scholarly journals Simultaneous extraction, separation and purification of microbial genomic DNA and total RNA from acidic habitat samples

2015 ◽  
Vol 7 (3) ◽  
pp. 909-917 ◽  
Author(s):  
Jianping Xie ◽  
Hui Yun ◽  
Haigang Dong ◽  
Wenya Zhao ◽  
Guohua Wang ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Molecular Size ◽  
Total Nucleic Acid ◽  
Separation And Purification ◽  
Simultaneous Extraction ◽  
Dna And Rna ◽  
Molecular Size Marker ◽  
Extraction Separation ◽  
Microbial Genomic ◽  
Size Marker

DNA and RNA simultaneously extracted fromA. fusing the optimised method. (a) Total nucleic acid extracted fromA. f: lane M1, 1 kb ladder; lane M2,HindIII-cut lambda molecular size marker; lanes 1–4, biological replicates. (b) DNA precipitated by isopropanol. (c) RNA precipitated by LiCl.

scholarly journals A paradoxical synergism between Resveratrol and copper (II) with respect to degradation of DNA and RNA

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 1145 ◽  
Author(s):  
Siddharth Subramaniam ◽  
Iqbal Vohra ◽  
Aishwarya Iyer ◽  
Naveen K Nair ◽  
Indraneel Mittra
Keyword(s):  
Synergistic Effect ◽  
Plasmid Dna ◽  
Genomic Dna ◽  
Oxygen Species ◽  
Molar Ratios ◽  
Dna Cleaving ◽  
Dna And Rna ◽  
Fixed Concentration ◽  
Anti Cancer ◽  
Low Levels

Resveratrol (R), a plant polyphenol, is known to reduce Cu (II) to Cu (I) generating reactive oxygen species that can cleave plasmid DNA. Here we report a surprising observation of a paradoxical synergistic effect between R and Cu whereby plasmid DNA cleaving / degrading activity of R-Cu increased progressively as the ratio of R to Cu was increased i.e., the concentration of Cu was successively reduced with respect to a fixed concentration R. Whereas cleavage of plasmid DNA occurred at low molar ratios of R to Cu, at higher ratios, complete degradation of DNA was achieved. By further increasing the ratio, whereby the concentration of Cu was reduced to very low levels, the DNA degrading activity of R-Cu was lost. This paradoxical synergistic effect is also seen with respect to eukaryotic genomic DNA and RNA. Since R-Cu may have anti-cancer and anti-viral activities, our findings may not only help to improve the therapeutic efficacy of R-Cu but also reduce its toxic side effects with the use of low concentration of Cu.

scholarly journals Liquid Biphasic System: A Recent Bioseparation Technology

Processes ◽  
2020 ◽  
Vol 8 (2) ◽  
pp. 149 ◽  
Author(s):  
Kuan Shiong Khoo ◽  
Hui Yi Leong ◽  
Kit Wayne Chew ◽  
Jun-Wei Lim ◽  
Tau Chuan Ling ◽  
...  
Keyword(s):  
Future Development ◽  
Future Prospect ◽  
Fundamental Principle ◽  
Present Review ◽  
Biphasic System ◽  
Separation And Purification ◽  
Separation Techniques ◽  
System A ◽  
Extraction Separation ◽  
Further Development

A well-known bioseparation technique namely liquid biphasic system (LBS) has attracted many researchers’ interest for being an alternative bioseparation technology for various kinds of biomolecules. The present review begins with an in-depth discussion on the fundamental principle of LBS and this is followed by the discussion on further development of various phase-forming components in LBS. Additionally, the implementation of various advance technologies to the LBS that is beneficial towards the efficiency of LBS for the extraction, separation, and purification of biomolecules was discussed. The key parameters affecting the LBS were presented and evaluated. Moreover, future prospect and challenges were highlighted to be a useful guide for future development of LBS. The efforts presented in this review will provide an insight for future researches in liquid-liquid separation techniques.

