling of charges. For this analysis, theoretical models for quantum tunneling are combined with transition voltage spectroscopy to obtain measurable parameters unique to the molecule within an electronic junction. Scanning tunneling spectroscopy is then used to measure these nine biophysical parameters for DNA nucleotides, and a modified machine learning algorithm identified nucleobases. The new parameters significantly improve base calling over merely using LUMO and HOMO frontier orbital energies. Furthermore, high accuracies for identifying DNA nucleobases were observed at different pH conditions. These results have significant implications for developing a robust and accurate high-throughput nanoelectronic DNA sequencing technique.
Collapse
Affiliation(s)
- Lee E Korshoj
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80309, USA
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, SEEC 27 UCB Suite N321, Boulder, CO, 80309, USA
| | - Sepideh Afsari
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80309, USA
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, SEEC 27 UCB Suite N321, Boulder, CO, 80309, USA
| | - Sajida Khan
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80309, USA
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, SEEC 27 UCB Suite N321, Boulder, CO, 80309, USA
| | - Anushree Chatterjee
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80309, USA
- BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave., Boulder, CO, 80303, USA
| | - Prashant Nagpal
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80309, USA
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, SEEC 27 UCB Suite N321, Boulder, CO, 80309, USA
- BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave., Boulder, CO, 80303, USA
- Materials Science and Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80309, USA
| |
Collapse
|
31
|
Abstract
In this review, we focus on an important aspect of ion mobility (IM) research, namely the reporting of quantitative ion mobility measurements in the form of the gas-phase collision cross section (CCS), which has provided a common basis for comparison across different instrument platforms and offers a unique form of structural information, namely size and shape preferences of analytes in the absence of bulk solvent. This review surveys the over 24,000 CCS values reported from IM methods spanning the era between 1975 to 2015, which provides both a historical and analytical context for the contributions made thus far, as well as insight into the future directions that quantitative ion mobility measurements will have in the analytical sciences. The analysis was conducted in 2016, so CCS values reported in that year are purposely omitted. In another few years, a review of this scope will be intractable, as the number of CCS values which will be reported in the next three to five years is expected to exceed the total amount currently published in the literature.
Collapse
Affiliation(s)
- Jody C May
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University , Nashville, Tennessee 37235, United States
| | - Caleb B Morris
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University , Nashville, Tennessee 37235, United States
| | - John A McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University , Nashville, Tennessee 37235, United States
| |
Collapse
|
32
|
Lee CH, Kim IH, Moon JC, Seo SY, Kim SH, Kim SW, Lee SO, Lee ST, Kim DG, Yang JD, Yu HC. 3-Dimensional liver volume assessment in patients with hepatitis B virus-related liver cirrhosis during long-term oral nucleos(t)ide analogues therapy. World J Gastroenterol 2017; 23:297-305. [PMID: 28127203 PMCID: PMC5236509 DOI: 10.3748/wjg.v23.i2.297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/22/2016] [Accepted: 12/08/2016] [Indexed: 02/06/2023] Open
Abstract
AIM To assess the effect of long-term oral nucleos(t)ide analogues (NUCs) therapy on liver volume change in patients with suppress hepatitis B virus (HBV)-related liver cirrhosis.
METHODS We reviewed the data of naïve patients with HBV-related liver cirrhosis, who had taken oral NUCs therapy, between 2003 and 2007 at Chonbuk University Hospital. We analyzed two consecutive sets of abdominal computerized tomography scans-one at the time of treatment initiation and another at the second-year follow-up. Liver volume was calculated by 3-dimensional liver extraction volumetry program.
RESULTS A total of 55 patients (34 males) were included. There was 114.3 mL ± 167.8 mL (12.9% ± 17.9%) of increase in liver volume during the two years of NUCs therapy (993.8 mL ± 242.8 mL at baseline vs 1108.1 mL ± 263.3 mL at two-year follow-up, P < 0.001). The ratio of the measured baseline liver volume to the estimated standard liver volume was improved from 70.8% to 78.0%. An increase in liver volume was shown not only in patients with compensated cirrhosis (P = 0.046) but also in those with decompensated cirrhosis (P < 0.001). Significant factors for volume increases were Child-Turcotte-Pugh grade and model for end-stage liver disease score improvement without virological breakthrough. In multiple linear regression analysis, delta albumin and delta alanine aminotransferase levels showed a significant association with the increase in liver volume (P = 0.002 and 0.005, respectively).
CONCLUSION Long-term oral NUCs therapy in patients with HBV-related liver cirrhosis lead to significant increase in liver volume assessed with 3-dimensional liver extraction volumetry program.
