Buffer Flow Research Articles

The cardioprotective potential of soluble urokinase Plasminogen Activator Receptor (suPAR) in myocardial ischemia

Abstract Background and aims: Increased circulating soluble urokinase plasminogen activator receptor (suPAR) levels are associated with adverse cardiovascular outcomes, however, any cardiovascular-related functions remain unknown. This study aimed to (i) document haemodynamic profiles in isolated rat hearts under the influence of suPAR, and to (ii) explore any mechanisms triggered by suPAR following myocardial ischaemia-reperfusion. Methods We undertook a 4-pronged approach (Figure 1). A Langendorff isolated rat heart model was used to perfuse all hearts with Krebs-Henseleit solution flowing retrogradely through the aorta at 37°C. A balloon inserted into the left ventricle allowed measurements of ventricular pressure, and a pressure transducer placed above the aorta recorded perfusion pressure for coronary flow rates. The experimental protocol consisted an initial 30-minute stabilisation period, followed by 40 minutes of ischemia via buffer flow cessation. Hearts were subsequently recovered during 90 minutes of reperfusion, receiving either suPAR treatment or perfusion buffer as controls. An inhibitor arm comprising co-infusion of suPAR and a monoclonal antibody capable of binding to suPAR was also assessed. Troponin T was measured in outflow perfusates collected at specific intervals. Proteins from hearts in treatment groups were separated using gel electrophoresis, with Western blotting to visualise the phosphorylation status of kinases (Akt, STAT). High-flow respirometry and fluorometry were investigated in cardiac mitochondria to determine respiration rates and ATP production in ischaemia reperfusion under the influence of suPAR. Statistical analysis was conducted with ANOVA using SPSS. Results Hearts receiving suPAR infusion at reperfusion (n = 16) showed a significant increase in developed pressure (p = .017) and lower perfusion pressure (p = .02) compared to controls (n = 16), revealing that suPAR-treated hearts recovered with better contractility and vasodilatory properties post-ischaemia. suPAR’s haemodynamic profiles in the antibody group were similar to controls, attenuating suPAR-induced effects (n = 8). Outflow effluents in suPAR-treated hearts obtained >3 fold lower serial Troponin T values than controls (p < .001). Heart tissues receiving suPAR treatment revealed a 1.7-fold increase in Akt (p = .001) and a 3.8-fold increase in STAT3 phosphorylation compared to controls (p < .001) and the inhibitor group (p = .04). Finally, suPAR increased mitochondrial ATP production by 28% (p = .013) compared to controls after ischaemia. Conclusion This is a world-first demonstration of suPAR’s cardioprotective influences in isolated rat hearts recovering from ischaemia. suPAR’s ability to promote cardiac contractility and vasodilation was associated with lesser injury as shown by Troponin T reduction. Mechanistically, suPAR infusion upregulated two key cardioprotective pathways, which may also function to protect cardiac mitochondria.Figure 1 - Schematic of Methods

B-026 Transforming PCR protocols in pandemic response with automated non-contact liquid dispensing

