Gel Separation Research Articles

Preventing the mixed detergent micelle effect in two‐dimensional electrophoresis on Tris‐Tricine gels

Application of Tris-N-[Tris(hydroxymethyl)methyl]glycine gels for 2DE is hampered by formation of mixed CHAPS-SDS micelles resulting in typical swirling pattern in the low mass range, which makes reliable quantitative and qualitative gel evaluation impossible. Modification of 2DE strip equilibration procedure prevented the direct interaction between both detergents during equilibration process, thus substantially improving gel separation.

A Practical and Novel Method to Extract Genomic DNA from Blood Collection Kits for Plasma Protein Preservation

Laboratory tests can be done on the cellular or fluid portions of the blood. The use of different blood collection tubes determines the portion of the blood that can be analyzed (whole blood, plasma or serum). Laboratories involved in studying the genetic basis of human disorders rely on anticoagulated whole blood collected in EDTA-containing vacutainer as the source of DNA for genetic / genomic analysis. Because most clinical laboratories perform biochemical, serologic and viral testing as a first step in phenotypic outcome investigation, anticoagulated blood is also collected in heparin-containing tube (plasma tube). Therefore when DNA and plasma are needed for simultaneous and parallel analyses of both genomic and proteomic data, it is customary to collect blood in both EDTA and heparin tubes. If blood could be collected in a single tube and serve as a source for both plasma and DNA, that method would be considered an advancement to existing methods. The use of the compacted blood after plasma extraction represents an alternative source for genomic DNA, thus minimizing the amount of blood samples processed and reducing the number of samples required from each patient. This would ultimately save time and resources. The BD P100 blood collection system for plasma protein preservation were created as an improved method over previous plasma or serum collection tubes(1), to stabilize the protein content of blood, enabling better protein biomarker discovery and proteomics experimentation from human blood. The BD P100 tubes contain 15.8 ml of spray-dried K2EDTA and a lyophilized proprietary broad spectrum cocktail of protease inhibitors to prevent coagulation and stabilize the plasma proteins. They also include a mechanical separator, which provides a physical barrier between plasma and cell pellets after centrifugation. Few methods have been devised to extract DNA from clotted blood samples collected in old plasma tubes(2-4). Challenges from these methods were mainly associated with the type of separator inside the tubes (gel separator) and included difficulty in recovering the clotted blood, the inconvenience of fragmenting or dispersing the clot, and obstruction of the clot extraction by the separation gel. We present the first method that extracts and purifies genomic DNA from blood drawn in the new BD P100 tubes. We compare the quality of the DNA sample from P100 tubes to that from EDTA tubes. Our approach is simple and efficient. It involves four major steps as follows: 1) the use of a plasma BD P100 (BD Diagnostics, Sparks, MD, USA) tube with mechanical separator for blood collection, 2) the removal of the mechanical separator using a combination of sucrose and a sterile paperclip metallic hook, 3) the separation of the buffy coat layer containing the white cells and 4) the isolation of the genomic DNA from the buffy coat using a regular commercial DNA extraction kit or a similar standard protocol.

Association of aldosterone synthase (CYP11B2) gene −344T/C polymorphism with the risk of primary chronic glomerulonephritis in the Polish population

