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Piantanida L, Liddle JA, Hughes WL, Majikes JM. DNA nanostructure decoration: a how-to tutorial. NANOTECHNOLOGY 2024; 35:273001. [PMID: 38373400 DOI: 10.1088/1361-6528/ad2ac5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 02/18/2024] [Indexed: 02/21/2024]
Abstract
DNA Nanotechnology is being applied to multiple research fields. The functionality of DNA nanostructures is significantly enhanced by decorating them with nanoscale moieties including: proteins, metallic nanoparticles, quantum dots, and chromophores. Decoration is a complex process and developing protocols for reliable attachment routinely requires extensive trial and error. Additionally, the granular nature of scientific communication makes it difficult to discern general principles in DNA nanostructure decoration. This tutorial is a guidebook designed to minimize experimental bottlenecks and avoid dead-ends for those wishing to decorate DNA nanostructures. We supplement the reference material on available technical tools and procedures with a conceptual framework required to make efficient and effective decisions in the lab. Together these resources should aid both the novice and the expert to develop and execute a rapid, reliable decoration protocols.
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Affiliation(s)
- Luca Piantanida
- Faculty of Applied Science, School of Engineering, University of British Columbia, Kelowna, B.C., V1V 1V7, Canada
| | - J Alexander Liddle
- National Institute of Standards and Technology, Gaithersburg, MD, 20878, United States of America
| | - William L Hughes
- Faculty of Applied Science, School of Engineering, University of British Columbia, Kelowna, B.C., V1V 1V7, Canada
| | - Jacob M Majikes
- National Institute of Standards and Technology, Gaithersburg, MD, 20878, United States of America
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Tripathy S, Nagari A, Chiu SP, Nandu T, Camacho CV, Mahendroo M, Kraus WL. Relaxin Modulates the Genomic Actions and Biological Effects of Estrogen in the Myometrium by Reducing Estrogen Receptor Alpha Phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589654. [PMID: 38659934 PMCID: PMC11042280 DOI: 10.1101/2024.04.15.589654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Estradiol (E2) and relaxin (Rln) are steroid and polypeptide hormones, respectively, with important roles in the female reproductive tract, including myometrium. Some actions of Rln, which are mediated by its membrane receptor RXFP1, require or are augmented by E2 signaling through its cognate nuclear steroid receptor, estrogen receptor alpha (ERα). In contrast, other actions of Rln act in opposition to the effects of E2. Here we explore the molecular and genomic mechanisms that underlie the functional interplay between E2 and Rln in the myometrium. We used both ovariectomized female mice and immortalized human myometrial cells expressing wild type or mutant ERα (hTERT-HM-ERα cells). Our results indicate that Rln attenuates the genomic actions and biological effects of estrogen in the myometrium and myometrial cells by reducing phosphorylation ERα on serine 118 (S118). Interestingly, we observed a potent inhibitory effect of Rln on the E2-dependent binding of ERα across the genome. The reduction in ERα binding was associated with changes in the hormone-regulated transcriptome, including a decrease in the E2-dependent expression of neighboring genes. The inhibitory effects of Rln cotreatment on the E2-dependent phosphorylation of ERα required the nuclear dual-specificity phosphatases DUSP1 and DUSP5. Moreover, the inhibitory effects of Rln were reflected in a concomitant inhibition of the E2-dependent contraction of myometrial cells. Collectively, our results identify a pathway that integrates Rln/RXFP1 and E2/ERα signaling, resulting in a convergence of membrane and nuclear signaling pathways to control genomic and biological outcomes.
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Affiliation(s)
- Sudeshna Tripathy
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Laboratory of Cervical Remodeling and Preterm Birth, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Section of Laboratory Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Anusha Nagari
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Computational Core Facility, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shu-Ping Chiu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Computational Core Facility, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cristel V. Camacho
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Section of Laboratory Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mala Mahendroo
- Laboratory of Cervical Remodeling and Preterm Birth, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Section of Laboratory Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W. Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Section of Laboratory Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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Asaeda Y, Shiraga K, Suzuki M, Sambongi Y, Ogino H, Igawa T. Rapid and collective determination of the complete "hot-spring frog" mitochondrial genome containing long repeat regions using Nanopore sequencing. PLoS One 2023; 18:e0280090. [PMID: 37906558 PMCID: PMC10617713 DOI: 10.1371/journal.pone.0280090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/25/2023] [Indexed: 11/02/2023] Open
Abstract
The mitochondrial genome (mt-genome) is one of the promising molecular markers for phylogenetics and population genetics. Recently, various mt-genomes have been determined rapidly by using massively parallel sequencers. However, the control region (CR, also called D-loop) in mt-genomes remain difficult to precisely determine due to the presence of repeat regions. Here, using Nanopore sequencing, we succeeded in rapid and collective determination of complete mt-genome of the hot-spring frog, Buergeria japonica, and found that its mt-genome size was 22,274 bp including CR (6,929 bp) with two types of tandem repeat motifs forming repeat regions. Comparison of assembly strategies revealed that the long- and short-read data combined together enabled efficient determination of the CR, but the short-read data alone did not. The B. japonica CR was longer than that of a congenic species inhabiting cooler climate areas, Buergeria buergeri, because of the long repeat regions in the former. During the thermal adaptation of B. japonica, the longer repeat regions in its CR may have accumulated within a period after divergence from B. buergeri.
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Affiliation(s)
- Yuka Asaeda
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Kento Shiraga
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Makoto Suzuki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yoshihiro Sambongi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hajime Ogino
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, Japan
| | - Takeshi Igawa
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, Japan
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Vaskó D, Domján J, Szűcs B, Bakk L, Hajdinák P, Marosi G, Nagy ZK, Hirsch E, Fehér C. Development and Comparison of Alternative Methods for the Purification of Adalimumab Directly from Harvested Cell Culture Fluid. Food Technol Biotechnol 2023; 61:339-349. [PMID: 38022883 PMCID: PMC10666952 DOI: 10.17113/ftb.61.03.23.8094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 07/11/2023] [Indexed: 12/01/2023] Open
Abstract
Research background Protein A affinity chromatography is a well-established method currently used in the pharmaceutical industry. However, the high costs usually associated with chromatographic separation of protein A and the difficulties in continuous operation make the investigation of alternative purification methods very important. Experimental approach In this study, extraction/back-extraction and precipitation/dissolution methods were developed and optimised. They were compared with protein A and cation exchange chromatography separations in terms of yield of monoclonal antibody (mAb) and amount of residual impurities, such as DNA and host cell proteins, and amount of mAb aggregates. For a comprehensive comparison of the different methods, experiments were carried out with the same cell-free fermentation broth containing adalimumab. Results and conclusions Protein A and cation exchange chromatographic separations resulted in high yield and purity of adalimumab. The precipitation-based process resulted in high yield but with lower purity. The extraction-based purification resulted in low yield and purity. Thus, the precipitation-based method proved to be more promising than the extraction-based method for direct purification of adalimumab from harvested cell culture fluid. Novelty and scientific contribution Although alternative purification methods may offer the advantages of simplicity and low-cost operation, further significant improvements are required to compete with the performance of chromatographic separations of adalimumab from true fermentation broth.
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Affiliation(s)
- Dorottya Vaskó
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111 Budapest, Hungary
| | - Júlia Domján
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111 Budapest, Hungary
| | - Bence Szűcs
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111 Budapest, Hungary
| | - László Bakk
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111 Budapest, Hungary
| | - Péter Hajdinák
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111 Budapest, Hungary
| | - György Marosi
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111 Budapest, Hungary
| | - Zsombor K. Nagy
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111 Budapest, Hungary
| | - Edit Hirsch
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111 Budapest, Hungary
| | - Csaba Fehér
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111 Budapest, Hungary
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Kamiya M, Kimura N, Umezawa N, Hasegawa H, Yasuda S. Muscle fiber necroptosis in pathophysiology of idiopathic inflammatory myopathies and its potential as target of novel treatment strategy. Front Immunol 2023; 14:1191815. [PMID: 37483632 PMCID: PMC10361824 DOI: 10.3389/fimmu.2023.1191815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/22/2023] [Indexed: 07/25/2023] Open
Abstract
Idiopathic inflammatory myopathies (IIMs), which are a group of chronic and diverse inflammatory diseases, are primarily characterized by weakness in the proximal muscles that progressively leads to persistent disability. Current treatments of IIMs depend on nonspecific immunosuppressive agents (including glucocorticoids and immunosuppressants). However, these therapies sometimes fail to regulate muscle inflammation, and some patients suffer from infectious diseases and other adverse effects related to the treatment. Furthermore, even after inflammation has subsided, muscle weakness persists in a significant proportion of the patients. Therefore, the elucidation of pathophysiology of IIMs and development of a better therapeutic strategy that not only alleviates muscle inflammation but also improves muscle weakness without increment of opportunistic infection is awaited. Muscle fiber death, which has been formerly postulated as "necrosis", is a key histological feature of all subtypes of IIMs, however, its detailed mechanisms and contribution to the pathophysiology remained to be elucidated. Recent studies have revealed that muscle fibers of IIMs undergo necroptosis, a newly recognized form of regulated cell death, and promote muscle inflammation and dysfunction through releasing inflammatory mediators such as damage-associated molecular patterns (DAMPs). The research on murine model of polymyositis, a subtype of IIM, revealed that the inhibition of necroptosis or HMGB1, one of major DAMPs released from muscle fibers undergoing necroptosis, ameliorated muscle inflammation and recovered muscle weakness. Furthermore, not only the necroptosis-associated molecules but also PGAM5, a mitochondrial protein, and reactive oxygen species have been shown to be involved in muscle fiber necroptosis, indicating the multiple target candidates for the treatment of IIMs acting through necroptosis regulation. This article overviews the research on muscle injury mechanisms in IIMs focusing on the contribution of necroptosis in their pathophysiology and discusses the potential treatment strategy targeting muscle fiber necroptosis.
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Shimbori EM, Giacomelli ADECS, Fernández-Triana JL, Watanabe IM, Santos EB, Santos JMD, Fazolin WX, Penteado-Dias AM. The Apanteles adelinamoralesae species group (Hymenoptera, Braconidae) from Brazil, with descriptions of three new species reared from fruit borers(Lepidoptera, Depressariidae). Zootaxa 2023; 5277:339-362. [PMID: 37518316 DOI: 10.11646/zootaxa.5277.2.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Indexed: 08/01/2023]
Abstract
With more than 633 species, Apanteles is the largest genus within the subfamily Microgastrinae (Hymenoptera, Braconidae). We describe three new species reared from pests of commercial fruits, Apanteles ahuacatl Shimbori, Giacomelli & Fernández-Triana sp. n., A. aratiku Shimbori sp. n., and A. mayochinchipe Shimbori sp. n. They parasitize caterpillars in the subfamily Stenomatinae (Depressariidae): the soursop moth Cerconota anonella (Sepp), in fruits of sweetsop (Annona squamosa L.) and atemoya (Annona squamosa x Annona cherimola Mill.) (Annonaceae), the avocado borer Stenoma catenifer Walsingham, in fruits of avocado (Persea americana Mill.) (Lauraceae), and the cacao shoot borer Stenoma decora Zeller, in fruits and shoots of cacao (Theobroma cacao L.) (Malvaceae). The new Apanteles species are included in an expanded version of the key provided by Fernández-Triana et al. (2014) for the Apanteles adelinamoralesae species group. In addition, the previous record of Apanteles stenomae Muesebeck in Brazil is revised and considered to actually represent the species A. yolandarojasae Fernández-Triana.
