1
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Ji J, Sharma A, Pokhrel P, Karna D, Pandey S, Zheng YR, Mao H. Dynamic Structures and Fast Transition Kinetics of Oxidized G-Quadruplexes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2400485. [PMID: 38678502 PMCID: PMC11357892 DOI: 10.1002/smll.202400485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/04/2024] [Indexed: 05/01/2024]
Abstract
8-oxoguanines (8-oxoG) in cells form compromised G-quadruplexes (GQs), which may vary GQ mediated gene regulations. By mimicking molecularly crowded cellular environment using 40% DMSO or sucrose, here it is found that oxidized human telomeric GQs have stabilities close to the wild-type (WT) GQs. Surprisingly, while WT GQs show negative formation cooperativity between a Pt(II) binder and molecularly crowded environment, positive cooperativity is observed for oxidized GQ formation. Single-molecule mechanical unfolding reveals that 8-oxoG sequence formed more diverse and flexible structures with faster folding/unfolding transition kinetics, which facilitates the Pt(II) ligand to bind the best-fit structures with positive cooperativity. These findings offer new understanding on structures and properties of oxidized G-rich species in crowded environments. They also provide insights into the design of better ligands to target oxidized G-rich structures formed under oxidative cell stress.
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Affiliation(s)
- Jiahao Ji
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Arpit Sharma
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Pravin Pokhrel
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Deepak Karna
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Shankar Pandey
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Yao-Rong Zheng
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Hanbin Mao
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
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2
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Lau MH, Madika A, Zhang Y, Minton NP. Parageobacillus thermoglucosidasius Strain Engineering Using a Theophylline Responsive RiboCas for Controlled Gene Expression. ACS Synth Biol 2024; 13:1237-1245. [PMID: 38517011 PMCID: PMC11036489 DOI: 10.1021/acssynbio.3c00735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/23/2024]
Abstract
The relentless increase in atmospheric greenhouse gas concentrations as a consequence of the exploitation of fossil resources compels the adoption of sustainable routes to chemical and fuel manufacture based on biological fermentation processes. The use of thermophilic chassis in such processes is an attractive proposition; however, their effective exploitation will require improved genome editing tools. In the case of the industrially relevant chassis Parageobacillus thermoglucosidasius, CRISPR/Cas9-based gene editing has been demonstrated. The constitutive promoter used, however, accentuates the deleterious nature of Cas9, causing decreased transformation and low editing efficiencies, together with an increased likelihood of off-target effects or alternative mutations. Here, we rectify this issue by controlling the expression of Cas9 through the use of a synthetic riboswitch that is dependent on the nonmetabolized, nontoxic, and cheap inducer, theophylline. We demonstrate that the riboswitches are dose-dependent, allowing for controlled expression of the target gene. Through their use, we were then able to address the deleterious nature of Cas9 and produce an inducible system, RiboCas93. The benefits of RiboCas93 were demonstrated by increased transformation efficiency of the editing vectors, improved efficiency in mutant generation (100%), and a reduction of Cas9 toxicity, as indicated by a reduction in the number of single nucleotide polymorphisms (SNPs) observed. This new system provides a quick and efficient way to produce mutants in P. thermoglucosidasius.
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Affiliation(s)
- Matthew
S. H. Lau
- BBSRC/EPSRC
Synthetic Biology Research Centre (SBRC), Biodiscovery Institute,
School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K.
| | - Abubakar Madika
- BBSRC/EPSRC
Synthetic Biology Research Centre (SBRC), Biodiscovery Institute,
School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K.
- Department
of Microbiology, Faculty of Life Sciences, Ahmadu Bello University, Zaria 810107, Nigeria
| | - Ying Zhang
- BBSRC/EPSRC
Synthetic Biology Research Centre (SBRC), Biodiscovery Institute,
School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K.
| | - Nigel P. Minton
- BBSRC/EPSRC
Synthetic Biology Research Centre (SBRC), Biodiscovery Institute,
School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K.
- NIHR
Nottingham Biomedical Research Centre, Nottingham
University Hospitals NHS Trust and The University of Nottingham, Nottingham NG7 2RD, U.K.
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3
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Mathur N, Singh A, Singh N. Force-induced unzipping of DNA in the presence of solvent molecules. Biophys Chem 2024; 307:107175. [PMID: 38244296 DOI: 10.1016/j.bpc.2024.107175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 01/22/2024]
Abstract
The melting of double-stranded DNA (dsDNA) in the presence of solvent molecules is a fundamental process with significant implications for understanding the thermal and mechanical behavior of DNA and its interactions with the surrounding environment. The solvents play an essential role in the structural transformation of DNA subjected to a pulling force. In this study, we simulate the thermal and force induced denaturation of dsDNA and elucidate the solvent dependent melting behavior, identifying key factors that influence the stability of DNA melting in presence of solvent molecules. Using a statistical model, we first find the melting profile of short heterogeneous DNA molecules in the presence of solvent molecules in Force ensemble. We also investigate the effect of solvent's strengths on the melting profile of DNA. In the force ensemble, we consider two homogeneous DNA chains and apply the force on different locations along the chain in the presence of solvent molecules. Different pathways manifest the melting of the molecule in both ensembles, and we found several interesting features of melting DNA in a constant force ensemble, such as lower critical force when the chain is pulled from the base pair close to a solvent molecule. The results provide new insights into the force-induced unzipping of DNA and could be used to develop new methods for controlling the unzipping process. By providing a better understanding of melting and unzipping of dsDNA in the presence of solvent molecules, this study provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA nanostructures.
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Affiliation(s)
- Neha Mathur
- Birla Institute of Technology & Science, Pilani 333031, India
| | - Amar Singh
- Birla Institute of Technology & Science, Pilani 333031, India.
| | - Navin Singh
- Birla Institute of Technology & Science, Pilani 333031, India
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4
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Xu MR, Sun FC, Yang BC, Chen HJ, Lin CH, Cheng JH, Lee MS. Genetic Authentication of the Medicinal Plant Portulaca oleracea Using a Quick, Precise, and Sensitive Isothermal DNA Amplification Assay. Int J Mol Sci 2023; 24:10730. [PMID: 37445904 DOI: 10.3390/ijms241310730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Portulaca oleracea (PO) is a commonly known medicinal crop that is an important ingredient for traditional Chinese medicine (TCM) due to its use as a vegetable in the diet. PO has been recorded to be frequently adulterated by other related species in the market of herbal plants, distorting the PO plant identity. Thus, identification of the botanical origin of PO is a crucial step before pharmaceutical or functional food application. In this research, a quick assay named "loop-mediated isothermal amplification (LAMP)" was built for the specific and sensitive authentication of PO DNA. On the basis of the divergences in the internal transcribed spacer 2 (ITS2) sequence between PO and its adulterant species, the LAMP primers were designed and verified their specificity, sensitivity, and application for the PO DNA authentication. The detection limit of the LAMP assay for PO DNA identification specifically was 100 fg under isothermal conditions at 63 °C for 30 min. In addition, different heat-processed PO samples can be applied for use in PO authentication in the LAMP assay. These samples of PO were more susceptible to the effect of steaming in authentication by PCR than boiling and drying treatment. Furthermore, commercial PO samples pursued from herbal markets were used to display their applicability of the developed LAMP analysis for PO postharvest authentication, and the investigation found that approximately 68.4% of PO specimens in the marketplace of herbal remedies were adulterated. In summary, the specific, sensitive, and rapid LAMP assay for PO authentication was first successfully developed herein, and its practical application for the inspection of adulteration in PO samples from the herbal market was shown. This LAMP assay created in this study will be useful to authenticate the botanical origin of PO and its commercial products.
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Affiliation(s)
- Mo-Rong Xu
- Department of Chinese Pharmaceutical Science and Chinese Medicine Resources, China Medical University, Taichung 40402, Taiwan
| | - Fang-Chun Sun
- Department of Medicinal Botanicals and Foods on Health Applications, Da-Yeh University, Changhua 515006, Taiwan
| | - Bo-Cheng Yang
- Department of Chinese Pharmaceutical Science and Chinese Medicine Resources, China Medical University, Taichung 40402, Taiwan
| | - Hsi-Jien Chen
- Department of Safety, Health and Environmental Engineering, Ming Chi University of Technology, New Taipei City 24301, Taiwan
| | - Chia-Hsin Lin
- Department of Chinese Pharmaceutical Science and Chinese Medicine Resources, China Medical University, Taichung 40402, Taiwan
| | - Jai-Hong Cheng
- Center for Shockwave Medicine and Tissue Engineering, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung 833, Taiwan
| | - Meng-Shiou Lee
- Department of Chinese Pharmaceutical Science and Chinese Medicine Resources, China Medical University, Taichung 40402, Taiwan
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5
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Chen L, Wang Y, Yang G. Locally Denatured DNA Compaction by Divalent Cations. J Phys Chem B 2023. [PMID: 37205854 DOI: 10.1021/acs.jpcb.3c01858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The denaturation of DNA is a critical process in biology and has many biotechnological applications. We investigated the compaction of locally denatured DNA by a chemical denaturation agent, dimethyl sulfoxide (DMSO), using magnetic tweezers (MTs), atomic force microscopy (AFM), and dynamic light scattering (DLS). Our results show that DMSO not only is capable of denaturing DNA but also able to compact DNA directly. When the DMSO concentration is above 10%, DNA condensation occurs due to the reduction in the persistence length of DNA and excluded volume interactions. Meanwhile, locally denatured DNA is easily condensed by divalent cations, such as magnesium ions (Mg2+), contrasting with no native DNA condensation by the classical divalent cations. Specifically, the addition of more than 3 mM Mg2+ to a 5% DMSO solution leads to DNA condensation. The critical condensing force (FC) increases from 6.4 to 9.5 pN when the Mg2+ concentration grows from 3 to 10 mM. However, FC decreases gradually with a further increase in Mg2+ concentration. For 3% DMSO solution, above 30 mM Mg2+ is needed to compact DNA and a weaker condensing force was measured. With increasing Mg2+ concentration, the morphology of the DMSO partially denatured DNA complex changes from loosely random coils to a dense network structure, even forming a spherical condensation nucleus, and finally to a partially disintegrated network. These findings show that the elasticity of DNA plays an important role in its denaturation and condensation behavior.