We evaluate whether angiotensinogen AGT M235T (rs699), angiotensin-converting enzyme ACE (I/D) (rs4646994) and aldosterone synthase CYP11B2 -344C/T (rs1799998) polymorphisms can be genetic risk factors of chronic glomerulonephritis (GN) in the Polish population. The study was conducted in 140 patients with primary chronic GN: mesangial proliferative GN (MesPGN) (n = 49), IgA nephropathy (IgAN) (n = 31), membranous nephropathy (MN) (n = 27), focal segmental glomerulosclerosis (FSGS) (n = 25), membranoproliferative GN (MPGN) (n = 4), and minimal change disease (MCD) (n = 4), and controls (n = 187). Genotypes were determined by HRM curve analysis for AGT M235T, by PCR and agarose gel separation for ACE (I/D), and by PCR-RFLP for CYP11B2 -344C/T. We found a significant association of the CYP11B2 -344C/T polymorphism in the recessive model with all subtypes of GN (OR = 1.925 (95% CI = 1.152-3.219, p = 0.0118, p(corr) = 0.0354)). We also observed that the CYP11B2 -344C/T polymorphism in the recessive model may also be an independent significant risk factor of IgAN (OR = 2.743 (95% CI = 1.219-6.172, p = 0.0122, p(corr) = 0.0366)), FSGS (OR = 2.895 (95% CI = 1.200-6.985, p = 0.0145, p(corr) = 0.0435)), and all proliferative GNs (MesPGN, IgAN, MPGN) (OR = 2.171 (95% CI = 1.211-3.894, p = 0.0084, p(corr) = 0.0252)). Our results suggest that the CYP11B2 -344C/T polymorphism might be an independent risk factor of IgAN, FSGS and all proliferative chronic GNs.

Quality Impact on Diagnostic Blood Specimen Collection Using a New Device to Relieve Venipuncture Pain

A new device called Buzzy(®) has been recently presented that combines a cooling ice pack and a vibrating motor in order to relieve the venipuncture pain. The aim of this study was to evaluate the impact of Buzzy(®) use during diagnostic blood specimen collection by venipuncture for routine immunochemistry tests. Blood was collected from 100 volunteers by a single, expert phlebotomist. A vein was located on the left forearm without applying tourniquet, in order to prevent any interference from venous stasis, and blood samples were collected using a 20-G straight needle directly into 5mL vacuum tubes with clot activator and gel separator. In sequence, external cold and vibration by Buzzy(®) was applied on the right forearm-5cm above the chosen puncture site-for 1min before venipuncture and continued until the end of the same procedure already done in the left forearm. The panel of tests included the following: glucose, total cholesterol, HDL-cholesterol, triglycerides, total protein, albumin, c-reactive protein, urea, creatinine, uric acid, alkaline phosphatase, amylase, AST, ALT, g-glutamyltransferase, lactate dehydrogenase, creatine kinase, total bilirubin, phosphorus, calcium, magnesium, iron, sodium, potassium, chloride, lipase, cortisol, insulin, thyroid-stimulating hormone, total triiodothyronine, free triiodothyronine, total thyroxine, free thyroxine and haemolysis index. Clinically significant differences between samples were found only for: total protein, albumin and transferrin. The Buzzy(®) can be used during diagnostic blood specimens collection by venipuncture for the majority of the routine immunochemistry tests. We only suggest avoiding this device during blood collection when protein, albumin and transferrin determinations should be performed.

Perfil hematológico, bioquímico sérico, proteína C reativa e cortisol de ararajubas (Guaroba guarouba) mantidas em cativeiro

Objetivou-se determinar os valores hematológicos, bioquímicos séricos, proteína C reativa e cortisol de 14 ararajubas (Guaroba guarouba) clinicamente saudáveis mantidas em cativeiro no zoológico do Parque Estadual de Dois Irmãos Recife/PE. Amostras de sangue foram obtidas da veia jugular com volume médio de 0,8ml, fracionando em duas porções, a primeira depositada em tubo MiniCollect®CE contendo EDTA e a outra tubo com gel separador, para a separação do soro sanguíneo. Os indicadores bioquímicos e PCR foram determinados através do analisador ARCHITECT c8000. O cortisol foi analisado no Cobas E411 da Roche. Para a determinação dos números de eritrócitos e leucócitos, foi utilizada a metodologia da contagem em câmara de Neubauer. O hematócrito foi avaliado pelo método do microhematócrito e a hemoglobina pelo método da cianometahemoglobulina. Para a contagem diferencial de leucócitos, foi utilizada a técnica de Shilling. Os índices hematimétricos (VCM, HCM E CHCM) foram determinados com os valores encontrados na série eritrocítica. Os dados foram caracterizados por dispersão de freqüências, utilizando-se as seguintes medidas de tendência central: Média, desvio-padrão, mediana e percentil de 25 e percentil 75. A determinação de alguns parâmetros como ferro, triglicerídeos, PCR e cortisol foram identificados como sendo pioneiramente referenciados nesta espécie de ave. Os dados são apresentados como sendo de referência para a ararajuba (Guaroba guarouba) criada em cativeiro em condições similares de manejo e higidez e ainda pode contribuir para os trabalhos de conservação ex situ desta espécie.