Collapse
|
33
|
BELL LG. THE SITE OF A DIFFUSIBLE NUCLEOTIDE REVEALED BY A COMPARISON OF CHEMICALLY FIXED TISSUE WITH FROZEN AND DRIED TISSUE. J Histochem Cytochem 2016; 6:435-7. [PMID: 13598880 DOI: 10.1177/6.6.435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
1. Using unfixed frozen and dried tissue as a standard it is shown that acid alcohol fixation extracts a diffusible nucleotide from the vicinity of the chromosomes. 2. It is shown that the denuded area contains protein and that the end groups are not available for reaction with protein reagents.
Collapse
|
34
|
Wojnicz A, Avendaño-Ortiz J, de Pascual R, Ruiz-Pascual L, García AG, Ruiz-Nuño A. Simultaneous monitoring of monoamines, amino acids, nucleotides and neuropeptides by liquid chromatography-tandem mass spectrometry and its application to neurosecretion in bovine chromaffin cells. J Mass Spectrom 2016; 51:651-664. [PMID: 28239974 DOI: 10.1002/jms.3794] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/20/2016] [Accepted: 05/28/2016] [Indexed: 06/06/2023]
Abstract
The primary functions of adrenal medullary chromaffin cells are the synthesis and storage in their chromaffin vesicles of the catecholamines noradrenaline (NA) and adrenaline (AD), and their subsequent release into the bloodstream by Ca2+ -dependent exocytosis under conditions of fear or stress (fight or flight response). Several monoamines, nucleotides and opiates, such as leucine-enkephalin (LENK) and methionine-enkephalin (MENK), are also co-stored and co-released with the catecholamines. However, other neurotransmitters have not been studied in depth. Here, we present a novel high-resolution liquid chromatography-tandem mass spectrometry approach for the simultaneous monitoring of 14 compounds stored and released in bovine chromaffin cells (BCCs). We validated the analytical method according to the recommendations of the EMA and FDA by testing matrix effect, selectivity, sensitivity, precision, accuracy, stability and carry-over. After testing on six batches of BCCs from different cultures, the method enabled simultaneous quantitative determination of monoamines (AD, NA, dopamine, serotonin, 5-hydroxyindoleacetic acid, histamine and metanephrine), amino acids (L-glutamic acid, γ-aminobutyric acid), nucleotides (adenosine 5'-diphosphate, adenosine 5'-monophosphate, cyclic adenosine 5'-monophosphate) and neuropeptides (LENK and MENK) in the intracellular content, basal secretion and acetylcholine induced secretion of BBCs. The high-resolution approach used here enabled us to determine the levels of 14 compounds in the same BCC batch in only 16 min. This novel approach will make it possible to study the regulatory mechanisms of Ca2+ signaling, exocytosis and endocytosis using different neurotrophic factors and/or secretagogues as stimuli in primary BCC cultures. Our method is actually being applied to human plasma samples of different therapeutic areas where sympathoadrenal axis is involved in stress situations such as Alzheimer's disease, migraine or cirrhosis, to improve diagnosis and clinical practice. Copyright © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Aneta Wojnicz
- Instituto-Fundación Teófilo Hernando, Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Farmacología y Terapéutica, Facultad de Medicina, Universidad Autónoma de Madrid, Spain
- Servicio de Farmacología Clínica, Instituto de Investigación Sanitaria, Hospital Universitario de la Princesa, Universidad Autónoma de Madrid, Madrid, Spain
| | - José Avendaño-Ortiz
- Instituto-Fundación Teófilo Hernando, Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Farmacología y Terapéutica, Facultad de Medicina, Universidad Autónoma de Madrid, Spain
| | - Ricardo de Pascual
- Instituto-Fundación Teófilo Hernando, Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Farmacología y Terapéutica, Facultad de Medicina, Universidad Autónoma de Madrid, Spain
| | - Lucía Ruiz-Pascual
- Instituto-Fundación Teófilo Hernando, Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Farmacología y Terapéutica, Facultad de Medicina, Universidad Autónoma de Madrid, Spain
| | - Antonio G García
- Instituto-Fundación Teófilo Hernando, Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Farmacología y Terapéutica, Facultad de Medicina, Universidad Autónoma de Madrid, Spain
- Servicio de Farmacología Clínica, Instituto de Investigación Sanitaria, Hospital Universitario de la Princesa, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ana Ruiz-Nuño
- Instituto-Fundación Teófilo Hernando, Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Farmacología y Terapéutica, Facultad de Medicina, Universidad Autónoma de Madrid, Spain
- Servicio de Farmacología Clínica, Instituto de Investigación Sanitaria, Hospital Universitario de la Princesa, Universidad Autónoma de Madrid, Madrid, Spain
| |
Collapse
|
35
|
Abstract
BACKGROUND RNA viruses have genomes with a distinct nucleotide composition and codon usage. We present the global characteristics of the RNA genome of Zika virus (ZIKV), an emerging pathogen within the Flavivirus genus. ZIKV was first isolated in 1947 in Uganda, caused a widespread epidemic in South and Central America and the Caribbean in 2015 and has recently been associated with microcephaly in newborns. METHODS The nearly 11 kb positive-stranded RNA genome of ZIKV was analyzed for its nucleotide composition, also in the context of the folded RNA molecule. Nucleotide trends were investigated along the genome length by skew analyses and we analyzed the codons used for translation of the ZIKV proteins. RESULTS ZIKV RNA has a biased nucleotide composition in being purine-rich and pyrimidine-poor. This preference for purines is a general characteristic of the mosquito-borne and tick-borne flaviviruses. The virus-specific nucleotide bias is further enriched in the unpaired, single-stranded regions of the structured ZIKV RNA genome, thus further imposing this ZIKV-specific signature. The codons used for translation of the ZIKV proteins is also unusual, but we show that it is the underlying bias in nucleotide composition of the viral RNA that largely dictates these codon preferences. CONCLUSIONS The ZIKV RNA genome has a biased nucleotide composition that dictates the codon usage of this flavivirus. We discuss the evolutionary scenarios and molecular mechanisms that may be responsible for these distinctive ZIKV RNA genome features.