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Affiliation(s)
- Ling Chen
- Department of Physics, Wenzhou University, Wenzhou, Zhejiang 325035, China
| | - Yanwei Wang
- Department of Physics, Wenzhou University, Wenzhou, Zhejiang 325035, China
| | - Guangcan Yang
- Department of Physics, Wenzhou University, Wenzhou, Zhejiang 325035, China
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6
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Xu M, Dai T, Wang Y, Yang G. The incipient denaturation mechanism of DNA. RSC Adv 2022; 12:23356-23365. [PMID: 36090395 PMCID: PMC9383117 DOI: 10.1039/d2ra02480b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/19/2022] [Indexed: 11/21/2022] Open
Abstract
DNA denaturation is related to many important biological phenomena, such as its replication, transcription and the interaction with some specific proteins for single-stranded DNA. Dimethyl sulfoxide (DMSO) is a common chemical agent for DNA denaturation. In the present study, we investigate quantitatively the effects of different concentrations of DMSO on plasmid and linear DNA denaturation by atomic force microscopy (AFM) and UV spectrophotometry. We found that persistent length of DNA decreases significantly by adding a small amount of DMSO before ensemble DNA denaturation occurs; the persistence length of DNA in 3% DMSO solution decreases to 12 nm from about 50 nm without DMSO in solution. And local DNA denaturation occurs even at very low DMSO concentration (such as 0.1%), which can be directly observed in AFM imaging. Meanwhile, we observed the forming process of DNA contacts between different parts for plasmid DNA with increasing DMSO concentration. We suggest the initial mechanism of DNA denaturation as follows: DNA becomes more flexible due to the partial hydrogen bond braking in the presence of DMSO before local separation of the two complementary nucleotide chains. The persistent length of DNA decreases significantly by adding small amount of DMSO. Local DNA denaturation occurs even at very low DMSO concentration, which can be observed by atomic force microscopy directly.![]()
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Affiliation(s)
- Min Xu
- Department of Physics, Wenzhou University, Wenzhou 325035, China
| | - Tinghui Dai
- Department of Physics, Wenzhou University, Wenzhou 325035, China
| | - Yanwei Wang
- Department of Physics, Wenzhou University, Wenzhou 325035, China
| | - Guangcan Yang
- Department of Physics, Wenzhou University, Wenzhou 325035, China
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7
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Kennedy‐Darling J, Bhate SS, Hickey JW, Black S, Barlow GL, Vazquez G, Venkataraaman VG, Samusik N, Goltsev Y, Schürch CM, Nolan GP. Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction. Eur J Immunol 2021; 51:1262-1277. [PMID: 33548142 PMCID: PMC8251877 DOI: 10.1002/eji.202048891] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 11/21/2020] [Accepted: 02/04/2021] [Indexed: 01/04/2023]
Abstract
Multiparameter tissue imaging enables analysis of cell-cell interactions in situ, the cellular basis for tissue structure, and novel cell types that are spatially restricted, giving clues to biological mechanisms behind tissue homeostasis and disease. Here, we streamlined and simplified the multiplexed imaging method CO-Detection by indEXing (CODEX) by validating 58 unique oligonucleotide barcodes that can be conjugated to antibodies. We showed that barcoded antibodies retained their specificity for staining cognate targets in human tissue. Antibodies were visualized one at a time by adding a fluorescently labeled oligonucleotide complementary to oligonucleotide barcode, imaging, stripping, and repeating this cycle. With this we developed a panel of 46 antibodies that was used to stain five human lymphoid tissues: three tonsils, a spleen, and a LN. To analyze the data produced, an image processing and analysis pipeline was developed that enabled single-cell analysis on the data, including unsupervised clustering, that revealed 31 cell types across all tissues. We compared cell-type compositions within and directly surrounding follicles from the different lymphoid organs and evaluated cell-cell density correlations. This sequential oligonucleotide exchange technique enables a facile imaging of tissues that leverages pre-existing imaging infrastructure to decrease the barriers to broad use of multiplexed imaging.
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Affiliation(s)
- Julia Kennedy‐Darling
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Akoya Biosciences1505 O'Brien DriveMenlo ParkCAUSA
| | - Salil S. Bhate
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
- Department of BioengineeringStanford UniversityStanfordCAUSA
| | - John W. Hickey
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
| | - Sarah Black
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
| | - Graham L. Barlow
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
| | - Gustavo Vazquez
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
| | - Vishal G. Venkataraaman
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
| | - Nikolay Samusik
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Becton DickinsonSan JoseCAUSA
| | - Yury Goltsev
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
| | - Christian M. Schürch
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
- Department of Pathology and NeuropathologyUniversity Hospital and Comprehensive Cancer Center TübingenTübingenGermany
| | - Garry P. Nolan
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
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8
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Baek MS, Lee KH, Byun JY, Shin YB, Kim DM. Aptamer-linked in vitro expression assay for ultrasensitive detection of biomarkers. Anal Chim Acta 2020; 1146:118-123. [PMID: 33461706 DOI: 10.1016/j.aca.2020.12.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 12/02/2020] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
Signal amplification is a key step that determines the sensitivity of molecular assays. Although studies on aptamers have mostly focused on their target-binding ability, taking advantage of the gene-coding function of nucleic acids, we demonstrate here that aptamers can be engineered into diagnostic reagents that can both recognize a target and generate highly amplified detection signals. We developed a strategy that employs a 'readable' aptamer that consists of a single-stranded aptamer and a double-stranded reporter gene. After binding to its target via the aptamer region, the reporter gene of the readable aptamer produces amplified number of signal-generating enzymes through a subsequent in vitro expression reaction. In contrast to conventional enzyme-conjugation methods, this method allows the generation of far more amplified detection signals, thereby markedly increasing the sensitivity of detection enough to analyze a target present in aM concentrations.
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Affiliation(s)
- Min-Seok Baek
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 34134, South Korea
| | - Kyung-Ho Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 34134, South Korea
| | - Ju-Young Byun
- BioNano Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea
| | - Yong-Beom Shin
- BioNano Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea; BioNano Health Guard Research Center (H-GUARD), Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 34141, South Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 34134, South Korea.
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9
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Smith LD, Willard MC, Smith JP, Cunningham BT. Development of a Linker-Mediated Immunoassay Using Chemically Transitioned Nanosensors. Anal Chem 2020; 92:3627-3635. [DOI: 10.1021/acs.analchem.9b04518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Lucas D. Smith
- Department of Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro & Nanotechnology Lab, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- EnterpriseWorks, University of Illinois at Urbana−Champaign, Champaign, Illinois 61820, United States
| | - Michael C. Willard
- EnterpriseWorks, University of Illinois at Urbana−Champaign, Champaign, Illinois 61820, United States
| | - Jordan P. Smith
- EnterpriseWorks, University of Illinois at Urbana−Champaign, Champaign, Illinois 61820, United States
| | - Brian T. Cunningham
- Department of Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro & Nanotechnology Lab, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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10
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Schlichting N, Reinhardt F, Jager S, Schmidt M, Kabisch J. Optimization of the experimental parameters of the ligase cycling reaction. Synth Biol (Oxf) 2019; 4:ysz020. [PMID: 32995543 PMCID: PMC7445781 DOI: 10.1093/synbio/ysz020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 05/22/2019] [Accepted: 06/18/2019] [Indexed: 11/23/2022] Open
Abstract
The ligase cycling reaction (LCR) is a scarless and efficient method to assemble plasmids from fragments of DNA. This assembly method is based on the hybridization of DNA fragments with complementary oligonucleotides, so-called bridging oligos (BOs), and an experimental procedure of thermal denaturation, annealing and ligation. In this study, we explore the effect of molecular crosstalk of BOs and various experimental parameters on the LCR by utilizing a fluorescence-based screening system. The results indicate an impact of the melting temperatures of BOs on the overall success of the LCR assembly. Secondary structure inhibitors, such as dimethyl sulfoxide and betaine, are shown to negatively impact the number of correctly assembled plasmids. Adjustments of the annealing, ligation and BO-melting temperature further improved the LCR. The optimized LCR was confirmed by validation experiments. Based on these findings, a step-by-step protocol is offered within this study to ensure a routine for high efficient LCR assemblies.
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Affiliation(s)
- Niels Schlichting
- Department of Biology, Computer-Aided Synthetic Biology, TU Darmstadt, Darmstadt, Germany
| | - Felix Reinhardt
- Department of Physics, Computational Biology and Simulation, TU Darmstadt, Darmstadt, Germany
| | - Sven Jager
- Department of Physics, Computational Biology and Simulation, TU Darmstadt, Darmstadt, Germany
| | - Michael Schmidt
- Department of Physics, Computational Biology and Simulation, TU Darmstadt, Darmstadt, Germany
| | - Johannes Kabisch
- Department of Biology, Computer-Aided Synthetic Biology, TU Darmstadt, Darmstadt, Germany
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11
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Taemaitree L, Shivalingam A, El-Sagheer AH, Brown T. An artificial triazole backbone linkage provides a split-and-click strategy to bioactive chemically modified CRISPR sgRNA. Nat Commun 2019; 10:1610. [PMID: 30962447 PMCID: PMC6453947 DOI: 10.1038/s41467-019-09600-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 03/18/2019] [Indexed: 12/26/2022] Open
Abstract
As the applications of CRISPR-Cas9 technology diversify and spread beyond the laboratory to diagnostic and therapeutic use, the demands of gRNA synthesis have increased and access to tailored gRNAs is now restrictive. Enzymatic routes are time-consuming, difficult to scale-up and suffer from polymerase-bias while existing chemical routes are inefficient. Here, we describe a split-and-click convergent chemical route to individual or pools of sgRNAs. The synthetic burden is reduced by splitting the sgRNA into a variable DNA/genome-targeting 20-mer, produced on-demand and in high purity, and a fixed Cas9-binding chemically-modified 79-mer, produced cost-effectively on large-scale, a strategy that provides access to site-specific modifications that enhance sgRNA activity and in vivo stability. Click ligation of the two components generates an artificial triazole linkage that is tolerated in functionally critical regions of the sgRNA and allows efficient DNA cleavage in vitro as well as gene-editing in cells with no unexpected off-target effects.