Abstract Background During the COVID-19 pandemic, effective Polymerase Chain Reaction (PCR) protocols were crucial for detecting SARS-CoV-2 in clinical samples, playing a key role in rapid infection control and easing the strain on healthcare services. However, with the critical need for fast and accurate pathogen surveillance, the manual execution of PCR workflows presented numerous challenges, including limited throughput, risk of human error and variability, and risk to human health. Several automated liquid handling systems from a range of vendors were considered to prepare extraction plates for this process. Ultimately, RFL decided on dragonfly® discovery, a non-contact positive displacement dispenser. Methods The analytical sensitivity for the UltraDx SARS-CoV-2 N1/N2/RP assay was evaluated by the RFL development team using RNA extracted from a panel of virus inputs from a Qnostics Analytical Q Panel, Product Number: SCV2AQP. Samples were extracted using a modified RNA extraction procedure for Thermo MagMax reagents and consumables with dragonfly discovery. dragonfly discovery was utilized to distribute a combination of inactivation buffer and beads into a 96-well kingfisher flex plate. This process was accomplished using a peristaltic pump and a 6-way Auto Feed Reservoir (AFR) to ensure a constant buffer flow. Simultaneously, the AFR ensured that the beads were kept in constant suspension, resulting in precise dispensing across all wells. The EPCR assay, UltraDx SARS-CoV-2 N1/N2/RP assay (LGC, Biosearch Technologies), utilized two CDC-characterized amplicon primer sets alongside two additional probes using fluorescence-based (FAM dye) detection. The input RNA extracted from clinical samples was combined with RT-PCR reaction mixes, before the reaction arrays were amplified. The reactions were then measured by a single scan on a multi-channel fluorescence reader. Results The UltraDx SARS-CoV-2 N1/N2/RP assay (when performed using the manufacturer method and in the absence of dragonfly discovery) has an LoD of 80 copies per reaction for the N1 assay, and 20 copies per reaction for the N2 assay, across 20 replicates for each copy number tested. Using the same/equivalent reagents and control materials, inclusion of dragonfly discovery showed an LoD of 70 copies/mL (0.9 copies/reaction) sensitivity when compared to the LoD suggested by the manufacture. Conclusions Integrating dragonfly discovery into the UltraDx SARS-CoV-2 N1/N2/RP assay led to an 80-fold reduction in the limit of detection for the N1 assay compared to the reagent manufacturer's recommendation. Some of this improvement can be attributed to dragonfly discovery's non-contact positive displacement dispensing, coupled with the AFR pump mechanism that ensures a continuous suspension of magnetic beads, enhancing accuracy and precision. dragonfly discovery's versatility supports a robust business-as-usual (BAU) process and is easily scalable for pandemic-level testing. Its user-friendly software interface requires zero computer programming knowledge, providing end-users with the flexibility to run multiple protocols on the same instrument, making it ideal for BAU assay processing. The instrument played a pivotal role in the UltraDx SARS-CoV-2 N1/N2/RP assay conducted by UKHSA during the pandemic, and SPT Labtech will continue to support UKHSA in their mission to protect communities from the impact of health threats.

Genetic algorithm optimization of langevin thermostat and thermal properties of graphene-aluminum nanocomposites: a molecular dynamics

Abstract The thermal properties of a laminated structure of graphene-coated aluminum composite nanomaterial were investigated through non-equilibrium molecular dynamics (NEMD) simulations to address the problem of temperature deviation in the thermostat volume applied. This paper presents a new insight into the best values of timestep and Langevin thermostat damping parameters for each atom in the nanomaterial with different size configurations using the genetic algorithm (GA) method by considering the timestep and thermostat damping parameters for each atom type, as well as the thickness of the nanomaterial, the thermostat, buffer, and heat flow lengths. The initial population results indicate that the thermostat temperature deviation increases with higher thermostat damping coefficients and timestep. However, the deviation decreases significantly with increased heat flow and thermostat lengths. Variations in buffer length and aluminum thickness do not have a significant effect on temperature. The application of a GA for optimization leads to a decrease in thermostat temperature deviation. The optimized parameters resulted in better thermostat temperature deviations when analyzing the temperature, aluminum thickness, and both buffer and thermostat lengths. Additionally, the thermal conductivity of aluminum-graphene nanomaterial decreases with increasing temperature, buffer length, and aluminum thickness, but increases by up to 9.85% with increasing thermostat length.

Stability Indicating RP-HPLC Method for Posaconazole Assay Using QbD Approach.

The development and optimization of analytical techniques utilizing the quality by design methodology is essential in the pharmaceutical industry. This approach helps in the direction of identifying and optimizing critical parameters during drug development and assesses their impact on key quality attributes. A stability-indicating RP-HPLC method was developed for quantifying posaconazole in bulk and tablet forms utilizing the quality-by-design approach. The Box-Behnken design optimized buffer flow rate, organic modifier percentage, and temperature, affecting retention time, theoretical plate count, and symmetry factor. Chromatography was performed on a Symmetry C18 column with a mobile phase of 0.01N potassium dihydrogen phosphate and acetonitrile (57.4:42.6% v/v), at a flow rate of 1.11 mL/min, detection at 220 nm, and column temperature of 30°C. Posaconazole’s retention time was 3.663 minutes, with precise, accurate, and linear signals (R² = 0.999). The method is simple, fast, cost-effective, and ideal for routine quality control.

