Gel Separation Research Articles

Retraction Note: NF-κB activation impairs somatic cell reprogramming in ageing.

We, the authors, are retracting this Article due to issues that have come to our attention regarding data availability, data description and figure assembly. Specifically, original numerical data are not available for the majority of the graphs presented in the paper. Although original data were available for most EMSA and immunoblot experiments, those corresponding to the published EMSA data of Supplementary Fig. 8a, the independent replicate immunoblots of Fig. 8b and Supplementary Fig. 1e, and the independent replicate EMSA data of Supplementary Figs 6e, 8b, 8c and 8d, are unavailable. Mistakes were detected in the presentation of Figs 3c, 4i and Supplementary Figs 6a, 8a, 8d, 9, and in some cases the β-actin immunoblots were erroneously described in the figure legends as loading controls, rather than as sample processing controls that were run on separate gels. Although we, the authors, believe that the key findings of the paper are still valid, given the issues with data availability we have concluded that the most appropriate course of action is to retract the Article. We deeply regret these errors and apologize to the scientific community for any confusion this publication may have caused. All authors agree with the retraction.

Direct antimicrobial susceptibility tests of bacteria and yeasts from positive blood cultures by using serum separator gel tubes and MALDI–TOF MS

Early and appropriate antimicrobial treatment can effectively reduce the mortality rate caused by bloodstream infections (BSIs) and is critical for favorable patient outcomes. In general, >90% of positive blood cultures will show positive results within 48 h after incubation in the BACTECTM FX system. However, an additional 6–8 h are required to obtain clones of the bacterium and another 10–24 h to obtain antimicrobial susceptibility test (AST) results. In this study, direct ASTs of bacteria and yeasts from positive blood cultures were performed by using serum separator gel tubes and matrix-assisted laser desorption ionization–time of flight mass spectrometry(MALDI-TOF MS). 153 BSI cases were caused by a single pathogen. The coincidence rates of genus and species identification between the direct method (from positive blood cultures) and reference method (from subcultured clones) were 86.9% and 83%, respectively. On average, 98.6% of the direct ASTs in 88 Gram-negative bacteria tested had an accurate result compared to the reference method. In Gram- positive bacteria and yeasts, the accuracy rates were 99.2% and 100%, respectively. MALDI-TOF MS combined with serum separator gel tubes can be used for rapidly identifying and performing ASTs on positive blood cultures.

Screening & analysis of anionic peptides from Foeniculum vulgare Mill by mass spectroscopy.

Fennel (Foeniculum vulgare Mill.) member from the family Umbelliferae (Apiaceae) and has been used in Saudi Arabia as an medicine as of the from the tradition. Our previous work with seed extracts of this plant generated DEAE-ion exchange purified proteins that exhibited antibacterial properties. The current study moves this work forward by using 2-D gel separation and MALDI TOF/TOF to identify proteins in this active extract. Fourteen protein spots were excised, digested, and identified. Several putative functions were identified, including: a copper-trans locating ATPase PAA1 chloroplastic-like isoform X1; a cytosolic enolase; a putative pentatricopeptide repeat-containing protein; an NADP-requiring isocitrate dehydrogenase; two proteins annotated as being encoded downstream from Son-like proteins; three probable nuclear proteins 5–1; and four predicted/ unidentified proteins. Future efforts will further characterize their relevant antimicrobial properties with the aim of cloning and high throughput synthesis of the antimicrobial element(s).

Applications of Pillar[n]arene-Based Supramolecular Assemblies.

Macrocycles are an important player in supramolecular chemistry. In 2008, a new class of macrocycles, "pillar[n]arenes", were first discovered. Research efforts in the area of pillar[n]arenes have elucidated key properties, such as their shape, reaction mechanism, host-guest properties, and their versatile functionality, which has contributed to the development of pillar[n]arene chemistry and their applications to various fields. This Minireview describes how pillar[n]arene-based supramolecular assemblies can be applied to supramolecular gel formation, reactions, light-harvesting systems, drug-delivery systems, biochemical applications, separation and storage materials, and surface chemistry.