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Affiliation(s)
- Lapatrada Taemaitree
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Arun Shivalingam
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez, 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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12
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Duchemin N, Skiredj A, Mansot J, Leblanc K, Vasseur J, Beniddir MA, Evanno L, Poupon E, Smietana M, Arseniyadis S. DNA‐Templated [2+2] Photocycloaddition: A Straightforward Entry into the Aplysinopsin Family of Natural Products. Angew Chem Int Ed Engl 2018; 57:11786-11791. [DOI: 10.1002/anie.201806357] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Nicolas Duchemin
- Queen Mary University of LondonSchool of Biological and Chemical Sciences Mile End Road London E1 4NS UK
| | - Adam Skiredj
- Laboratoire de Pharmacognosie associé au CNRS, UMR 8076 BioCISUniversité Paris-SudUniversité Paris-Saclay 5 rue Jean-Baptiste Clément 92296 Châtenay-Malabry France
| | - Justine Mansot
- Institut des Biomolécules Max MousseronCNRS, UMR 5247 Université de MontpellierENSCM Place Eugène Bataillon 34095 Montpellier France
| | - Karine Leblanc
- Laboratoire de Pharmacognosie associé au CNRS, UMR 8076 BioCISUniversité Paris-SudUniversité Paris-Saclay 5 rue Jean-Baptiste Clément 92296 Châtenay-Malabry France
| | - Jean‐Jacques Vasseur
- Institut des Biomolécules Max MousseronCNRS, UMR 5247 Université de MontpellierENSCM Place Eugène Bataillon 34095 Montpellier France
| | - Mehdi A. Beniddir
- Laboratoire de Pharmacognosie associé au CNRS, UMR 8076 BioCISUniversité Paris-SudUniversité Paris-Saclay 5 rue Jean-Baptiste Clément 92296 Châtenay-Malabry France
| | - Laurent Evanno
- Laboratoire de Pharmacognosie associé au CNRS, UMR 8076 BioCISUniversité Paris-SudUniversité Paris-Saclay 5 rue Jean-Baptiste Clément 92296 Châtenay-Malabry France
| | - Erwan Poupon
- Laboratoire de Pharmacognosie associé au CNRS, UMR 8076 BioCISUniversité Paris-SudUniversité Paris-Saclay 5 rue Jean-Baptiste Clément 92296 Châtenay-Malabry France
| | - Michael Smietana
- Institut des Biomolécules Max MousseronCNRS, UMR 5247 Université de MontpellierENSCM Place Eugène Bataillon 34095 Montpellier France
| | - Stellios Arseniyadis
- Queen Mary University of LondonSchool of Biological and Chemical Sciences Mile End Road London E1 4NS UK
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13
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Duchemin N, Skiredj A, Mansot J, Leblanc K, Vasseur JJ, Beniddir MA, Evanno L, Poupon E, Smietana M, Arseniyadis S. DNA-Templated [2+2] Photocycloaddition: A Straightforward Entry into the Aplysinopsin Family of Natural Products. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806357] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Nicolas Duchemin
- Queen Mary University of London; School of Biological and Chemical Sciences; Mile End Road London E1 4NS UK
| | - Adam Skiredj
- Laboratoire de Pharmacognosie associé au CNRS, UMR 8076 BioCIS; Université Paris-Sud; Université Paris-Saclay; 5 rue Jean-Baptiste Clément 92296 Châtenay-Malabry France
| | - Justine Mansot
- Institut des Biomolécules Max Mousseron; CNRS, UMR 5247 Université de Montpellier; ENSCM; Place Eugène Bataillon 34095 Montpellier France
| | - Karine Leblanc
- Laboratoire de Pharmacognosie associé au CNRS, UMR 8076 BioCIS; Université Paris-Sud; Université Paris-Saclay; 5 rue Jean-Baptiste Clément 92296 Châtenay-Malabry France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron; CNRS, UMR 5247 Université de Montpellier; ENSCM; Place Eugène Bataillon 34095 Montpellier France
| | - Mehdi A. Beniddir
- Laboratoire de Pharmacognosie associé au CNRS, UMR 8076 BioCIS; Université Paris-Sud; Université Paris-Saclay; 5 rue Jean-Baptiste Clément 92296 Châtenay-Malabry France
| | - Laurent Evanno
- Laboratoire de Pharmacognosie associé au CNRS, UMR 8076 BioCIS; Université Paris-Sud; Université Paris-Saclay; 5 rue Jean-Baptiste Clément 92296 Châtenay-Malabry France
| | - Erwan Poupon
- Laboratoire de Pharmacognosie associé au CNRS, UMR 8076 BioCIS; Université Paris-Sud; Université Paris-Saclay; 5 rue Jean-Baptiste Clément 92296 Châtenay-Malabry France
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron; CNRS, UMR 5247 Université de Montpellier; ENSCM; Place Eugène Bataillon 34095 Montpellier France
| | - Stellios Arseniyadis
- Queen Mary University of London; School of Biological and Chemical Sciences; Mile End Road London E1 4NS UK
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14
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Belahbib H, Summers ZM, Fardeau ML, Joseph M, Tamburini C, Dolla A, Ollivier B, Armougom F. Towards a congruent reclassification and nomenclature of the thermophilic species of the genus Pseudothermotoga within the order Thermotogales. Syst Appl Microbiol 2018; 41:555-563. [PMID: 29801938 DOI: 10.1016/j.syapm.2018.04.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 04/20/2018] [Accepted: 04/27/2018] [Indexed: 11/24/2022]
Abstract
The phylum Thermotogae gathers thermophilic, hyperthermophic, mesophilic, and thermo-acidophilic anaerobic bacteria that are mostly originated from geothermally heated environments. The metabolic and phenotypic properties harbored by the Thermotogae species questions the evolutionary events driving the emergence of this early branch of the universal tree of life. Recent reshaping of the Thermotogae taxonomy has led to the description of a new genus, Pseudothermotoga, a sister group of the genus Thermotoga within the order Thermotogales. Comparative genomics of both Pseudothermotoga and Thermotoga spp., including 16S-rRNA-based phylogenetic, pan-genomic analysis as well as signature indel conservation, provided evidence that Thermotoga caldifontis and Thermotoga profunda species should be reclassified within the genus Pseudothermotoga and renamed as Pseudothermotoga caldifontis comb. nov. (type strain=AZM44c09T) and Pseudothermotoga profunda comb. nov. (type strain=AZM34c06T), respectively. In addition, based upon whole-genome relatedness indices and DNA-DNA Hybridization results, the reclassification of Pseudothermotoga lettingae and Pseudothermotoga subterranea as latter heterotypic synonyms of Pseudothermotoga elfii is proposed. Finally, potential genetic elements resulting from the distinct evolutionary story of the Thermotoga and Pseudothermotoga clades are discussed.
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Affiliation(s)
- Hassiba Belahbib
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Zarath M Summers
- ExxonMobil Research and Engineering Company, 1545 Route 22 East, Annandale, NJ 08801, United States
| | | | - Manon Joseph
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | | | - Alain Dolla
- Aix Marseille Univ, CNRS, LCB, Marseille, France
| | - Bernard Ollivier
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Fabrice Armougom
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France.
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15
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Šmidlehner T, Piantanida I, Pescitelli G. Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids - tutorial. Beilstein J Org Chem 2018; 14:84-105. [PMID: 29441133 PMCID: PMC5789433 DOI: 10.3762/bjoc.14.5] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/13/2017] [Indexed: 01/19/2023] Open
Abstract
The structural characterization of non-covalent complexes between nucleic acids and small molecules (ligands) is of a paramount significance to bioorganic research. Highly informative methods about nucleic acid/ligand complexes such as single crystal X-ray diffraction or NMR spectroscopy cannot be performed under biologically compatible conditions and are extensively time consuming. Therefore, in search for faster methods which can be applied to conditions that are at least similar to the naturally occurring ones, a set of polarization spectroscopy methods has shown highly promising results. Electronic circular dichroism (ECD) is the most commonly used method for the characterization of the helical structure of DNA and RNA and their complexes with ligands. Less common but complementary to ECD, is flow-oriented linear dichroism (LD). Other methods such as vibrational CD (VCD) and emission-based methods (FDCD, CPL), can also be used for suitable samples. Despite the popularity of polarization spectroscopy in biophysics, aside several highly focused reviews on the application of these methods to DNA/RNA research, there is no systematic tutorial covering all mentioned methods as a tool for the characterization of adducts between nucleic acids and small ligands. This tutorial aims to help researchers entering the research field to organize experiments accurately and to interpret the obtained data reliably.
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Affiliation(s)
- Tamara Šmidlehner
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute; P. O. Box 180, 10002 Zagreb, Croatia
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute; P. O. Box 180, 10002 Zagreb, Croatia
| | - Gennaro Pescitelli
- Department of Chemistry, University of Pisa, via Moruzzi 13, Pisa, Italy
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16
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Ouattara AS, Le Mer J, Joseph M, Macarie H. Transfer of Pseudomonas pictorum Gray and Thornton 1928 to genus Stenotrophomonas as Stenotrophomonas pictorum comb. nov., and emended description of the genus Stenotrophomonas. Int J Syst Evol Microbiol 2017. [PMID: 28629502 DOI: 10.1099/ijsem.0.001880] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic taxonomic approach including analysis of phenotypic, physiological and genotypic characteristics, 16S rRNA gene sequence and DNA-DNA hybridization analysis was used to determine the most consistent affiliation of Pseudomonas pictorum. Pseudomonas pictorum ATCC 23328T exhibited phenotypic traits of members of the genus Stenotrophomonas including cellular fatty acid composition, quinone and limited range of substrates that could be used. Antibiotic susceptibility and physiological characteristics were determined. The DNA G+C content was 65.7 mol%. Phylogenetic analysis revealed that the type strains of Stenotrophomonas terrae, Stenotrophomonashumi, Stenotrophomonasnitritireducens and Stenotrophomonasacidaminiphila were the nearest relatives (16S rRNA gene sequence similarity of 98.0 to 98.8 %). All the other type strains of species of the genus Stenotrophomonas showed high 16S rRNA gene sequence similarities (96.8 to 97.2 %). DNA-DNA hybridizations revealed 31.0, 32.0, 43.3 and 43.6 % reassociation between Pseudomonas pictorum ATCC 23328T and the type strains of S. terrae, S. humi, S. nitritireducens and S. acidaminiphila, respectively. Our overall results indicate that Pseudomonas pictorum should be transferred to the genus Stenotrophomonas as a novel species of this genus, Stenotrophomonas pictorum comb. nov. Since the original description of the genus Stenotrophomonaswas made with only one species (Stenotrophomonasmaltophilia), an emendation of the genus description is proposed in order to match better with the characteristics of the eleven novel species assigned to this genus since then.