Stability-Indicating HPLC Method for Quantifying Process-Related Impurities in Fedratinib and Identification of Its Forced Degradation Products Using LC-MS/MS

Background: Pharmaceutical industry is characterized by rigorous quality standards to ensure the safety and efficacy of drugs. Despite stringent manufacturing processes, the presence of impurities or generation of degradation products (DPs) in pharmaceutical products remains a concern. This necessitates a comprehensive and systematic approach to analysis impurities and DPs. Objectives: This study deals with the optimization of the stable HPLC method for quantification of fedratinib impurities and its DPs characterization through LC-MS/MS. Method: Method optimization studies were conducted by analyzing standard solutions in various method parameters. The results noticed in every varied method condition were tabulated for finalizing the appropriate conditions for analyzing fedratinib. The mass spectral response of DPs was interpreted carefully for structural conformation of DPs. Results: The method is optimized as HIQSIL C18 (250mm×4.6mm;5µ) column employing 1.0 mL/min flow of phosphate buffer (pH 5.2) and acetonitrile in 45:65 (v/v) and 257 nm. This method elutes 5.4, 2.6, 9.2 and 3.5 min for fedratinib, impurity 1, 2 and 3 respectively. Method sensitivity was verified to be very sensitive that can evaluate up to 0.003, 0.015 and 0.004 µg/mL for impurity 1, 2 and 3 respectively. Well correlated calibration curve achieved in 50-200 µg/mL for fedratinib and 0.05-0.20 µg/mL for impurities. Various stress studies produce four stress DPs and were identified using LC-MS/MS. The molecular mass (g/mol) and formula of DPs were identified as 426 and C21H25N5O3S, 312 and C17H22N5O, 354 and C17H14N4O3S, 215 and C11H11N4O respectively for DP 1 to 4. Conclusion: The method proposed can successfully be helpful for quantifying the pharmaceutical impurities and DPs of fedratinib in bulk batch samples and formulations.

Investigation of a microfluidic free-flow electrophoresis chip of glass substrate with integrated indium tin oxide electrodes

Free-flow electrophoresis (FFE) is a unique form of electrophoresis that allows continuous electrophoresis separation. Small scale FFE is very practical for processing of limited amounts of samples for analytical purposes. In this work, glass substrate was designed as a chip FFE and its performance was visually demonstrated and characterized using fluorescent probes. The chip consisted of two pieces of glass substrate. One of them was patterned with a planar indium tin oxide (ITO) electrodes, and the other glass was designed with inlets for sample infusion and electrolyte transfer. The depth of the separation channel (15 × 60 mm) is defined by a tape spacer of 85 μm. Since the integrated ITO electrodes in direct contact with the working solution in the separation channel, a voltage as high as 600 V can be applied without bubbling problems. The main operation factors such as buffer concentration, pH, voltage, and flow rate were optimized to separate the probes, and the results were compared with capillary electrophoresis. The role of EOF and electrolysis was also discussed. Compared to photolithographic wet etching, this design is easier to implement, and it enables effective FFE operation. This chip FFE system has potential application in processing and cell sorting.