Glucose variation in centrifuged serum and lithium-heparin gel tubes stored for up to 96 hours at room temperature or 4 °C

This study aimed to verify glucose stability within centrifuged serum and lithium-heparin tubes stored at room temperature (RT) or 4 °C. Sixty paired serum (plus gel separator), lithium-heparin (plus gel separator) and K2-EDTA tubes were centrifuged within 30 min from collection. Thirty serum and lithium-heparin tubes were then stored at RT, whilst the other 30 serum and lithium-heparin tubes were kept at 4 °C. Complete cell blood count was performed in serum and plasma after centrifugation, as well as in K2-EDTA paired whole blood tubes. Glucose was measured immediately after centrifugation and 3, 6, 24, 48, 72 and 96 h afterwards. Immeasurable blood cells values were found in serum, whilst residual leukocytes and platelets were present in lithium-heparin plasma. Regardless of storage conditions, glucose concentration decreased 3 h after centrifugation in lithium-heparin tubes, displaying uninterrupted reduction until 96 h. Mean decrease per hour was higher in plasma tubes stored at RT than at 4 °C. Performance specification was exceeded between 6 and 24 h of storage in most plasma tubes. Glucose concentration significantly decreased in serum tubes between 24 and 48 h, regardless of storage conditions. The mean glucose variation never exceeded performance specification throughout the study period. Mean glucose decrease per hour in plasma was not associated with blood cells counts before and after centrifugation, and was probably attributable to the presence of blood cells entrapped within the gel. Delayed glucose measurement in centrifuged serum tubes may be clinically viable up to 96 h, whilst it may be unadvisable in centrifuged lithium-heparin tubes.

Fabrication of single gel with different mechanical stiffness using three-dimensional mold.

The hydrogel is considering as functional substrates for three-dimensional (3D) environment mimicking the native tissue in vitro. To get the cell or tissue culture result in different stiffness, researchers used separate gel at different times. Sometimes these results are manipulated by surrounding environment. To overcome this, we prepared a single hydrogel with different young modulus using a 3 D printed mold and cell culture and tissue culture was performed to check the functional capacity. In this proposed device we successfully produced a multiproperties agarose hydrogel on a single platform. We designed different mold pattern to confirm that this gel formation technique can be used for any types of design and many different concentrated hydrogels can be combined together. The cell and tissue culture results showed that even in same planer surface, each gel solely maintains their own physical properties and control the cell and tissue adherence and proliferation behavior. The protocol is fairly simple and reproducible. The design helps to produce consistent gel thickness, shape, and size. This 3 D mold has provided a new way tostudy the fundamental cellular responses to engineered microenvironments that may have a high implementation in both biological and healthcare-related applications. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 107A: 6-11, 2019.

The right blood collection tube for therapeutic drug monitoring and toxicology screening procedures: Standard tubes, gel or mechanical separator?

Stability data of toxics or drugs in gel-based or mechanical separation blood collection tubes are lacking, especially for therapeutic drug monitoring and clinical toxicology procedures. According to ISO 15189 accreditation standard, laboratories need to master the entire preanalytical process including the stability of analytes in a specific tube. Here we explored the impact of BD PST™ II and Barricor™ separator tubes on the stability of 167 therapeutic compounds and common drugs of abuse in plasma samples using LC-MS/MS. Forty drugs were significantly affected by the use of PST™ II tubes, including antidepressants (11/26), neuroleptics (9/13), cardiovascular drugs (5/26), anxiolytics and hypnotics (4/25) and some drugs of abuse (5/26). Six compounds exhibited significant reduction by the mechanical Barricor™ tubes. Ten drugs exhibited low (<85%) but non-significant recoveries due to inter-assay variability. Besides, a logP > 3.3 was determined as a cut-off value to predict a potential lack of stability in PST™ II gel tubes with an 86.4% sensitivity and a 61.4% specificity. As a consequence, determination of drugs with a logP > 3.3 should be carried out with caution in plasma samples withdrawn on PST™ II. The study showed the Barricor™ and non-gel tubes cause less drug interference and are recommended for the drugs studied.