Collapse
Affiliation(s)
- Formijn van Hemert
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
| |
Collapse
|
36
|
Hijaz F, Manthey JA, Van der Merwe D, Killiny N. Nucleotides, micro- and macro-nutrients, limonoids, flavonoids, and hydroxycinnamates composition in the phloem sap of sweet orange. Plant Signal Behav 2016; 11:e1183084. [PMID: 27171979 PMCID: PMC4976783 DOI: 10.1080/15592324.2016.1183084] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Currently, the global citrus production is declining due to the spread of Huanglongbing (HLB). HLB, otherwise known as citrus greening, is caused by Candidatus Liberibacter asiaticus (CLas) and is transmitted by the Asian citrus psyllids (ACP), Diaphorina citri Kuwayama. ACP transmits CLas bacterium while feeding on the citrus phloem sap. Multiplication of CLas in the phloem of citrus indicates that the sap contains all the essential nutrients needed for CLas. In this study, we investigated the micro- and macro-nutrients, nucleotides, and others secondary metabolites of phloem sap from pineapple sweet orange. The micro- and macro-nutrients were analyzed using inductively coupled plasma-mass spectroscopy (ICP-MS) and inductively coupled plasma-optical emission spectroscopy (ICP-OES). Nucleotides and other secondary metabolites analysis was accomplished by reversed phase HPLC coupled with UV, fluorescence detection, or negative mode electrospray ionization mass spectrometry (ESI-MS). Calcium (89 mM) was the highest element followed by potassium (38.8 mM) and phosphorous (24 mM). Magnesium and sulfur were also abundant and their concentrations were 15 and 9 mM, respectively. The rest of the elements were found in low amounts (< 2mM). The concentrations of ATP, ADP, and AMP were 16, 31, and 3 µ mole/Kg fwt, respectively. GTP, GMP. NAD, FMN, FAD, and riboflavin were found at concentrations below (3 µ mole/Kg fwt). The phloem was rich in nomilin 124 mM and limonin 176 µ mole/Kg fwt. Hesperidin, vicenin-2, sinensetin, and nobiletin were the most predominant flavonoids. In addition, several hydroxycinnamates were detected. The results of this study will increase our knowledge about the nature and the chemical composition of citrus phloem sap.
Collapse
Affiliation(s)
- Faraj Hijaz
- Citrus Research and Education Center, University of Florida, IFAS, Lake Alfred, FL, USA
| | - John A. Manthey
- US Horticultural Research Laboratory, USDA, ARS, Fort Pierce, FL, USA
| | - Deon Van der Merwe
- Department of Diagnostic Medicine/Pathobiology, Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Nabil Killiny
- Citrus Research and Education Center, University of Florida, IFAS, Lake Alfred, FL, USA
- CONTACT Nabil Killiny, , Plant Pathology Department, Citrus Research & Education Center, University of Florida, Lake Alfred, FL, USA
| |
Collapse
|
37
|
Yuan F, Zhao H, Zang H, Ye F, Quan X. Three-Dimensional Graphene Supported Bimetallic Nanocomposites with DNA Regulated-Flexibly Switchable Peroxidase-Like Activity. ACS Appl Mater Interfaces 2016; 8:9855-9864. [PMID: 27018504 DOI: 10.1021/acsami.6b00306] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A synergistic bimetallic enzyme mimetic catalyst, three-dimensional (3D) graphene/Fe3O4-AuNPs, was successfully fabricated which exhibited flexibly switchable peroxidase-like activity. Compared to the traditional 2D graphene-based monometallic composite, the introduced 3D structure, which was induced by the addition of glutamic acid, and bimetallic anchoring approach dramatically improved the catalytic activity, as well as the catalysis velocity and its affinity for substrate. Herein, Fe3O4NPs acted as supporters for AuNPs, which contributed to enhance the efficiency of electron transfer. On the basis of the measurement of Mott-Schottky plots of graphene and metal anchored hybrids, the catalysis mechanism was elucidated by the decrease of Fermi level resulted from the chemical doping behavior. Notably, the catalytic activity was able to be regulated by the adsorption and desorption of single-stranded DNA molecules, which laid a basis for its utilization in the construction of single-stranded DNA-based colorimetric biosensors. This strategy not only simplified the operation process including labeling, modification, and imprinting, but also protected the intrinsic affinity between the target and biological probe. Accordingly, based on the peroxidase-like activity and its controllability, our prepared nanohybrids was successfully adopted in the visualized and label-free sensing detections of glucose, sequence-specific DNA, mismatched nucleotides, and oxytetracycline.