scholarly journals Biodiversity of Active and Inactive Bacteria in the Gut Flora of Wood-Feeding Huhu Beetle Larvae (Prionoplus reticularis)

2011 ◽  
Vol 77 (19) ◽  
pp. 7000-7006 ◽  
Author(s):  
Nicola M. Reid ◽  
Sarah L. Addison ◽  
Lucy J. Macdonald ◽  
Gareth Lloyd-Jones
Keyword(s):  
Genomic Dna ◽  
Data Sets ◽  
Data Set ◽  
Content Type ◽  
Dna And Rna ◽  
New Information ◽  
Related Organism ◽  
The Family ◽  
Insect Symbionts ◽  
Derived Data

ABSTRACTHuhu grubs (Prionoplus reticularis) are wood-feeding beetle larvae endemic to New Zealand and belonging to the family Cerambycidae. Compared to the wood-feeding lower termites, very little is known about the diversity and activity of microorganisms associated with xylophagous cerambycid larvae. To address this, we used pyrosequencing to evaluate the diversity of metabolically active and inactive bacteria in the huhu larval gut. Our estimate, that the gut harbors at least 1,800 phylotypes, is based on 33,420 sequences amplified from genomic DNA and reverse-transcribed RNA. Analysis of genomic DNA- and RNA-derived data sets revealed that 71% of all phylotypes (representing 95% of all sequences) were metabolically active. Rare phylotypes contributed considerably to the richness of the community and were also largely metabolically active, indicating their participation in digestive processes in the gut. The dominant families in the active community (RNA data set) includedAcidobacteriaceae(24.3%),Xanthomonadaceae(16.7%),Acetobacteraceae(15.8%),Burkholderiaceae(8.7%), andEnterobacteriaceae(4.1%). The most abundant phylotype comprised 14% of the active community and affiliated withDyella ginsengisoli(Gammaproteobacteria), suggesting that aDyella-related organism is a likely symbiont. This study provides new information on the diversity and activity of gut-associated microorganisms that are essential for the digestion of the nutritionally poor diet consumed by wood-feeding larvae. Many huhu gut phylotypes affiliated with insect symbionts or with bacteria present in acidic environments or associated with fungi.

Simultaneous extraction of DNA and RNA from Escherichia coli BL 21 based on silica-coated magnetic nanoparticles

2015 ◽  
Vol 58 (11) ◽  
pp. 1774-1778 ◽  
Author(s):  
Jiuhai Wang ◽  
Zeeshan Ali ◽  
Nianyue Wang ◽  
Wenbiao Liang ◽  
Hongna Liu ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Magnetic Nanoparticles ◽  
Simultaneous Extraction ◽  
Dna And Rna

A comparative hybridization analysis of yeast DNA with Paramecium parafusin- and different phosphoglucomutase-specific probes

2000 ◽  
Vol 78 (6) ◽  
pp. 683-690 ◽  
Author(s):  
Elzbieta Wyroba ◽  
Birgit H Satir
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Nucleotide Sequence ◽  
Genomic Dna ◽  
Pcr Amplification ◽  
Molecular Size ◽  
Molecular Probes ◽  
Hybridization Analysis ◽  
Yeast Genome ◽  
Specific Primers ◽  
Genome Database

Molecular probes designed for the parafusin (PFUS), the Paramecium exocytic-sensitive phospho glyco protein, gave distinct hybridization patterns in Saccharomyces cerevisiae genomic DNA when compared with different phosphoglucomutase specific probes. These include two probes identical to segments of yeast phosphoglucomutase (PGM) genes 1 and 2. Neither of the PGM probes revealed the 7.4 and 5.9 kb fragments in Bgl II-cut yeast DNA digest detected with the 1.6 kb cloned PFUS cDNA and oligonucleotide constructed to the PFUS region (insertion 3 – I-3) not found in other species. PCR amplification with PFUS-specific primers generated yeast DNA-species of the predicted molecular size which hybridized to the I-3 probe. A search of the yeast genome database produced an unassigned nucleotide sequence that showed 55% identity to parafusin gene and 37% identity to PGM2 (the major isoform of yeast phosphoglucomutase) within the amplified region.Key words: parafusin, phosphoglucomutase, yeast, hybridization, PCR.