In situ measurement of localization error in particle tracking microrheology

A method is presented to estimate the static error 𝜖 in a multiple particle tracking microrheology experiment. This in situ estimate of 𝜖 is measured under the same conditions of the material under test, and without any additional experiments. The correction of the mean-squared displacement by the in situ method is potentially more reliable than methods that rely on characterizing 𝜖 in a separate gel sample. With the true mean-squared displacements accessible at short lag times, experimental artifacts introduced by static error can be distinguished from true rheological properties, even in highly viscous (>10,000 mPa⋅s) samples.

Cross-Linked Ionomer Gel Separators for Polysulfide Shuttle Mitigation in Magnesium–Sulfur Batteries: Elucidation of Structure–Property Relationships

Cross-linked ionomer networks of varying poly(ethylene glycol) diacrylate cross-linker chain length, ionic comonomer chemistry, and comonomer ratio have been studied for their use as polysulfide shuttle inhibiting separators in magnesium–sulfur (Mg–S) batteries. Through the use of X-ray scattering, polysulfide diffusion experiments, conductivity measurements, and Mg–S cell cycling, it was determined that inclusion of tethered anions in polymer networks mitigates the polysulfide shuttle effect. Polysulfide crossover through networks into a bulk electrolyte can be reduced by absorption into the polymer gel, steric rejection, and electrostatic rejection, with the predominance of these mechanisms dictated by polymer composition and structure. The best network composition allowed an initial Mg–S cell discharge capacity of 522 mAh/g compared to a discharge capacity of 365 mAh/g using a literature standard glass fiber separator. The ionomer cell saw 67% capacity retention after three cycles, whereas the glass fi...

Graphite nanoparticles paper supercapacitor based on gel electrolyte

In this study, three-type paper supercapacitors based on the polyvinylidene fluoride (PVDF) and polyvinyl alcohol (PVA)/phosphoric acid (H3PO4) gel electrolytes and graphite nanoparticles (GNPs) electrodes have been fabricated. The gel electrolytes and electrodes films have been coated on the paper using push coating and then characterized by scanning electron microscopy (SEM). In two types of the paper supercapacitors, on the PVDF gel electrolyte film, a layer of PVA/water and BaTiO3 as a gel separator film has been coated. The specific capacitance of the paper supercapacitors using cyclic voltammetry (CV) and galvanostatic (charge–discharge) methods at the scan rates 20 and 150 mV s−1 have been investigated. The paper supercapacitor based on the BaTiO3 separator film showed higher specific capacitance (312 F g−1) compared to other samples. Also, using electrochemical impedance spectroscopy (EIS), the Nyquist and Bode curves of paper supercapacitors have been measured. For the paper supercapacitors based on the PVDF gel electrolyte film and BaTiO3 separator film using the Nyquist curves, the equivalent series resistance (ESR) was 306 Ω and 125 Ω, respectively. The paper supercapacitor based on BaTiO3 gel separator structure represents a new type of flexible supercapacitor with high performance that can be applied to electronic devices.

Systematic Glycolytic Enzyme Activity Analysis from Human Serum with PEP Technology.

A functional proteomics technology was used to systematically monitor metabolic enzyme activities from resolved serum proteins produced by a modified 2-D gel separation and subsequent Protein Elution Plate, a method collectively called PEP. Both qualitative and quantitative differences in the metabolic enzyme activity could be detected between cancer patient and control group, providing excellent biomarker candidates for cancer diagnosis and drug development. This technology has a wide range of applications; it can be used for rapid functional protein purification and characterization as well as drug target identification and validation. The ability for the PEP technology to efficiently separate and recover functional proteins makes it useful for the analysis of any proteins and its variants; this is especially advantageous for enzyme families with large number of enzymes such as protein kinases, phosphatases, proteases, and metabolic enzymes.

Preanalytical stability of [-2]proPSA in whole blood stored at room temperature before separation of serum and plasma: implications to Phi determination.