Collapse
Affiliation(s)
- Fang Yuan
- Key Laboratory of Industrial Ecology and Environment Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology , Dalian 116024, China
| | - Huimin Zhao
- Key Laboratory of Industrial Ecology and Environment Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology , Dalian 116024, China
| | - Hongmei Zang
- Key Laboratory of Industrial Ecology and Environment Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology , Dalian 116024, China
| | - Fei Ye
- Key Laboratory of Industrial Ecology and Environment Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology , Dalian 116024, China
| | - Xie Quan
- Key Laboratory of Industrial Ecology and Environment Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology , Dalian 116024, China
| |
Collapse
|
38
|
Sun J, Ding ZQ, Gao Q, Xun H, Tang F, Xia ED. Major Chemical Constituents of Bamboo Shoots (Phyllostachys pubescens): Qualitative and Quantitative Research. J Agric Food Chem 2016; 64:2498-2505. [PMID: 26551795 DOI: 10.1021/acs.jafc.5b05167] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Bamboo shoots are a delicacy in Asia. Two novel compounds, adenine-(1'R,2'R,3'R)-cyclic butanetetraol carbonate (16) and (-)-(7R,8S)-(4-hydroxy-3-methoxyphenylglycerol 9-O-β-D-[6-O-4-hydroxy-3-methoxybenzoyl])-glucopyranoside (20), together with 12 known nucleosides (1-12), 3 amino acids (13-15), β-carboline (17), and 2 megastigmane glycosides (18, 19) were isolated from bamboo shoots (Phyllostachys pubescens). Their structures and absolute configurations were rigorously determined by detailed spectroscopic analysis, and the composition of carbohydrates in bamboo shoots was qualitatively detected and quantitatively analyzed with ion chromatography. A simple, rapid, sensitive, and accurate HPLC-UV analysis was built for routine edible quality control of bamboo shoots, and 12 major components of bamboo shoots were quantitatively analyzed. The major chemical constituents of bamboo shoots were determined to be carbohydrates, amino acids, and nucleotides. These findings are correctives to the usual view of bamboo shoots chemical composition, and the previous research reports about the chemical composition of bamboo shoots may have taken the aromatic amino acids and nucleotides for flavonoids and phenolic acids.
Collapse
Affiliation(s)
- Jia Sun
- State Forestry Administration Key Open Laboratory, International Centre for Bamboo and Rattan , Beijing 100102, China
| | - Zhao-Qing Ding
- Anhui Key Laboratory of Agricultural Products, School of Resource and Environment, Anhui Agricultural University , Hefei 230036, China
| | - Quan Gao
- Anhui Key Laboratory of Agricultural Products, School of Resource and Environment, Anhui Agricultural University , Hefei 230036, China
| | - Hang Xun
- State Forestry Administration Key Open Laboratory, International Centre for Bamboo and Rattan , Beijing 100102, China
| | - Feng Tang
- State Forestry Administration Key Open Laboratory, International Centre for Bamboo and Rattan , Beijing 100102, China
| | - Er-Dong Xia
- State Forestry Administration Key Open Laboratory, International Centre for Bamboo and Rattan , Beijing 100102, China
| |
Collapse
|
39
|
Yanagi I, Oura T, Haga T, Ando M, Yamamoto J, Mine T, Ishida T, Hatano T, Akahori R, Yokoi T, Anazawa T. Side-gated ultrathin-channel nanopore FET sensors. Nanotechnology 2016; 27:115501. [PMID: 26876025 DOI: 10.1088/0957-4484/27/11/115501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A side-gated, ultrathin-channel nanopore FET (SGNAFET) is proposed for fast and label-free DNA sequencing. The concept of the SGNAFET comprises the detection of changes in the channel current during DNA translocation through a nanopore and identifying the four types of nucleotides as a result of these changes. To achieve this goal, both p- and n-type SGNAFETs with a channel thicknesses of 2 or 4 nm were fabricated, and the stable transistor operation of both SGNAFETs in air, water, and a KCl buffer solution were confirmed. In addition, synchronized current changes were observed between the ionic current through the nanopore and the SGNAFET's drain current during DNA translocation through the nanopore.