Avoidance to wipe alcohol before venipuncture is not a source of spurious hemolysis

BackgroundIt is still uncertain whether or not avoidance to let disinfectant alcohol dry at the site of venipuncture is a source of spurious hemolysis when drawing venous blood.Methods:In a consecutive series of 52 outpatients referred for routine laboratory testing, venous blood was drawn by direct venipuncture with (odd group) or without (pair group) wiping 70% isopropyl alcohol at the site of venipuncture. A 3.5 mL evacuated tube with clot activator and gel separator was drawn from a vein of the upper limb, serum was immediately separated with standard centrifugation and tested for potassium, lactate dehydrogenase (LD), aspartate aminotransferase (AST) and hemolysis index (HI) on Roche Cobas.Results:No specimen was discarded for unsatisfactory venipuncture. No differences for age and gender were observed between groups. As regards the four parameters investigated, no significant differences could be observed between patients in whom blood was drawn with or without letting the alcohol dry. It is also noteworthy that no sample in both groups exceeded the conventional sample rejection threshold of cell-free hemoglobin.Conclusions:The results of our prospective, randomized study attest that failure to wipe alcohol at the site of venipuncture should not be considered as a potential source of spurious hemolysis when drawing blood.

Incorrect order of draw could be mitigate the patient safety: a phlebotomy management case report

Procedures involving phlebotomy are critical for obtaining diagnostic blood specimens and represent a well known and recognized problem, probably among the most important issues in laboratory medicine. The aim of this report is to show spurious hyperkalemia and hypocalcemia due to inadequate phlebotomy procedure. The diagnostic blood specimens were collected from a male outpatient 45 years old, with no clinical complaints. The tubes drawing order were as follows: i) clot activator and gel separator (serum vacuum tube), ii) K3EDTA, iii) a needleless blood gas dedicated-syringe with 80 I.U. lithium heparin, directly connected to the vacuum tube holder system. The laboratory testing results from serum vacuum tube and dedicated syringe were 4.8 and 8.5 mmol/L for potassium, 2.36 and 1.48 mmol/L for total calcium, respectively. Moreover 0.15 mmol/L of free calcium was observed in dedicated syringe. A new blood collection was performed without K3EDTA tube. Different results were found for potassium (4.7 and 4.5 mmol/L) and total calcium (2.37 and 2.38 mmol/L) from serum vacuum tube and dedicated syringe, respectively. Also free calcium showed different concentration (1.21 mmol/L) in this new sample when compared with the first blood specimen. Based on this case we do not encourage the laboratory managers training the phlebotomists to insert the dedicated syringes in needle-holder system at the end of all vacuum tubes. To avoid double vein puncture the dedicated syringe for free calcium determination should be inserted immediately after serum tubes before EDTA vacuum tubes.

A reverse membrane emulsification process based on a hierarchically porous monolith for high efficiency water–oil separation

A hierarchically porous monolith with macro- and meso-pores was synthesized via a sol–gel and phase separation process. Due to the surface modification by organic silanes, the wettability of the silica material was effectively controlled. A series of hydrophobic porous silica monoliths (HPSM) were obtained. Using a “reverse membrane emulsification” process, the HPSM not only cleared oil away from water, but also broke the micro-emulsion efficiently, even when emulsion stabilizer was in the system. As the filtration layer, 1.0 g of HPSM could treat 944 mL of oil containing water or 667 mL of surfactant-stabilized micro-emulsion. HPSM materials could remove at maximum 96.5% of the oil in water and 100% surfactant in the micro-emulsion. In addition, the material could be reused through a simple treatment. The excellent separating effect was kept even after 8 times of regeneration. Special selectivity, easy operation and excellent recyclability make the material have great potential for practical application.