Background [-2]proPSA seems to outperform free/total prostate-specific antigen (PSA) ratio in prostate cancer diagnosis. However, [-2]proPSA stability remains an underestimated issue. We examined [-2]proPSA stability over time in whole blood before separation of serum and plasma and its implications for prostate health index (Phi) determination. Total PSA (tPSA) and free PSA (fPSA) stabilities were also assessed. Methods Blood was drawn from 26 patients and separated in two tubes for plasma (K2EDTA and K2EDTA plus protease inhibitors - P100) and one for serum (clot activator plus gel separator). Tubes were stored at room temperature before centrifugation 1, 3 and 5 h for serum and EDTA plasma or 1 and 5 h for P100 plasma. To investigate the influence of gel separator on markers' stability, blood was collected from 10 patients in three types of tubes to obtain serum: tubes with clot activator plus gel separator, with silica particles or glass tubes. Biomarkers were assayed with chemiluminescent immunoassays. Results [-2]proPSA and Phi levels significantly and progressively increased over time in serum (+4.81% and +8.2% at 3 h; +12.03% and +14.91% at 5 h, respectively, vs. 1 h; p<0.001). Conversely, [-2]proPSA levels did not change in plasma (EDTA or P100). tPSA levels did not change over time in serum or plasma, whereas fPSA decreased in serum. All markers were higher in plasma than in serum at any time point. This difference did not seem to be attributable to the use of gel for serum preparation. Conclusions EDTA prevented spurious in vitro modifications in PSA-related isoforms, confirming that a stabilized blood sample is a prerequisite for [-2]proPSA measurement and Phi determination.

Discovery, Characterization, and Linkage Mapping of Simple Sequence Repeat Markers In Hazelnut

From the genome sequence of hazelnut (Corylus avellana), 192 new polymorphic simple sequence repeat (SSR) markers were developed, characterized, and used to investigate genetic diversity in 50 accessions. Next-generation sequencing allows inexpensive sequencing of plant genomes and transcriptomes, and efficient development of polymorphic SSR markers, also known as microsatellite markers, at low cost. A search of the genome sequence of ‘Jefferson’ hazelnut identified 9094 fragments with long repeat motifs of 4, 5, or 6 base pairs (bp), from which polymorphic SSR markers were developed. The repeat regions in the ‘Jefferson’ genome were used as references to which genomic sequence reads of seven additional cultivars were aligned in silico. Visual inspection for variation in repeat number among the aligned reads identified 246 as polymorphic, for which primer pairs were designed. Polymerase chain reaction (PCR) amplification followed by agarose gel separation indicated polymorphism at 195 loci, for which fluorescent forward primers were used to amplify the DNA of 50 hazelnut accessions. Amplicons were post-PCR multiplexed for capillary electrophoresis, and allele sizes were determined for 50 accessions. After eliminating three, 192 were confirmed as polymorphic, and 169 showed only one or two alleles in each of the 50 cultivars, as expected in a diploid. At these 169 SSRs, a total of 843 alleles were found, for an average of 4.99 and a range of 2 to 17 alleles per locus. The mean observed heterozygosity, expected heterozygosity, polymorphism information content, and the frequency of null alleles were 0.51, 0.53, 0.47, and 0.03, respectively. An additional 25 primer pairs produced more than two bands in some accessions with an average of 6.8 alleles. The UPGMA dendrogram revealed a wide genetic diversity and clustered the 50 accessions according to their geographic origin. Of the new SSRs, 132 loci were placed on the linkage map. These new markers will be useful for diversity and parentage studies, cultivar fingerprinting, marker-assisted selection, and aligning the linkage map with scaffolds of the genome sequence.

User-friendly tool kits for protein gel electrophoresis techniques: A training program for high school students.

