High Salt Buffer Research Articles

CABS1 Is Essential for Progressive Motility and the Integrity of Fibrous Sheath in Mouse Epididymal Spermatozoa.

The calcium-binding protein spermatid-associated 1 (CABS1) localizes to the principal piece of mature sperm flagella. Deletion of CABS1 results in subfertility in male mice, possibly due to an impaired annulus in the sperm flagella. However, it is unknown whether there are other mechanisms by which CABS1 affects male fertility. Our current investigation has uncovered that CABS1 is located in the midsection of the flagellum in testicular sperm and the principal piece in epididymal sperm. Moreover, male mice lacking CABS1 exhibit a defect in the progressive motility of sperm. Furthermore, the regulation of calcium levels, which has been reported to have a significant impact on sperm motility, capacitation, and the acrosome reaction, is also affected when sperm are exposed to alkalized high-salt buffer (pH 8.0) and progesterone (100 μM) in Cabs1-null spermatozoa. This alteration in calcium response may contribute to changes in the phosphorylation of PKA substrates and subsequent phosphorylation of tyrosine residues. Additionally, the absence of CABS1 leads to a defective fibrous sheath and abnormal configuration of doublet microtubules in post-testicular sperm. These findings indicate that the absence of CABS1 also disrupts the structural integrity of the fibrous sheath, resulting in male subfertility. The highly conserved nature of CABS1 in humans suggests that it could potentially be a contributing factor to asthenozoospermia in men.

Purification of hepatitis C virus core protein in non-denaturing condition

Hepatitis C virus (HCV) is the major cause of chronic hepatitis and hepatocellular carcinoma. Among its structural proteins, the HCV core protein has been implicated in liver disease. Understanding the role of HCV core proteins in viral diseases is crucial to elucidating disease mechanisms and identifying potential drug targets. However, purification challenges hinder the comprehensive elucidation of the structure and biochemical properties of HCV core proteins. In this study, we successfully solubilized bacterially expressed core protein using a high-salt and detergent-containing buffer and bypassed the denaturing-refolding process. Size-exclusion chromatography revealed three distinct peaks in the HCV-infected cell lysate, with the bacterially expressed soluble core protein corresponding to its second peak. Using a combination of affinity, size exclusion, and multi-modal chromatography purification techniques, we achieved a purity of > 95% for the core protein. Analytical ultracentrifugation revealed monomer formation in the solution. Far UV Circular dichroism spectroscopy identified 25.53% alpha helices and 20.26% beta sheets. These findings strongly suggest that the purified core proteins retained one of the native structures observed in HCV-infected cells.

Alternative direct-to-amplification cell lysis techniques for forensically relevant non-sperm cells.

While efforts have been made to reduce the pervasive backlog of sexual assault evidence collection kits, the actual laboratory process remains very time-consuming due to the requirement of a differential lysis step before DNA purification, as well as intricate mixture analysis towards the end of the DNA workflow. Recently, an alternative, direct-to-amplification sperm lysis method (using 1 M NaOH) was identified. However, a direct cell lysis method for non-sperm cells has not been identified yet. Thus, the primary objective of this work was to find an alternative method that is quick, inexpensive, and does not require multiple purification steps for the lysis of non-sperm cells in sexual assault samples. In this study, vaginal swab samples were lysed with the control method, prepGEM™, as well as six alternative reagents: alkaline buffer with 25-200 mM NaOH, high-salt stain extraction buffer, modified radioimmunoprecipitation assay (RIPA) buffer, mammalian protein extraction reagent (M-PER™), digitonin buffer, and urea/thiourea buffer. Quantification using Quantifiler® Trio of vaginal and semen lysates revealed that the alkaline (25 mM NaOH) and M-PER™ methods were efficient for the lysis of vaginal epithelial cells without substantial sperm cell lysis. Following quantification, analysis of STR profiles from vaginal lysates revealed that the M-PER™ method showed promising results across all metrics examined, including the percentage of detected STR alleles, mean peak heights, peak height ratio, and interlocus balance. Thus, this method was recommended as an alternative to the traditional differential lysis method for non-sperm cells given its ability to produce amplification-ready lysates without any DNA purification step.