Frequency of Macroprolactinemia in Hyperprolactinemic Women Presenting with Menstrual Irregularities, Galactorrhea, and/or Infertility: Etiology and Clinical Manifestations

Aim. To determine the frequency of macroprolactinemia, its etiology, and the clinical manifestations in patients with hyperprolactinemia presenting with menstrual irregularities, galactorrhea, and/or infertility who were attended by the gynecology-endocrinology service. Methods. In a cross-sectional study, 326 hyperprolactinemic women were tested for serum prolactin (PRL) concentrations before and after chromatographic separation (gel filtration and affinity with protein G) and extraction of free PRL with polyethylene glycol (PEG). Results. Sera from 57 patients (17.5%) were found to have macroprolactinemia. The presence of macroprolactinemia was attributable to anti-PRL autoantibodies in 54 (94.7%) patients. The median serum PRL levels were similar in patients with or without macroprolactinemia (42.0 versus 38.1 ng/mL). In contrast, patients with macroprolactinemia had lower serum-free PRL levels (median 9.2 versus 31.7 ng/mL, P < 0.001). Patients without macroprolactinemia had a higher frequency of galactorrhea and abnormal pituitary imagine findings (P < 0.002). Conclusions. We can conclude that macroprolactinemia should be considered as a benign variant, and it must be ruled out in women presenting with menstrual irregularities, galactorrhea, and/or infertility in order to investigate other causes different than hyperprolactinemia. Serum PRL precipitated with PEG is a convenient and simple procedure to screen for the presence of macroprolactinemia.

Fractionation of ethylcellulose oleogels during setting

The use of ethylcellulose (EC) polymers as a means to structure edible oils for fat replacement is beginning to show great promise and the use of these 'oleogels' has recently been shown to be feasible in food products. These gels are very versatile, as the mechanical properties can be tailored by altering either the fatty acid profile of the oil component, or the viscosity or concentration of the polymer component. Here we report the observation that certain formulation of EC oleogels tend to separate into two distinct phases; a soft interior core surrounded by a firm exterior sheath. It was found that the extent of this effect depends on EC viscosity, and can also be induced through the addition of certain surfactants, such as sorbitan monostearate and sorbitan monooleate, though not by glycerol monooleate. Although the two visually distinct regions were shown to be chemically indistinct, the cooling rate during gel setting was found to play a large role; rapid setting of the gels reduces the fractionation effect, while slow cooling produced a completely homogeneous structure. In addition, by reheating only the soft region of the gel, a firm and soft fractionated gel could again be produced. Finally, it was observed that oleogels prepared with castor oil or mineral oil have the ability to remove or induce the gel separation, respectively. Taken together, these results indicate chemical interactions may incite the separation into two distinct phases, but the process also seems to be driven by the cooling conditions during gel setting. These findings lend insight into the EC-oleogel gelation process and should provide a stepping stone for future research into the manufacturing of these products.

Impact of Blood Sample Collection and Processing Methods on Glucose Levels in Community Outreach Studies

Glucose obtained from unprocessed blood samples can decrease by 5%–7% per hour due to glycolysis. This study compared the impact of glucose degradation on measured glucose values by examining two different collection methods. For the first method, blood samples were collected in tubes containing sodium fluoride (NaF), a glycolysis inhibitor. For the second method, blood samples were collected in tubes containing a clot activator and serum gel separator and were centrifuged to separate the serum and plasma 20 minutes after sample collection. The samples used in the two methods were collected during the same blood draw and were assayed by the clinical laboratory 2–4 hours after the samples were obtained. A total of 256 pairs of samples were analyzed. The average glucose reading for the centrifuged tubes was significantly higher than the NaF tubes by 0.196 ± 0.159 mmol/L (P < 0.01) or 4.2%. This study demonstrates the important role collection methods play in accurately assessing glucose levels of blood samples collected in the field, where working environment may be suboptimal. Therefore, blood samples collected in the field should be promptly centrifuged before being transported to clinical labs to ensure accurate glucose level measurements.