Recent advancements in biochemical sciences have helped the researchers to explore the molecular logic of life inclusive of its multifarious expressions and explain many facts about the structure and functions of cellular macromolecules. Due to its simple and cost-effective nature, polyacrylamide gel electrophoresis (PAGE) has become the most favored technique for qualitative and quantitative examination of macromolecules. Major drawbacks of such modifications are the cost and operational complexities faced by naïve students. Many interlinking laboratory equipment are needed in the school laboratories for the conduct of even simple scientific experiment. Some of these costly modern equipment are inaccessible for students of small laboratories, and their alternatives are not easily available. Many of these laboratory equipment required for routine gel electrophoresis technique can be fabricated in their simplest form using off-the-shelf components. A short term biochemistry training program was executed for high school students to provide them "hands-on" training using newly modified equipment, which was proved to be an exciting way of learning biochemical gel separation techniques. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):566-577, 2018.

Comparative 1D Blue-Native electrophoresis analysis of Plasmodium falciparum and human proteins associated with cytoadherence

BackgroundTo understand more about changes to the molecular components that occur when host endothelium interacts with Plasmodium falciparum-infected erythrocytes, a combined technique of protein separation (1D Blue-Native electrophoresis) and mass spectrometry of infected erythrocytes with endothelial cells (EC) in a co-culture system has been used.MethodsNative proteins were extracted from co-cultures and identified by mass spectrometry. Proteomic data from different parasite strains, either adhesion proficient (to endothelial cells) or non-adherent, were analysed in parallel to reveal protein associations linked to cytoadherence. Informatic approaches were developed to facilitate this comparison.ResultsBlue-Native gel separation and LC/MS/MS identification revealed major differences in samples produced from endothelial cell co-culture with adherent and non-adherent parasite strains. This approach enabled us to identify protein associations seen only with the adhesion proficient parasite strain.ConclusionsThe combination of proteomic and analytical approaches has identified differences between adherent and non-adherent parasite lines in co-culture with EC, providing potential candidates for complexes or associations formed during cytoadherence involved in cell structure, signalling and apoptosis.

Doxorubicin/gold nanoparticles coated with liposomes for chemo-photothermal synergetic antitumor therapy

Hybrid liposome/metal nanoparticles are promising candidate drug-carriers for therapy of various diseases due to their unique photothermal effect. In this study, self-crystallized gold nanoparticles (Au NPs) and doxorubicin (DOX) were co-encapsulated within liposomes (Au/DOX−Lips) by thin film hydration and gel separation technology. The surface plasmon resonance bands of drug-carriers were controllable in the near-infrared (NIR) zone. When the complex liposome/metallic hybrids were irradiated by NIR light, they displayed higher endocytosis efficiency following the fracture of liposomal membranes and the release of Au NPs. Then, the Au NPs penetrated further into deeper tumor tissue to accomplish photothermal treatment. The Au/DOX−Lips showed an excellent antitumor effect, whose inhibition rate for tumor cells was up to 78.28%. In experiments on mice bearing tumors, the Au/DOX−Lips treated mice exhibited superior tumor suppression. This novel drug system provides huge potential for biomedical application.

SINTESIS DAN KARAKTERISASI SILIKA GEL DARI LIMBAH KACA SERTA APLIKASINYA PADA KROMATOGRAFI KOLOM

Silica gel synthesis from glass waste have been carried out with activation and purification method by using hydrochloride acid. Hydrochloride acid were varied 8 N, 10 N, and 12 N to observe optimum concentration in purification of silica gel and component separation in chromatography column. Gravimetric analysis result showed 12 N hydrochloride acid produce ~100 % silica. XRD and FTIR analysis revealed that synthetic gel silica was amorphous where its IR absorption bands were at 3426 cm-1, 1620 cm-1, 1080 cm-1, 772 cm-1 and 478 cm-1. The absorption bands agreed to standard gel silica and spectrum. The most effective HCl in gel silica synthesis was 12 N, caused by its ability to separate color component in a column. The synthetic silica that can be applied as stationary phase in column chromatography.