Collapse
Affiliation(s)
- Itaru Yanagi
- Hitachi Ltd, Research & Development Group, Center for Technology Innovation-Healthcare, 1-280, Higashi-Koigakubo, Kokubunji, Tokyo, 185-8603, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Frańska M. Electrospray ionization-collision-induced dissociation-tandem mass spectrometry study of lead complexes with deprotonated nucleobases. Eur J Mass Spectrom (Chichester) 2016; 22:175-180. [PMID: 27882882 DOI: 10.1255/ejms.1424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The complexes between the lead cation and deprotonated nucleobases (and deprotonated nucleosides) are studied by using electrospray ionization-collision-induced dissociation-tandem mass spectrometry. It has been found that the deprotonated N9 atom is not the site of lead cation attachment. In ions [A - H + Pb]+ and [C - H + Pb]+, the lead cation is coordinated by the adenine N1 atom and cytosine N3 atom and interaction between the lead cation and deprotonated amino groups seems very likely. Deprotonated thymine shows a higher affinity toward lead cation than deprotonated uracil. In the lead-nucleoside complexes lead cation interacts with a sugar moiety.
Collapse
Affiliation(s)
- Magdalena Frańska
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965 Poznań, Poland.
| |
Collapse
|
41
|
Feng J, Liu K, Bulushev RD, Khlybov S, Dumcenco D, Kis A, Radenovic A. Identification of single nucleotides in MoS2 nanopores. Nat Nanotechnol 2015; 10:1070-6. [PMID: 26389660 DOI: 10.1038/nnano.2015.219] [Citation(s) in RCA: 278] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 08/20/2015] [Indexed: 05/19/2023]
Abstract
The size of the sensing region in solid-state nanopores is determined by the size of the pore and the thickness of the pore membrane, so ultrathin membranes such as graphene and single-layer molybdenum disulphide could potentially offer the necessary spatial resolution for nanopore DNA sequencing. However, the fast translocation speeds (3,000-50,000 nt ms(-1)) of DNA molecules moving across such membranes limit their usability. Here, we show that a viscosity gradient system based on room-temperature ionic liquids can be used to control the dynamics of DNA translocation through MoS2 nanopores. The approach can be used to statistically detect all four types of nucleotide, which are identified according to current signatures recorded during their transient residence in the narrow orifice of the atomically thin MoS2 nanopore. Our technique, which exploits the high viscosity of room-temperature ionic liquids, provides optimal single nucleotide translocation speeds for DNA sequencing, while maintaining a signal-to-noise ratio higher than 10.
Collapse
Affiliation(s)
- Jiandong Feng
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne 1015, Switzerland
| | - Ke Liu
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne 1015, Switzerland
| | - Roman D Bulushev
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne 1015, Switzerland
| | - Sergey Khlybov
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne 1015, Switzerland
| | - Dumitru Dumcenco
- Laboratory of Nanoscale Electronics and Structure, Institute of Electrical Engineering, School of Engineering, EPFL, Lausanne 1015, Switzerland
| | - Andras Kis
- Laboratory of Nanoscale Electronics and Structure, Institute of Electrical Engineering, School of Engineering, EPFL, Lausanne 1015, Switzerland
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne 1015, Switzerland
| |
Collapse
|
42
|
Craig JM, Laszlo AH, Derrington IM, Ross BC, Brinkerhoff H, Nova IC, Doering K, Tickman BI, Svet MT, Gundlach JH. Direct Detection of Unnatural DNA Nucleotides dNaM and d5SICS using the MspA Nanopore. PLoS One 2015; 10:e0143253. [PMID: 26588074 PMCID: PMC4654578 DOI: 10.1371/journal.pone.0143253] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/02/2015] [Indexed: 11/19/2022] Open
Abstract
Malyshev et al. showed that the four-letter genetic code within a living organism could be expanded to include the unnatural DNA bases dNaM and d5SICS. However, verification and detection of these unnatural bases in DNA requires new sequencing techniques. Here we provide proof of concept detection of dNaM and d5SICS in DNA oligomers via nanopore sequencing using the nanopore MspA. We find that both phi29 DNA polymerase and Hel308 helicase are capable of controlling the motion of DNA containing dNaM and d5SICS through the pore and that single reads are sufficient to detect the presence and location of dNaM and d5SICS within single molecules.