Rheological properties of low fat yogurt containing cress seed gum

Yogurt—a milk based mix fermented by lactic acid bacteria is a valuable health food for both young and old. Milk is the main ingredient of yogurt. However, most yogurts contain additional solids such as milk solids nonfat to boost the nonfat milk solids. Stabilizers such as natural gums are added to improve and maintain gel firmness and consistency, while also for many people to improve appearance and mouth feel. Hydrocolloidsspecifically stabilize gel structure, increaseviscosity and either from networks with milk constituents and establish a separate gel structure. In current research, a natural local plant Iranian hydrocolloid, cress seed gum, is added to yogurt formulation and its rheological propertiesare evaluated using a rotational viscometer. Different famous rheological models have beenused to fit shear stress-shear rate data’s. The results demonstrated that cress seed gum has a good potential to be used as a stabilizer in yogurt formula.

Photopatterned free-standing polyacrylamide gels for microfluidic protein electrophoresis

Designed for compatibility with slab-gel polyacrylamide gel electrophoresis (PAGE) reagents and instruments, we detail development of free-standing polyacrylamide gel (fsPAG) microstructures supporting electrophoretic performance rivalling that of microfluidic platforms. For the protein electrophoresis study described here, fsPAGE lanes are comprised of a sample reservoir and contiguous separation gel. No enclosed microfluidic channels are employed. The fsPAG devices (120 μm tall) are directly photopatterned atop of and covalently attached to planar polymer or glass surfaces. Leveraging the fast <1 h design-prototype-test cycle - significantly faster than mold based fabrication techniques - we optimize the fsPAG architecture to minimize injection dispersion for rapid (<1 min) and short (1 mm) protein separations. The facile fabrication and prototyping of the fsPAGE provides researchers a powerful tool for developing custom analytical assays. We highlight the utility of assay customization by fabricating a polyacrylamide gel with a spatial pore-size distribution and demonstrate the resulting enhancement in separation performance over a uniform gel. Further, we up-scale from a unit separation to an array of 96 concurrent fsPAGE assays in 10 min run time driven by one electrode pair. The fsPAG array layout matches that of a 96-well plate to facilitate integration of the planar free standing gel array with multi-channel pipettes while remaining compatible with conventional slab-gel PAGE reagents, such as staining for label-free protein detection. Notably, the entire fsPAGE workflow from fabrication, to operation, and readout uses readily available materials and instruments - making this technique highly accessible.

Sodium chloride concentration on the rheological and dynamic properties of aloe vera gel

Aloe vera gel is a highly medicinal gel which is in high demand in the cosmetics and pharmaceutical industry. Mathematical models were developed to simulate the rheological and dynamic properties of aloe vera gel in relation to the addition of sodium chloride (NaCl – common salt) at various concentrations. The result from the investigation shows the effect of sodium chloride concentration on the density, viscosity, shear rate, shear stress and flow concentration of the aloe vera gel; hence, giving the manufacturers of aloe vera products an insight and awareness of aloe vera gel rheology and dynamic properties. The mucilaginous fluid samples were obtained from aloe vera bardadensis miller leaves, washed and wiped dry and mechanical analysis were conducted on the samples for the purpose of separation of aloe juice and aloe gel from the sample. Increase in the concentration of sodium chloride result to a change in the concentration of aloe vera gel mixture (viscosity and density). The result obtained from the analysis revealed the sudden change in aloe versa gel concentration alongside with rheological and dynamic characteristics of the aloe vera gel mixture were attributed to increase in salt added. The developed models obtained from the investigation were found useful in monitoring and predicting the quality of aloe vera products. Key words: Modeling, sodium chloride concentration, rheology, dynamic property, aloe vera products.

