Precipitation of DNA by polyethylene glycol and ethanol

Paithankar, Khanderao; Prasad, K.

doi:10.1093/nar/19.6.1346

Cited by 188 publications

(99 citation statements)

References 3 publications

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“…DNA of the biofilms and activated sludge was separately extracted by a modified CTAB-PEG protocol (Paithankar and Prasad, 1991;Griffiths et al, 2000). The biofilm and sludge samples were collected at two time points of low TMP stage (7 and 10 kPa) and two time points of high TMP stage (30 and 60 kPa).…”

Section: Dna Extractionmentioning

confidence: 99%

Characterization of the archaeal community fouling a membrane bioreactor

Luo

Zhang

Tan

et al. 2015

Journal of Environmental Sciences

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Biofilm formation, one of the primary causes of biofouling, results in reduced membrane flux or increased transmembrane pressure and thus represents a major impediment to the wider implementation of membrane bioreactor (MBR) technologies for water purification. Most studies have focused on the role of bacteria in membrane fouling as they are the most dominant and best studied organisms present in the MBR. In contrast, there is limited information on the role of the archaeal community in biofilm formation in MBRs. This study investigated the composition of the archaeal community during the process of biofouling in an MBR. The archaeal community was observed to have lower richness and diversity in the biofilm than the sludge during the establishment of biofilms at low transmembrane pressure (TMP). Clustering of the communities based on the Bray-Curtis similarity matrix indicated that a subset of the sludge archaeal community formed the initial biofilms. The archaeal community in the biofilm was mainly composed of Thermoprotei, Thermoplasmata, Thermococci, Methanopyri, Methanomicrobia and Halobacteria. Among them, the Thermoprotei and Thermoplasmata were present at higher relative proportions in the biofilms than they were in the sludge. Additionally, the Thermoprotei, Thermoplasmata and Thermococci were the dominant organisms detected in the initial biofilms at low TMP, while as the TMP increased, the Methanopyri, Methanomicrobia, Aciduliprofundum and Halobacteria were present at higher abundances in the biofilms at high TMP.

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Section: Dna Extractionmentioning

confidence: 99%

Characterization of the archaeal community fouling a membrane bioreactor

Luo

Zhang

Tan

et al. 2015

Journal of Environmental Sciences

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“…A DNA fragment containing 757 bp of IHHNV nonstructural protein (nucleotide 1215 to 1971) was cloned in the pGEM-T-Easy vector (Promega, Madison, WI, USA) and designated as pIHHNV-P4. The plasmid was purified with alkaline lysis and polyethylene glycol-NaCl precipitation (Paithankar & Prasad 1991) and sequenced to confirm that it contained the sequence for PCR primers and TaqMan probe. The concentration of pIHHNV-P4 was then determined by measurement of OD at 260 nm and confirmed with agarose gel electrophoresis.…”

Section: Shrimp and Virusesmentioning

confidence: 99%

Detection and quantification of infectious hypodermal and hematopoietic necrosis virus in penaeid shrimp by real-time PCR

Tang¹,

Lightner²

2001

Dis. Aquat. Org.

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A real-time PCR method using a fluorogenic 5' nuclease assay and a PE Applied Biosystems GeneAmp 5700 sequence detector was developed to detect infectious hypodermal and hematopoietic necrosis virus (IHHNV) in penaeid shrimp. A pair of PCR primers to amplify an 81 bp DNA fragment and a fluorogenic probe (TaqMan probe) were selected from ORF1 (open reading frame 1) of the IHHNV genome. The primers and TaqMan probe used in this assay were shown to be specific for IHHNV and did not react with either hepatopancreatic parvovirus (HPV), white-spot syndrome virus (WSSV), or shrimp DNA. A plasmid, pIHHNV-P4, containing the target IHHNV sequence was constructed and used as a positive control. The concentration of pIHHNV-P4 was determined through spectrophotometric analysis and the plasmid was used for quantitative studies. This real-time PCR assay had a detection limit of 10 copies and a log-linear range up to 5 × 10 7 copies of IHHNV DNA. The assay was then used to quantify IHHNV in infected shrimp collected from 5 locations: Hawaii, Panama, Mexico, Guam, and the Philippines. The quantitative analysis showed that wild-caught, large juvenile Penaeus stylirostris collected from the Gulf of California (Mexico) in 1996 were naturally infected with IHHNV and contained up to 10 9 copies of IHHNV µg -1 of DNA. Similar quantities of IHHNV were detected in hatchery-raised, small juvenile P. stylirostris collected from Guam in 1995 and in farm-raised, post-larval P. monodon from the Philippines in 1996. Laboratory-infected P. stylirostris contained approximately 10 8 copies of IHHNV 31 d after being fed with IHHNV-infected shrimp tissue. In contrast, individuals of Super Shrimp ® , a line of P. stylirostris selected for IHHNV resistance, showed no signs of infection 32 d after ingesting IHHNV-infected shrimp tissue. Laboratory-infected P. vannamei also contained approximately 10 8 copies of IHHNV 30 d after being fed infected shrimp tissue. A time-course study of IHHNV replication in juvenile P. vannamei showed that the doubling time in the exponential growth phase was approximately 22 h.

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“…Poly‐ethylene glycol (PEG) is an uncharged chemical polymer with broad application in biotechnology, biophysics, nanotechnology and biomedical research, not only as a common precipitant for proteins1 and nucleic acids2 but also for hydrophilic coating of particles or surfaces, preparation of hydrogels3 and, in particular, for conjugation to biopharmaceuticals 4, 5. Prominent features of PEG are its strong hydrophilicity, its disordered conformation in a dissolved state, which causes an expanded hydrodynamic volume as well as “crowding effect,” the availability in a variety of average sizes and its largely inert chemical and biological behavior 6…”

Section: Introductionmentioning

confidence: 99%

The polypeptide biophysics of proline/alanine‐rich sequences (PAS): Recombinant biopolymers with PEG‐like properties

Breibeck

Skerra

2017

Biopolymers

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PAS polypeptides comprise long repetitive sequences of the small L‐amino acids proline, alanine and/or serine that were developed to expand the hydrodynamic volume of conjugated pharmaceuticals and prolong their plasma half‐life by retarding kidney filtration. Here, we have characterized the polymer properties both of the free polypeptides and in fusion with the biopharmaceutical IL‐1Ra. Data from size exclusion chromatography, dynamic light scattering, circular dichroism spectroscopy and quantification of hydrodynamic and polar properties demonstrate that the biosynthetic PAS polypeptides exhibit random coil behavior in aqueous solution astonishingly similar to the chemical polymer poly‐ethylene glycol (PEG). The solvent‐exposed PAS peptide groups, in the absence of secondary structure, account for strong hydrophilicity, with negligible contribution by the Ser side chains. Notably, PAS polypeptides exceed PEG of comparable molecular mass in hydrophilicity and hydrodynamic volume while exhibiting lower viscosity. Their uniform monodisperse composition as genetically encoded polymers and their biological nature, offering biodegradability, render PAS polypeptides a promising PEG mimetic for biopharmaceutical applications.

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Precipitation of DNA by polyethylene glycol and ethanol

Cited by 188 publications

References 3 publications

Characterization of the archaeal community fouling a membrane bioreactor

Characterization of the archaeal community fouling a membrane bioreactor

Detection and quantification of infectious hypodermal and hematopoietic necrosis virus in penaeid shrimp by real-time PCR

The polypeptide biophysics of proline/alanine‐rich sequences (PAS): Recombinant biopolymers with PEG‐like properties

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