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Affiliation(s)
- Eduardo Mitio Shimbori
- Departamento de Entomologia e Acarologia; Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ); Universidade de São Paulo (USP); Piracicaba; São Paulo; Brazil.
| | - Arthuro DE Castro Stolf Giacomelli
- Departamento de Entomologia e Acarologia; Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ); Universidade de São Paulo (USP); Piracicaba; São Paulo; Brazil.
| | - José L Fernández-Triana
- Canadian National Collection of Insects; Arachnids and Nematodes; 960 Carling Ave.; Ottawa; ON K1A 0C6 Canada.
| | - Isabela Midori Watanabe
- Departamento de Ecologia e Biologia Evolutiva; Universidade Federal de São Carlos (UFSCar); São Carlos; São Paulo; Brazil.
| | - Eliaber Barros Santos
- Departamento de Ciências Agrárias e Ambientais; Universidade Estadual de Santa Cruz; Rodovia Jorge Amado; km 16; Bairro Salobrinho; Ilhéus; Bahia; Brazil CEP 45662-900.
| | - Jakeline Maria Dos Santos
- AgroVerde Soluções Agrícolas Ltda; Rua Rivadavia Carnauba 91 Sala 04; Pinheiro; Maceió; Alagoas; Brazil; CEP 57057-260.
| | - Wilian Xavier Fazolin
- Departamento de Entomologia e Acarologia; Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ); Universidade de São Paulo (USP); Piracicaba; São Paulo; Brazil.
| | - Angélica Maria Penteado-Dias
- Departamento de Ecologia e Biologia Evolutiva; Universidade Federal de São Carlos (UFSCAR); Rodovia Washington Luiz; Km 235; CEP 13.565-905; São Carlos; SP; Brazil.
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Liu D, Li Q, Luo J, Huang Q, Zhang Y. An SPRI beads-based DNA purification strategy for flexibility and cost-effectiveness. BMC Genomics 2023; 24:125. [PMID: 36927488 PMCID: PMC10022144 DOI: 10.1186/s12864-023-09211-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Current solid-phase reversible immobilization (SPRI) beads technology is widely used in molecular biology due to its convenience for DNA manipulation. However, the high performance commercial SPRI beads have no price advantage over our method. Furthermore, the use of commercially available SPRI beads standards does not provide the flexibility required for a number of specific nucleic acid handling scenarios. RESULTS We report an efficient DNA purification strategy by combining home-made beads-suspension buffer with SPRI beads. The method tests the critical concentrations of polyethylene glycol (PEG) 8000 and beads to maximise recovery. And the composition of the SPRI beads DNA purification system (SDPS) was determined at 20% PEG 8000, 2 M NaCl and 16.3 mM MgCl2, and 1.25 mg/ml beads (1/8th original concentration). Then, we tested the DNA recovery of the SDPS, and the result showed that it was comparable to the control (AMPure XP beads). In the study, we have also developed an adjustment SPRI beads DNA purification system (ASDPS), the volume of ASDPS per reaction is 0.6× reaction volume (beads/samples). The performance of ASDPS is similar to SDPS and the control. But the cost of our methods is only about 1/24th of the control. To further assess its performance, we prepare the DNA-seq libraries to evaluate the yield, library quality, capture efficiency and consistency. We have compared all these results with the performance of the control and confirmed its efficiency. CONCLUSION We have proposed an alternative DNA purification approach with great flexibility, allowing researchers to manipulate DNA in different conditions. And ultimately, its application will benefit molecular biology research in the future.
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Affiliation(s)
- Danli Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng, Shenzhen, 518120, China
| | - Qiujia Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jing Luo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng, Shenzhen, 518120, China
| | - Qitong Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng, Shenzhen, 518120, China
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, 6708PB, Netherlands
| | - Yubo Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng, Shenzhen, 518120, China.
- College of Life Science and Engineering, Foshan University, Foshan, China.
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Schleif R. A Career's Work, the l-Arabinose Operon: How It Functions and How We Learned It. EcoSal Plus 2022; 10:eESP00122021. [PMID: 36519894 DOI: 10.1128/ecosalplus.esp-0012-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/20/2021] [Indexed: 06/17/2023]
Abstract
Very few labs have had the good fortune to have been able to focus for more than 50 years on a relatively narrow research topic and to be in a field in which both basic knowledge and the research technology and methods have progressed as rapidly as they have in molecular biology. My research group, first at Brandeis University and then at Johns Hopkins University, has had this opportunity. In this review, therefore, I will describe largely the work from my laboratory that has spanned this period and which was carried out by 40 plus graduate students, several postdoctoral associates, my technician, and me. In addition to presenting the scientific findings or results, I will place many of the topics in scientific context and, because we needed to develop a good many of the experimental methods behind our findings, I will also describe some of these methods and their importance. Also included will be occasional comments on how the research community or my research group functioned. Because a wide variety of approaches were used throughout our work, no ideal organization of this review is apparent. Therefore, I have chosen to use a hybrid structure in which there are six sections. Within each of the sections, experiments and findings will be described roughly in chronological order. Frequent cross references between parts and sections will be made because some findings and experimental approaches could logically have been described in more than one place.
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Dey S, Batisse C, Shukla J, Webster MW, Takacs M, Saint-André C, Weixlbaumer A. Structural insights into RNA-mediated transcription regulation in bacteria. Mol Cell 2022; 82:3885-3900.e10. [DOI: 10.1016/j.molcel.2022.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/07/2022] [Accepted: 09/19/2022] [Indexed: 11/06/2022]
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DNA Polymerase ζ without the C-Terminus of Catalytic Subunit Rev3 Retains Characteristic Activity, but Alters Mutation Specificity of Ultraviolet Radiation in Yeast. Genes (Basel) 2022; 13:genes13091576. [PMID: 36140745 PMCID: PMC9498848 DOI: 10.3390/genes13091576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/16/2022] [Accepted: 08/27/2022] [Indexed: 11/17/2022] Open
Abstract
DNA polymerase ζ (pol ζ) plays a central role in replicating damaged genomic DNA. When DNA synthesis stalls at a lesion, it participates in translesion DNA synthesis (TLS), which helps replication proceed. TLS prevents cell death at the expense of new mutations. The current model indicates that pol ζ-dependent TLS events are mediated by Pol31/Pol32 pol ζ subunits, which are shared with replicative polymerase pol δ. Surprisingly, we found that the mutant rev3-ΔC in yeast, which lacks the C-terminal domain (CTD) of the catalytic subunit of pol ζ and, thus, the platform for interaction with Pol31/Pol32, retains most pol ζ functions. To understand the underlying mechanisms, we studied TLS in normal templates or templates with abasic sites in vitro in primer extension reactions with purified four-subunit pol ζ versus pol ζ with Rev3-ΔC. We also examined the specificity of ultraviolet radiation (UVR)-induced mutagenesis in the rev3-ΔC strains. We found that the absence of Rev3 CTD reduces activity levels, but does not alter the basic biochemical properties of pol ζ, and alters the mutation spectrum only at high doses of UVR, alluding to the existence of mechanisms of recruitment of pol ζ to UVR-damaged sites independent of the interaction of Pol31/Pol32 with the CTD of Rev3.
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Masukawa M, Sato Y, Yu F, Tsumoto K, Yoshikawa K, Takinoue M. Water-in-water droplets selectively uptake self-assembled DNA nano/microstructures: a versatile method for purification in DNA nanotechnology. Chembiochem 2022; 23:e202200240. [PMID: 35686962 PMCID: PMC9544409 DOI: 10.1002/cbic.202200240] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/08/2022] [Indexed: 11/10/2022]
Abstract
DNA is an excellent material for constructing self-assembled nano/microstructures. Owing to the widespread use of DNA as a building block in laboratories and industry, it is desirable to increase the efficiency of all steps involved in producing self-assembled DNA structures. One of the bottlenecks is the purification required to separate the excess components from the target structures. This paper describes a purification method based on the fractionation by water-in-water (W/W) droplets composed of phase-separated dextran-rich droplets in a polyethylene glycol (PEG)-rich continuous phase. The dextran-rich droplets facilitate the selective uptake of self-assembled DNA nano/microstructures and allow the separation of the target structure. This study investigates the ability to purify DNA origami, DNA hydrogels, and DNA microtubes. The W/W-droplet fractionation allows the purification of structures of a broad size spectrum without changes to the protocol. By quantifying the activity of deoxyribozyme-modified DNA origami after W/W-droplet purification, this study demonstrates that this method sufficiently preserves the accessibility to the surface of a functional DNA nanostructure. It is considered that the W/W-droplet fractionation could become one of the standard methods for the purification of self-assembled DNA nano/microstructures for biomedical and nanotechnology applications owing to its low cost and simplicity.
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Affiliation(s)
- Marcos Masukawa
- Tokyo Institute of Technology: Tokyo Kogyo Daigaku, Computer Science, JAPAN
| | - Yusuke Sato
- Kyushu Institute of Technology - Iizuka Campus: Kyushu Kogyo Daigaku - Iizuka Campus, Intelligent and Control Systems, JAPAN
| | - Fujio Yu
- Tokyo Institute of Technology: Tokyo Kogyo Daigaku, Computer Science, JAPAN
| | - Kanta Tsumoto
- Mie University: Mie Daigaku, Chemistry for Materials, JAPAN
| | - Kenichi Yoshikawa
- Kyoto University: Kyoto Daigaku, Center for Integrative Medicine and Physics, Institute for Advanced Study, JAPAN
| | - Masahiro Takinoue
- Tokyo Institute of Technology, Department of Computer Science, 4259-J2-36 Nagatsuta-cho, Midori-ku, 226-8502, Yokohama, JAPAN
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12
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LaSarre B, Olawole OI, Paulsen AA, Halverson LJ, Gleason ML, Beattie GA. Complete Genome Sequences of Four Strains of Erwinia tracheiphila: A Resource for Studying a Bacterial Plant Pathogen with a Highly Complex Genome. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:500-504. [PMID: 35491948 DOI: 10.1094/mpmi-01-22-0008-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Breah LaSarre
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011-1101, U.S.A
| | - Olakunle I Olawole
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011-1101, U.S.A
| | - Ashley A Paulsen
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011-1101, U.S.A
| | - Larry J Halverson
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011-1101, U.S.A
| | - Mark L Gleason
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011-1101, U.S.A
| | - Gwyn A Beattie
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011-1101, U.S.A
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13
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Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P. Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory. Nat Struct Mol Biol 2022; 29:493-501. [PMID: 35581345 PMCID: PMC9113941 DOI: 10.1038/s41594-022-00768-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 04/01/2022] [Indexed: 01/17/2023]
Abstract
Throughout the genome, nucleosomes often form regular arrays that differ in nucleosome repeat length (NRL), occupancy of linker histone H1 and transcriptional activity. Here, we report cryo-EM structures of human H1-containing tetranucleosome arrays with four physiologically relevant NRLs. The structures show a zig-zag arrangement of nucleosomes, with nucleosomes 1 and 3 forming a stack. H1 binding to stacked nucleosomes depends on the NRL, whereas H1 always binds to the non-stacked nucleosomes 2 and 4. Short NRLs lead to altered trajectories of linker DNA, and these altered trajectories sterically impair H1 binding to the stacked nucleosomes in our structures. As the NRL increases, linker DNA trajectories relax, enabling H1 contacts and binding. Our results provide an explanation for why arrays with short NRLs are depleted of H1 and suited for transcription, whereas arrays with long NRLs show full H1 occupancy and can form transcriptionally silent heterochromatin regions. Cryo-EM structures of human H1-containing tetranucleosome arrays with distinct, physiological nucleosome repeat lengths reveal that nucleosomes assume a zig-zag arrangement and H1 binds to stacked nucleosomes with longer linker DNA.