LC and LC-MS/MS Studies for Identification and Characterisation of Related Substances and Degradation Products of Abrocitinib

In the pharmaceutical industry, Related Substances (RCs), impurities or Degradation Products (DPs) are associated with the Active Pharmaceutical Ingredient (API) in the final drug product. These compounds must be within permissible limits for safe therapeutic use for consumers. Hence there is a need to quantify these compounds using an appropriate analytical method. No method is reported in the literature for quantification of these compounds in abrocitinib which is a medical drug prescribed to treat severe atopic dermatitis in adults. This study includes the optimisation of stability indicating the HPLC method for resolution and subsequent quantification of abrocitinib RCs and structural characterisation of stressinduced DPs of abrocitinib. The method was optimised by varying mobile phase solvents, pH, flow rate and wavelength of the detector. The finalised conditions were validated and applied for the resolution and evaluation of stress-induced DPs. The stress was induced in abrocitinib pure drug HCl (0.1M), NaOH (0.1M), hydrogen peroxide (3%), 80°C in an air oven and 254nm in a UV chamber. The generated DPs were structurally characterised with the LCMS experiment. Abrocitinib and DPs along with known RCs were resolved on ACE Ultra Core Super C18 250mm column using 0.9mL/min gradient flow of methanol (Solvent A), acetonitrile and buffer (Solvent B). The resolved compounds were detected through a UV detector at 295nm and a mass detector at NMR positive mode. The method identifies 5.85min, 3.13min, 6.60min and 4.38min respectively for abrocitinib, related compounds 1 to 3 respectively with acceptable system suitability. A very high correlate (< 0.999) linear graph was achieved within 5 to 30 μg/mL concentration level for abrocitinib and 0.05 to 0.3μg/ mL for related compounds. Three DPs with molecular mass and formula of C10H13N5 (203.2 g/mol), C11H14N4 (202.2 g/mol) and C13H19N5O2S (309.3 g/mol) in acid-induced stress study and two DPs of C12H21N5O2S (299.3 g/mol) and C11H19N5O2S (285.3 g/mol) in peroxide-induced stress study and one DP of C10H14N4 (190.2 g/mol) in base induced stress study were successfully characterised. The method proposed in this study can effectively resolve unknown degradation products, and known related compounds along with abrocitinib and is hence applicable for quality control analysis of abrocitinib.

Abstract 7495: Validation of microfluidic isolation of circulating pancreatic tumor cells from blood

Abstract Background. Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis and is the fourth leading cause of cancer-related deaths in the US. PDAC is diagnosed in the late stages, which limits treatment options and yields poor clinical outcomes. Recurrence is a significant issue for patients undergoing surgery for PDAC. Circulating tumor cells (CTCs) are thought to be a potential mediator of recurrence, facilitating the formation of secondary tumor sites after surgery. Thus, there is a need to isolate CTCs to improve understanding of disease recurrence, to ultimately improve outcomes. Herein, we aim to validate our inertial microfluidic (iMF) system for isolating pancreatic CTCs from blood. We also benchmark our iMF system to a commercially available immunomagnetic negative selection system, EasySep™, and quantify target cell recovery and cell enrichment. Methods. Our iMF system employs the differential cell sizes of CTCs from blood cells and inertial migration of such cells in a straight microchannel (150 µm × 50 µm × 24 mm) to enrich CTCs from blood. The iMF system sample flow rate used is 100 µL/min, with a 200 µL/min PBS buffer flow rate. The EasySep™ Direct Human CTC Enrichment kit targets CD2, CD14, CD16, CD19, CD45, CD61, CD66b, and Glycophorin to remove blood cells from the sample using magnetic particles, thereby separating them from CTCs. We spiked low cell concentrations of 50, 100, and 500 Hoechst-stained pancreatic carcinoma cells, PANC1, in 1 mL of healthy blood then captured using either EasySep™ or iMF. Cell enumeration was performed after centrifugation or Cytospin. Results. PANC1 cells and WBCs have average sizes of 18 µm and 8.4 µm, respectively. We characterized our iMF device to capture cells ≥ 12 µm, which yields capture of most PANC1 cells. Indeed, our iMF system achieved 82.8±19.2%, 72.5±16.3%, and 59.3±3.8% recovery for 50, 100, and 500 cell-spikes in lysed blood, respectively. For the same 50, 100, and 500 cell-spikes, the total iMF CTC yields after Cytospin were 46.3±11.8, 44.3±9.1, and 32.7±2.1%, while the total CTC yields from EasySep™ were 4.6±3, 5.3±2.1, 8.3±1%, respectively. When we processed whole blood directly, EasySep™ had lower cell recovery, 3.8±0.2, 4.6±1, and 3.3±0.4%, respectively. Our system also demonstrated 8 × higher target cell enrichment compared to EasySep™. Blood lysis before iMF separation did not drastically affect the recovery of target cells. Conclusions. We determined that our system has improved performance over the commercial isolation system, EasySep™, thereby validating the effectiveness of microfluidic isolation for PDAC. In future studies, we can then use our iMF system in CTC isolation from routine blood draws from PDAC patients undergoing surgical resection. We may then isolate real patient samples and study relevant phenotypes of PDAC CTCs which may therefore be used for identifying certain mechanisms of PDAC progression. Citation Format: Celine Macaraniag, Ifra Khan, Jian Zhou, Pier Cristoforo Giulianotti, Alain Borgeat, Gina Votta-Velis, Ian Papautsky. Validation of microfluidic isolation of circulating pancreatic tumor cells from blood [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7495.