Optimization of the Method for Simultaneous Extraction Bioleaching Bacteria DNA and RNA

2013 ◽  
Vol 825 ◽  
pp. 177-181
Author(s):  
Jian Ping Xie ◽  
Hui Yun ◽  
Guan Zhou Qiu ◽  
Xin Xing Liu
Keyword(s):  
Simultaneous Extraction ◽  
Dna And Rna

scholarly journals Selective Microbial Genomic DNA Isolation Using Restriction Endonucleases

PLoS ONE ◽  
2014 ◽  
Vol 9 (10) ◽  
pp. e109061 ◽  
Author(s):  
Helen E. Barnes ◽  
Guohong Liu ◽  
Christopher Q. Weston ◽  
Paula King ◽  
Long K. Pham ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Dna Isolation ◽  
Restriction Endonucleases ◽  
Genomic Dna Isolation ◽  
Microbial Genomic

Detection of Multiple Myeloma Cells in Peripheral Blood Using High-Throughput Sequencing Assay

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 321-321
Author(s):  
Amitabha Mazumder ◽  
Malek Faham ◽  
Mark Fiala ◽  
Mark Klinger ◽  
Thomas Martin ◽  
...  
Keyword(s):  
Peripheral Blood ◽  
High Frequency ◽  
Genomic Dna ◽  
Research Funding ◽  
High Throughput Sequencing ◽  
Plasma Dna ◽  
Employment Equity ◽  
Clonal Rearrangement ◽  
Dna And Rna ◽  
Equity Ownership

Abstract Abstract 321 Background: Multiple myeloma (MM) is characterized by the presence of monoclonal protein (M-protein) in serum and/or urine, clonal plasma cell accumulation in bone marrow (BM), and related organ or tissue impairment. MM patients are monitored during therapy and posttherapy using immunoglobulin, M-protein and free light chain assays. Assessing pathological myeloma cells using flow cytometry and RT-PCR has been shown to have superior prognostic value. However, the sensitivity of these techniques has generally limited their use to assessment of BM. In order to determine whether myeloma minimal residual disease could be detected in peripheral blood (PB), we assessed a cohort of MM patients using a sequencing based platform, LymphoSIGHT, with a sensitivity of 1 cancer cell per million leukocytes. Methods: We obtained from 4 sources (UCSF, NYU, Washington Univ, commercial source) pairs of BM and PB samples from 60 MM patients at different points of disease. BM samples were used to identify the clonal MM sequence and detection of that sequence in the PB was assessed. For some patients BM/PB sample pairs were obtained from >1 time point resulting in a total of 78 pairs. In addition blood and bone marrow plasma samples were available for 44 and 6 patients, respectively, to assess presence of the myeloma clonotype in cell free DNA. Altogether there were 206 samples. BM samples were either available as BM mononuclear cells (BMMC) or bead enriched CD138+ cells. Using universal primer sets, we amplified IgH@ variable (V), diversity (D), and joining (J) gene segments from genomic DNA and/or RNA samples, the incomplete IgH rearrangement (DJ), and IgK from genomic DNA. Amplified products were sequenced to obtain >1 million reads and analyzed using standardized algorithms for clonotype determination. Myeloma-specific IgH, IgK, and DJ clonotypes were identified for each patient based on their high frequency in BM samples. The presence of the myeloma clonotype was then assessed in all PBMC (DNA and RNA), BM plasma (DNA), and PB plasma (DNA) samples using the same IgH and in some samples using the IgK sequencing assays. A quantitative and standardized measure of clone level among all leukocytes in each PB or BM sample was determined using internal reference DNA. Here we describe data on 46/60 patients; data from all 60 patients will be presented. Results: In BM samples, we detected the myeloma clonal rearrangement of at least one receptor (“calibrating receptor”) in 34/46 (74%) of MM patients (Table 1). The calibration rate varied by receptor, with 30/46 (65%) patients calibrating with IgH, 14/43 (33%) with IgH DJ, and 22/43 (51%) with IgK (Table 1). Identification of myeloma-specific clonal rearrangement is based on presence at high frequency and may not occur in samples from patients with low disease load (e.g., post-treatment). Of the 12 non-calibrating patients, only 3 had high disease load. The myeloma clonotype that was identified in the BM was also detected in PBMC in 22/30 (73%) and 28/30 (93%) patients with the DNA and RNA IgH analysis, respectively (Table 2). IgK DNA analysis showed the presence of the myeloma clonotype in 9/10 PBMC samples, all of which were concordant with IgH results. The myeloma clonotype that was identified in the BM was also detected in the cell-free BM and PB samples in 5/5 and 7/11 patients, respectively, using the IgH DNA assay. The evaluation of blood plasma and PBMC were at times complementary in detecting the myeloma. Conclusions: Results from the application of a high-throughput sequencing method for detection of myeloma-specific clonotypes in 46 MM patients are shown. A clonal rearrangement was detected in 74% of MM BM samples. Importantly, 93% of peripheral blood samples from 30 patients showed evidence of circulating myeloma in PBMC. Analysis of BM and PB samples from 14 additional MM patients as well as association of the level of myeloma in PBMC and BM with clinical measures is ongoing. Disclosures: Faham: Sequenta, Inc.: Employment, Equity Ownership, Research Funding. Klinger:Sequenta, Inc.: Employment, Equity Ownership, Research Funding.