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Affiliation(s)
- Aboubakar Sidiki Ouattara
- Laboratoire de Microbiologie et de Biotechnologie Microbienne, Ecole Doctorale Sciences et Technologies, Université Ouaga 1 Pr Joseph KI ZERBO, 03 BP 7021, Ouagadougou 03, Burkina Faso
| | - Jean Le Mer
- Aix Marseille Univ, Univ Toulon, CNRS, IRD, MIO, Marseille, France
| | - Manon Joseph
- Aix Marseille Univ, Univ Toulon, CNRS, IRD, MIO, Marseille, France
| | - Hervé Macarie
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
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17
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Fuller JR, Rice PA. Target DNA bending by the Mu transpososome promotes careful transposition and prevents its reversal. eLife 2017; 6. [PMID: 28177285 PMCID: PMC5357137 DOI: 10.7554/elife.21777] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/07/2017] [Indexed: 12/19/2022] Open
Abstract
The transposition of bacteriophage Mu serves as a model system for understanding DDE transposases and integrases. All available structures of these enzymes at the end of the transposition reaction, including Mu, exhibit significant bends in the transposition target site DNA. Here we use Mu to investigate the ramifications of target DNA bending on the transposition reaction. Enhancing the flexibility of the target DNA or prebending it increases its affinity for transpososomes by over an order of magnitude and increases the overall reaction rate. This and FRET confirm that flexibility is interrogated early during the interaction between the transposase and a potential target site, which may be how other DNA binding proteins can steer selection of advantageous target sites. We also find that the conformation of the target DNA after strand transfer is involved in preventing accidental catalysis of the reverse reaction, as conditions that destabilize this conformation also trigger reversal. DOI:http://dx.doi.org/10.7554/eLife.21777.001 Pieces of DNA called transposons can move or copy themselves around the genome. Some viruses – such as HIV and Mu (a virus that infects bacteria) – act as transposons to hide their DNA by inserting it into their host’s genome. Mu, HIV and many transposons all work in the same, somewhat unusual way. Like many chemical reactions, joining DNAs together needs a source of energy to make it happen, yet these viruses and transposons do not need high energy inputs to work. In addition, they do not look for a specific DNA sequence to insert their DNA into. This gives them the advantage of inserting copies of their DNA anywhere in the host’s genome, but also means that multiple copies might mistakenly insert into each other. Visualizations of the insertion process show that the DNA that the viruses insert their DNA into is always bent like a U-turn. Why does this bending occur? It may be that the bending helps the virus to choose where in the DNA to insert and acts as a way to power the chemical reaction that joins the DNA. To investigate this possibility, Fuller and Rice performed experiments using purified fragments of DNA and the enzyme from Mu that does the DNA joining chemistry. The results revealed that making the insertion site DNA easier to bend made the insertion much faster. Furthermore, a mutant enzyme that struggled to bend the DNA had trouble keeping the chemistry going, and so the viral DNA would accidentally pop back out after it was joined. Thus the insertion site DNA is like a spring: the enzyme puts a lot of energy into bending it, but once the viral DNA has been inserted that energy is released to power the reaction to completion. Fuller and Rice conclude that if other proteins were to pre-bend or otherwise make the DNA more flexible, this would tell the DNA-joining enzyme where to insert, which helps explain the roles of known targeting proteins for Mu and HIV. Further work is now needed to investigate whether these other targeting proteins exist for other viruses and transposons, and to identify them. DOI:http://dx.doi.org/10.7554/eLife.21777.002
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Affiliation(s)
- James R Fuller
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
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18
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The structural stability and catalytic activity of DNA and RNA oligonucleotides in the presence of organic solvents. Biophys Rev 2016; 8:11-23. [PMID: 28510143 DOI: 10.1007/s12551-015-0188-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/03/2015] [Indexed: 01/02/2023] Open
Abstract
Organic solvents and apolar media are used in the studies of nucleic acids to modify the conformation and function of nucleic acids, to improve solubility of hydrophobic ligands, to construct molecular scaffolds for organic synthesis, and to study molecular crowding effects. Understanding how organic solvents affect nucleic acid interactions and identifying the factors that dominate solvent effects are important for the creation of oligonucleotide-based technologies. This review describes the structural and catalytic properties of DNA and RNA oligonucleotides in organic solutions and in aqueous solutions with organic cosolvents. There are several possible mechanisms underlying the effects of organic solvents on nucleic acid interactions. The reported results emphasize the significance of the osmotic pressure effect and the dielectric constant effect in addition to specific interactions with nucleic acid strands. This review will serve as a guide for the selection of solvent systems based on the purpose of the nucleic acid-based experiments.
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19
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Burmudžija A, Ratković Z, Muškinja J, Janković N, Ranković B, Kosanić M, Đorđević S. Ferrocenyl based pyrazoline derivatives with vanillic core: synthesis and investigation of their biological properties. RSC Adv 2016. [DOI: 10.1039/c6ra18977f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Synthesis of four novel series of ferrocenyl based pyrazoline derivatives with vanillic core are described and microbiological, BSA and DNA binding studies conducted.
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Affiliation(s)
- Adrijana Burmudžija
- Faculty of Science
- University of Kragujevac
- Department of Chemistry
- 34000 Kragujevac
- Serbia
| | - Zoran Ratković
- Faculty of Science
- University of Kragujevac
- Department of Chemistry
- 34000 Kragujevac
- Serbia
| | - Jovana Muškinja
- Faculty of Science
- University of Kragujevac
- Department of Chemistry
- 34000 Kragujevac
- Serbia
| | - Nenad Janković
- Faculty of Science
- University of Kragujevac
- Department of Chemistry
- 34000 Kragujevac
- Serbia
| | - Branislav Ranković
- Faculty of Science
- University of Kragujevac
- Department of Biology and Ecology
- 34000 Kragujevac
- Serbia
| | - Marijana Kosanić
- Faculty of Science
- University of Kragujevac
- Department of Biology and Ecology
- 34000 Kragujevac
- Serbia
| | - Snežana Đorđević
- National Poison Control Centre
- Military Medical Academy
- 11000 Belgrade
- Republic of Serbia
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20
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Song C, Castellanos-Rizaldos E, Bejar R, Ebert BL, Makrigiorgos GM. DMSO Increases Mutation Scanning Detection Sensitivity of High-Resolution Melting in Clinical Samples. Clin Chem 2015; 61:1354-62. [PMID: 26432802 DOI: 10.1373/clinchem.2015.245357] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/17/2015] [Indexed: 02/02/2023]
Abstract
BACKGROUND Mutation scanning provides the simplest, lowest-cost method for identifying DNA variations on single PCR amplicons, and it may be performed before sequencing to avoid screening of noninformative wild-type samples. High-resolution melting (HRM) is the most commonly used method for mutation scanning. With PCR-HRM, however, mutations less abundant than approximately 3%-10% that can still be clinically significant may often be missed. Therefore, enhancing HRM detection sensitivity is important for mutation scanning and its clinical application. METHODS We used serial dilution of cell lines containing the TP53 exon 8 mutation to demonstrate the improvement in detection sensitivity for conventional-PCR-HRM in the presence of DMSO. We also conducted coamplification at lower denaturation temperature (COLD)-PCR with an extra step for cross-hybridization, followed by preferential denaturation and amplification at optimized critical temperature (full-COLD-PCR), to further enrich low-level mutations before HRM with or without DMSO, and we used droplet-digital PCR to derive the optimal conditions for mutation enrichment. Both conventional PCR-HRM and full-COLD-PCR-HRM with and without DMSO were used for mutation scanning of TP53 exon 8 in cancer samples containing known mutations and myelodysplastic syndrome samples with unknown mutations. Mutations in other genes were also examined. RESULTS The detection sensitivity of PCR-HRM scanning increases 2- to 5-fold in the presence of DMSO, depending on mutation type and sequence context, and can typically detect mutation abundance of approximately 1%. When mutation enrichment is applied during amplification with full-COLD-PCR followed by HRM in the presence of DMSO, mutations with 0.2%-0.3% abundance in TP53 exon 8 can be detected. CONCLUSIONS DMSO improves HRM mutation scanning sensitivity with saturating dyes. When full-COLD-PCR is used, followed by DMSO-HRM, the overall improvement is about 20-fold compared with conventional PCR-HRM.
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Affiliation(s)
- Chen Song
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Elena Castellanos-Rizaldos
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Rafael Bejar
- Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, CA
| | - Benjamin L Ebert
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA;
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21
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Marques S, Huss VAR, Pfisterer K, Grosse C, Thompson G. Internal transcribed spacer sequence-based rapid molecular identification of Prototheca zopfii and Prototheca blaschkeae directly from milk of infected cows. J Dairy Sci 2015; 98:3001-9. [PMID: 25726118 DOI: 10.3168/jds.2014-9271] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 01/23/2015] [Indexed: 11/19/2022]
Abstract
The increasing incidence of rare mastitis-causing pathogens has urged the implementation of fast and efficient diagnostic and control measures. Prototheca algae are known to be associated with diseases in humans and animals. In the latter, the most prevalent form of protothecosis is bovine mastitis with Prototheca zopfii and Prototheca blaschkeae representing the most common pathogenic species. These nonphotosynthetic and colorless green algae are ubiquitous in different environments and are widely resistant against harmful conditions and antimicrobials. Hence, the association of Prototheca with bovine mastitis represents a herd problem, requiring fast and easy identification of the infectious agent. The purpose of this study was to develop a reliable and rapid method, based on the internal transcribed spacer (ITS) sequences of ribosomal DNA, for molecular identification and discrimination between P. zopfii and P. blaschkeae in bovine mastitic milk. The complete ITS sequences of 32 Prototheca isolates showed substantial interspecies but moderate intraspecies variability facilitating the design of species-specific PCR amplification primers. The species-specific PCR was successfully applied to the identification of P. zopfii and P. blaschkeae directly from milk samples. The intraspecific ITS phylogeny was compared for each species with the geographical distribution of the respective Prototheca isolates, but no significant correlation was found.
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Affiliation(s)
- S Marques
- Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto (CIBIO/UP), InBio Laboratório Associado Campus Agrário de Vairão, Rua Padre Armando Quintas, n 7, 4485-661 Vairão, Portugal; Laboratório de Doenças Infecciosas do Departamento de Clínicas Veterinárias, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, n 228, 4050-313 Porto, Portugal.