High-throughput selection of sperm with improved DNA integrity and rapidly progressive motility using a butterfly-shaped chip compared to the swim-up method.

Microfluidics provides unique opportunities for the high throughput selection of motile sperm with improved DNA integrity for assisted reproductive technologies (ARTs). Here, through a parametric study on dimensions and geometrical angles, a butterfly-shaped chip (BSC) is presented to isolate sperm with high progressive motility and intact DNA at a separation rate of 1125 sperm per minute. Using finite element simulations, the flow field and shear rates in the device were optimized to leverage the inherent motility characteristics of sperm for maximum selection throughput. The device incorporates a triple selection mechanism in series, initially activating sperm rheotaxis by rotation against the semen flow, penetrating the counter buffer flow and swimming against the direction of the buffer flow, leaving dead cells and debris behind, and subsequently leveraging boundary-following behavior to direct progressively motile sperm to swim along the walls and reach the device outlet. The device selects over 4.1 million sperm per mL within 20 minutes, with 29.2%, 68.2%, and 57.3% improvement in total motility, DNA integrity, and velocity parameter (VCL), as compared with the conventional swim-up method, respectively. Overall, the performance of the device to separate sperm with approximately 95.9% total motility, 97.8% viability, and 96.6% DNA integrity at high concentrations demonstrates its potential for enhancing the efficiency of conventional treatment methods.

Interaction of Staphylococcus aureus and Candida albicans with surface-modified silica studied by ultra-high frequency acoustic wave biosensor.

In this work the bacteria S. aureus and fungi C. albicans were allowed to interact with quartz-based biosensor devices under different flow rates, with and without an anti-fouling coating. These experiments were conducted in order to determine if the level of fouling observed was affected by the flow rate. The biosensor used was an ultra-high frequency acoustic wave device (EMPAS) for investigation of device surface initial interaction of S. aureus or C. albicans under flow of PBS buffer at flow rates between 50 and 200 μL min-1. Surface-bound microbes were also visualized by fluorescence microscopy following these experiments. S. aureus bacteria was able to foul the bare quartz sensors at each flow rate tested, with the greatest degree of fouling observed at a flow rate of 100 μL min-1. C. albicans showed far less fouling of bare devices with the maximum fouling observed at a flow rate of 75 μL min-1. Antifouling MEG-OH coated sensors showed greatly reduced fouling for S. aureus, with between a 90 and 99% reduction in observed frequency change depending on the flow rate used, and between 22 and 90% for C. albicans. Fluorescence images of the microbes following the experiments correlated well with the frequency data, showing a marked decrease in the amount of bacteria seen on MEG-OH-coated surfaces compared to controls.

Loading characteristics of streptavidin on polypropylene capillary channeled polymer fibers and capture performance towards biotinylated proteins.