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Affiliation(s)
- Marco Dombrowski
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Maik Engeholm
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Christian Dienemann
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Svetlana Dodonova
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany. .,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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14
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Hanke M, Hansen N, Chen R, Grundmeier G, Fahmy K, Keller A. Salting-Out of DNA Origami Nanostructures by Ammonium Sulfate. Int J Mol Sci 2022; 23:ijms23052817. [PMID: 35269959 PMCID: PMC8911265 DOI: 10.3390/ijms23052817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 12/16/2022] Open
Abstract
DNA origami technology enables the folding of DNA strands into complex nanoscale shapes whose properties and interactions with molecular species often deviate significantly from that of genomic DNA. Here, we investigate the salting-out of different DNA origami shapes by the kosmotropic salt ammonium sulfate that is routinely employed in protein precipitation. We find that centrifugation in the presence of 3 M ammonium sulfate results in notable precipitation of DNA origami nanostructures but not of double-stranded genomic DNA. The precipitated DNA origami nanostructures can be resuspended in ammonium sulfate-free buffer without apparent formation of aggregates or loss of structural integrity. Even though quasi-1D six-helix bundle DNA origami are slightly less susceptible toward salting-out than more compact DNA origami triangles and 24-helix bundles, precipitation and recovery yields appear to be mostly independent of DNA origami shape and superstructure. Exploiting the specificity of ammonium sulfate salting-out for DNA origami nanostructures, we further apply this method to separate DNA origami triangles from genomic DNA fragments in a complex mixture. Our results thus demonstrate the possibility of concentrating and purifying DNA origami nanostructures by ammonium sulfate-induced salting-out.
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Affiliation(s)
- Marcel Hanke
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (M.H.); (N.H.); (R.C.); (G.G.)
| | - Niklas Hansen
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (M.H.); (N.H.); (R.C.); (G.G.)
| | - Ruiping Chen
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (M.H.); (N.H.); (R.C.); (G.G.)
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (M.H.); (N.H.); (R.C.); (G.G.)
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstrasse 400, 01328 Dresden, Germany;
- Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01062 Dresden, Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (M.H.); (N.H.); (R.C.); (G.G.)
- Correspondence: ; Tel.: +49-5251-605722
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15
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Trick AY, Ngo HT, Nambiar AH, Morakis MM, Chen FE, Chen L, Hsieh K, Wang TH. Filtration-assisted magnetofluidic cartridge platform for HIV RNA detection from blood. LAB ON A CHIP 2022; 22:945-953. [PMID: 35088790 PMCID: PMC9035341 DOI: 10.1039/d1lc00820j] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The ability to detect and quantify HIV RNA in blood is essential to sensitive detection of infections and monitoring viremia throughout treatment. Current options for point-of-care HIV diagnosis (i.e. lateral flow rapid tests) lack sensitivity for early detection and are unable to quantify viral load. HIV RNA diagnostics typically require extensive pre-processing of blood to isolate plasma and extract nucleic acids, in addition to expensive equipment for conducting nucleic acid amplification and fluorescence detection. Therefore, molecular HIV diagnostics is still mainly limited to clinical laboratories and there is an unmet need for high sensitivity point-of-care screening and at-home HIV viral load quantification. In this work, we outline a streamlined workflow for extraction of plasma from whole blood coupled with HIV RNA extraction and quantitative polymerase chain reaction (qPCR) in a portable magnetofluidic cartridge platform for use at the point-of-care. Viral particles were isolated from blood using manual filtration through a 3D-printed filter module in seconds followed by automated nucleic acid capture, purification, and transfer to qPCR using magnetic beads. Both nucleic acid extraction and qPCR were integrated within cartridges using compact instrumentation consisting of a motorized magnet arm, miniaturized thermocycler, and image-based fluorescence detection. We demonstrated detection down to 1000 copies of HIV viral particles from whole blood in <30 minutes.
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Affiliation(s)
- Alexander Y Trick
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Hoan Thanh Ngo
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Anju H Nambiar
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Marisa M Morakis
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Fan-En Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Liben Chen
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
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16
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Kerachian MA, Azghandi M, Mozaffari-Jovin S, Thierry AR. Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA. Clin Epigenetics 2021; 13:193. [PMID: 34663458 PMCID: PMC8525023 DOI: 10.1186/s13148-021-01182-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/04/2021] [Indexed: 02/06/2023] Open
Abstract
Methylation analysis of circulating cell-free DNA (cirDNA), as a liquid biopsy, has a significant potential to advance the detection, prognosis, and treatment of cancer, as well as many genetic disorders. The role of epigenetics in disease development has been reported in several hereditary disorders, and epigenetic modifications are regarded as one of the earliest and most significant genomic aberrations that arise during carcinogenesis. Liquid biopsy can be employed for the detection of these epigenetic biomarkers. It consists of isolation (pre-analytical) and detection (analytical) phases. The choice of pre-analytical variables comprising cirDNA extraction and bisulfite conversion methods can affect the identification of cirDNA methylation. Indeed, different techniques give a different return of cirDNA, which confirms the importance of pre-analytical procedures in clinical diagnostics. Although novel techniques have been developed for the simplification of methylation analysis, the process remains complex, as the steps of DNA extraction, bisulfite treatment, and methylation detection are each carried out separately. Recent studies have noted the absence of any standard method for the pre-analytical processing of methylated cirDNA. We have therefore conducted a comprehensive and systematic review of the important pre-analytical and analytical variables and the patient-related factors which form the basis of our guidelines for analyzing methylated cirDNA in liquid biopsy.
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Affiliation(s)
- Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.
| | - Marjan Azghandi
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Sina Mozaffari-Jovin
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alain R Thierry
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France.
- INSERM, U1194, Montpellier, France.
- University of Montpellier, Montpellier, France.
- ICM, Regional Institute of Cancer of Montpellier, Montpellier, France.
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17
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Yu AD, Galatsis K, Zheng J, Le JQ, Ma D, Perlman S, Rosbash M. Development of a Saliva-Optimized RT-LAMP Assay for SARS-CoV-2. J Biomol Tech 2021; 32:102-113. [PMID: 35027868 PMCID: PMC8730519 DOI: 10.7171/jbt.21-3203-005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Conventional reverse transcription quantitative polymerase chain reaction (RT-qPCR) technology has struggled to fulfill the unprecedented need for diagnostic testing created by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Complexity and cost hinder access to testing, and long turnaround time decreases its utility. To ameliorate these issues, we focus on saliva and introduce several advances to colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) technology; RT-LAMP offers a minimal equipment alternative to RT-qPCR. First, we validated the use of the novel dye LAMPShade Violet (LSV), which improves the visual clarity and contrast of the colorimetric readout. Second, we compared different inactivation conditions on infectivity and RNA yield from saliva. Third, we developed a 10-minute RNA purification protocol from saliva. We call this magnetic bead protocol SalivaBeads. Finally, we developed a magnetic stick, StickLAMP, which provides reliable bead-based RNA purification as well as simple and low-cost access to scalable testing from saliva.
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Affiliation(s)
- Albert D. Yu
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, Massachusetts, USA
| | - Kristina Galatsis
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, Massachusetts, USA
| | - Jian Zheng
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Jasmine Quynh Le
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, Massachusetts, USA
| | - Dingbang Ma
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, Massachusetts, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, Massachusetts, USA
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18
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Rego NDFC, Chahad-Ehlers S, Campanini EB, Torres FR, de Brito RA. VRILLE shows high divergence among Higher Diptera flies but may retain role as transcriptional repressor of clock. JOURNAL OF INSECT PHYSIOLOGY 2021; 133:104284. [PMID: 34256034 DOI: 10.1016/j.jinsphys.2021.104284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
In the circadian system, the clock gene vrille (vri) is an essential component of the second feedback loop, being responsible in Drosophila for the rhythmicity of the Clock (Clk) gene transcription by its repression. Here we studied vri in a fruit fly pest, the Tephritidae Anastrepha fraterculus, aimingtoinvestigate its molecular evolution and expression patterns from whole-head extracts. We used a combination of transcriptomic, genomic and gene walking strategies to sequence and characterize Afravri in male and female head transcriptomes of A. fraterculus and detected two putative isoforms that may correspond to A and D vri isoforms of Drosophila. Both isoforms produced a full-length sequence that translates to 842 amino acids. While the protein sequence showed significant divergence to orthologous sequences from other organisms, the bZIP domain was highly conserved. Molecular evolutionary analyses showed that vri in higher Diptera flies has been evolving under positive selection. A more detailed analysis showed positive selection also in Tephritidae with 29 sites evolving under positive selection in comparison with Drosophilidae. Real time expression analysis in LD and DD conditions showed cyclic expression of Afravri mRNA with oscillation opposite to AfraClk, suggesting that VRI may also behave in Anastrepha as a transcriptional repressor of Clk, providing another indication that higher Diptera might share common interlocked transcript-translation feedback loops (TTFLs) mechanisms that differ from other insects in target genes.
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Affiliation(s)
| | - Samira Chahad-Ehlers
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, Brazil.
| | - Emeline Boni Campanini
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, Brazil
| | - Felipe Rafael Torres
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil.
| | - Reinaldo Alves de Brito
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, Brazil.
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19
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Elnasser Z, Elsamarneh R, Obeidat H, Amarin Z, Jaradat S, Kaplan N. In-vitro activity of tigecycline against multidrug-resistant Gram negative bacteria: The experience of a university hospital. J Infect Public Health 2021; 14:478-483. [PMID: 33743369 DOI: 10.1016/j.jiph.2020.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 12/05/2020] [Accepted: 12/08/2020] [Indexed: 01/04/2023] Open
Abstract
The emergence of multidrug-resistant Gram negative bacteria has given rise to significant therapeutic challenges. These pathogens may have developed resistance to tigecycline, which is an alternative antibiotic used empirically in the treatment of serious infections. The objectives of this study were to identify the in-vitro activity of tigecycline against multidrug-resistant Gram negative strains isolated from clinical specimens and their related genes, at a university hospital. For this, 150 clinical isolates of multidrug-resistant Gram negative cultures from various clinical specimens were collected. Bacterial isolates were cultured, identified and their antibiotic susceptibilities were determined. Polymerase chain reaction was performed to amplify AcrB, AmpC, RamR, MexR, AdeB, TetA genes. Results revealed that all isolates were multidrug-resistant. The resistance of isolates was 91.4% to aztreonam, 94.6% to piperacillin, 34% to imipenem, 38.7% to meropenem, 71.3% to levofloxacin, 97.3% to ceftriaxone, 94.7% to cefepime, 9.3% to colistin, 78% to tetracycline, 21.4% to tigecycline and 68% to trimethoprim. AcrB, AmpC, RamR, MexR, AdeB, TetA genes were present in multidrug-resistant Gram negative bacteria. AcrB, RamR, TetA genes were related to tigecycline resistance. It is concluded that infections caused by multidrug-resistant Gram negative bacteria occur at a high rate. Most isolates were multi drug resistant, with 21.4% being resistant to tigecycline.