In-Gel Nonspecific Proteolysis for Elucidating Glycoproteins: A Method for Targeted Protein-Specific Glycosylation Analysis in Complex Protein Mixtures

Determining protein-specific glycosylation in protein mixtures remains a difficult task. A common approach is to use gel electrophoresis to isolate the protein followed by glycan release from the identified band. However, gel bands are often composed of several proteins. Hence, release of glycans from specific bands often yields products not from a single protein but a composite. As an alternative, we present an approach whereby glycans are released with peptide tags allowing verification of glycans bound to specific proteins. We term the process in-gel nonspecific proteolysis for elucidating glycoproteins (INPEG). INPEG combines rapid gel separation of a protein mixture with in-gel nonspecific proteolysis of protein bands followed by tandem mass spectrometry (MS) analysis of the resulting N- and O-glycopeptides. Here, in-gel digestion is shown for the first time with nonspecific and broad specific proteases such as Pronase, proteinase K, pepsin, papain, and subtilisin. Tandem MS analysis of the resulting glycopeptides separated on a porous graphitized carbon (PGC) chip was achieved via nanoflow liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (nano-LC/Q-TOF MS). In this study, rapid and automated glycopeptide assignment was achieved via an in-house software (Glycopeptide Finder) based on a combination of accurate mass measurement, tandem MS data, and predetermined protein identification (obtained via routine shotgun analysis). INPEG is here initially validated for O-glycosylation (κ casein) and N-glycosylation (ribonuclease B). Applications of INPEG were further demonstrated for the rapid determination of detailed site-specific glycosylation of lactoferrin and transferrin following gel separation and INPEG analysis on crude bovine milk and human serum, respectively.

Proteomic Identification of Matrix Metalloproteinase Substrates in the Human Vasculature

Matrix metalloproteinases (MMPs) play a key role in cardiovascular disease, in particular aneurysm formation and plaque rupture. Surprisingly, little is known about MMP substrates in the vasculature. We used a proteomics approach to identify vascular substrates for 3 MMPs, 1 of each of the 3 major classes of MMPs: Human arteries were incubated with MMP-3 (a member of stromelysins), MMP-9 (considered a gelatinase), and MMP-14 (considered a member of the collagenases and of the membrane-bound MMPs). Candidate substrates were identified by mass spectrometry based on increased release from the arterial tissue on digestion, spectral evidence for proteolytic degradation after gel separation, and identification of nontryptic cleavage sites. Using this approach, novel candidates were identified, including extracellular matrix proteins associated with the basement membrane, elastic fibers (emilin-1), and other extracellular proteins (periostin, tenascin-X). Seventy-four nontryptic cleavage sites were detected, many of which were shared among different MMPs. The proteomics findings were validated by immunoblotting and by digesting recombinant/purified proteins with exogenous MMPs. As proof-of-principle, results were related to in vivo pathology by searching for corresponding degradation products in human aortic tissue with different levels of endogenous MMP-9. The application of proteomics to identify MMP targets is a new frontier in cardiovascular research. Our current classification of MMPs based on few substrates is an oversimplification of a complex area of biology. This study provides a more comprehensive assessment of potential MMP substrates in the vasculature and represents a valuable resource for future investigations.

Succinate dehydrogenase assembly factor 2 is needed for assembly and activity of mitochondrial complex II and for normal root elongation in Arabidopsis

Mitochondria complex II (succinate dehydrogenase, SDH) plays a central role in respiratory metabolism as a component of both the electron transport chain and the tricarboxylic acid cycle. We report the identification of an SDH assembly factor by analysis of T-DNA insertions in At5g51040, a protein with unknown function that was identified by mass spectrometry analysis as a low abundance mitochondrial protein. This gene is co-expressed with a number of genes encoding mitochondrial proteins, including SDH1-1, and has low partial sequence similarity to human SDHAF2, a protein required for flavin-adenine dinucleotide (FAD) insertion into SDH. In contrast to observations of other SDH deficient lines in Arabidopsis, the sdhaf2 line did not affect photosynthetic rate or stomatal conductance, but instead showed inhibition of primary root elongation with early lateral root emergence, presumably due to the low SDH activity caused by the reduced abundance of SDHAF2. Both roots and leaves showed succinate accumulation but different responses in the abundance of other organic acids and amino acids assayed. Isolated mitochondria showed lowered SDH1 protein abundance, lowered maximal SDH activity and less protein-bound flavin-adenine dinucleotide (FAD) at the molecular mass of SDH1 in the gel separation. The short root phenotype and SDH function of sdhaf2 was fully complemented by transformation with SDHAF2. Application of the SDH inhibitor, malonate, phenocopied the sdhaf2 root architecture in WT. Whole root respiratory assays showed no difference between WT and sdhaf2, but micro-respirometry of the tips of roots clearly showed low oxygen consumption in sdhaf2 which could explain a metabolic deficit responsible for root tip growth.

