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Gabriel L, Koschella A, Tied A, Pfeifer A, Heinze T. Sulfoethylation of polysaccharides-A comparative study. Carbohydr Polym 2020; 246:116533. [PMID: 32747232 DOI: 10.1016/j.carbpol.2020.116533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 11/18/2022]
Abstract
The heterogeneous sulfoethylation of cellulose, xylan, α-1,3-glucan, glucomannan, pullulan, curdlan, galactoglucomannan, and agarose was studied using sodium vinylsulfonate (NaVS) as reagent in presence of sodium hydroxide and iso-propanol (i-PrOH) as slurry medium. The influence of the concentration of polymer, water, and NaOH (solid or aqueous solution) on the degree of substitution (DS) was investigated. The sulfoethylation rendered the polysaccharides studied water-soluble. Sulfoethylation of heteropolysaccharides yielded products with higher DS compared to the conversion of homopolysaccharides. Structure characterization was carried out by means of 13C-NMR spectroscopy.
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Affiliation(s)
- Lars Gabriel
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University of Jena, Centre of Excellence for Polysaccharide Research, Humboldtstraße 10, D-07743, Jena, Germany
| | - Andreas Koschella
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University of Jena, Centre of Excellence for Polysaccharide Research, Humboldtstraße 10, D-07743, Jena, Germany
| | - Antje Tied
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University of Jena, Centre of Excellence for Polysaccharide Research, Humboldtstraße 10, D-07743, Jena, Germany
| | - Annett Pfeifer
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University of Jena, Centre of Excellence for Polysaccharide Research, Humboldtstraße 10, D-07743, Jena, Germany
| | - Thomas Heinze
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University of Jena, Centre of Excellence for Polysaccharide Research, Humboldtstraße 10, D-07743, Jena, Germany.
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Serwer P, Wright ET. In-Gel Isolation and Characterization of Large (and Other) Phages. Viruses 2020; 12:v12040410. [PMID: 32272774 PMCID: PMC7232213 DOI: 10.3390/v12040410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/02/2020] [Accepted: 04/05/2020] [Indexed: 12/13/2022] Open
Abstract
We review some aspects of the rapid isolation of, screening for and characterization of jumbo phages, i.e., phages that have dsDNA genomes longer than 200 Kb. The first aspect is that, as plaque-supporting gels become more concentrated, jumbo phage plaques become smaller. Dilute agarose gels are better than conventional agar gels for supporting plaques of both jumbo phages and, prospectively, the even larger (>520 Kb genome), not-yet-isolated mega-phages. Second, dilute agarose gels stimulate propagation of at least some jumbo phages. Third, in-plaque techniques exist for screening for both phage aggregation and high-in-magnitude, negative average electrical surface charge density. The latter is possibly correlated with high phage persistence in blood. Fourth, electron microscopy of a thin section of a phage plaque reveals phage type, size and some phage life cycle information. Fifth, in-gel propagation is an effective preparative technique for at least some jumbo phages. Sixth, centrifugation through sucrose density gradients is a relatively non-destructive jumbo phage purification technique. These basics have ramifications in the development of procedures for (1) use of jumbo phages for phage therapy of infectious disease, (2) exploration of genomic diversity and evolution and (3) obtaining accurate metagenomic analyses.
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Serwer P, Hunter B, Wright ET. Cell-gel interactions of in-gel propagating bacteria. BMC Res Notes 2018; 11:699. [PMID: 30286794 PMCID: PMC6172759 DOI: 10.1186/s13104-018-3811-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/30/2018] [Indexed: 11/17/2022] Open
Abstract
Objective Our immediate objective is to test the data-suggested possibility that in-agarose gel bacterial propagation causes gel fiber dislocation and alteration of cell distribution. We also test the further effect of lowering water activity. We perform these tests with both Gram-negative and Gram-positive bacteria. Data are obtained via electron microscopy of thin sections, which provides the first images of both bacteria and gel fibers in gel-supported bacterial lawns. The long-term objective is analysis of the effects of in-gel propagation on the DNA packaging of phages. Results We find that agarose gel-supported cells in lawns of Escherichia coli and Lysinibacillus (1) are primarily in clusters that increase in size with time and are surrounded by gel fibers, and (2) sometimes undergo gel-induced, post-duplication rotation and translation. Bacterial growth-induced dislocation of gel fibers is observed. One reason for clustering is that clustering promotes growth by increasing the growth-derived force applied to the gel fibers. Reactive force exerted by gel on cells explains cell movement. Finally, addition to growth medium of 0.94 M sucrose causes cluster-associated E. coli cells to become more densely packed and polymorphic. Shape is determined, in part, by neighboring cells, a novel observation to our knowledge.