| | - V A R Huss
- Department of Biology, Molecular Plant Physiology, University of Erlangen-Nürnberg, Staudtstrasse 5, D-91058 Erlangen, Germany
| | - K Pfisterer
- Department of Biology, Molecular Plant Physiology, University of Erlangen-Nürnberg, Staudtstrasse 5, D-91058 Erlangen, Germany
| | - C Grosse
- Department of Biology, Molecular Plant Physiology, University of Erlangen-Nürnberg, Staudtstrasse 5, D-91058 Erlangen, Germany
| | - G Thompson
- Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto (CIBIO/UP), InBio Laboratório Associado Campus Agrário de Vairão, Rua Padre Armando Quintas, n 7, 4485-661 Vairão, Portugal; Laboratório de Doenças Infecciosas do Departamento de Clínicas Veterinárias, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, n 228, 4050-313 Porto, Portugal
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22
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Venil CK, Nordin N, Zakaria ZA, Ahmad WA. Chryseobacterium artocarpi sp. nov., isolated from the rhizosphere soil of Artocarpus integer. Int J Syst Evol Microbiol 2014; 64:3153-3159. [DOI: 10.1099/ijs.0.063594-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated UTM-3T, isolated from the rhizosphere soil of Artocarpus integer (cempedak) in Malaysia was studied to determine its taxonomic position. Cells were Gram-stain-negative, non-spore-forming rods, devoid of flagella and gliding motility, that formed yellow-pigmented colonies on nutrient agar and contained MK-6 as the predominant menaquinone. Comparative analysis of the 16S rRNA gene sequence of strain UTM-3T with those of the most closely related species showed that the strain constituted a distinct phyletic line within the genus
Chryseobacterium
with the highest sequence similarities to Chryseobacterium lactis NCTC 11390T, Chryseobacterium viscerum 687B-08T, Chryseobacterium tructae 1084-08T, Chryseobacterium arthrosphaerae CC-VM-7T, Chryseobacterium oncorhynchi 701B-08T, Chryseobacterium vietnamense GIMN1.005T, Chryseobacterium bernardetii NCTC 13530T, Chryseobacterium nakagawai NCTC 13529T, Chryseobacterium gallinarum LMG 27808T, Chryseobacterium culicis R4-1AT, Chryseobacterium flavum CW-E2T, Chryseobacterium aquifrigidense CW9T, Chryseobacterium ureilyticum CCUG 52546T, Chryseobacterium indologenes NBRC 14944T, Chryseobacterium gleum CCUG 14555T, Chryseobacterium jejuense JS17-8T, Chryseobacterium oranimense H8T and Chryseobacterium joostei LMG 18212T. The major whole-cell fatty acids were iso-C15 : 0 and iso-C17 : 1ω9c, followed by summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1ω7t) and iso-C17 : 0 3-OH, and the polar lipid profile consisted of phosphatidylethanolamine and several unknown lipids. The DNA G+C content strain UTM-3T was 34.8 mol%. On the basis of the phenotypic and phylogenetic evidence, it is concluded that the isolate represents a novel species of the genus
Chryseobacterium
, for which the name Chryseobacterium
artocarpi sp. nov. is proposed. The type strain is UTM-3T ( = CECT 8497T = KCTC 32509T).
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Affiliation(s)
| | - Nordiana Nordin
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia
| | - Zainul Akmar Zakaria
- Institute of Bioproduct Development, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia
| | - Wan Azlina Ahmad
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia
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23
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Kok SD, Stanton LH, Slaby T, Durot M, Holmes VF, Patel KG, Platt D, Shapland EB, Serber Z, Dean J, Newman JD, Chandran SS. Rapid and reliable DNA assembly via ligase cycling reaction. ACS Synth Biol 2014; 3:97-106. [PMID: 24932563 DOI: 10.1021/sb4001992] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Assembly of DNA parts into DNA constructs is a foundational technology in the emerging field of synthetic biology. An efficient DNA assembly method is particularly important for high-throughput, automated DNA assembly in biofabrication facilities and therefore we investigated one-step, scarless DNA assembly via ligase cycling reaction (LCR). LCR assembly uses single-stranded bridging oligos complementary to the ends of neighboring DNA parts, a thermostable ligase to join DNA backbones, and multiple denaturation-annealing-ligation temperature cycles to assemble complex DNA constructs. The efficiency of LCR assembly was improved ca. 4-fold using designed optimization experiments and response surface methodology. Under these optimized conditions, LCR enabled one-step assembly of up to 20 DNA parts and up to 20 kb DNA constructs with very few single-nucleotide polymorphisms (<1 per 25 kb) and insertions/deletions (<1 per 50 kb). Experimental comparison of various sequence-independent DNA assembly methods showed that circular polymerase extension cloning (CPEC) and Gibson isothermal assembly did not enable assembly of more than four DNA parts with more than 50% of clones being correct. Yeast homologous recombination and LCR both enabled reliable assembly of up to 12 DNA parts with 60-100% of individual clones being correct, but LCR assembly provides a much faster and easier workflow than yeast homologous recombination. LCR combines reliable assembly of many DNA parts via a cheap, rapid, and convenient workflow and thereby outperforms existing DNA assembly methods. LCR assembly is expected to become the method of choice for both manual and automated high-throughput assembly of DNA parts into DNA constructs.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Sunil S. Chandran
- Amyris, Inc., 5885 Hollis
Street, Suite 100, Emeryville, California 94608, United States
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24
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Hakil F, Amin-Ali O, Hirschler-Réa A, Mollex D, Grossi V, Duran R, Matheron R, Cravo-Laureau C. Desulfatiferula berrensis sp. nov., a n-alkene-degrading sulfate-reducing bacterium isolated from estuarine sediments. Int J Syst Evol Microbiol 2014; 64:540-544. [DOI: 10.1099/ijs.0.057174-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel sulfate-reducing bacterium designated strain BE2801T was isolated from oil-polluted estuarine sediments (Berre Lagoon, France). Cells were Gram-stain-negative, motile, slightly curved or vibrioid rods. Optimal growth of strain BE2801T occurred at 30–32 °C, 0.5–1.5% NaCl (w/v) and pH 7.2–7.4. Strain BE2801T grew with C4 to C20 fatty acids or C12 to C20
n-alkenes as electron donors. Acetate and carbon dioxide were the oxidation products. The major cellular fatty acids were C16 : 0, C16 : 1ω7c and C18 : 1ω7. The DNA G+C content was 50.2 mol%. 16S rRNA and dsrAB gene sequence analysis indicated that strain BE2801T was a member of the family
Desulfobacteraceae
within the class
Deltaproteobacteria
. DNA–DNA hybridization with the most closely related taxon demonstrated 14.8 % relatedness. Based on phenotypic and phylogenetic evidence, strain BE2801T ( = DSM 25524T = JCM 18157T) is proposed to be a representative of a novel species of the genus
Desulfatiferula
, for which the name Desulfatiferula
berrensis sp. nov. is suggested.
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Affiliation(s)
- Florence Hakil
- Equipe Environnement et Microbiologie, IPREM UMR 5254, IBEAS Université de Pau et des Pays de l’Adour, BP1155, 64013 Pau cedex, France
| | - Oulfat Amin-Ali
- Université de Toulon, Université du Sud Toulon‐Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 83957 La Garde, France
- Aix-Marseille Université, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France
| | - Agnès Hirschler-Réa
- Université de Toulon, Université du Sud Toulon‐Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 83957 La Garde, France
- Aix-Marseille Université, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France
| | - Damien Mollex
- Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement, UMR CNRS 5276, Université Claude Bernard Lyon 1, Campus de la Doua, 69622 Villeurbanne, France
| | - Vincent Grossi
- Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement, UMR CNRS 5276, Université Claude Bernard Lyon 1, Campus de la Doua, 69622 Villeurbanne, France
| | - Robert Duran
- Equipe Environnement et Microbiologie, IPREM UMR 5254, IBEAS Université de Pau et des Pays de l’Adour, BP1155, 64013 Pau cedex, France
| | - Robert Matheron
- Aix-Marseille Université, IMBE, UMR 7263, UR-IRD 237, 13397 Marseille cedex 20, France
| | - Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie, IPREM UMR 5254, IBEAS Université de Pau et des Pays de l’Adour, BP1155, 64013 Pau cedex, France
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25
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Nakano SI, Miyoshi D, Sugimoto N. Effects of molecular crowding on the structures, interactions, and functions of nucleic acids. Chem Rev 2013; 114:2733-58. [PMID: 24364729 DOI: 10.1021/cr400113m] [Citation(s) in RCA: 369] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Shu-ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) and Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University , 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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26
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Properties of Halococcus salifodinae, an Isolate from Permian Rock Salt Deposits, Compared with Halococci from Surface Waters. Life (Basel) 2013; 3:244-59. [PMID: 25371342 PMCID: PMC4187196 DOI: 10.3390/life3010244] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 02/07/2013] [Accepted: 02/14/2013] [Indexed: 11/17/2022] Open
Abstract
Halococcus salifodinae BIpT DSM 8989T, an extremely halophilic archaeal isolate from an Austrian salt deposit (Bad Ischl), whose origin was dated to the Permian period, was described in 1994. Subsequently, several strains of the species have been isolated, some from similar but geographically separated salt deposits. Hcc. salifodinae may be regarded as one of the most ancient culturable species which existed already about 250 million years ago. Since its habitat probably did not change during this long period, its properties were presumably not subjected to the needs of mutational adaptation. Hcc. salifodinae and other isolates from ancient deposits would be suitable candidates for testing hypotheses on prokaryotic evolution, such as the molecular clock concept, or the net-like history of genome evolution. A comparison of available taxonomic characteristics from strains of Hcc. salifodinae and other Halococcus species, most of them originating from surface waters, is presented. The cell wall polymer of Hcc. salifodinae was examined and found to be a heteropolysaccharide, similar to that of Hcc. morrhuae. Polyhydroxyalkanoate granules were present in Hcc. salifodinae, suggesting a possible lateral gene transfer before Permian times.
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27
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Leonard CW, Hajdin CE, Karabiber F, Mathews DH, Favorov O, Dokholyan NV, Weeks KM. Principles for understanding the accuracy of SHAPE-directed RNA structure modeling. Biochemistry 2013; 52:588-95. [PMID: 23316814 PMCID: PMC3578230 DOI: 10.1021/bi300755u] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Accurate RNA structure modeling is an important, incompletely solved, challenge. Single-nucleotide resolution SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) yields an experimental measurement of local nucleotide flexibility that can be incorporated as pseudo-free energy change constraints to direct secondary structure predictions. Prior work from our laboratory has emphasized both the overall accuracy of this approach and the need for nuanced interpretation of modeled structures. Recent studies by Das and colleagues [Kladwang, W., et al. (2011) Biochemistry 50, 8049; Nat. Chem. 3, 954], focused on analyzing six small RNAs, yielded poorer RNA secondary structure predictions than expected on the basis of prior benchmarking efforts. To understand the features that led to these divergent results, we re-examined four RNAs yielding the poorest results in this recent work: tRNA(Phe), the adenine and cyclic-di-GMP riboswitches, and 5S rRNA. Most of the errors reported by Das and colleagues reflected nonstandard experiment and data processing choices, and selective scoring rules. For two RNAs, tRNA(Phe) and the adenine riboswitch, secondary structure predictions are nearly perfect if no experimental information is included but were rendered inaccurate by the SHAPE data of Das and colleagues. When best practices were used, single-sequence SHAPE-directed secondary structure modeling recovered ~93% of individual base pairs and >90% of helices in the four RNAs, essentially indistinguishable from the results of the mutate-and-map approach with the exception of a single helix in the 5S rRNA. The field of experimentally directed RNA secondary structure prediction is entering a phase focused on the most difficult prediction challenges. We outline five constructive principles for guiding this field forward.