The development of higher-throughput, potentially lower-cost means to isolate proteins, for a variety of end uses, is of continuing emphasis. Polypropylene (PP) capillary-channeled polymer (C-CP) fiber columns are modified with the biotin-binding protein streptavidin (SAV) to capture biotinylated proteins. The loading characteristics of SAV on fiber supports were determined using breakthrough curves and frontal analysis. Based on adsorption data, a 3-min on-column loading at a flow rate of 0.5 mL min-1 (295.2 cm h-1) with a SAV feed concentration of 0.5 mg mL-1 produces a SAV loading capacity of 1.4 mg g-1 fiber. SAV has an incredibly high affinity for the small-molecule biotin (10-14 M), such that this binding relationship can be exploited by labeling a target protein with biotin via an Avi-tag. To evaluate the capture of the biotinylated proteins on the modified PP surface, the biotinylated versions of bovine serum albumin (b-BSA) and green fluorescent protein (b-GFP) were utilized as probe species. The loading buffer composition and flow rate were optimized towards protein capture. The non-ionic detergent Tween-20 was added to the deposition solutions to minimize non-specific binding. Values of 0.25-0.50% (v/v) Tween-20 in PBS exhibited better capture efficiency, while minimizing the non-specific binding for b-BSA and b-GFP, respectively. The C-CP fiber platform has the potential to provide a fast and low-cost method to capture targeted proteins for applications including protein purification or pull-down assays.

Continuous production of gamma aminobutyric acid by engineered and immobilized Escherichia coli whole-cells in a small-scale reactor system

γ-Amino butyric acid (GABA) is a non-proteinogenic amino acid and a human neurotransmitter. Recently, increasing demand for food additives and biodegradable bioplastic monomers, such as nylon 4, has been reported. Consequently, considerable efforts have been made to produce GABA through fermentation and bioconversion. To realize bioconversion, wild-type or recombinant strains harboring glutamate decarboxylase were paired with the cheap starting material monosodium glutamate, resulting in less by-product formation and faster production compared to fermentation. To increase the reusability and stability of whole-cell production systems, this study used an immobilization and continuous production system with a small-scale continuous reactor for gram-scale production. The cation type, alginate concentration, barium concentration, and whole-cell concentration in the beads were optimized and this optimization resulted in more than 95 % conversion of 600 mM monosodium glutamate to GABA in 3 h and reuse of the immobilized cells 15 times, whereas free cells lost all activity after the ninth reaction. When a continuous production system was applied after optimizing the buffer concentration, substrate concentration, and flow rate, 165 g of GABA was produced after 96 h of continuous operation in a 14-mL scale reactor. Our work demonstrates the efficient and economical production of GABA by immobilization and continuous production in a small-scale reactor.

Effect of Flow Rate and Ionic Strength on the Stabilities of YOYO-1 and YO-PRO-1 Intercalated in DNA Molecules.

Single-molecule DNA studies have improved our understanding of the DNAs' structure and their interactions with other molecules. A variety of DNA labeling dyes are available for single-molecule studies, among which the bis-intercalating dye YOYO-1 and mono-intercalating dye YO-PRO-1 are widely used. They have an extraordinarily strong affinity toward DNA and are bright with a high quantum yield (>0.5) when bound to DNAs. However, it is still not clear how these dyes behave in DNA molecules under higher ionic strength and strong buffer flow. Here, we have studied the effect of ionic strength and flow rate of buffer on their binding in single DNA molecules. The larger the flow rate and the higher the ionic strength, the faster the intercalated dyes are washed away from the DNAs. In the buffer with 1 M ionic strength, YOYO-1 and YO-PRO-1 are mostly washed away from DNA within 2 min of moderate buffer flow.