Collapse
Affiliation(s)
- Jonathan M. Craig
- Department of Physics, University of Washington, Seattle, Washington, United States of America
| | - Andrew H. Laszlo
- Department of Physics, University of Washington, Seattle, Washington, United States of America
| | - Ian M. Derrington
- Department of Physics, University of Washington, Seattle, Washington, United States of America
| | - Brian C. Ross
- Department of Physics, University of Washington, Seattle, Washington, United States of America
| | - Henry Brinkerhoff
- Department of Physics, University of Washington, Seattle, Washington, United States of America
| | - Ian C. Nova
- Department of Physics, University of Washington, Seattle, Washington, United States of America
| | - Kenji Doering
- Department of Physics, University of Washington, Seattle, Washington, United States of America
| | - Benjamin I. Tickman
- Department of Physics, University of Washington, Seattle, Washington, United States of America
| | - Mark T. Svet
- Department of Physics, University of Washington, Seattle, Washington, United States of America
| | - Jens H. Gundlach
- Department of Physics, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| |
Collapse
|
43
|
Abstract
The CRISPR/Cas9 system has been rapidly adopted for genome editing. However, one major issue with this system is the lack of robust bioinformatics tools for design of single guide RNA (sgRNA), which determines the efficacy and specificity of genome editing. To address this pressing need, we analyze CRISPR RNA-seq data and identify many novel features that are characteristic of highly potent sgRNAs. These features are used to develop a bioinformatics tool for genome-wide design of sgRNAs with improved efficiency. These sgRNAs as well as the design tool are freely accessible via a web server, WU-CRISPR ( http://crispr.wustl.edu ).
Collapse
Affiliation(s)
- Nathan Wong
- Department of Biomedical Engineering, Washington University, St Louis, MO, 63130, USA
- Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO, 63108, USA
| | - Weijun Liu
- Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO, 63108, USA
| | - Xiaowei Wang
- Department of Biomedical Engineering, Washington University, St Louis, MO, 63130, USA.
- Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO, 63108, USA.
| |
Collapse
|
44
|
Zheng LH, Huang LY, Chen Y, Lin SE, Huang BL. [Determination of Nucleosides and Nucleobases in Natural, Cultured and Tissue Culture Anoectochilus roxburghii Using LC-MS]. Zhong Yao Cai 2015; 38:2269-2273. [PMID: 27356374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
OBJECTIVE To establish a method for simultaneous determination of nucleosides and nucleobases in natural, cultured and tissue culture Anoectochilus roxburghii by high performance liquid chromatography-electrospray ionization/ion trap mass spectrometry (HPLC-ESI/MS). METHODS The separation was performed on a Welch Ultimate XB-C18 column (250 mm x 4.6 mm,5 μm). 20 mmol/L ammonium acetate solution and methanol were adopted as the mobile phase with gradient elution. The flow rate was 1.0 mL/min. The injection volume was 20 μL. The column temperature and UV wavelength were set at 30 degrees C and 260 nm, respectively. RESULTS Cytosine, uracil, cytidine, uridine, hypoxanthine, adenine, inosine, guanosine,fl-thymidine and adenosine were identified in natural, cultured and tissue culture Anoectochilus roxburghii. The total content of nucleosides and nucleotides in Anoectochilus roxburghii were 1.6639, 1.8568 and 2.2013 mg/g,respectively. CONCLUSION The contents of nucleosides and nucleobases in herb are affected by its growth pattern. The total content of nucleosides and nucleotides was tissue culture herb > cultured herb > natural herb. This investigation would provide the theoretic basis for quality standards and applications of Anoectochilus roxburghii in clinical research.
Collapse
|
45
|
Abstract
A collaborative study was conducted on AOAC First Action Method 2011.20: 5'-Mononucleotides in Infant Formula and Adult/Pediatric Nutritional Formula. After the successful analysis of National Institute of Standards and Technology (NIST) 1849a Standard Reference Material (SRM) as a practice sample, 12 laboratories participated in the analysis of duplicate samples of six different infant formula products. The samples were dissolved in high-salt solution to inhibit protein and fat interactions, with the nucleotides [uridine 5'-monophosphate (UMP), inosine 5'-monophosphate (IMP), adenosine 5'-monophosphate (AMP), guanosine 5'-monophosphate (GMP), and cytidine 5'-monophosphate (CMP)] separated from the sample matrix by strong-anion exchange SPE, followed by chromatographic analysis using a C18 stationary phase with gradient elution, UV detection, and quantitation by an internal standard technique using thymidine 5'-monophosphate. For nucleotide-supplemented products, precision is within the Standard Method Performance RequirementsSM (SMPR) 2011.008 target reproducibility limit of ≤11%, with the reproducibility RSD (RSDR) estimated at 7.1-8.7% for CMP, 7.9-9.0% for UMP, 2.8-7.7% for GMP, 5.5-10.3% for IMP, and 2.7-6.2% for AMP, and Horwitz ratio (HorRat) values of 0.9-1.0 for CMP, 0.9-1.0 for UMP, 0.3-0.7 for GMP, 0.6-1.0 for IMP, and 0.3-0.7 for AMP.