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Affiliation(s)
- Z Elnasser
- Pathology and Microbiology Department, Jordan University of Science and Technology, Jordan.
| | - R Elsamarneh
- Medical Laboratory Sciences Department, Jordan University of Science and Technology, Jordan
| | - H Obeidat
- Medical Laboratory Sciences Department, Jordan University of Science and Technology, Jordan
| | - Z Amarin
- Department of Obstetrics and Gynecology, Jordan University of Science and Technology, Jordan
| | - S Jaradat
- Department of Biotechnology and Genetic Engineering, Jordan university of Science and Technology, Jordan
| | - N Kaplan
- Pathology and Microbiology Department, Jordan University of Science and Technology, Jordan
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20
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Muzzopappa F, Hertzog M, Erdel F. DNA length tunes the fluidity of DNA-based condensates. Biophys J 2021; 120:1288-1300. [PMID: 33640380 PMCID: PMC8059207 DOI: 10.1016/j.bpj.2021.02.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/31/2021] [Accepted: 02/15/2021] [Indexed: 02/09/2023] Open
Abstract
Living organisms typically store their genomic DNA in a condensed form. Mechanistically, DNA condensation can be driven by macromolecular crowding, multivalent cations, or positively charged proteins. At low DNA concentration, condensation triggers the conformational change of individual DNA molecules into a compacted state, with distinct morphologies. Above a critical DNA concentration, condensation goes along with phase separation into a DNA-dilute and a DNA-dense phase. The latter DNA-dense phase can have different material properties and has been reported to be rather liquid-like or solid-like depending on the characteristics of the DNA and the solvent composition. Here, we systematically assess the influence of DNA length on the properties of the resulting condensates. We show that short DNA molecules with sizes below 1 kb can form dynamic liquid-like assemblies when condensation is triggered by polyethylene glycol and magnesium ions, binding of linker histone H1, or nucleosome reconstitution in combination with linker histone H1. With increasing DNA length, molecules preferentially condense into less dynamic more solid-like assemblies, with phage λ-DNA with 48.5 kb forming mostly solid-like assemblies under the conditions assessed here. The transition from liquid-like to solid-like condensates appears to be gradual, with DNA molecules of roughly 1–10 kb forming condensates with intermediate properties. Titration experiments with linker histone H1 suggest that the fluidity of condensates depends on the net number of attractive interactions established by each DNA molecule. We conclude that DNA molecules that are much shorter than a typical human gene are able to undergo liquid-liquid phase separation, whereas longer DNA molecules phase separate by default into rather solid-like condensates. We speculate that the local distribution of condensing factors can modulate the effective length of chromosomal domains in the cell. We anticipate that the link between DNA length and fluidity established here will improve our understanding of biomolecular condensates involving DNA.
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Affiliation(s)
- Fernando Muzzopappa
- MCD, Center for Integrative Biology (CBI), University of Toulouse, CNRS, Toulouse, France
| | - Maud Hertzog
- MCD, Center for Integrative Biology (CBI), University of Toulouse, CNRS, Toulouse, France
| | - Fabian Erdel
- MCD, Center for Integrative Biology (CBI), University of Toulouse, CNRS, Toulouse, France.
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21
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Wang X, Yang X. A Simple Blocking PCR-Based Method for the Synthesis of High-Copy dsDNA Tandem Repeats. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2003671. [PMID: 33006262 DOI: 10.1002/smll.202003671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/26/2020] [Indexed: 06/11/2023]
Abstract
DNA tandem repeats are frequently found in eukaryotic genomes. High-copy DNA repeats can serve as building blocks of complex DNA structures, but the in vitro synthesis of DNA repeats has been challenging due to complicated procedures and the high cost. Here, a new, simple method is developed using the strategy of blocking polymerase chain reaction for highly efficient DNA repeat expansion (BPRE). With BPRE, dsDNA fragments composed of more than 40 copies of the repeat sequence can be quickly produced, while the cost is reduced by at least 90%. As a typical application, reannealing of the dsDNA repeats generates elastic hydrogels, which shows a high capacity for doxycycline absorption and prolonged release.
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Affiliation(s)
- Xin Wang
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xuerui Yang
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
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22
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Hidden diversity in Prochilodus nigricans: A new genetic lineage within the Tapajós River basin. PLoS One 2020; 15:e0237916. [PMID: 32842138 PMCID: PMC7447553 DOI: 10.1371/journal.pone.0237916] [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: 01/07/2020] [Accepted: 08/06/2020] [Indexed: 11/23/2022] Open
Abstract
Highly spread through the Amazon River basin, Prochilodus nigricans have had its taxonomic validity recently questioned, when genetic differences between Western and Eastern Amazon populations from the Brazilian shield were detected. This area has been seeing as a region of high ichthyofaunal diversity and endemism, in which the hybrid origin of the Tapajós River basin has been raised. In this paper, we report a new molecular lineage within P. nigricans of Tapajós River, highlighting this region still hides taxonomically significant diversity. Haplotype networks were reconstructed using the mitochondrial COI and ATP6/8 markers, which were also used to calculate genetic distances among clusters. We additionally conducted a delimiting species approach by employing a Generalized Mixed Yule-Coalescent model (GMYC) with COI sequences produced here, and previous ones published for individuals sampled across the Amazon River basin. In addition to the genetic differentiation within P. nigricans, our findings favor the hypothesis of hybrid origin of the Tapajós River basin and reaffirm the importance of studies aiming to investigate hidden diversity to address taxonomic and biogeographic issues, that certainly benefit better biodiversity conservation actions.
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23
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Dodonova SO, Zhu F, Dienemann C, Taipale J, Cramer P. Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function. Nature 2020; 580:669-672. [PMID: 32350470 DOI: 10.1038/s41586-020-2195-y] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/18/2020] [Indexed: 02/02/2023]
Abstract
'Pioneer' transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming1,2. Pioneer factors can bind nucleosomal DNA to enable gene expression from regions of the genome with closed chromatin. SOX2 is a prominent pioneer factor that is essential for pluripotency and self-renewal of embryonic stem cells3. Here we report cryo-electron microscopy structures of the DNA-binding domains of SOX2 and its close homologue SOX11 bound to nucleosomes. The structures show that SOX factors can bind and locally distort DNA at superhelical location 2. The factors also facilitate detachment of terminal nucleosomal DNA from the histone octamer, which increases DNA accessibility. SOX-factor binding to the nucleosome can also lead to a repositioning of the N-terminal tail of histone H4 that includes residue lysine 16. We speculate that this repositioning is incompatible with higher-order nucleosome stacking, which involves contacts of the H4 tail with a neighbouring nucleosome. Our results indicate that pioneer transcription factors can use binding energy to initiate chromatin opening, and thereby facilitate nucleosome remodelling and subsequent transcription.
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Affiliation(s)
- Svetlana O Dodonova
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Fangjie Zhu
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Christian Dienemann
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jussi Taipale
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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24
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Pyne P, Samanta N, Patra A, Das A, Sen P, Mitra RK. Polyethylene glycols affect electron transfer rate in phenosafranin-DNA complex. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 225:117464. [PMID: 31465973 DOI: 10.1016/j.saa.2019.117464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/06/2019] [Accepted: 08/09/2019] [Indexed: 06/10/2023]
Abstract
Long distance electron transfer (ET) between small ligands and DNA is a much studied phenomenon and is principally believed to occur through electron (or hole) hopping. Several studies have been carried out in aqueous environments while in real biological milieu the DNA molecules experience a more dense and heterogeneous environment containing otherwise indifferent molecular crowders. It is therefore expected that the ET could get modified in the presence of crowding agent and to investigate that we have made elaborate studies on steady state and time-resolved (picosecond (ps) and femtosecond (fs)-resolved) emission properties of a phenosafranine (PSF) intercalated to calf thymus (CT) DNA in the presence of ethylene glycol (EG) and polyethylene glycols (PEG) of different chain lengths (PEG 200, 400 and 1000). The emission of PSF gets considerably quenched when intercalated to DNA; the quenching is released when PEGs are added into it. The structural integrity of the CT DNA has been established using circular dichroism spectroscopy. CD measurements have evidenced only marginal changes in the DNA structure upon the addition of PEGs. ps-Resolved fluorescence measurements show significant decrease in the contribution of the DNA induced quenched time-constant of PSF upon the addition of PEGs, however, fs-resolved measurements show less noticeable changes in the time constants. Our study shows that the electron hopping rate through the guanine base in DNA core remains unaffected whereas the 'through space' electron transfer process does get affected in the presence of molecular crowders.
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Affiliation(s)
- Partha Pyne
- Department of Chemical, Biological and Macromolecular Sciences, S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 106, India
| | - Nirnay Samanta
- Department of Chemical, Biological and Macromolecular Sciences, S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 106, India
| | - Animesh Patra
- Department of Chemical, Biological and Macromolecular Sciences, S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 106, India
| | - Aritra Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India.
| | - Rajib Kumar Mitra
- Department of Chemical, Biological and Macromolecular Sciences, S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 106, India.
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Figueiredo RMPD, Souza VCD, Nascimento VAD, Naveca FG. Human parvovirus B19 genotype 1 in suspected dengue patients of Tefé, Amazonas State, Brazil. Rev Soc Bras Med Trop 2019; 52:e20190304. [PMID: 31508787 DOI: 10.1590/0037-8682-0304-2019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/02/2019] [Indexed: 01/30/2023] Open
Abstract
INTRODUCTION Human parvovirus B19 (B19V) is a common pathogen, which on infection causes variety of clinical conditions from benign self-limiting exanthematous disease and other similar pathologies to fetal death. METHODS We collected 341 serum samples between the first and fourth day after the onset of symptoms from all patients suspected of dengue fever who were attended at Regional Hospital of Tefé. Initially, patients were screened for malaria by blood smear test and negative samples were sent to Fundação de Medicina Tropical Doutor Heitor Vieira Dourado (FMT-HVD) situated in Manaus (AM) for dengue testing using semi-nested multiplex PCR. Further, we investigated 44 malaria and dengue-negative samples of children for B19V DNA by nested-PCR. Positive samples were analyzed by BLAST against entire public non-redundant nucleotide database and genotyped by phylogenetic analyses using neighbor-joining clustering method. RESULTS Eight samples (18.2%) were found to be PCR positive. Fever, headache, ocular pain, and/or muscle pain were reported as the most frequent symptoms by the patients and none were diagnosed with rash at the time of sample collection. Phylogenetic analysis of major capsid protein 2 (VP2) and VP3 coding region showed high similarity with B19V genotype 1. CONCLUSIONS Our results reveal the spread of B19V genotype 1 in Tefé. Moreover, our results emphasize the significance of laboratorial differential diagnosis using molecular techniques in patients with acute febrile, and thereby aid the health surveillance system in improving patient care even in the remote areas of Amazon.