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Affiliation(s)
| | - Christine E. Hajdin
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290
| | - Fethullah Karabiber
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290
| | - David H. Mathews
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642
| | - Oleg Favorov
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599-3290
| | - Nikolay V. Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-3290
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290
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28
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Inan K, Belduz AO, Canakci S. Anoxybacillus kaynarcensissp. nov., a moderately thermophilic, xylanase producing bacterium. J Basic Microbiol 2012; 53:410-9. [DOI: 10.1002/jobm.201100638] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 01/29/2012] [Indexed: 11/06/2022]
Affiliation(s)
- Kadriye Inan
- Karadeniz Technical University, Faculty of Science, Department of Biology; Trabzon; Turkey
| | - Ali Osman Belduz
- Karadeniz Technical University, Faculty of Science, Department of Biology; Trabzon; Turkey
| | - Sabriye Canakci
- Karadeniz Technical University, Faculty of Science, Department of Biology; Trabzon; Turkey
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29
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Brogaard KR, Xi L, Wang JP, Widom J. A chemical approach to mapping nucleosomes at base pair resolution in yeast. Methods Enzymol 2012; 513:315-34. [PMID: 22929776 DOI: 10.1016/b978-0-12-391938-0.00014-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Most eukaryotic DNA exists in DNA-protein complexes known as nucleosomes. The exact locations of nucleosomes along the genome play a critical role in chromosome functions and gene regulation. However, the current methods for nucleosome mapping do not provide the necessary accuracy to identify the precise nucleosome locations. Here we describe a new experimental approach that directly maps nucleosome center locations in vivo genome-wide at single base pair resolution.
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Affiliation(s)
- Kristin R Brogaard
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA.
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30
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Grégoire P, Fardeau ML, Guasco S, Lagière J, Cambar J, Michotey V, Bonin P, Ollivier B. Desulfosoma profundi sp. nov., a thermophilic sulfate-reducing bacterium isolated from a deep terrestrial geothermal spring in France. Antonie van Leeuwenhoek 2011; 101:595-602. [DOI: 10.1007/s10482-011-9675-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 11/08/2011] [Indexed: 11/29/2022]
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31
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Grégoire P, Bohli M, Cayol JL, Joseph M, Guasco S, Dubourg K, Cambar J, Michotey V, Bonin P, Fardeau ML, Ollivier B. Caldilinea tarbellica sp. nov., a filamentous, thermophilic, anaerobic bacterium isolated from a deep hot aquifer in the Aquitaine Basin. Int J Syst Evol Microbiol 2011; 61:1436-1441. [DOI: 10.1099/ijs.0.025676-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An anaerobic, thermophilic, filamentous (0.45 × >100 µm) bacterium, designated D1-25-10-4T, was isolated from a deep hot aquifer in France. Cells were non-motile and Gram-negative. Growth was observed at 43–65 °C (optimum 55 °C), at pH 6.8–7.8 (optimum pH 7.0) and with 0–5 g NaCl l−1 (optimum 0 g NaCl l−1). Strain D1-25-10-4T was a chemo-organotroph and fermented ribose, maltose, glucose, galactose, arabinose, fructose, mannose, sucrose, raffinose, xylose, glycerol, fumarate, peptone, starch and xylan. Yeast extract was required for growth. Sulfate, thiosulfate, sulfite, elemental sulfur, nitrate, nitrite and fumarate were not used as terminal electron acceptors. The G+C content of the DNA was 61.9 mol%. The major cellular fatty acids of strain D1-25-10-4T were C17 : 0, C18 : 0, C16 : 0 and iso-C17 : 0. The closest phylogenetic relative of strain D1-25-10-4T was Caldilinea aerophila STL-6-O1T (97.9 % 16S rRNA gene sequence similarity). DNA–DNA relatedness between strain D1-25-10-4T and Caldilinea aerophila DSM 14535T was 8.7±1 %. On the basis of phylogenetic, genotypic and phenotypic characteristics, strain D1-25-10-4T represents a novel species within the genus Caldilinea, class Caldilineae, phylum Chloroflexi, for which the name Caldilinea tarbellica sp. nov. is proposed. The type strain is D1-25-10-4T ( = DSM 22659T = JCM 16120T).
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Affiliation(s)
- Patrick Grégoire
- Institut du Thermalisme, Université Victor Segalen Bordeaux 2, 8 rue Sainte Ursule, 40100 Dax, France
- Laboratoire de Microbiologie et de Biotechnologie des Environnements Chauds UMR 180, IRD, Universités de Provence et de la Méditerranée, ESIL case 925, 163 avenue de Luminy, 13288 Marseille, France
| | - Malek Bohli
- Laboratoire de Microbiologie et de Biotechnologie des Environnements Chauds UMR 180, IRD, Universités de Provence et de la Méditerranée, ESIL case 925, 163 avenue de Luminy, 13288 Marseille, France
| | - Jean-Luc Cayol
- Laboratoire de Microbiologie et de Biotechnologie des Environnements Chauds UMR 180, IRD, Universités de Provence et de la Méditerranée, ESIL case 925, 163 avenue de Luminy, 13288 Marseille, France
| | - Manon Joseph
- Laboratoire de Microbiologie et de Biotechnologie des Environnements Chauds UMR 180, IRD, Universités de Provence et de la Méditerranée, ESIL case 925, 163 avenue de Luminy, 13288 Marseille, France
| | - Sophie Guasco
- LMGEM, UMR 6117, Centre d’Océanologie de Marseille, Université Aix Marseille 2 Campus de Luminy - Case 901, 163 Avenue de Luminy, 13288 Marseille, France
| | - Karine Dubourg
- Institut du Thermalisme, Université Victor Segalen Bordeaux 2, 8 rue Sainte Ursule, 40100 Dax, France
| | - Jean Cambar
- Institut du Thermalisme, Université Victor Segalen Bordeaux 2, 8 rue Sainte Ursule, 40100 Dax, France
| | - Valérie Michotey
- LMGEM, UMR 6117, Centre d’Océanologie de Marseille, Université Aix Marseille 2 Campus de Luminy - Case 901, 163 Avenue de Luminy, 13288 Marseille, France
| | - Patricia Bonin
- LMGEM, UMR 6117, Centre d’Océanologie de Marseille, Université Aix Marseille 2 Campus de Luminy - Case 901, 163 Avenue de Luminy, 13288 Marseille, France
| | - Marie-Laure Fardeau
- Laboratoire de Microbiologie et de Biotechnologie des Environnements Chauds UMR 180, IRD, Universités de Provence et de la Méditerranée, ESIL case 925, 163 avenue de Luminy, 13288 Marseille, France
| | - Bernard Ollivier
- Laboratoire de Microbiologie et de Biotechnologie des Environnements Chauds UMR 180, IRD, Universités de Provence et de la Méditerranée, ESIL case 925, 163 avenue de Luminy, 13288 Marseille, France
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Maune MW, Tanner RS. Description of Anaerobaculum hydrogeniformans sp. nov., an anaerobe that produces hydrogen from glucose, and emended description of the genus Anaerobaculum. Int J Syst Evol Microbiol 2011; 62:832-838. [PMID: 21602364 DOI: 10.1099/ijs.0.024349-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel anaerobic, moderately thermophilic, NaCl-requiring fermentative bacterium, strain OS1T, was isolated from oil production water collected from Alaska, USA. Cells were Gram-negative, non-motile, non-spore-forming rods (1.7-2.7×0.4-0.5 µm). The G+C content of the genomic DNA of strain OS1T was 46.6 mol%. The optimum temperature, pH and NaCl concentration for growth of strain OS1T were 55 °C, pH 7 and 10 g l(-1), respectively. The bacterium fermented D-fructose, D-glucose, maltose, D-mannose, α-ketoglutarate, L-glutamate, malonate, pyruvate, L-tartrate, L-asparagine, Casamino acids, L-cysteine, L-histidine, L-leucine, L-phenylalanine, L-serine, L-threonine, L-valine, inositol, inulin, tryptone and yeast extract. When grown on D-glucose, 3.86 mol hydrogen and 1.4 mol acetate were produced per mol substrate. Thiosulfate, sulfur and L-cystine were reduced to sulfide, and crotonate was reduced to butyrate with glucose as the electron donor. 16S rRNA gene sequence analysis indicated that strain OS1T was related to Anaerobaculum thermoterrenum (99.7 % similarity to the type strain), a member of the phylum Synergistetes. DNA-DNA hybridization between strain OS1T and A. thermoterrenum DSM 13490T yielded 68 % relatedness. Unlike A. thermoterrenum, strain OS1T fermented malonate, maltose, tryptone, L-leucine and L-phenylalanine, but not citrate, fumarate, lactate, L-malate, glycerol, pectin or starch. The major cellular fatty acid of strain OS1T was iso-C15:0 (91 % of the total). Strain OS1T also contained iso-C13:0 3-OH (3 %), which was absent from A. thermoterrenum, and iso-C13:0 (2 %), which was absent from Anaerobaculum mobile. On the basis of these results, strain OS1T represents a novel species of the genus Anaerobaculum, for which the name Anaerobaculum hydrogeniformans sp. nov. is proposed. The type strain is OS1T (=DSM 22491T=ATCC BAA-1850T). An emended description of the genus Anaerobaculum is also given.
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Affiliation(s)
- Matthew W Maune
- Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
| | - Ralph S Tanner
- Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
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Bouanane-Darenfed A, Fardeau ML, Grégoire P, Joseph M, Kebbouche-Gana S, Benayad T, Hacene H, Cayol JL, Ollivier B. Caldicoprobacter algeriensis sp. nov. a new thermophilic anaerobic, xylanolytic bacterium isolated from an Algerian hot spring. Curr Microbiol 2010; 62:826-32. [PMID: 20981546 DOI: 10.1007/s00284-010-9789-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 10/08/2010] [Indexed: 11/30/2022]
Abstract
A thermophilic anaerobic bacterium (strain TH7C1(T)) was isolated from the hydrothermal hot spring of Guelma in the northeast of Algeria. Strain TH7C1(T) stained Gram-positive, was a non-motile rod appearing singly, in pairs, or as long chains (0.7-1 × 2-6 μm(2)). Spores were never observed. It grew at temperatures between 55 and 75°C (optimum 65°C) and at pH between 6.2 and 8.3 (optimum 6.9). It did not require NaCl for growth, but tolerated it up to 5 g l(-1). Strain TH7C1(T) is an obligatory heterotroph fermenting sugars including glucose, galactose, lactose, raffinose, fructose, ribose, xylose, arabinose, maltose, mannitol, cellobiose, mannose, melibiose, saccharose, but also xylan, and pyruvate. Fermentation of sugars only occurred in the presence of yeast extract (0.1%). The end-products from glucose fermentation were acetate, lactate, ethanol, CO(2), and H(2). Nitrate, nitrite, thiosulfate, elemental sulfur, sulfate, and sulfite were not used as electron acceptors. The G+C content of the genomic DNA was 44.7 mol% (HPLC techniques). Phylogenetic analysis of the small-subunit ribosomal RNA (rRNA) gene sequence indicated that strain TH7C1(T) was affiliated to Firmicutes, order Clostridiales, family Caldicoprobacteraceae, with Caldicoprobacter oshimai (98.5%) being its closest relative. Based on phenotypic, phylogenetic, and genetic characteristics, strain TH7C1(T) is proposed as a novel species of genus Caldicoprobacter, Caldicoprobacter algeriensis, sp. nov. (strain TH7C1(T) = DSM 22661(T) = JCM 16184(T)).