Collapse
Affiliation(s)
- Brendon D Gill
- Fonterra Co-operative Group Ltd, PO Box 7, Waitoa 3341, New Zealand
| | | |
Collapse
|
46
|
Al-Shehri SS, Knox CL, Liley HG, Cowley DM, Wright JR, Henman MG, Hewavitharana AK, Charles BG, Shaw PN, Sweeney EL, Duley JA. Breastmilk-Saliva Interactions Boost Innate Immunity by Regulating the Oral Microbiome in Early Infancy. PLoS One 2015; 10:e0135047. [PMID: 26325665 PMCID: PMC4556682 DOI: 10.1371/journal.pone.0135047] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 07/16/2015] [Indexed: 01/06/2023] Open
Abstract
INTRODUCTION Xanthine oxidase (XO) is distributed in mammals largely in the liver and small intestine, but also is highly active in milk where it generates hydrogen peroxide (H2O2). Adult human saliva is low in hypoxanthine and xanthine, the substrates of XO, and high in the lactoperoxidase substrate thiocyanate, but saliva of neonates has not been examined. RESULTS Median concentrations of hypoxanthine and xanthine in neonatal saliva (27 and 19 μM respectively) were ten-fold higher than in adult saliva (2.1 and 1.7 μM). Fresh breastmilk contained 27.3 ± 12.2 μM H2O2 but mixing baby saliva with breastmilk additionally generated >40 μM H2O2, sufficient to inhibit growth of the opportunistic pathogens Staphylococcus aureus and Salmonella spp. Oral peroxidase activity in neonatal saliva was variable but low (median 7 U/L, range 2-449) compared to adults (620 U/L, 48-1348), while peroxidase substrate thiocyanate in neonatal saliva was surprisingly high. Baby but not adult saliva also contained nucleosides and nucleobases that encouraged growth of the commensal bacteria Lactobacillus, but inhibited opportunistic pathogens; these nucleosides/bases may also promote growth of immature gut cells. Transition from neonatal to adult saliva pattern occurred during the weaning period. A survey of saliva from domesticated mammals revealed wide variation in nucleoside/base patterns. DISCUSSION AND CONCLUSION During breast-feeding, baby saliva reacts with breastmilk to produce reactive oxygen species, while simultaneously providing growth-promoting nucleotide precursors. Milk thus plays more than a simply nutritional role in mammals, interacting with infant saliva to produce a potent combination of stimulatory and inhibitory metabolites that regulate early oral-and hence gut-microbiota. Consequently, milk-saliva mixing appears to represent unique biochemical synergism which boosts early innate immunity.
Collapse
Affiliation(s)
- Saad S Al-Shehri
- School of Pharmacy, The University of Queensland, Brisbane, Australia; College of Applied Medical Science, Taif University, Taif, Saudi Arabia
| | - Christine L Knox
- Institute of Health and Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - Helen G Liley
- Mater Research Institute, Mater Health Services, Brisbane, Australia
| | - David M Cowley
- Mater Research Institute, Mater Health Services, Brisbane, Australia
| | - John R Wright
- School of Veterinary Science, The University of Queensland, Gatton, Australia
| | - Michael G Henman
- Mater Research Institute, Mater Health Services, Brisbane, Australia
| | | | - Bruce G Charles
- School of Pharmacy, The University of Queensland, Brisbane, Australia
| | - Paul N Shaw
- School of Pharmacy, The University of Queensland, Brisbane, Australia
| | - Emma L Sweeney
- Institute of Health and Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - John A Duley
- School of Pharmacy, The University of Queensland, Brisbane, Australia; Mater Research Institute, Mater Health Services, Brisbane, Australia
| |
Collapse
|
47
|
Abstract
In angiosperms, gene conversion has been known to reduce the mutational load of plastid genomes (the plastomes). Particularly, more frequent gene conversions in inverted repeat (IR) than in single copy (SC) regions result in contrasting substitution rates between these two regions. However, little has been known about the effect of gene conversion in the evolution of gymnosperm plastomes. Cycads (Cycadophyta) are the second largest gymnosperm group. Evolutionary study of their plastomes is limited to the basal cycad genus, Cycas. In this study, we addressed three questions. 1) Do the plastomes of other cycad genera evolve slowly as previously observed in the plastome of Cycas taitungensis? 2) Do substitution rates differ between their SC and IR regions? And 3) Does gene conversion occur in the cycad plastomes? If yes, is it AT-biased or GC-biased? Plastomes of eight species from other eight genera of cycads were sequenced. These plastomes are highly conserved in genome organization. Excluding ginkgo, cycad plastomes have significantly lower synonymous and nonsynonymous substitution rates than other gymnosperms, reflecting their evolutionary stasis in nucleotide mutations. In the IRs of cycad plastomes, the reduced substitution rates and GC-biased mutations are associated with a GC-biased gene conversion (gBGC) mechanism. Further investigations suggest that in cycads, gBGC is able to rectify plastome-wide mutations. Therefore, this study is the first to uncover the plastomic gBGC in seed plants. We also propose a gBGC model to interpret the dissimilar evolutionary patterns as well as the compositionally biased mutations in the SC and IR regions of cycad plastomes.