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Affiliation(s)
| | - Victor Costa de Souza
- Fundação Oswaldo Cruz Amazônia, Instituto Leônidas e Maria Deane, Manaus, AM, Brasil
| | | | - Felipe Gomes Naveca
- Fundação Oswaldo Cruz Amazônia, Instituto Leônidas e Maria Deane, Manaus, AM, Brasil
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Bastos E, Schneider M, de Quadros DPC, Welz B, Batista MB, Horta PA, Rörig LR, Barufi JB. Phytoremediation potential of Ulva ohnoi (Chlorophyta): Influence of temperature and salinity on the uptake efficiency and toxicity of cadmium. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 174:334-343. [PMID: 30849653 DOI: 10.1016/j.ecoenv.2019.01.130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 01/18/2019] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
Ulva ohnoi is a green macroalga with fast growth and high rates of nitrogen and phosphorus absorption. Recently, this species has been recorded in several places with record green tide formation in some of them. Using molecular tools, we herein report the first occurrence of this species in Brazil and demonstrate its potential for phytoremediation in typical environmental concentrations of Cd (0.625-15 µg L-1). Similarly, the effects of physicochemical parameters (salinity and temperature) on the toxicity and uptake efficiency of this species were evaluated. Molecular analysis of two sequences (1141 bp) obtained corroborates another 34 sequences for U. ohnoi obtained from GenBank. The addition of Cd in the medium affected photosynthetic parameters and reduced growth rate. U. ohnoi showed resistance to Cd when cultivated at 18 °C, S15 and 18-25 °C, S35, at concentrations between 0.625 and 2.5 μg. L-1 of Cd; yet, positive growth rate was maintained. Dose-dependent accumulation was observed in all combinations of factors used with a maximum value of 4.20 μg Cd per gram of dry seaweed at 15 μg. L-1 of Cd at 18 °C and S35. Maximum value of the concentration factor was 81.3 ± 1.1% of Cd added at the concentration of 0.625 μg. L-1 to S15 and 18 °C. Our results demonstrate the potential of using U. ohnoi in the phytoremediation of Cd in saltwater or brackish water.
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Affiliation(s)
- Eduardo Bastos
- Programa de Pós-Graduação em Biotecnologia e Biociências, Universidade Federal de Santa Catarina, Florianópolis CEP:88040-970, Brazil.
| | - Mauana Schneider
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Daiane Paula Cunha de Quadros
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Brazil; Instituto Federal de Educação, Ciência e Tecnologia Catarinense, Ibirama, Brazil
| | - Bernhard Welz
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Brazil; Instituto Nacional de Ciência e Tecnologia do CNPq - INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA, Brazil
| | - Manuela Bernardes Batista
- Programa de Pós-Graduação em Ecologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Paulo Antunes Horta
- Departamento de Botânica, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Leonardo Rubi Rörig
- Departamento de Botânica, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - José Bonomi Barufi
- Departamento de Botânica, Universidade Federal de Santa Catarina, Florianópolis, Brazil
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High-resolution, strand-specific R-loop mapping via S9.6-based DNA-RNA immunoprecipitation and high-throughput sequencing. Nat Protoc 2019; 14:1734-1755. [PMID: 31053798 DOI: 10.1038/s41596-019-0159-1] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 02/28/2019] [Indexed: 11/08/2022]
Abstract
R-loops are prevalent three-stranded non-B DNA structures composed of an RNA-DNA hybrid and a single strand of DNA. R-loops are implicated in various basic nuclear processes, such as class-switch recombination, transcription termination and chromatin patterning. Perturbations in R-loop metabolism have been linked to genomic instability and have been implicated in human disorders, including cancer. As a consequence, the accurate mapping of these structures has been of increasing interest in recent years. Here, we describe two related immunoprecipitation-based methods for mapping R-loop structures: basic DRIP-seq (DNA-RNA immunoprecipitation followed by high-throughput DNA sequencing), an easy, robust, but resolution-limited technique; and DRIPc-seq (DNA-RNA immunoprecipitation followed by cDNA conversion coupled to high-throughput sequencing), a high-resolution and strand-specific iteration of the method that permits accurate R-loop mapping genome wide. Briefly, after gentle DNA extraction and restriction digestion with a cocktail of enzymes, R-loop structures are immunoprecipitated with the anti-RNA-DNA hybrid S9.6 antibody. Compared with DRIP-seq, in which the immunoprecipitated DNA is directly sequenced, DRIPc-seq permits the recovery of the RNA moiety of R-loops, and these RNA strands are subjected to strand-specific RNA sequencing (RNA-seq) analysis. DRIPc-seq can be performed in 5 d and can be applied to any cell type, provided sufficient starting material can be collected. Accurately mapping R-loop distribution in various cell lines and under varied conditions is essential to understanding the formation, roles and dynamic resolution of these important structures.
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Abstract
In this review, we compare the circular dichroism (CD) spectra of liquid-crystalline dispersion (LCD) particles formed in PEG-containing aqueous-salt solutions with the purpose of determining the packing of ds DNA molecules in these particles. Depending on the osmotic pressure of the solution, the phase exclusion of ds DNA molecules at room temperature results in the formation of LCD particles with the cholesteric or the hexagonal packing of molecules. The heating of dispersion particles with the hexagonal packing of the ds DNA molecules results in a new phase transition, accompanied by an appearance of a new optically active phase of ds DNA molecules. Our results are rationalized by way of a concept of orientationally ordered “quasinematic” layers formed by ds DNA molecules, with a parallel alignment in the hexagonal structure. These layers can adopt a twisted configuration with a temperature increase; and as a result of this process, a new, helicoidal structure of dispersion particle is formed (termed as the “re-entrant” cholesteric phase). To prove the cholesteric pattern of ds DNA molecules in this phase, the “liquid-like” state of the dispersion particles was transformed into its “rigid” counterpart.
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Oberacker P, Stepper P, Bond DM, Höhn S, Focken J, Meyer V, Schelle L, Sugrue VJ, Jeunen GJ, Moser T, Hore SR, von Meyenn F, Hipp K, Hore TA, Jurkowski TP. Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extraction and manipulation. PLoS Biol 2019; 17:e3000107. [PMID: 30629605 PMCID: PMC6343928 DOI: 10.1371/journal.pbio.3000107] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 01/23/2019] [Indexed: 01/10/2023] Open
Abstract
Current molecular biology laboratories rely heavily on the purification and manipulation of nucleic acids. Yet, commonly used centrifuge- and column-based protocols require specialised equipment, often use toxic reagents, and are not economically scalable or practical to use in a high-throughput manner. Although it has been known for some time that magnetic beads can provide an elegant answer to these issues, the development of open-source protocols based on beads has been limited. In this article, we provide step-by-step instructions for an easy synthesis of functionalised magnetic beads, and detailed protocols for their use in the high-throughput purification of plasmids, genomic DNA, RNA and total nucleic acid (TNA) from a range of bacterial, animal, plant, environmental and synthetic sources. We also provide a bead-based protocol for bisulfite conversion and size selection of DNA and RNA fragments. Comparison to other methods highlights the capability, versatility, and extreme cost-effectiveness of using magnetic beads. These open-source protocols and the associated webpage (https://bomb.bio) can serve as a platform for further protocol customisation and community engagement. This Community Page article presents open-source nucleic acid purification and handling protocols based on functionalised magnetic beads, with the aim of transforming life science research practice and its economics.
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Affiliation(s)
- Phil Oberacker
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Peter Stepper
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Donna M. Bond
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Sven Höhn
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Jule Focken
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Vivien Meyer
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Luca Schelle
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | | | - Gert-Jan Jeunen
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Tim Moser
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | | | - Ferdinand von Meyenn
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom and Department of Medical and Molecular Medicine, Kings College London, Guys Hospital, London, United Kingdom
| | - Katharina Hipp
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Timothy A. Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand
- * E-mail: (TPJ); (TAH)
| | - Tomasz P. Jurkowski
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
- * E-mail: (TPJ); (TAH)
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Schalamun M, Nagar R, Kainer D, Beavan E, Eccles D, Rathjen JP, Lanfear R, Schwessinger B. Harnessing the MinION: An example of how to establish long-read sequencing in a laboratory using challenging plant tissue from Eucalyptus pauciflora. Mol Ecol Resour 2019; 19:77-89. [PMID: 30118581 PMCID: PMC7380007 DOI: 10.1111/1755-0998.12938] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 08/08/2018] [Accepted: 08/10/2018] [Indexed: 11/28/2022]
Abstract
Long-read sequencing technologies are transforming our ability to assemble highly complex genomes. Realizing their full potential is critically reliant on extracting high-quality, high-molecular-weight (HMW) DNA from the organisms of interest. This is especially the case for the portable MinION sequencer which enables all laboratories to undertake their own genome sequencing projects, due to its low entry cost and minimal spatial footprint. One challenge of the MinION is that each group has to independently establish effective protocols for using the instrument, which can be time-consuming and costly. Here, we present a workflow and protocols that enabled us to establish MinION sequencing in our own laboratories, based on optimizing DNA extraction from a challenging plant tissue as a case study. Following the workflow illustrated, we were able to reliably and repeatedly obtain >6.5 Gb of long-read sequencing data with a mean read length of 13 kb and an N50 of 26 kb. Our protocols are open source and can be performed in any laboratory without special equipment. We also illustrate some more elaborate workflows which can increase mean and average read lengths if this is desired. We envision that our workflow for establishing MinION sequencing, including the illustration of potential pitfalls and suggestions of how to adapt it to other tissue types, will be useful to others who plan to establish long-read sequencing in their own laboratories.
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Affiliation(s)
- Miriam Schalamun
- Research School of BiologyThe Australian National UniversityActonACTAustralia
- Present address:
University of Natural Resources and Life SciencesViennaAustria
| | - Ramawatar Nagar
- Research School of BiologyThe Australian National UniversityActonACTAustralia
| | - David Kainer
- Research School of BiologyThe Australian National UniversityActonACTAustralia
| | - Eleanor Beavan
- Research School of BiologyThe Australian National UniversityActonACTAustralia
| | - David Eccles
- Malaghan Institute of Medical ResearchWellingtonNew Zealand
- Present address:
Malaghan Institute of Medical ResearchWellingtonNew Zealand
| | - John P. Rathjen
- Research School of BiologyThe Australian National UniversityActonACTAustralia
| | - Robert Lanfear
- Research School of BiologyThe Australian National UniversityActonACTAustralia
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Díaz F, Luís A. Lima A, Nakamura AM, Fernandes F, Sobrinho I, de Brito RA. Evidence for Introgression Among Three Species of the Anastrepha fraterculus Group, a Radiating Species Complex of Fruit Flies. Front Genet 2018; 9:359. [PMID: 30250479 PMCID: PMC6139333 DOI: 10.3389/fgene.2018.00359] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 08/21/2018] [Indexed: 12/13/2022] Open
Abstract
Introgression should no longer be considered as rare a phenomenon as once thought, since several studies have recently documented gene flow between closely related and radiating species. Here, we investigated evolutionary relationships among three closely related species of fruit flies of the Anastrepha fraterculus group (Anastrepha fraterculus, A. obliqua and A. sororcula). We sequenced a set of 20 genes and implemented a combined populational and phylogenetic inference with a model selection approach by an ABC framework in order to elucidate the demographic history of these species. The phylogenetic histories inferred from most genes showed a great deal of discordance and substantial shared polymorphic variation. The analysis of several population and speciation models reveal that this shared variation is better explained by introgression rather than convergence by parallel mutation or incomplete lineage sorting. Our results consistently showed these species evolving under an isolation with migration model experiencing a continuous and asymmetrical pattern of gene flow involving all species pairs, even though still showed a more closely related relationship between A. fraterculus and A. sororcula when compared with A. obliqua. This suggests that these species have been exchanging genes since they split from their common ancestor ∼2.6 MYA ago. We also found strong evidence for recent population expansion that appears to be consequence of anthropic activities affecting host crops of fruit flies. These findings point that the introgression here found may have been driven by genetic drift and not necessary by selection, which has implications for tracking and managing fruit flies.