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Affiliation(s)
- Amel Bouanane-Darenfed
- Laboratoire de Biologie Cellulaire et Moléculaire (équipe de Microbiologie), Université des sciences et de la technologie Houari Boumédiènne, Bab Ezzouar, Algiers, Algeria
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Guzmán D, Quillaguamán J, Muñoz M, Hatti-Kaul R. Halomonas andesensis sp. nov., a moderate halophile isolated from the saline lake Laguna Colorada in Bolivia. Int J Syst Evol Microbiol 2010; 60:749-753. [DOI: 10.1099/ijs.0.014522-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A moderately halophilic, motile, Gram-negative, rod-shaped bacterium, strain LC6T, was isolated from a water sample of lake Laguna Colorada in the Bolivian Andes. The major cellular fatty acids were C18 : 1
ω7c, iso-C16 : 1
ω7c 2-OH, C16 : 0 and C12 : 0 3-OH. The respiratory ubiquinones found in strain LC6T were Q-9 (97 %) and Q-8 (3 %). Strain LC6T was aerobic, heterotrophic, and able to utilize various carbohydrates and other substrates as carbon source. The G+C content of the genomic DNA of strain LC6T was 52.5 mol%. The organism was able to grow at pH 6.0–11.0 (optimum, pH 7.0–8.0), at 4–45 °C (optimum, 30–35 °C) and in the presence of 0.5–20 % (w/v) NaCl (optimum, 1–3 %, w/v). Based on 16S rRNA gene sequence analysis, strain LC6T was most closely related to Halomonas hydrothermalis DSM 15725T and Halomonas venusta DSM 4743T (98.8 % similarity), followed by Halomonas aquamarina DSM 30161T, Halomonas axialensis DSM 15723T and Halomonas meridiana DSM 5425T (98.4 %). However, levels of DNA–DNA relatedness between strain LC6T and the above type strains were low (<31 %). Strain LC6T resembled recognized Halomonas species with respect to various physiological, biochemical and nutritional characteristics. Combined phenotypic data and DNA–DNA hybridization data supported the conclusion that strain LC6T represents a novel species of the genus Halomonas, for which the name Halomonas andesensis is proposed. The type strain is LC6T (=CCUG 54844T=LMG 24243T=DSM 19434T).
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Affiliation(s)
- Daniel Guzmán
- Centro de Biotecnología, Facultad de Ciencias y Tecnología, Universidad Mayor de San Simón, Cochabamba, Bolivia
- Department of Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, PO Box 124, SE-221 00 Lund, Sweden
| | - Jorge Quillaguamán
- Centro de Biotecnología, Facultad de Ciencias y Tecnología, Universidad Mayor de San Simón, Cochabamba, Bolivia
- Department of Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, PO Box 124, SE-221 00 Lund, Sweden
| | - Marlene Muñoz
- Department of Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, PO Box 124, SE-221 00 Lund, Sweden
| | - Rajni Hatti-Kaul
- Department of Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, PO Box 124, SE-221 00 Lund, Sweden
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Alazard D, Joseph M, Battaglia-Brunet F, Cayol JL, Ollivier B. Desulfosporosinus acidiphilus sp. nov.: a moderately acidophilic sulfate-reducing bacterium isolated from acid mining drainage sediments. Extremophiles 2010; 14:305-12. [PMID: 20358236 DOI: 10.1007/s00792-010-0309-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Accepted: 03/12/2010] [Indexed: 11/29/2022]
Affiliation(s)
- Didier Alazard
- IRD, UMR 180, Universités de Provence et de la Méditerranée, ESIL, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 9, France.
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Vecherskaya M, Dijkema C, Saad HR, Stams AJM. Microaerobic and anaerobic metabolism of a Methylocystis parvus strain isolated from a denitrifying bioreactor. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:442-449. [PMID: 23765898 DOI: 10.1111/j.1758-2229.2009.00069.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
An obligate methanotrophic bacterium, strain MTS, was isolated from a methane-fed microaerobic denitrifying bioreactor. 16S rRNA and DNA-DNA hybridization analysis revealed that this organism was most closely related to Methylocystis parvus, a Type II methanotroph, belonging to the α-subclass of the Proteobacteria. The metabolism of the bacterium under microaerobic and anaerobic conditions was studied by (13) C-NMR. (13) C-labelled poly-β-hydroxybutyrate (PHB) formation occurred in cell suspensions incubated with (13) C-labelled methane at low (5-10%) oxygen concentration. Under these conditions low levels of succinate, acetate and 2,3-butanediol were formed and excreted into the culture medium. Intracellular PHB degradation was observed in intact cells under anaerobic conditions in the absence of an exogenous carbon source during a long-term incubation of 90 days. Multiple (13) C-labelled β-hydroxybutyrate, butyrate, acetate, acetone, isopropanol, 2,3-butanediol and succinate were identified as products in in vivo(13) C-NMR spectra and in the spectra of culture medium during the dynamic PHB degradation. The isolated obligate methanotroph clearly shows a fermentative metabolism of PHB under anaerobic conditions. The excreted products may serve as substrates for denitrifying bacteria.
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Affiliation(s)
- Margarita Vecherskaya
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, the Netherlands. Laboratory of Biophysics, Wageningen University, Dreijenplein 3, 6703 HA, Wageningen, the Netherlands. Department of Biological Systems, Universidad Autónoma Metropolitana, 06960 Mexico City, Mexico
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Isolation and characterization of a new CO-utilizing strain, Thermoanaerobacter thermohydrosulfuricus subsp. carboxydovorans, isolated from a geothermal spring in Turkey. Extremophiles 2009; 13:885-94. [PMID: 19701714 PMCID: PMC2767516 DOI: 10.1007/s00792-009-0276-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2009] [Accepted: 08/03/2009] [Indexed: 11/26/2022]
Abstract
A novel anaerobic, thermophilic, Gram-positive, spore-forming, and sugar-fermenting bacterium (strain TLO) was isolated from a geothermal spring in Ayaş, Turkey. The cells were straight to curved rods, 0.4–0.6 μm in diameter and 3.5–10 μm in length. Spores were terminal and round. The temperature range for growth was 40–80°C, with an optimum at 70°C. The pH optimum was between 6.3 and 6.8. Strain TLO has the capability to ferment a wide variety of mono-, di-, and polysaccharides and proteinaceous substrates, producing mainly lactate, next to acetate, ethanol, alanine, H2, and CO2. Remarkably, the bacterium was able to grow in an atmosphere of up to 25% of CO as sole electron donor. CO oxidation was coupled to H2 and CO2 formation. The G + C content of the genomic DNA was 35.1 mol%. Based on 16S rRNA gene sequence analysis and the DNA–DNA hybridization data, this bacterium is most closely related to Thermoanaerobacter thermohydrosulfuricus and Thermoanaerobacter siderophilus (99% similarity for both). However, strain TLO differs from Thermoanaerobacter thermohydrosulfuricus in important aspects, such as CO-utilization and lipid composition. These differences led us to propose that strain TLO represents a subspecies of Thermoanaerobacter thermohydrosulfuricus, and we therefore name it Thermoanaerobacter thermohydrosulfuricus subsp. carboxydovorans.
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Pseudomonas extremaustralis sp. nov., a Poly(3-hydroxybutyrate) Producer Isolated from an Antarctic Environment. Curr Microbiol 2009; 59:514-9. [DOI: 10.1007/s00284-009-9469-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 07/08/2009] [Accepted: 07/20/2009] [Indexed: 10/20/2022]
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Fu X, Li M, Zheng G, Le Y, Wang L. Waste recombinant DNA: effectiveness of thermo-treatment to manage potential gene pollution. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2009; 157:2536-2541. [PMID: 19342135 DOI: 10.1016/j.envpol.2009.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Revised: 02/25/2009] [Accepted: 03/02/2009] [Indexed: 05/27/2023]
Abstract
Heating at 100 degrees C for 5-10 min is a common method for treating wastewater containing recombinant DNA in many bio-laboratories in China. In this experiment, plasmid pET-28b was used to investigate decay efficiency of waste recombinant DNA during thermo-treatment. The results showed that the decay half-life of the plasmid was 2.7-4.0 min during the thermo-treatment, and even heating for 30 min the plasmids still retained some transforming activity. Low pH promoted the decay of recombinant DNA, but NaCl, bovine serum albumin and EDTA, which existed in the most wastewater from bio-laboratories, protected DNA from degradation. Thus, the decay half-life of plasmid DNA may be longer than 2.7-4.0 min practically. These results suggest that the effectiveness of heating at 100 degrees C for treating waste recombinant DNA is low and a gene pollution risk remains when those thermo-treated recombinant DNAs are discharged into the environment. Therefore other simple and effective methods should be developed.
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Affiliation(s)
- Xiaohua Fu
- School of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, 1239 Siping road, Shanghai 200092, China
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40
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Ehrmann MA, Freiding S, Vogel RF. Leuconostoc palmae sp. nov., a novel lactic acid bacterium isolated from palm wine. Int J Syst Evol Microbiol 2009; 59:943-7. [PMID: 19406772 DOI: 10.1099/ijs.0.005983-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel lactic acid bacterium, strain TMW 2.694(T), was isolated among other lactic acid bacteria from palm wine, an alcoholic beverage produced from the sap of various palm tree species. Strain TMW 2.694(T) is a Gram-positive, facultatively anaerobic, catalase-negative, non-spore-forming coccus, occurring in long chains. Phylogenetic analysis based on 16S rRNA gene sequencing positioned strain TMW 2.694(T) in a distinct line of descent within the genus Leuconostoc, with the closest neighbours being Leuconostoc lactis JCM 6123(T) (98.7 % sequence similarity) and Leuconostoc citreum DSM 5577(T) (98.8 % sequence similarity). Comparative sequencing of the additional phylogenetic markers dnaK and recA confirmed the 16S rRNA gene tree topology. Genomic DNA-DNA similarities of strain TMW 2.694(T) to L. lactis DSM 20202(T) and L. citreum DSM 5577(T) were 45.1 and 17.7 %, respectively. The DNA G+C content is 36.4 mol%. Thus, we propose a novel species within the genus Leuconostoc, with the name Leuconostoc palmae sp. nov. and the type strain TMW 2.694(T) (=DSM 21144(T) =LMG 24510(T)).