Collapse
Affiliation(s)
- Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
48
|
Ogura R, Kumano S, Matsuzaki T, Sakata T. High-pressure liquid chromatography of free nucleotide patterns in normal and abnormal keratinocytes. Curr Probl Dermatol 2015; 10:279-93. [PMID: 6165523 DOI: 10.1159/000396296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A method for analyzing free nucleotides in the epidermis of the guinea pig is presented. Free nucleotides were extracted by using a methylalethanol mixture, and the analysis was carried out by high-pressure liquid chromatography on a column of Lichrosorb-NH2 with a single buffer of potassium phosphate. The concentration of total free nucleotides in the epidermis is about 4 times greater than that in the liver, kidney, spleen, or intestinal epithelium.l The free nucleotide level is markedly elevated in the hyperkeratotic epidermis induced by n-hexadecane. The alternation of free nucleotides in hyperkeratotic epidermis is discussed in relation to nucleic acid content, DNase, disc-electrophoretic properties of DNase, and salvage pathway enzymatic activity. Significant increases in the enzyme activity of the salvage pathway and in neutral DNase were observed in the hyperkeratotic stage. However, the DNA content and acid DNase activity were decreased. It is suggested that the pool size of free nucleotides in the epidermis is affected by the salvage enzyme system.
Collapse
|
49
|
Reichenberger ER, Rosen G, Hershberg U, Hershberg R. Prokaryotic nucleotide composition is shaped by both phylogeny and the environment. Genome Biol Evol 2015; 7:1380-9. [PMID: 25861819 PMCID: PMC4453058 DOI: 10.1093/gbe/evv063] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2015] [Indexed: 02/07/2023] Open
Abstract
The causes of the great variation in nucleotide composition of prokaryotic genomes have long been disputed. Here, we use extensive metagenomic and whole-genome data to demonstrate that both phylogeny and the environment shape prokaryotic nucleotide content. We show that across environments, various phyla are characterized by different mean guanine and cytosine (GC) values as well as by the extent of variation on that mean value. At the same time, we show that GC-content varies greatly as a function of environment, in a manner that cannot be entirely explained by disparities in phylogenetic composition. We find environmentally driven differences in nucleotide content not only between highly diverged environments (e.g., soil, vs. aquatic vs. human gut) but also within a single type of environment. More specifically, we demonstrate that some human guts are associated with a microbiome that is consistently more GC-rich across phyla, whereas others are associated with a more AT-rich microbiome. These differences appear to be driven both by variations in phylogenetic composition and by environmental differences-which are independent of these phylogenetic composition differences. Combined, our results demonstrate that both phylogeny and the environment significantly affect nucleotide composition and that the environmental differences affecting nucleotide composition are far subtler than previously appreciated.
Collapse
Affiliation(s)
- Erin R Reichenberger
- Department of Biomedical Engineering, Science & Health Systems, Drexel University
| | - Gail Rosen
- Department of Computer and Electrical Engineering, Drexel University
| | - Uri Hershberg
- Department of Biomedical Engineering, Science & Health Systems, Drexel University Department of Microbiology and Immunology, Drexel University College of Medicine
| | - Ruth Hershberg
- Rachel and Menachem Mendelovitch Evolutionary Processes of Mutation and Natural Selection Research Laboratory, Department of Genetics and Developmental Biology, The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| |
Collapse
|
50
|
Kolodziej K, Romanowska J, Stawinski J, Kraszewski A, Sobkowski M. The case of triethylammonium cation loss during purification of certain nucleotide analogues: a cautionary note. Anal Bioanal Chem 2015; 407:1775-80. [PMID: 25542580 PMCID: PMC4329187 DOI: 10.1007/s00216-014-8397-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 11/20/2014] [Accepted: 12/08/2014] [Indexed: 10/25/2022]
Abstract
Nucleotides, their analogues, and other phosphate esters and phosphoramidates often contain the triethylammonium cation as a counterion. We found that this may be lost during chromatographic purification or concentration of solutions, yielding products in acidic forms or containing sub-stoichiometric amounts of the counterion. This in turn may be detrimental, e.g., due to possible decomposition of a compound or inaccurate sample preparation. Correlations between the structure of studied compounds and their susceptibility for cation loss were analyzed. Modifications in preparative techniques were developed to obtain the studied compounds with stoichiometric anion to cation ratios.
Collapse
Affiliation(s)
- Krystian Kolodziej
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Joanna Romanowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Jacek Stawinski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Adam Kraszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Michal Sobkowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| |
Collapse
|