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Affiliation(s)
- Fernando Díaz
- Department of Entomology, University of Arizona, Tucson, AZ, United States
| | - André Luís A. Lima
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Aline M. Nakamura
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Fernanda Fernandes
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Iderval Sobrinho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Reinaldo A. de Brito
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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Application of steric exclusion chromatography on monoliths for separation and purification of RNA molecules. J Chromatogr A 2018; 1574:50-59. [PMID: 30195858 DOI: 10.1016/j.chroma.2018.08.063] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/22/2018] [Accepted: 08/31/2018] [Indexed: 11/23/2022]
Abstract
Steric exclusion chromatography (SXC) is a method for separation of large target solutes based on their association with a hydrophilic stationary phase through mutual steric exclusion of polyethylene glycol (PEG). Selectivity in SXC is determined by the size or shape (or both) of the solutes alongside the size and concentration of PEG molecules. Elution is achieved by decreasing the PEG concentration. In this study, SXC applicability for the separation and purification of single-stranded (ss) and double-stranded (ds) RNA molecules was evaluated for the first time. The retention of ssRNA and dsRNA molecules of different lengths on convective interaction media (CIM) monolithic columns was systematically studied under variable PEG-6000 and NaCl concentrations. We determined that over 90% of long ssRNAs (700-6374 nucleotides) and long dsRNAs (500-6374 base pairs) are retained on the stationary phase in 15% PEG-6000 and ≥0.4 M NaCl. dsDNA and dsRNA molecules of the same length were partially separated by SXC. Separation of RNA molecules below 100 nucleotides from longer RNA species is easily achieved by SXC. Furthermore, SXC has the potential to separate dsRNAs from ssRNAs of the same length. We also demonstrated that SXC is suitable for the enrichment of ssRNA (PRR1 bacteriophage) and dsRNA (Phi6 bacteriophage) viral genomes from contaminating cellular RNA species. In summary, SXC on CIM monolithic columns is an appropriate tool for rapid RNA separation and concentration.
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Barletta-Naveca RH, Naveca FG, de Almeida VA, Porto JIR, da Silva GAV, Ogusku MM, Sadahiro A, Ramasawmy R, Boechat AL. Toll-Like Receptor-1 Single-Nucleotide Polymorphism 1805T/G Is Associated With Predisposition to Multibacillary Tuberculosis. Front Immunol 2018; 9:1455. [PMID: 29988507 PMCID: PMC6026633 DOI: 10.3389/fimmu.2018.01455] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/12/2018] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis (TB), caused by mycobacterial species of the Mycobacterium tuberculosis complex, is a serious global health issue. Brazil is among the 22 countries with the highest number of TB cases, and the state of Amazonas has the highest incidence of TB cases in the country. Toll-like receptors (TLRs) are important pattern recognition receptors of the innate immunity and play a key role in orchestrating an effective immune response. We investigated whether the single-nucleotide polymorphisms (SNPs) 1805T/G TLR1, 2258G/A TLR2, 896A/G and 1196C/T of TLR4, 745T/C TLR6, and −1237A/G and −1486A/G of TLR9 are associated with the predisposition to TB and/or bacillary load. The SNPs genotyping was performed by nucleotide sequencing in 263 TB patients and 232 healthy controls residing in the state of Amazonas. Alleles and genotypes frequencies were similar between patients and healthy individuals for most of the investigated SNPs. Stratification of the TB patients according to their bacillary load showed that the genotype 1805TT TLR1 (rs5743618) was prevalent among paucibacillary patients [odds ratio (OR) = 0.38; 95% confidence interval (CI) = 0.19–0.76; p = 0.009] while the genotype 1805TG was common among multibacillary patients (OR = 3.72; CI = 1.65–8.4; p = 0.004). Comparison of demographic characteristics of patients to controls showed that TB is strongly associated with smoking (OR = 6.55; 95% CI = 3.2–13.6; p < 0.0001); alcohol use disorder (OR = 7.14; 95% CI = 3.7–13.9; p < 0.0001); and male gender (OR = 3.66; 95% CI = 2.52–5.3; p < 0.0001). Multivariate logistic regression demonstrated that alcoholism (OR = 2.93; 95% CI = 1.05–8.16; p = 0.03) and the 1805G allele (OR = 2.75; 95% CI = 1.33–5.7; p = 0.006) are predictive variables for multibacillary TB. Altogether, we suggest that the TLR1 1805G allele may be a relevant immunogenetic factor for the epidemiology of TB together with environmental, sociodemographic, and behavioral factors.
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Affiliation(s)
- Raphaela Honorato Barletta-Naveca
- Laboratório de Micobacteriologia, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil.,Programa de Pós-graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz Amazônia, Manaus, Brazil.,Programa de Pós-Graduação em Biologia da Interação Patógeno-Hospedeiro, Instituto Leônidas e Maria Deane, Fiocruz Amazônia, Manaus, Brazil.,Programa de Pós-Graduação em Imunologia Básica e Aplicada, Universidade Federal do Amazonas, Manaus, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Vanessa Alves de Almeida
- Laboratório de Micobacteriologia, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil.,Programa de Pós-Graduação em Imunologia Básica e Aplicada, Universidade Federal do Amazonas, Manaus, Brazil
| | - Jorge Ivan Rebelo Porto
- Programa de Pós-graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil.,Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia (INPA/CPBA), Manaus, Brazil
| | | | - Mauricio Morishi Ogusku
- Laboratório de Micobacteriologia, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
| | - Aya Sadahiro
- Laboratório de Micobacteriologia, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil.,Programa de Pós-Graduação em Imunologia Básica e Aplicada, Universidade Federal do Amazonas, Manaus, Brazil.,Laboratório de Imunologia Molecular, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Brazil
| | - Rajendranath Ramasawmy
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Universidade Federal do Amazonas, Manaus, Brazil.,Faculdade de Medicina, Universidade Nilton Lins, Manaus, Brazil.,Fundação de Medicina Tropical Doutor Heitor Vieira Dourado (FMT-HVD), Manaus, Brazil
| | - Antonio Luiz Boechat
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Universidade Federal do Amazonas, Manaus, Brazil.,Laboratório de Imunoquímica, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Brazil
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Mondin LADC, Machado CB, de Resende EK, Marques DKS, Galetti PM. Genetic Pattern and Demographic History of Salminus brasiliensis: Population Expansion in the Pantanal Region during the Pleistocene. Front Genet 2018; 9:1. [PMID: 29387083 PMCID: PMC5776086 DOI: 10.3389/fgene.2018.00001] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 01/03/2018] [Indexed: 11/13/2022] Open
Abstract
Pleistocene climate changes were major historical events that impacted South American biodiversity. Although the effects of such changes are well-documented for several biomes, it is poorly known how these climate shifts affected the biodiversity of the Pantanal floodplain. Fish are one of the most diverse groups in the Pantanal floodplains and can be taken as a suitable biological model for reconstructing paleoenvironmental scenarios. To identify the effects of Pleistocene climate changes on Pantanal's ichthyofauna, we used genetic data from multiple populations of a top-predator long-distance migratory fish, Salminus brasiliensis. We specifically investigated whether Pleistocene climate changes affected the demography of this species. If this was the case, we expected to find changes in population size over time. Thus, we assessed the genetic diversity of S. brasiliensis to trace the demographic history of nine populations from the Upper Paraguay basin, which includes the Pantanal floodplain, that form a single genetic group, employing approximate Bayesian computation (ABC) to test five scenarios: constant population, old expansion, old decline, old bottleneck following by recent expansion, and old expansion following by recent decline. Based on two mitochondrial DNA markers, our inferences from ABC analysis, the results of Bayesian skyline plot, the implications of star-like networks, and the patterns of genetic diversity (high haplotype diversity and low-to-moderate nucleotide diversity) indicated a sudden population expansion. ABC allowed us to make strong quantitative inferences about the demographic history of S. brasiliensis. We estimated a small ancestral population size that underwent a drastic fivefold expansion, probably associated with the colonization of newly formed habitats. The estimated time of this expansion was consistent with a humid and warm phase as inferred by speleothem growth phases and travertine records during Pleistocene interglacial periods. The strong concordance between our genetic inferences and this historical data could represent the first genetic record of a humid and warm phase in the Pantanal in the period since the Last Interglacial to 40 ka.
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Affiliation(s)
| | - Carolina B Machado
- Laboratório de Biodiversidade Molecular e Conservação, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Emiko K de Resende
- Embrapa Pantanal, Empresa Brasileira de Pesquisa Agropecuária, Corumbá, Brazil
| | - Debora K S Marques
- Embrapa Pantanal, Empresa Brasileira de Pesquisa Agropecuária, Corumbá, Brazil
| | - Pedro M Galetti
- Laboratório de Biodiversidade Molecular e Conservação, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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35
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Green MR, Sambrook J. Preparation of Single-Stranded Bacteriophage M13 DNA by Precipitation with Polyethylene Glycol. Cold Spring Harb Protoc 2017; 2017:pdb.prot093419. [PMID: 29093199 DOI: 10.1101/pdb.prot093419] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacteriophage M13 single-stranded DNA is prepared from virus particles secreted by infected bacteria into the surrounding medium. Several methods are available to purify the polymorphic filamentous particles. In this protocol, the particles are concentrated by precipitation with polyethylene glycol (PEG) in the presence of high salt. Subsequent extraction with phenol releases the single-stranded DNA, which is then collected by precipitation with ethanol. The resulting preparation is pure enough to be used as a template for DNA sequencing. A yield of 5-10 µg of single-stranded DNA/mL of infected cells may be expected from recombinant bacteriophages bearing inserts of 300-1000 nt.
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Oh YS, Park JH, Han SW, Kim SK, Lee YA. Retained binding mode of various DNA-binding molecules under molecular crowding condition. J Biomol Struct Dyn 2017; 36:3035-3046. [DOI: 10.1080/07391102.2017.1375992] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Ye Sol Oh
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
| | - Jin Ha Park
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
| | - Sung Wook Han
- Department of Health & Biotechnology, Kyungwoon University, Kumi City, Gyeong-buk 39253, Republic of Korea
| | - Seog K. Kim
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
| | - Young-Ae Lee
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
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Evolutionary coincidence of adaptive changes in exuperantia and the emergence of bicoid in Cyclorrhapha (Diptera). Dev Genes Evol 2017; 227:355-365. [PMID: 28894941 PMCID: PMC5597691 DOI: 10.1007/s00427-017-0594-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 08/20/2017] [Indexed: 11/15/2022]
Abstract
The great radiation in the infraorder Cyclorrhapha involved several morphological and molecular changes, including important changes in anterior egg development. During Drosophila oogenesis, exuperantia (exu) is critical for localizing bicoid (bcd) messenger RNA (mRNA) to the anterior region of the oocyte. Because it is phylogenetically older than bcd, which is exclusive to Cyclorrhapha, we hypothesize that exu has undergone adaptive changes to enable this new function. Although exu has been well studied in Drosophila, there is no functional or transcriptional information about it in any other Diptera. Here, we investigate exu in the South American fruit fly Anastrepha fraterculus, a Cyclorrhapha of great agricultural importance that have lost bcd, aiming to understand the evolution of exu in this infraorder. We assessed its pattern of gene expression in A. fraterculus by analyzing transcriptomes from cephalic and reproductive tissues. A combination of next-generation data with classical sequencing procedures enabled identification of the structure of exu and its alternative transcripts in this species. In addition to the sex-specific isoforms described for Drosophila, we found that not only exu is expressed in heads, but this is mediated by two transcripts with a specific 5′UTR exon—likely a result from usage of a third promoter. Furthermore, we tested the hypothesis that exu is evolving under positive selection in Cyclorrhapha after divergence from lower Diptera. We found evidence of positive selection at two important exu domains, EXO-like and SAM-like, both involved with mRNA binding during bcd mRNA localization in Drosophila, which could reflect its cooptation for the new function of bcd mRNA localization in Cyclorrhapha.