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Affiliation(s)
- Philip Serwer
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA.
| | - Barbara Hunter
- Department of Pathology, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Elena T Wright
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
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Licata NA, Mohari B, Fuqua C, Setayeshgar S. Diffusion of Bacterial Cells in Porous Media. Biophys J 2016; 110:247-57. [PMID: 26745427 DOI: 10.1016/j.bpj.2015.09.035] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 09/22/2015] [Accepted: 09/30/2015] [Indexed: 12/24/2022] Open
Abstract
The chemotaxis signal transduction network regulates the biased random walk of many bacteria in favorable directions and away from harmful ones through modulating the frequency of directional reorientations. In mutants of diverse bacteria lacking the chemotaxis response, migration in classic motility agar, which constitutes a fluid-filled porous medium, is compromised; straight-swimming cells unable to tumble become trapped within the agar matrix. Spontaneous mutations that restore spreading have been previously observed in the enteric bacterium Escherichia coli, and recent work in other bacterial species has isolated and quantified different classes of nonchemotacting mutants exhibiting the same spreading phenotype. We present a theoretical description of bacterial diffusion in a porous medium-the natural habitat for many cell types-which elucidates how diverse modifications of the motility apparatus resulting in a nonzero tumbling frequency allows for unjamming of otherwise straight-swimming cells at internal boundaries and leads to net migration. A unique result of our analysis is increasing diffusive spread with increasing tumbling frequency in the small pore limit, consistent with earlier experimental observations but not captured by previous models. Our theoretical results, combined with a simple model of bacterial diffusion and growth in agar, are compared with our experimental measurements of swim ring expansion as a function of time, demonstrating good quantitative agreement. Our results suggest that the details of the cellular tumbling process may be adapted to enable bacteria to propagate efficiently through complex environments. For engineered, self-propelled microswimmers that navigate via alternating straight runs and changes in direction, these results suggest an optimal reorientation strategy for efficient migration in a porous environment with a given microarchitecture.
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Affiliation(s)
- Nicholas A Licata
- Department of Physics, Indiana University, Bloomington, Indiana; Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, Michigan
| | - Bitan Mohari
- Department of Biology, Indiana University, Bloomington, Indiana
| | - Clay Fuqua
- Department of Biology, Indiana University, Bloomington, Indiana
| | - Sima Setayeshgar
- Department of Physics, Indiana University, Bloomington, Indiana.
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Li F, Allison SA, Hill RJ. Nanoparticle gel electrophoresis: Soft spheres in polyelectrolyte hydrogels under the Debye–Hückel approximation. J Colloid Interface Sci 2014; 423:129-42. [DOI: 10.1016/j.jcis.2014.02.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 02/05/2014] [Accepted: 02/09/2014] [Indexed: 11/24/2022]
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Chaudhary JP, Kondaveeti S, Gupta V, Prasad K, Meena R. Preparation and functional evaluation of agarose derivatives. J Appl Polym Sci 2014. [DOI: 10.1002/app.40630] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jai Prakash Chaudhary
- Scale-Up and Process Engineering Unit; CSIR-Central Salt and Marine Chemicals Research Institute, G. B. Marg; Bhavnagar 364002 Gujarat India
| | - Stalin Kondaveeti
- Marine Biotechnology and Ecology Discipline; CSIR-Central Salt and Marine Chemicals Research Institute, G. B. Marg; Bhavnagar 364002 Gujarat India
| | - Vishal Gupta
- Marine Biotechnology and Ecology Discipline; CSIR-Central Salt and Marine Chemicals Research Institute, G. B. Marg; Bhavnagar 364002 Gujarat India
| | - Kamalesh Prasad
- Marine Biotechnology and Ecology Discipline; CSIR-Central Salt and Marine Chemicals Research Institute, G. B. Marg; Bhavnagar 364002 Gujarat India
- Academy of Scientific and Innovative Research, CSIR-Central Salt & Marine Chemicals Research Institute, G. B Marg; Bhavnagar 364002 Gujarat India
| | - Ramavatar Meena
- Scale-Up and Process Engineering Unit; CSIR-Central Salt and Marine Chemicals Research Institute, G. B. Marg; Bhavnagar 364002 Gujarat India
- Academy of Scientific and Innovative Research, CSIR-Central Salt & Marine Chemicals Research Institute, G. B Marg; Bhavnagar 364002 Gujarat India
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Gai H, Griess GA, Demeler B, Weintraub ST, Serwer P. Routine fluorescence microscopy of single untethered protein molecules confined to a planar zone. J Microsc 2007; 226:256-62. [PMID: 17535264 DOI: 10.1111/j.1365-2818.2007.01776.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
To bypass limitations of ensemble averaging biochemical analysis, microscopy-based detection and tracking are needed for single protein molecules that are diffusing in aqueous solution. Confining the molecules to a planar zone dramatically assists tracking. Procedures of microscopy should be routine enough so that effort is focused on the biochemistry. Fluorescence microscopy and partial planar confinement of single, untethered, aqueous protein molecules have been achieved here by use of a routine procedure. With this procedure, multiple thermally diffusing Alexa 488-stained bovine serum albumin molecules were observed during partial confinement to a thin aqueous zone next to a cover slip. The procedure produces confinement by partial re-swelling of a previously dried agarose gel on the microscope slide. Confinement was confirmed through analysis that revealed thermal motion lower in the third dimension than it was in the plane of observation.