A new fluorescence labeling method for molecular analysis of double-stranded DNA

In this study, a double-stranded DNA (dsDNA) fluorescent labeling method was developed using the fusion proteins of fluorescent protein (FP), and 7 kDa DNA-binding family members including Sso7d from Sulfolobus solfataricus, Aho7c from Acidianus hospitalis, ATSV7 from Acidianus tailed spindle virus and Sto7 from Sulfolobus tokodaii. Using this fluorescent DNA labeling method, we succeeded in single-molecule imaging of bacteriophage λDNA molecules stretched on glass surfaces. The fluorescence of the λDNA with FP fusion proteins decayed 2.4- to 6.4-fold slower than that of the typical intercalating method with SYTOX Green (SxG). In addition, the dynamic behaviors of FP-fused Aho7c-λDNA were relaxed and stretched with and without buffer flow, respectively, in microflow channels and were similar to that with typical intercalating dye, such as YOYO-1 and SxG. this fluorescent DNA labeling method. This fluorescent DNA labeling method can solve the problem of rapid fluorescence decay due to the intercalating dyes and therefore can be expected as an alternative to compound-based fluorescent dye. Thus, this study establishes FP fusion proteins as useful fluorescent DNA probes at the single-molecule level.

Stabilization of DNA fork junctions by Smc5/6 complexes revealed by single-molecule imaging.

SMC complexes play key roles in genome maintenance, where they ensure efficient genome replication and segregation. The SMC complex Smc5/6 is a crucial player in DNA replication and repair, yet many molecular features that determine its roles are unclear. Here, we use single-molecule microscopy to investigate Smc5/6's interaction with DNA. We find that Smc5/6 forms oligomers that dynamically redistribute on dsDNA by 1D diffusion and statically bind to ssDNA. Using combined force manipulation and single-molecule microscopy, we generate ssDNA-dsDNA junctions that mimic structures present in DNA repair intermediates or replication forks. We show that Smc5/6 accumulates at these junction sites, stabilizes the fork, and promotes the retention of RPA. Our observations provide a model for the complex's enrichment at sites of replication stress and DNA lesions from where it coordinates the recruitment and activation of downstream repair proteins.

Microfluidic vortex focusing for high throughput synthesis of size-tunable liposomes

Control over vesicle size during nanoscale liposome synthesis is critical for defining the pharmaceutical properties of liposomal nanomedicines. Microfluidic technologies capable of size-tunable liposome generation have been widely explored, but scaling these microfluidic platforms for high production throughput without sacrificing size control has proven challenging. Here we describe a microfluidic-enabled process in which highly vortical flow is established around an axisymmetric stream of solvated lipids, simultaneously focusing the lipids while inducing rapid convective and diffusive mixing through application of the vortical flow field. By adjusting the individual buffer and lipid flow rates within the system, the microfluidic vortex focusing technique is capable of generating liposomes with precisely controlled size and low size variance, and may be operated up to the laminar flow limit for high throughput vesicle production. The reliable formation of liposomes as small as 27 nm and mass production rates over 20 g/h is demonstrated, offering a path toward production-scale liposome synthesis using a single continuous-flow vortex focusing device.

Analysis of Tau/Nucleoporin Interactions by Surface Plasmon Resonance Spectroscopy.

Tau, a soluble and predominantly neuronal protein, is best known for its microtubule (MT)-binding function in the cytosol, where it decisively contributes to stability as well as modulation of MT dynamics. In Alzheimer's disease and other tauopathies, Tau is altered into forming intracellular neurofibrillary tangles; additionally, also a mislocalization from the cytosol to the nucleus has been observed where interactions of Tau with the nucleus become possible. Using surface plasmon resonance (SPR), it was recently shown that Tau can directly interact with certain nucleoporins (e.g., Nup98), components of the nuclear pore complex (NPC). The NPC constitutes large regulated pores in the nuclear envelope that facilitate the bidirectional exchange of proteins, nucleic acids, and other biomolecules between the inner section of the nucleus and the cytosol, the nucleocytoplasmic transport. The mechanism of Tau/Nup interactions is as yet unknown, and a systematic interaction analysis of Tau with different Nups can be of high value to decipher the molecular binding mechanism of Tau to Nups. SPR is a useful tool to analyze binding affinities and kinetic parameters in a label-free environment. While one interaction partner is immobilized on a sensor chip, the second is supplied within a constant flow of buffer. Binding of mobile molecules to immobilized ones changes the refractive index of the medium close to the sensor surface with the signal being proportional to the bound mass. In this chapter, we describe the application of the SPR technique for the investigation of Tau binding to nucleoporins.

SMC complexes can traverse physical roadblocks bigger than their ring size.