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Tessarolli LP, Bagatini IL, Bianchini-Jr. I, Vieira AAH. Bacterial degradation of dissolved organic matter released by Planktothrix agardhii (Cyanobacteria). BRAZ J BIOL 2017; 78:108-116. [DOI: 10.1590/1519-6984.07616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/23/2016] [Indexed: 11/22/2022] Open
Abstract
Abstract Although Planktothrix agardhii often produces toxic blooms in eutrophic water bodies around the world, little is known about the fate of the organic matter released by these abundant Cyanobacteria. Thus, this study focused in estimating the bacterial consumption of the DOC and DON (dissolved organic carbon and dissolved organic nitrogen, respectively) produced by axenic P. agardhii cultures and identifying some of the bacterial OTUs (operational taxonomic units) involved in the process. Both P. agardhii and bacterial inocula were sampled from the eutrophic Barra Bonita Reservoir (SP, Brazil). Two distinct carbon degradation phases were observed: during the first three days, higher degradation coefficients were calculated, which were followed by a slower degradation phase. The maximum value observed for particulate bacterial carbon (POC) was 11.9 mg L-1, which consisted of 62.5% of the total available DOC, and its mineralization coefficient was 0.477 day-1 (t½ = 1.45 days). A similar pattern of degradation was observed for DON, although the coefficients were slightly different. Changes in the OTUs patterns were observed during the different steps of the degradation. The main OTUs were related to the classes Alphaproteobacteria (8 OTUs), Betaproteobacteria (2 OTUs) and Gammaproteobacteria (3 OTUs). The genus Acinetobacter was the only identified organism that occurred during the whole process. Bacterial richness was higher at the slower degradation phase, which could be related to the small amounts of DOM (dissolved organic matter) available, particularly carbon. The kinetics of the bacterial degradation of P. agardhii-originated DOM suggests minimal loss of DOM from the Barra Bonita reservoir.
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Chahad-Ehlers S, Arthur LP, Lima ALA, Gesto JSM, Torres FR, Peixoto AA, de Brito RA. Expanding the view of Clock and cycle gene evolution in Diptera. INSECT MOLECULAR BIOLOGY 2017; 26:317-331. [PMID: 28234413 DOI: 10.1111/imb.12296] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We expanded the view of Clock (Clk) and cycle (cyc) gene evolution in Diptera by studying the fruit fly Anastrepha fraterculus (Afra), a Brachycera. Despite the high conservation of clock genes amongst insect groups, striking structural and functional differences of some clocks have appeared throughout evolution. Clk and cyc nucleotide sequences and corresponding proteins were characterized, along with their mRNA expression data, to provide an evolutionary overview in the two major groups of Diptera: Lower Diptera and Higher Brachycera. We found that AfraCYC lacks the BMAL (Brain and muscle ARNT-like) C-terminus region (BCTR) domain and is constitutively expressed, suggesting that AfraCLK has the main transactivation function, which is corroborated by the presence of poly-Q repeats and an oscillatory pattern. Our analysis suggests that the loss of BCTR in CYC is not exclusive of drosophilids, as it also occurs in other Acalyptratae flies such as tephritids and drosophilids, however, but it is also present in some Calyptratae, such as Muscidae, Calliphoridae and Sarcophagidae. This indicates that BCTR is missing from CYC of all higher-level Brachycera and that it was lost during the evolution of Lower Brachycera. Thus, we can infer that CLK protein may play the main role in the CLK\CYC transcription complex in these flies, like in its Drosophila orthologues.
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Affiliation(s)
- S Chahad-Ehlers
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - L P Arthur
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - A L A Lima
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - J S M Gesto
- Laboratório de Biologia Molecular de Insetos, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - F R Torres
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - A A Peixoto
- Laboratório de Biologia Molecular de Insetos, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - R A de Brito
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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Yevdokimov YM, Skuridin SG, Semenov SV, Dadinova LA, Salyanov VI, Kats EI. Re-entrant cholesteric phase in DNA liquid-crystalline dispersion particles. J Biol Phys 2017; 43:45-68. [PMID: 28028733 PMCID: PMC5323345 DOI: 10.1007/s10867-016-9433-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 10/18/2016] [Indexed: 11/24/2022] Open
Abstract
In this research, we observe and rationalize theoretically the transition from hexagonal to cholesteric packing of double-stranded (ds) DNA in dispersion particles. The samples were obtained by phase exclusion of linear ds DNA molecules from water-salt solutions of poly(ethylene glycol)-PEG-with concentrations ranging from 120 mg ml-1 to 300 mg ml-1. In the range of PEG concentrations from 120 mg ml-1 to 220 mg ml-1 at room temperature, we find ds DNA molecule packing, typical of classical cholesterics. The corresponding parameters for dispersion particles obtained at concentrations greater than 220 mg ml-1 indicate hexagonal packing of the ds DNA molecules. However, slightly counter-intuitively, the cholesteric-like packing reappears upon the heating of dispersions with hexagonal packing of ds DNA molecules. This transition occurs when the PEG concentration is larger than 220 mg ml-1. The obtained new cholesteric structure differs from the classical cholesterics observed in the PEG concentration range 120-220 mg ml-1 (hence, the term 're-entrant'). Our conclusions are based on the measurements of circular dichroism spectra, X-ray scattering curves and textures of liquid-crystalline phases. We propose a qualitative (similar to the Lindemann criterion for melting of conventional crystals) explanation of this phenomenon in terms of partial melting of so-called quasinematic layers formed by the DNA molecules. The quasinematic layers change their spatial orientation as a result of the competition between the osmotic pressure of the solvent (favoring dense, unidirectional alignment of ds DNA molecules) and twist Frank orientation energy of adjacent layers (favoring cholesteric-like molecular packing).
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Affiliation(s)
- Yuri M Yevdokimov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova St. 32, 119991, Moscow, Russia.
| | - Sergey G Skuridin
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova St. 32, 119991, Moscow, Russia
| | - Sergey V Semenov
- National Research Centre 'Kurchatov Institute', Kurchatova Sq. 1, 123182, Moscow, Russia
| | - Ljubov A Dadinova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of the Russian Academy of Sciences, Leninskii Ave. 59, 119333, Moscow, Russia
| | - Viktor I Salyanov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova St. 32, 119991, Moscow, Russia
| | - Efim I Kats
- Landau Institute for Theoretical Physics of the Russian Academy of Sciences, Kosygina St. 2, 119334, Moscow, Russia
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A streamlined method for the design and cloning of shRNAs into an optimized Dox-inducible lentiviral vector. BMC Biotechnol 2017; 17:24. [PMID: 28245848 PMCID: PMC5331646 DOI: 10.1186/s12896-017-0341-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 02/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Short hairpin RNA (shRNA) is an established and effective tool for stable knock down of gene expression. Lentiviral vectors can be used to deliver shRNAs, thereby providing the ability to infect most mammalian cell types with high efficiency, regardless of proliferation state. Furthermore, the use of inducible promoters to drive shRNA expression allows for more thorough investigations into the specific timing of gene function in a variety of cellular processes. Moreover, inducible knockdown allows the investigation of genes that would be lethal or otherwise poorly tolerated if constitutively knocked down. Lentiviral inducible shRNA vectors are readily available, but unfortunately the process of cloning, screening, and testing shRNAs can be time-consuming and expensive. Therefore, we sought to refine a popular vector (Tet-pLKO-Puro) and streamline the cloning process with efficient protocols so that researchers can more efficiently utilize this powerful tool. METHODS: First, we modified the Tet-pLKO-Puro vector to make it easy ("EZ") for molecular cloning (EZ-Tet-pLKO-Puro). Our primary modification was to shrink the stuffer region, which allows vector purification via polyethylene glycol precipitation thereby avoiding the need to purify DNA through agarose. In addition, we generated EZ-Tet-pLKO vectors with hygromycin or blasticidin resistance to provide greater flexibility in cell line engineering. Furthermore, we provide a detailed guide for utilizing these vectors, including shRNA design strategy and simplified screening methods. RESULTS Notably, we emphasize the importance of loop sequence design and demonstrate that the addition of a single mismatch in the loop stem can greatly improve shRNA efficiency. Lastly, we display the robustness of the system with a doxycycline titration and recovery time course and provide a cost/benefit analysis comparing our system with purchasing pre-designed shRNA vectors. CONCLUSIONS Our aim was twofold: first, to take a very useful shRNA vector and make it more amenable for molecular cloning and, secondly, to provide a streamlined protocol and rationale for cost-effective design, cloning, and screening of shRNAs. With this knowledge, anyone can take advantage of this powerful tool to inducibly knockdown any gene of their choosing.
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Machado CDB, Ishizuka TK, Freitas PDD, Valiati VH, Galetti PM. DNA barcoding reveals taxonomic uncertainty in Salminus (Characiformes). SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1254390] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Carolina De Barros Machado
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235 - SP-310, São Carlos, SP, 13565-905, Brazil
| | - Tamylin Kaori Ishizuka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235 - SP-310, São Carlos, SP, 13565-905, Brazil
| | - PatrÍcia Domingues De Freitas
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235 - SP-310, São Carlos, SP, 13565-905, Brazil
| | - Victor Hugo Valiati
- Laboratório de Biologia Molecular, Universidade do Vale do Rio dos Sinos, Avenida Unisinos, 950, São Leopoldo, RS, 93022-000, Brazil
| | - Pedro Manoel Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235 - SP-310, São Carlos, SP, 13565-905, Brazil
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Asymmetric flow field flow fractionation methods for virus purification. J Chromatogr A 2016; 1469:108-119. [PMID: 27697294 DOI: 10.1016/j.chroma.2016.09.055] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/07/2016] [Accepted: 09/23/2016] [Indexed: 12/25/2022]
Abstract
Detailed biochemical and biophysical characterization of viruses requires viral preparations of high quantity and purity. The optimization of virus production and purification is an essential, but laborious and time-consuming process. Asymmetric flow field flow fractionation (AF4) is an attractive alternative method for virus purification because it is a rapid and gentle separation method that should preserve viral infectivity. Here we optimized the AF4 conditions to be used for purification of a model virus, bacteriophage PRD1, from various types of starting materials. Our results show that AF4 is well suited for PRD1 purification as monitored by virus recovery and specific infectivity. Short analysis time and high sample loads enabled us to use AF4 for preparative scale purification of PRD1. Furthermore, we show that AF4 enables the rapid real-time analysis of progeny virus production in infected cells.