Nanoscale Electrochemical Imaging of Aligned Semiconducting and Metallic Single-Walled Carbon Nanotube Bundles

Carbon nanotubes have been studied in the variety of research fields from electronic devices to energy harvesting applications [1]. In general, their unique properties come from their ideal one-dimensional structure and tremendous metallic or semiconducting behavior depending upon their chirality. For energy application, it is an important issue to develop a good separation technique for the metallic and semiconducting single-walled carbon nanotubes (SWNTs) in large volume and to understand their electrochemical activities of both types of nanotubes. Recent progress for separation between metallic and semiconducting of has been developed. For example, a gel-based separation technique reported by Tanaka and co-workers [2]. Also, Unwin’s group has revealed the electrochemical activities for each type of the individual SWNT by scanning electrochemical cell microscopy [3]. In this study, we have at first created aligned SWNT bundles by dielectrophoresis [4] using by the commercially available suspension created by a gel separation technique. The aligned nanotube samples were prepared from either semiconducting or metallic nanotube suspension. Then, scanning electrochemical cell microscopy with a single-barrel nanopipette [5] was applied to each sample for the detection of the existence of the other property of the nanotube, referring to the difference in electrochemical activities between semiconducting and metallic nanotubes [3]. [1] M. F. L. De Volder et al., Science 339, 535, (2013). [2] T. Tanaka et al., Nano Lett. 9, 1497 (2009). [3] A. G. Guel et al., Nano Lett., 14, 220 (2014). [4] R. Krupke et al., Science 301, 344 (2003). [5] Y. Takahashi et al. Nat. Comm. 5:6450 (2014).

Hierarchically crosslinked ionic nanocomposite hydrogels with ultrahigh mechanical properties for underwater bioinspired capturing device

Various applications of nanocomposite hydrogels with a single crosslinked network have been largely limited by their poor comprehensive mechanical properties, despite their prominence in certain mechanical properties. Here, we introduce ferric ions into titania-based nanocomposite hydrogels to fabricate robust ionic nanocomposite hydrogels (INC gels) with hierarchically crosslinked networks. The introduction of ion crosslinkers into nanocomposite hydrogels dramatically improves their comprehensive mechanical properties. The mechanical attributes can be changed over wide ranges by adjusting hydrogel components and the optimal INC gel exhibits the super high strength of 13.0 MPa, elastic modulus of 26.8 MPa, and toughness of 34.3 MJ m−3. In addition, The INC gels show a good mechanical and volume stability in saline solutions due to the unique crosslinked network. The reversible phase separation in gels can be used for the achievement of the shape memory effect without significantly destroying the mechanical properties and enable the mussel shell-like hydrogel to imitate the self-protection behaviour of the mussel to grab the bead underwater. Therefore, these hydrogels will hold a great potential in underwater mechanical catching hands.

Thymopentin-loaded phospholipid-based phase separation gel with long-lasting immunomodulatory effects: in vitro and in vivo studies.

Thymopentin (TP5) is an effective immunomodulatory agent for autoimmune disease that has been used clinically for decades. However, its application is greatly limited by its extremely short half-life in vivo, poor membrane permeability and extensive metabolism in gastrointestinal tract, resulting in repeated injection and poor patient compliance. In the present study, we developed a TP5-loaded, phospholipid-based phase separation gel (PPSG) to achieve sustained drug release profile and long-lasting therapeutic effects. We firstly demonstrated the physiochemical characteristics of PPSG before and after phase transition by examining the viscosity and morphology change caused by the phase transition. Moreover, the PPSG exerted a low cytotoxicity in L929 cells and HUVECs, suggesting the biocompatibility of PPSG. A month-long drug release profile of TP5 PPSG was observed both in vitro and in vivo, revealing its sustained and controlled drug release property. Most importantly, in cyclophosphamide-induced immunosuppressive rats, a single dose of TP5 PPSG (15 mg/kg, sc) injected could normalize their T-SOD levels and CD4+/CD8+ ratio; such an immunoregulatory effect was comparable to that produced by repeated injection of TP5 solution (0.6 mg/kg per day, sc) for 14 consecutive days. Thus, TP5 PPSG has a great potential for sustained delivery of TP5 in clinical use because of its simple manufacture process, good biocompatibility and long-lasting immunomodulatory efficacy, which could greatly improve patient compliance.