A simplified quick microbial genomic DNA extraction via freeze–thawing cycles

2019 ◽  
Vol 47 (1) ◽  
pp. 703-709 ◽  
Author(s):  
Feifei Chen ◽  
Jianren Ye ◽  
Chonlong Chio ◽  
Wanhui Liu ◽  
Jiyuan Shi ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Genomic Dna ◽  
Genomic Dna Extraction ◽  
Microbial Genomic

scholarly journals Technologies for the Extraction, Separation and Purification of polyphenols – A Review

2019 ◽  
Vol 6 (1) ◽  
pp. 74-91 ◽  
Author(s):  
Shyam Suwal ◽  
Alice Marciniak
Keyword(s):  
Organic Molecules ◽  
Extraction Efficiency ◽  
Positive Impact ◽  
Cost Effective ◽  
Separation And Purification ◽  
Advantages And Disadvantages ◽  
Assisted Extraction ◽  
Extraction Separation ◽  
Current Context ◽  
Conventional Extraction

Polyphenols are high molecular weight, organic molecules mainly found in plant kingdom. They are mostly known for their positive impact on health, specifically for their antioxidant activity. Indeed, they are widely studied for the prevention of multiple diseases such as cancer, inflammatory, cardiovascular and neurodegenerative diseases. Nevertheless, extractions of these growing interest molecules remain challenging using conventional methods such as solvent extraction. That is why recent researches have focused on improving the extraction of polyphenol by using different technologies such as ultrasound, microwave, pressurized liquid, pulsed electric field, supercritical fluid and high hydrostatic pressure. In the current context, the assisted-extraction should demonstrate their potential to improve the extraction efficiency while being cost-effective and with a low environmental impact. To this end, technologies ought to, for instance, increase the solubility of polyphenol and the permeability of the cell wall. Consequently, this review is focused on the use and potential of these technologies to improve polyphenol extractions from plants as well as their purification using various methods. It discusses of the advantages and disadvantages with some examples of all these technologies assisted-extraction in comparison with conventional extraction method as well as purification technology.

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