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Affiliation(s)
- Matthias A Ehrmann
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Weihenstephaner Steig 16, 85350 Freising, Germany.
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41
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Cummings SP, Gyaneshwar P, Vinuesa P, Farruggia FT, Andrews M, Humphry D, Elliott GN, Nelson A, Orr C, Pettitt D, Shah GR, Santos SR, Krishnan HB, Odee D, Moreira FMS, Sprent JI, Young JPW, James EK. Nodulation of Sesbania species by Rhizobium (Agrobacterium) strain IRBG74 and other rhizobia. Environ Microbiol 2009; 11:2510-25. [PMID: 19555380 PMCID: PMC7163632 DOI: 10.1111/j.1462-2920.2009.01975.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Concatenated sequence analysis with 16S rRNA, rpoB and fusA genes identified a bacterial strain (IRBG74) isolated from root nodules of the aquatic legume Sesbania cannabina as a close relative of the plant pathogen Rhizobium radiobacter (syn. Agrobacterium tumefaciens). However, DNA:DNA hybridization with R. radiobacter, R. rubi, R. vitis and R. huautlense gave only 44%, 5%, 8% and 8% similarity respectively, suggesting that IRBG74 is potentially a new species. Additionally, it contained no vir genes and lacked tumour‐forming ability, but harboured a sym‐plasmid containing nifH and nodA genes similar to those in other Sesbania symbionts. Indeed, IRBG74 effectively nodulated S. cannabina and seven other Sesbania spp. that nodulate with Ensifer (Sinorhizobium)/Rhizobium strains with similar nodA genes to IRBG74, but not species that nodulate with Azorhizobium or Mesorhizobium. Light and electron microscopy revealed that IRBG74 infected Sesbania spp. via lateral root junctions under flooded conditions, but via root hairs under non‐flooded conditions. Thus, IRBG74 is the first confirmed legume‐nodulating symbiont from the Rhizobium (Agrobacterium) clade. Cross‐inoculation studies with various Sesbania symbionts showed that S. cannabina could form fully effective symbioses with strains in the genera Rhizobium and Ensifer, only ineffective ones with Azorhizobium strains, and either partially effective (Mesorhizobium huakii) or ineffective (Mesorhizobium plurifarium) symbioses with Mesorhizobium. These data are discussed in terms of the molecular phylogeny of Sesbania and its symbionts.
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Affiliation(s)
- Stephen P Cummings
- School of Applied Sciences, Ellison Building, University of Northumbria, Newcastle-upon-Tyne, UK
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Liu H, Zhou Y, Liu R, Zhang KY, Lai R. Bacillus solisalsi sp. nov., a halotolerant, alkaliphilic bacterium isolated from soil around a salt lake. Int J Syst Evol Microbiol 2009; 59:1460-4. [DOI: 10.1099/ijs.0.000653-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Peix A, Lang E, Verbarg S, Spröer C, Rivas R, Santa-Regina I, Mateos PF, Martínez-Molina E, Rodríguez-Barrueco C, Velázquez E. Acinetobacter strains IH9 and OCI1, two rhizospheric phosphate solubilizing isolates able to promote plant growth, constitute a new genomovar of Acinetobacter calcoaceticus. Syst Appl Microbiol 2009; 32:334-41. [PMID: 19467815 DOI: 10.1016/j.syapm.2009.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2009] [Indexed: 11/27/2022]
Abstract
During a screening of phosphate solubilizing bacteria (PSB) in agricultural soils, two strains, IH9 and OCI1, were isolated from the rhizosphere of grasses in Spain, and they showed a high ability to solubilize phosphate in vitro. Inoculation experiments in chickpea and barley were conducted with both strains and the results demonstrated their ability to promote plant growth. The 16S rRNA gene sequences of these strains were nearly identical to each other and to those of Acinetobacter calcoaceticus DSM 30006(T), as well as the strain CIP 70.29 representing genomospecies 3. Their phenotypic characteristics also coincided with those of strains forming the A. calcoaceticus-baumannii complex. They differed from A. calcoaceticus in the utilization of l-tartrate as a carbon source and from genomospecies 3 in the use of d-asparagine as a carbon source. The 16S-23S intergenic spacer (ITS) sequences of the two isolates showed nearly 98% identities to those of A. calcoaceticus, confirming that they belong to this phylogenetic group. However, the isolates appeared as a separate branch from the A. calcoaceticus sequences, indicating their molecular separation from other A. calcoaceticus strains. The analysis of three housekeeping genes, recA, rpoD and gyrB, confirmed that IH9 and OCI1 form a distinct lineage within A. calcoaceticus. These results were congruent with those from DNA-DNA hybridization, indicating that strains IH9 and OCI1 constitute a new genomovar for which we propose the name A. calcoaceticus genomovar rhizosphaerae.
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Affiliation(s)
- Alvaro Peix
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
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Yang SY, Liu H, Liu R, Zhang KY, Lai R. Saccharibacillus kuerlensis sp. nov., isolated from a desert soil. Int J Syst Evol Microbiol 2009; 59:953-7. [DOI: 10.1099/ijs.0.005199-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Probing the transcription mechanisms of reovirus cores with molecules that alter RNA duplex stability. J Virol 2009; 83:5659-70. [PMID: 19297468 DOI: 10.1128/jvi.02192-08] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mammalian reovirus (MRV) genome comprises 10 double-stranded RNA (dsRNA) segments, packaged along with transcriptase complexes inside each core particle. Effects of four small molecules on transcription by MRV cores were studied for this report, chosen for their known capacities to alter RNA duplex stability. Spermidine and spermine, which enhance duplex stability, inhibited transcription, whereas dimethyl sulfoxide and trimethylglycine, which attenuate duplex stability, stimulated transcription. Different mechanisms were identified for inhibition or activation by these molecules. With spermidine, one round of transcription occurred normally, but subsequent rounds were inhibited. Thus, inhibition occurred at the transition between the end of elongation in one round and initiation in the next round of transcription. Dimethyl sulfoxide or trimethylglycine, on the other hand, had no effect on transcription by a constitutively active fraction of cores in each preparation but activated transcription in another fraction that was otherwise silent for the production of elongated transcripts. Activation of this other fraction occurred at the transition between transcript initiation and elongation, i.e., at promoter escape. These results suggest that the relative stability of RNA duplexes is most important for certain steps in the particle-associated transcription cycles of dsRNA viruses and that small molecules are useful tools for probing these and probably other steps.
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van Houten BHGW, Meulepas RJW, van Doesburg W, Smidt H, Muyzer G, Stams AJM. Desulfovibrio paquesii sp. nov., a hydrogenotrophic sulfate-reducing bacterium isolated from a synthesis-gas-fed bioreactor treating zinc- and sulfate-rich wastewater. Int J Syst Evol Microbiol 2009; 59:229-33. [DOI: 10.1099/ijs.0.65616-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Li MN, Zheng GH, Wang L, Xiao W, Fu XH, Le YQ, Ren DM. Evaluation of the effectiveness and safety of the thermo-treatment process to dispose of recombinant DNA waste from biological research laboratories. THE SCIENCE OF THE TOTAL ENVIRONMENT 2009; 407:791-797. [PMID: 18849060 DOI: 10.1016/j.scitotenv.2008.08.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 07/18/2008] [Accepted: 08/06/2008] [Indexed: 05/26/2023]
Abstract
The discharge of recombinant DNA waste from biological laboratories into the eco-system may be one of the pathways resulting in horizontal gene transfer or "gene pollution". Heating at 100 degrees C for 5-10 min is a common method for treating recombinant DNA waste in biological research laboratories in China. In this study, we evaluated the effectiveness and the safety of the thermo-treatment method in the disposal of recombinant DNA waste. Quantitative PCR, plasmid transformation and electrophoresis technology were used to evaluate the decay/denaturation efficiency during the thermo-treatment process of recombinant plasmid, pET-28b. Results showed that prolonging thermo-treatment time could improve decay efficiency of the plasmid, and its decay half-life was 2.7-4.0 min during the thermo-treatment at 100 degrees C. However, after 30 min of thermo-treatment some transforming activity remained. Higher ionic strength could protect recombinant plasmid from decay during the treatment process. These results indicate that thermo-treatment at 100 degrees C cannot decay and inactivate pET-28b completely. In addition, preliminary results showed that thermo-treated recombinant plasmids were not degraded completely in a short period when they were discharged into an aquatic environment. This implies that when thermo-treated recombinant DNAs are discharged into the eco-system, they may have enough time to re-nature and transform, thus resulting in gene diffusion.
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Affiliation(s)
- Meng-Nan Li
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
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Li HB, Zhang LP, Chen SF. Halomonas korlensis sp. nov., a moderately halophilic, denitrifying bacterium isolated from saline and alkaline soil. Int J Syst Evol Microbiol 2008; 58:2582-8. [DOI: 10.1099/ijs.0.65711-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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49
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Characterization of a xylanase from a thermophilic strain of Anoxybacillus pushchinoensis A8. Biologia (Bratisl) 2008. [DOI: 10.2478/s11756-008-0134-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Evolution of Streptococcus pneumoniae and its close commensal relatives. PLoS One 2008; 3:e2683. [PMID: 18628950 PMCID: PMC2444020 DOI: 10.1371/journal.pone.0002683] [Citation(s) in RCA: 222] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2008] [Accepted: 06/18/2008] [Indexed: 11/19/2022] Open
Abstract
Streptococcus pneumoniae is a member of the Mitis group of streptococci which, according to 16S rRNA-sequence based phylogenetic reconstruction, includes 12 species. While other species of this group are considered prototypes of commensal bacteria, S. pneumoniae is among the most frequent microbial killers worldwide. Population genetic analysis of 118 strains, supported by demonstration of a distinct cell wall carbohydrate structure and competence pheromone sequence signature, shows that S. pneumoniae is one of several hundred evolutionary lineages forming a cluster separate from Streptococcus oralis and Streptococcus infantis. The remaining lineages of this distinct cluster are commensals previously collectively referred to as Streptococcus mitis and each represent separate species by traditional taxonomic standard. Virulence genes including the operon for capsule polysaccharide synthesis and genes encoding IgA1 protease, pneumolysin, and autolysin were randomly distributed among S. mitis lineages. Estimates of the evolutionary age of the lineages, the identical location of remnants of virulence genes in the genomes of commensal strains, the pattern of genome reductions, and the proportion of unique genes and their origin support the model that the entire cluster of S. pneumoniae, S. pseudopneumoniae, and S. mitis lineages evolved from pneumococcus-like bacteria presumably pathogenic to the common immediate ancestor of hominoids. During their adaptation to a commensal life style, most of the lineages gradually lost the majority of genes determining virulence and became genetically distinct due to sexual isolation in their respective hosts.
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