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Affiliation(s)
- Hongwei Gai
- Department of Biochemistry, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900, USA
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Cole KD, Akerman B. Enhanced capacity for electrophoretic capture of plasmid DNA by agarase treatment of agarose gels. Biomacromolecules 2002; 1:771-81. [PMID: 11710211 DOI: 10.1021/bm005594c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Agarase was used investigate the effect of increasing the number of polymer ends on the electrophoretic trapping of circular DNA in agarose gels. The electric field strength required to trap circular DNA was found to be the same in control and treated gels, indicating the treatment did not result in longer traps. Loading experiments indicated that treated gels had a significantly higher capacity for the open circular DNA. Electrophoretic mobility measurements using pulsed fields indicated a higher density of active traps for treated gels compared to controls. Linear dichroism experiments showed that impalement occurred by a fast and a slow process that had characteristic time constants in the one and tens of seconds ranges, respectively. The open circular DNA was more efficiently impaled in the treated gel compared to the control. The considerably higher efficiency of trapping indicated that agarase treatment increased the concentration of traps substantially.
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Affiliation(s)
- K D Cole
- Bioprocess Engineering Group, Biotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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Abstract
To build a foundation for the single-molecule fluorescence microscopy of protein complexes, the present study achieved fluorescence microscopy of single, nucleic acid-free protein capsids of bacteriophage T7. The capsids were stained with Alexa 488 (green emission). Manipulation of the capsids' thermal motion was achieved in three dimensions. The procedure for manipulation included embedding the capsids in an agarose gel. The data indicate that the thermal motion of capsids is reduced by the sieving of the gel. The thermal motion can be reduced to any desired level. A semilogarithmic plot of an effective diffusion constant as a function of gel concentration is linear. Single, diffusing T7 capsids were also visualized in the presence of single DNA molecules that had been both stretched and immobilized by gel-embedding. The DNA molecules were stained with ethidium (orange emission). This study shows that single-molecule (protein and DNA) analysis is possible for both packaging of DNA in a bacteriophage capsid and other events of DNA metabolism. The major problem is the maintenance of biochemical activity.
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Affiliation(s)
- S Huang
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229-3900, USA
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Abstract
Fractionation of DNA ladders by gel electrophoresis is limited by the progressive compressing of the long DNA end of a ladder. Improvement in the resolution of this DNA is achieved by use of the following two-step electrophoresis. Initially, the DNA ladder is fractionated by conventional constant field agarose gel electrophoresis. Subsequently, gel electrophoresis is performed in the reverse direction by pulsing the electrical field (PFGE). A newly developed type of pulsing is used, which causes inversion of a double-stranded DNA ladder: the distance migrated increases as the length of the DNA molecule increases. Thus, the resolution of DNA bands continues to increase during the PFGE. These two stages of electrophoresis are serially repeated. Eventually, both the short and the long DNA ends of the ladder migrate out of the gel while a selected region of the ladder undergoes progressive increase in resolution during back-and-forth migration. Improved resolution of DNA bands is achieved, without a known limit.
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Affiliation(s)
- G A Griess
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio 78284-7760, USA
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Kusukawa N, Ostrovsky MV, Garner MM. Effect of gelation conditions on the gel structure and resolving power of agarose-based DNA sequencing gels. Electrophoresis 1999; 20:1455-61. [PMID: 10424468 DOI: 10.1002/(sici)1522-2683(19990601)20:7<1455::aid-elps1455>3.0.co;2-l] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The effect of gelation conditions on the structure and resolving properties of agarose-based DNA sequencing gels were studied. Gels that were formed by rapid cooling gave separation patterns with sharp, well-defined bands, and resolved base repeats that were not separated on gels which were allowed to cool slowly. Analyses by electron microscopy indicated that the rapidly cooled gels have a homogeneous pore structure with a smaller average pore size than gels that were cooled slowly. The two types of gels also differ in optical clarity, and have significant differences in their melting characteristics as measured by differential scanning calorimetry.
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Affiliation(s)
- N Kusukawa
- FMC BioProducts, Rockland, ME 04841, USA.
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