Magnetic ionic liquids in applications of nucleic acid analysis: Sequence-specific extraction of DNA and preservation solvents of RNA

The selective extraction and accumulation of specific deoxyribonucleic acid (DNA) fragments is required for targeted nucleic acid analysis in order to minimize interferences from samples with abundant heterogeneous sequences. In addition, it is essential to isolate and preserve nucleic acid from biological sample containing numerous compounds such as endonucleases prior to sample analysis. Very recently, ionic liquid (IL) and magnetic ionic liquid (MIL) based materials have shown significant promise in the area of biological sample preparation and separation. In this thesis, various types of ILs and MILs are exhaustively descripted and utilized for two applications: 1) sequence-specific extraction of DNA and 2) RNA preservation. Functionalized oligonucleotide probes named as ion-tagged oligonucleotides (ITOs) and disubstituted ion-tagged oligonucleotides (DTOs) that hybridize with complementary DNA targets can be subsequently captured by a hydrophobic MIL support. The ITO- and DTO-MIL system is investigated for sequence-specific extraction of DNA in a relatively low concentration within multiple sample matrices such as blood and plasma. This particle- and aggregation-free extraction method is highly potential and beneficial for analysis based on microfluidic devices. In addition, RNA samples obtained from yeast cells can be extracted and preserved by several MILs simultaneously. RNA remains the high quantity and structural integrity within MILs at room temperature. Moreover, specific MILs can be used to reduce ribonuclease A (RNase A) degradation of RNA. This RNA preservation method reveals multiple advantages including energy-saving and equipment-independent which makes it applicable to in-field RNA sample preparation

Maximizing Ion-tagged Oligonucleotide Loading on Magnetic Ionic Liquid Supports for the Sequence-Specific Extraction of Nucleic Acids

Targeted nucleic acid analysis requires the highly selective extraction of desired DNA fragments in order to minimize interferences from samples with abundant heterogeneous sequences. We previously reported a method based on functionalized oligonucleotide probes known as ion-tagged oligonucleotides (ITOs) that hybridize with complementary DNA targets for subsequent capture using a hydrophobic magnetic ionic liquid (MIL) support. Although the ITO-MIL approach enriched specific DNA sequences in quantities comparable to a commercial magnetic bead-based method, the modest affinity of the ITO for the hydrophobic MIL limited the yield of DNA targets, particularly when stringent wash conditions were applied to remove untargeted DNA. Here, we report the synthesis and characterization of a series of ITOs in which functional groups were installed within the cation and anion components of the tag moiety in order to facilitate loading of the ITO to the MIL support phase. In addition to hydrophobic interactions, we demonstrate that π-π stacking and fluorophilic interactions can be exploited for loading oligonucleotide probes onto MILs. Using a disubstituted ion-tagged oligonucleotide (DTO) possessing two linear C8 groups, nearly quantitative loading of the probe onto the MIL support was achieved. The enhanced stability of the DTO within the MIL solvent permitted successive wash steps without the loss of the DNA target compared to a monosubstituted ITO with a single C8 group that was susceptible to increased loss of analyte. Furthermore the successful capture of a 120 bp KRAS fragment from human plasma samples followed by real-time quantitative polymerase chain reaction (qPCR) amplification is demonstrated

An Analysis of LED Light Distribution Based on Visual Spectral Characteristics

AbstractOn the analysis of the human visual structure characteristics and LED optical design principle, human visual color image model with background light was constructed in this paper, and the image sharpness function is defined. With high pressure sodium lamps, white light and green light LED as backlight, the model simulation of image sharpness is fulfilled. The results show that the green LED has better clarity and sensitivity with the same condition of radiation energy background light

The Silencing of RECK Gene is Associated with Promoter Hypermethylation and Poor Survival in Hepatocellular Carcinoma

Background: To evaluate the promoter methylation status of RECK gene and mRNA expression in patients with hepatocellular carcinoma (HCC)

Selenium nanoparticles decorated with Ulva lactuca polysaccharide potentially attenuate colitis by inhibiting NF-κB mediated hyper inflammation

Additional file 1. Supplemental information of ULP-SeNPs concerns their stability in physiological solutions, uptake by BMDMs and effect on NF-κB activation

Resolving the genetic paradox of invasions: Preadapted genomes and postintroduction hybridization of bigheaded carps in the Mississippi River Basin

The genetic paradox of biological invasions is complex and multifaceted. In particular, the relative role of disparate propagule sources and genetic adaptation through postintroduction hybridization has remained largely unexplored. To add resolution to this paradox, we investigate the genetic architecture responsible for the invasion of two invasive Asian carp species, bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) (bigheaded carps) that experience extensive hybridization in the Mississippi River Basin (MRB). We sequenced the genomes of bighead and silver carps (~1.08G bp and ~1.15G bp, respectively) and their hybrids collected from the MRB. We found moderate‐to‐high heterozygosity in bighead (0.0021) and silver (0.0036) carps, detected significantly higher dN/dS ratios of single‐copy orthologous genes in bigheaded carps versus 10 other species of fish, and identified genes in both species potentially associated with environmental adaptation and other invasion‐related traits. Additionally, we observed a high genomic similarity (96.3% in all syntenic blocks) between bighead and silver carps and over 90% embryonic viability in their experimentally induced hybrids. Our results suggest intrinsic genomic features of bigheaded carps, likely associated with life history traits that presumably evolved within their native ranges, might have facilitated their initial establishment of invasion, whereas ex-situ interspecific hybridization between the carps might have promoted their range expansion. This study reveals an alternative mechanism that could resolve one of the genetic paradoxes in biological invasions and provides invaluable genomic resources for applied research involving bigheaded carps

Magnetic ionic liquids in applications of nucleic acid analysis: Sequence-specific extraction of DNA and preservation solvents of RNA

The selective extraction and accumulation of specific deoxyribonucleic acid (DNA) fragments is required for targeted nucleic acid analysis in order to minimize interferences from samples with abundant heterogeneous sequences. In addition, it is essential to isolate and preserve nucleic acid from biological sample containing numerous compounds such as endonucleases prior to sample analysis. Very recently, ionic liquid (IL) and magnetic ionic liquid (MIL) based materials have shown significant promise in the area of biological sample preparation and separation. In this thesis, various types of ILs and MILs are exhaustively descripted and utilized for two applications: 1) sequence-specific extraction of DNA and 2) RNA preservation. Functionalized oligonucleotide probes named as ion-tagged oligonucleotides (ITOs) and disubstituted ion-tagged oligonucleotides (DTOs) that hybridize with complementary DNA targets can be subsequently captured by a hydrophobic MIL support. The ITO- and DTO-MIL system is investigated for sequence-specific extraction of DNA in a relatively low concentration within multiple sample matrices such as blood and plasma. This particle- and aggregation-free extraction method is highly potential and beneficial for analysis based on microfluidic devices. In addition, RNA samples obtained from yeast cells can be extracted and preserved by several MILs simultaneously. RNA remains the high quantity and structural integrity within MILs at room temperature. Moreover, specific MILs can be used to reduce ribonuclease A (RNase A) degradation of RNA. This RNA preservation method reveals multiple advantages including energy-saving and equipment-independent which makes it applicable to in-field RNA sample preparation.</p