Stability of AMH measurement in blood and avoidance of proteolytic changes

The new Gen II assay for anti-Müllerian hormone (AMH) shows good stability and reliability in serum, but analyses of stability in whole blood are lacking. Testing the effects of storage of whole-blood samples at room temperature revealed significant increases in the measured value of AMH of 31% over 4days (P<0.001). The effect is temperature dependent, with storage at 4°C showing markedly reduced increments. Further, samples collected into serum tubes with gel separators and centrifuged within 5h (blood cells and serum physically separated within the collection tube) showed reliable stability over a period of more than 5days.

Abstract 19380: Cardiac Contractile Protein Expression of the Right Ventricle in End Stage Human Heart Failure

Objectives: Little is known about right ventricular (RV) remodeling in human end-stage heart failure (HF). We sought to study RV contractile protein expression in HF. Methods: Western Blot (WB) analyses were performed on protein samples prepared from the RV and left ventricle (LV) free walls of 10 explanted human hearts (5 ischemic, ISC; 5 non-ischemic, N-ISC) and two normal (NOR) donor hearts. Tissues were homogenized in lysis buffer, subjected to electrophoresis gel separation and immune-blotted with antibodies against Myosin Heavy Chain 7 (MHC), Myosin Light Chain 3 (MLC), Troponin I type 3 (TNI), Tropomyosin 1 alpha (TRP), alpha Actinin-2 (ACT) and Desmin (DSM). GAPDH served as an internal loading control. The fluorescent intensity of reactive bands was detected by Li-Cor and band densities were quantified using Image Studio software. Results: We previously identified distinct RV and LV proteomic signatures in ISC in HF and confirmed these results by WB (Figure 1). In this study focused on the RV alone, we compared contractile protein expression in NOR, ISC and N-ISC RV (Figure 2). Expression of MHC and TNI was decreased and expression of MLC, TRP and DSM increased in both ISC and N-ISC RV compared to NOR. Expression of ACT was decreased in N-ISC RV but increased in ISC RV compared to NOR. Conclusions: RV contractile proteins exhibit distinctive expression patterns in human ISC and N-ISC HF compared to normal expression patterns in controls. In HF, RV expression of MLC and TRP is significantly increased and RV expression of MHC is significantly decreased. ACT RV expression is decreased only N-ISC HF.

A versatile cis-blocking and trans-activation strategy for ribozyme characterization

Synthetic RNA control devices that use ribozymes as gene-regulatory components have been applied to controlling cellular behaviors in response to environmental signals. Quantitative measurement of the in vitro cleavage rate constants associated with ribozyme-based devices is essential for advancing the molecular design and optimization of this class of gene-regulatory devices. One of the key challenges encountered in ribozyme characterization is the efficient generation of full-length RNA from in vitro transcription reactions, where conditions generally lead to significant ribozyme cleavage. Current methods for generating full-length ribozyme-encoding RNA rely on a trans-blocking strategy, which requires a laborious gel separation and extraction step. Here, we develop a simple two-step gel-free process including cis-blocking and trans-activation steps to support scalable generation of functional full-length ribozyme-encoding RNA. We demonstrate our strategy on various types of natural ribozymes and synthetic ribozyme devices, and the cleavage rate constants obtained for the RNA generated from our strategy are comparable with those generated through traditional methods. We further develop a rapid, label-free ribozyme cleavage assay based on surface plasmon resonance, which allows continuous, real-time monitoring of ribozyme cleavage. The surface plasmon resonance-based characterization assay will complement the versatile cis-blocking and trans-activation strategy to broadly advance our ability to characterize and engineer ribozyme-based devices.