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Liaw DJ, Yagudaeva E, Prostyakova A, Lazov M, Zybin D, Ischenko A, Zubov V, Chang CH, Huang YC, Kapustin D. Sorption behavior of polyaramides in relation to isolation of nucleic acids and proteins. Colloids Surf B Biointerfaces 2016; 145:912-921. [PMID: 27341305 DOI: 10.1016/j.colsurfb.2016.05.068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/29/2016] [Accepted: 05/25/2016] [Indexed: 12/23/2022]
Abstract
The effect of chemical composition and morphology of the surface layers of new polyaramide-containing sorbents on the mechanism of selective sorption of nucleic acids and proteins was investigated as compared to the previously studied sorbents modified with fluoropolymers and polyaniline (high-throughput materials providing one-step isolation of DNA from biological mixtures). A series of silica-based sorbents modified with polyaramides having consistently varying structure and containing the set of "key" structural elements (aromatic units and nitrogen atoms in the backbone, fluorinated groups), and various donor and acceptor moieties was prepared. The chemical composition of the polymer coatings was evaluated by X-ray photoelectron spectroscopy. The surface morphology was studied by scanning probe microscopy. The sorption properties were investigated by passing the mixtures containing DNA, RNA and proteins of different nature through the cartridges containing the obtained sorbents. All the investigated materials weakly retain double-stranded DNA but effectively retain RNA and proteins. The sorption capacity of the sorbents depends on the protein nature. The observed sorption behavior was shown to be determined by the chemical structure and not by the morphology of the polymer coating. It was proposed that similarity of the sorption properties of the series of chemically different polymers could be determined by similar total input of different sorption mechanisms.
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Affiliation(s)
- Der-Jang Liaw
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan
| | - Elena Yagudaeva
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - Anna Prostyakova
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - Michael Lazov
- Moscow Technological University, 119571 Moscow, Russia
| | - Dmitry Zybin
- Moscow Technological University, 119571 Moscow, Russia
| | | | - Vitaly Zubov
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; Moscow Technological University, 119571 Moscow, Russia
| | - Cheng-Hung Chang
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan
| | - Ying-Chi Huang
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan
| | - Dmitry Kapustin
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia.
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Bettinazzi S, Plazzi F, Passamonti M. The Complete Female- and Male-Transmitted Mitochondrial Genome of Meretrix lamarckii. PLoS One 2016; 11:e0153631. [PMID: 27083010 PMCID: PMC4833323 DOI: 10.1371/journal.pone.0153631] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 04/02/2016] [Indexed: 11/17/2022] Open
Abstract
Bivalve mitochondrial genomes show many uncommon features, like additional genes, high rates of gene rearrangement, high A-T content. Moreover, Doubly Uniparental Inheritance (DUI) is a distinctive inheritance mechanism allowing some bivalves to maintain and transmit two separate sex-linked mitochondrial genomes. Many bivalve mitochondrial features, such as gene extensions or additional ORFs, have been proposed to be related to DUI but, up to now, this topic is far from being understood. Several species are known to show this unusual organelle inheritance but, being widespread only among Unionidae and Mytilidae, DUI distribution is unclear. We sequenced and characterized the complete female- (F) and male-transmitted (M) mitochondrial genomes of Meretrix lamarckii, which, in fact, is the second species of the family Veneridae where DUI has been demonstrated so far. The two mitochondrial genomes are comparable in length and show roughly the same gene content and order, except for three additional tRNAs found in the M one. The two sex-linked genomes show an average nucleotide divergence of 16%. A 100-aminoacid insertion in M. lamarckii M-cox2 gene was found; moreover, additional ORFs have been found in both F and M Long Unassigned Regions of M. lamarckii. Even if no direct involvement in DUI process has been demonstrated so far, the finding of cox2 insertions and supernumerary ORFs in M. lamarckii both strengthens this hypothesis and widens the taxonomical distribution of such unusual features. Finally, the analysis of inter-sex genetic variability shows that DUI species form two separate clusters, namely Unionidae and Mytilidae+Veneridae; this dichotomy is probably due to different DUI regimes acting on separate taxa.
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Affiliation(s)
- Stefano Bettinazzi
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, BO, Italy
| | - Federico Plazzi
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, BO, Italy
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, BO, Italy
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Size-selective separation of DNA fragments by using lysine-functionalized silica particles. Sci Rep 2016; 6:22029. [PMID: 26911527 PMCID: PMC4766563 DOI: 10.1038/srep22029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/04/2016] [Indexed: 11/21/2022] Open
Abstract
In this work, a facile and efficient approach has been demonstrated for size-selective separation of DNA fragments by using lysine-functionalized silica particles. At a given pH, the environmental ionic strength can be utilized to alter the electrostatic interactions of lysine-functionalized silica particles with DNA fragments and in turn the DNA fragments on the silica particle surfaces, which exhibits a clear dependence on the DNA fragment sizes. By carefully adjusting the environmental pH and salt concentration, therefore, the use of the lysine-functionalized silica particles allows effective separation of binary and ternary DNA mixtures, for example, two different DNA fragments with sizes of 101 and 1073 bp, 101 and 745 bp, 101 and 408 bp, respectively, and three different DNA fragments with sizes of 101, 408 and 1073 bp.
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Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi. Anaerobe 2015; 38:39-46. [PMID: 26620247 DOI: 10.1016/j.anaerobe.2015.11.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/19/2015] [Accepted: 11/20/2015] [Indexed: 11/23/2022]
Abstract
Cell storage and DNA isolation are essential to developing an expanded suite of microorganisms for biotechnology. However, many features of non-model microbes, such as an anaerobic lifestyle and rigid cell wall, present formidable challenges to creating strain repositories and extracting high quality genomic DNA. Here, we establish accessible, high efficiency, and robust techniques to store lignocellulolytic anaerobic gut fungi long term without specialized equipment. Using glycerol as a cryoprotectant, gut fungal isolates were preserved for a minimum of 23 months at -80 °C. Unlike previously reported approaches, this improved protocol is non-toxic and rapid, with samples surviving twice as long with negligible growth impact. Genomic DNA extraction for these isolates was optimized to yield samples compatible with next generation sequencing platforms (e.g. Illumina, PacBio). Popular DNA isolation kits and precipitation protocols yielded preps that were unsuitable for sequencing due to carbohydrate contaminants from the chitin-rich cell wall and extensive energy reserves of gut fungi. To address this, we identified a proprietary method optimized for hardy plant samples that rapidly yielded DNA fragments in excess of 10 kb with minimal RNA, protein or carbohydrate contamination. Collectively, these techniques serve as fundamental tools to manipulate powerful biomass-degrading gut fungi and improve their accessibility among researchers.
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Camargo LF, Brito RA, Penteado-Dias AM. Redescription of Campoletis sonorensis (Cameron, 1886) (Hymenoptera, Ichneumonidae, Campopleginae), parasitoid of Spodoptera frugiperda (J. E. Smith, 1797) (Lepidoptera, Noctuidae) in Brazil. BRAZ J BIOL 2015; 75:989-98. [PMID: 26675917 DOI: 10.1590/1519-6984.04914] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 06/25/2014] [Indexed: 11/21/2022] Open
Abstract
The fall armyworm Spodoptera frugiperda (Lepidoptera; Noctuidae) is a voracious pest of numerous crops of economic importance throughout the New World. In Brazil, its larvae are attacked by several species of parasitoid wasps, making them potential candidate as biological control agents against this pest. A survey of the parasitoid fauna on S. frugiperda in maize crops throughout Brazil reveals two species of Campoletis, which are morphologicaly very similar species. In this paper we combine these data with pictures from the type material of C. sonorensis and C. flavicincta, as well as their descriptions to provide a redescription to Campoletis sonorensis (Cameron, 1886) using for this both morphological characters and DNA Barcoding (Hebert et al., 2003) information, in an attempt to help with the correct identification of the taxa to improve biological control studies.
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Affiliation(s)
- L F Camargo
- Programa de Pós-Graduação em Ecologia e Recursos Naturais, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - R A Brito
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - A M Penteado-Dias
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Carlos, São Carlos, SP, Brazil
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Song X, Ding T, Yao L, Lin M, Siew Tan RL, Liu C, Sokol K, Yu L, Lou XWD, Chen H. On the Origin and Underappreciated Effects of Ion Doping in Silica. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:4351-4365. [PMID: 26068983 DOI: 10.1002/smll.201500539] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 05/14/2015] [Indexed: 06/04/2023]
Abstract
The origin of selectivity in the hollowing of silica nanoparticles is investigated to further understand silica. It is realized that, during the synthesis, the silica precursors are essentially ion-paired polyelectrolytes, whose nucleation depends on the concentration of the counter ions, and most importantly, the size/length of the poly(silicic acid). Thus, the "silica" that nucleates out at the different stages of synthesis has different degrees of ion doping, which explains its solubility in water, its microporosity, and the selective etching phenomena. The etching of silica in water is shown to be a matter of silica solubility, which correlates to the relative amounts of solvent and to the solvent quality (the water/isopropanol ratio). Hollowing does not occur when the silica nanoparticles are incubated in solutions presaturated with "silica," ruling out surface reposition and Ostwald ripening as the hollowing mechanism. The embedded ions in silica are confirmed by elemental analysis (CHNS) and inductively coupled plasma-mass spectrometry. The high ionic doping ratios (N/Si = 2.3% for NH3 -catalyzed silica; Na/Si = 11.2% for NaOH-catalyzed silica) explain the unusual solubility of silica in neutral water. The new view of silica with the ionic impurities on the central stage allows for insights in silica properties and versatility in synthetic design.
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Affiliation(s)
- Xiaohui Song
- Division of Chemistry and Biological Chemistry, Nangyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Tao Ding
- Division of Chemistry and Biological Chemistry, Nangyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Lin Yao
- Division of Chemistry and Biological Chemistry, Nangyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Ming Lin
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), 3 Research Link, Singapore, S117602, Singapore
| | - Rachel Lee Siew Tan
- Division of Chemistry and Biological Chemistry, Nangyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Cuicui Liu
- Division of Chemistry and Biological Chemistry, Nangyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Katarzyna Sokol
- Division of Chemistry and Biological Chemistry, Nangyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Le Yu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459, Singapore
| | - Xiong Wen David Lou
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459, Singapore
| | - Hongyu Chen
- Division of Chemistry and Biological Chemistry, Nangyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
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Cohen IS, Bar C, Paz-Elizur T, Ainbinder E, Leopold K, de Wind N, Geacintov N, Livneh Z. DNA lesion identity drives choice of damage tolerance pathway in murine cell chromosomes. Nucleic Acids Res 2015; 43:1637-45. [PMID: 25589543 PMCID: PMC4330363 DOI: 10.1093/nar/gku1398] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
DNA-damage tolerance (DDT) via translesion DNA synthesis (TLS) or homology-dependent repair (HDR) functions to bypass DNA lesions encountered during replication, and is critical for maintaining genome stability. Here, we present piggyBlock, a new chromosomal assay that, using piggyBac transposition of DNA containing a known lesion, measures the division of labor between the two DDT pathways. We show that in the absence of DNA damage response, tolerance of the most common sunlight-induced DNA lesion, TT-CPD, is achieved by TLS in mouse embryo fibroblasts. Meanwhile, BP-G, a major smoke-induced DNA lesion, is bypassed primarily by HDR, providing the first evidence for this mechanism being the main tolerance pathway for a biologically important lesion in a mammalian genome. We also show that, far from being a last-resort strategy as it is sometimes portrayed, TLS operates alongside nucleotide excision repair, handling 40% of TT-CPDs in repair-proficient cells. Finally, DDT acts in mouse embryonic stem cells, exhibiting the same pattern—mutagenic TLS included—despite the risk of propagating mutations along all cell lineages. The new method highlights the importance of HDR, and provides an effective tool for studying DDT in mammalian cells.
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