Identification of prognostic signature with seven LncRNAs for papillary thyroid carcinoma.

Purpose: With the increasing incidence of thyroid cancer (TC), the prognostic risk assessment of thyroid cancer has been becoming more and more important. The aim of this study was to screen TC-related biomarkers and identify key multi-long non coding RNA (lncRNA) signature for prognostic risk assessment of papillary TC.

Material And Methods: The lncRNAs differentially expressed between TC tissue and adjacent normal tissue was identified by R language.

EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments.

Long non-coding RNAs (lncRNAs) play important functional roles in many diverse biological processes. However, not all expressed lncRNAs are functional. Thus, it is necessary to manually collect all experimentally validated functional lncRNAs (EVlncRNA) with their sequences, structures, and functions annotated in a central database.

Experimentally Validated Plant lncRNAs in EVLncRNAs Database.

Plant long noncoding RNAs (lncRNAs) play important functional roles in various biological processes. Most databases deposit all plant lncRNA candidates produced by high-throughput experimental and/or computational techniques. There are several databases for experimentally validated lncRNAs.

EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments.

Long non-coding RNAs (lncRNAs) play important functional roles in various biological processes. Early databases were utilized to deposit all lncRNA candidates produced by high-throughput experimental and/or computational techniques to facilitate classification, assessment and validation. As more lncRNAs are validated by low-throughput experiments, several databases were established for experimentally validated lncRNAs.

Real-time reliable determination of binding kinetics of DNA hybridization using a multi-channel graphene biosensor.

Reliable determination of binding kinetics and affinity of DNA hybridization and single-base mismatches plays an essential role in systems biology, personalized and precision medicine. The standard tools are optical-based sensors that are difficult to operate in low cost and to miniaturize for high-throughput measurement. Biosensors based on nanowire field-effect transistors have been developed, but reliable and cost-effective fabrication remains a challenge.

Target protein separation and preparation by free-flow electrophoresis coupled with charge-to-mass ratio analysis.

Herein, a novel strategy was developed to separate and prepare target protein from complex sample by free-flow electrophoresis (FFE), which mainly based on the charge-to-mass ratio (C/M) analysis of proteins. The C/M values of three model proteins, namely Cytochrome C (Cyt C), myoglobin (Mb) and bovine serum albumin (BSA) were analyzed under different pH and the separation of these proteins was predicted by CLC Protein Workbench software. Series of experiments were performed to validate the proposed method.

A tunable isoelectric focusing via moving reaction boundary for two-dimensional gel electrophoresis and proteomics.

Routine native immobilized pH gradient isoelectric focusing (IPG-IEF) and two-dimensional gel electrophoresis (2DE) are still suffering from unfortunate reproducibility, poor resolution (caused by protein precipitation) and instability in characterization of intact protein isoforms and posttranslational modifications. Based on the concept of moving reaction boundary (MRB), we firstly proposed a tunable non-IPG-IEF system to address these issues. By choosing proper pairs of catholyte and anolyte, we could achieve desired cathodic and anodic migrating pH gradients in non-IPG-IEF system, effectively eliminating protein precipitation and uncertainty of quantitation existing in routine IEF and 2DE, and enhancing the resolution and sensitivity of IEF.

Negative-pressure-induced collector for a self-balance free-flow electrophoresis device.

Uneven flow in free-flow electrophoresis (FFE) with a gravity-induced fraction collector caused by air bubbles in outlets and/or imbalance of the surface tension of collecting tubes would result in a poor separation. To solve these issues, this work describes a novel collector for FFE. The collector is composed of a self-balance unit, multisoft pipe flow controller, fraction collector, and vacuum pump.

A stable and high-resolution isoelectric focusing capillary array device for micropreparative separation of proteins.

A simple capillary array IEF device was developed for high resolution and micropreparative separation of trace amounts of proteins. Based on quasi-chip-scale manufacturing, the specific capillaries (600 μm i.d.

Theoretical and experimental studies on isotachophoresis in multi-moving chelation boundary system formed with metal ions and EDTA.

In this paper, a general mode and theory of moving chelation boundary based isotachophoresis (MCB-based ITP), together with the concept of decisive metal ion (DMI) having the maximum complexation constant (lg Kmax) with the chelator, were developed from a multi-MCB (mMCB) system. The theoretical deductions were: (i) the reaction boundary velocities in the mMCB system at steady state were equal to each other, resulting in a novel MCB-based ITP separation of metal ions; (ii) the boundary directions and velocities in the system were controlled by the fluxes of chelator and DMI, rather than other metal ions; and (iii) a controllable stacking of metal ions could be simultaneously achieved in the developed system. To demonstrate the deductions, a series of experiments were conducted by using model chelator of EDTA and metal ions of Cu(II) and Co(II) due to characteristic colors of blue [Cu-EDTA](2-) and pink [Co-EDTA](2-) complexes.

Study on stability mechanism of immobilized pH gradient in isoelectric focusing via the Svensson-Tiselius differential equation and moving reaction boundary.

An immobilized pH gradient (IPG) has strong power against instability (e.g., drifting and plateau) existing in classic isoelectric focusing (IEF).

A visual detection of protein content based on titration of moving reaction boundary electrophoresis.

A visual electrophoretic titration method was firstly developed from the concept of moving reaction boundary (MRB) for protein content analysis. In the developed method, when the voltage was applied, the hydroxide ions in the cathodic vessel moved towards the anode, and neutralized the carboxyl groups of protein immobilized via highly cross-linked polyacrylamide gel (PAG), generating a MRB between the alkali and the immobilized protein. The boundary moving velocity (V(MRB)) was as a function of protein content, and an acid-base indicator was used to denote the boundary displacement.

Studies on bioconjugation of quantum dots using capillary electrophoresis and fluorescence correlation spectroscopy.

In this paper, we systematically investigated the conjugation of quantum dots (QDs) with certain biomolecules using capillary electrophoresis (CE) and fluorescence correlation spectroscopy (FCS) methods. Commercial QDs and aqueous-synthesized QDs in our lab were used as labeling probes, certain bio-macromolecules, such as proteins, antibodies, and enzymes, were used as mode samples, and 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) and N-hydroxysulfo-succinimide (Sulfo-NHS) were used as linking reagents. We studied the effects of certain factors such as the isoelectric points (pIs) of bio-macromolecules and buffer pH on the bioconjugation of QDs, and found that the pIs of bio-macromolecules played an important role in the conjugation reaction.

A simple monolithic column electroelution for protein recovery from gel electrophoresis.

Protein recovery from gel electrophoresis plays an important role in functional genomics and proteomics but faces a series of issues (e.g., complex procedure, low recovery, long experimental time).

Purification of low-concentration phenazine-1-carboxylic acid from fermentation broth of Pseudomonas sp. M18 via free flow electrophoresis with gratis gravity.

The low-concentration phenazine-1-carboxylic acid (PCA) ( = 0.3 mM) extracted from fermentation broth of Pseudomonas sp. M18 was selected to be purified with a newly facile free flow electrophoresis (FFE) device with gratis gravity.