Ring-shaped structural maintenance of chromosomes (SMC) complexes like condensin and cohesin extrude loops of DNA. It remains, however, unclear how they can extrude DNA loops in chromatin that is bound with proteins. Here, we use invitro single-molecule visualization to show that nucleosomes, RNA polymerase, and dCas9 pose virtually no barrier to loop extrusion by yeast condensin. We find that even DNA-bound nanoparticles as large as 200nm, much bigger than the SMC ring size, also translocate into DNA loops during extrusion by condensin and cohesin. This even occurs for a single-chain version of cohesin in which the ring-forming subunits are covalently linked and cannot open to entrap DNA. The data show that SMC-driven loop extrusion has surprisingly little difficulty in accommodating large roadblocks into the loop. The findings also show that the extruded DNA does not pass through the SMC ring (pseudo)topologically, hence pointing to a nontopological mechanism for DNA loop extrusion.

Application of the SwitchSense Technique for the Study of Small Molecules' (Ethidium Bromide and Selected Sulfonamide Derivatives) Affinity to DNA in Real Time.

The discovery and introduction of the switchSense technique in the chemical laboratory have drawn well-deserved interest owing to its wide range of applications. Namely, it can be used to determine the diameter of proteins, alterations in their tertiary structures (folding), and many other conformational changes that are important from a biological point of view. The essence of this technique is based on its ability to study of the interactions between an analyte and a ligand in real time (in a buffer flow). Its simplicity, on the other hand, is based on the use of a signaling system that provides information about the ongoing interactions based on the changes in the fluorescence intensity. This technique can be extremely advantageous in the study of new pharmaceuticals. The design of compounds with biological activity, as well as the determination of their molecular targets and modes of interactions, is crucial in the search for new drugs and the fight against drug resistance. This article presents another possible application of the switchSense technique for the study of the binding kinetics of small model molecules such as ethidium bromide (EB) and selected sulfonamide derivatives with DNA in the static and dynamic modes at three different temperatures (15, 25, and 37 °C) each. The experimental results remain in very good agreement with the molecular dynamics docking ones. These physicochemical insights and applications obtained from the switchSense technique allow for the design of an effective strategy for molecular interaction assessments of small but pharmaceutically important molecules with DNA.

ANALYTICAL METHOD DEVELOPMENT AND VALIDATION FOR THE ESTIMATION OF CYAMEMAZINE TARTRATE IN FORMULATION BY RP-HPLC WITH STABILITY INDICATING

High-performance liquid chromatography (HPLC) technique for cyamemazine tartrate (CYMT) was developed and validated according to the International Conference on Harmonization (ICH) Q2 (R1) guidelines. The developed and validated method for estimating CYMT from a bulk and its pharmaceutical dosage form was found to be a simple, precise, accurate, fast, and stable reverse phase HPLC (RP-HPLC) approach. For chromatographic separation, a Hypersil BDS C18 (250 mm × 4.6 mm, particle size: 5 μm) column was employed with a mobile phase of methanol and buffer (80:20 v/v) flow rate at 1.0 ml/min at room temperature. For detection, a wavelength of 270 nm was utilized. With a run period of 10 min, the CYMT was eluted at 4.38 min. With a correlation coefficient (r2) of above 0.9996, and limits of detection and quantitation (LOD and LOQ) of 0.27 and 0.80 μg, respectively, the method exhibited a dynamic linear response across 30–90 μg/ml. The repeatability of batch injections for intra- and inter-assay precision and accuracy testing was likewise satisfactory. The stability of CYMT was studied under thermal, acid, alkali, and oxidation conditions, as well as photodegradation conditions. The stability of the approach is demonstrated by the presence of CYMT and its breakdown products. The recommended technique exhibited great linearity, accuracy, precision, robustness, LOD, LOQ, and system suitability within the acceptance limit. The study’s findings indicate that the method is rapid, simple, accurate, exact, and linearly stable, implying that an HPLC method for CYMT has been developed and validated, and that it may be used for routine quality control analysis.