Simple two-step purification and characterisation of peroxidase from Citrullus colocynthis

Peroxidase is a biotechnologically important enzyme. The purification of peroxidase from the root of Citrullus colocynthis was carried out in a simple two-step process with maximum purity level. The sample was extracted in a high salt buffer, and the enzyme was partially purified with a Q-Sepharose anion exchange column. Final purification was carried out with HighLoad 16/600 Superdex G-75 column. The purified protein was analysed with SDS gel electrophoresis, which suggested a single band of approximately 35 kDa. Further, the enzyme was identified with the help of Mass spectrometric analysis using an ESI-QTOF Mass spectrometer. The study will be helpful for the isolation and its commercial uses in biotechnology.

Monoclonal Antibody Purification with Reduced Turbidity by using High-salt Elution Buffer During Protein a Chromatography

During purification of monoclonal antibodies, viral inactivation/removal step is a mandatory step to comply with the regulatory guidelines which commonly performs at low pH about 3.5 and further neutralizes it to a pH about 7.0. Neutralization of monoclonal antibodies results formation of high turbidity which is troublesome for further processing such as filtration and other chromatography processes and it eventually leads to filter clogging and increases column back pressure. In this work, we propose a new optimized process of affinity chromatography (Protein A) by using a high salt elution buffer which reduces turbidity more than 80%. A systematic study of different concentration of salts were analysed and it reveals that salt concentration greater than 100mM in Protein A elution buffer reduces turbidity during neutralization of monoclonal antibodies when compared to low salt concentration of elution buffer. We also found that elution of monoclonal antibodies during Protein A chromatography at pH 3.5 results higher reduction of turbidity compared to pH 3.0. These findings provide both cost and time effective for large scale production of monoclonal antibodies as it eliminates the use of multiple filters throughout the purification process.

Silica reinforced core-shell quorum quenching beads to control biofouling in an MBR

Quorum quenching (QQ) is a strategy to alleviate membrane biofouling in membrane bioreactors (MBRs). As a stable inorganic material with a large specific surface area, silica is often used to prepare of microbial immobilization composites. This study selected two different sizes of silica materials (silica beads and Nano-silica) to make the core encapsulate a QQ bacterial strain (Rhodococcus sp. BH4). The compressive strength and stability under extreme environments were characterized, and the positive effect of silica on QQ beads was verified. The results showed that both QQ beads could resist the impact of high pressure, acid, alkali, salt and EDTA buffer. It was proved that they have the potential to quench effectively continuously. Both beads were still more than 70 % QQ activity after five months of use. In the lab-scale continuous MBR experiment, the time of transmembrane pressure (TMP) reaching 50 kPa in both experimental groups was more than 3 times that in the blank group. The TMP contamination time was extended from 5 to 6 days in the blank group to 18–19 days. Among them, silica beads greatly improve the compressive strength of the beads, and also have a better performance in QQ.

Generation of Ions from Aqueous Taylor Cones near the Minimum Flow Rate: "True Nanoelectrospray" without Narrow Capillary.

Generating ultrafine charged droplets using electrospray is crucial for attaining high ionization efficiency for mass spectrometry. The size of the precursor charged droplets depends on the spray flow rate, and conventional wisdom holds that an electrospray of a nL/min flow rate (nanoelectrospray) is only possible using narrow capillaries with an inner diameter of ∼1 μm or smaller. Here, the electrospray of aqueous solutions with high electric conductivities generated from a large off-line capillary of 0.4 mm i.d. has been performed using a high-pressure ion source. The electric discharge is avoided by operating the ion source at 2.5 bar gauge pressure. The highly stable Taylor cone can be tuned to a near-hydrostatic state that exhibits the "true nanoelectrospray" properties, i.e., high salt tolerance and minimal ion suppression. The Q1/2 scaling law describing the electrospray current I and flow rate Q is found to be valid down to the nanoflow regime under a condition that is free of electric discharge. For a given solution, the flow rate and the size of the initial droplets and ionization species can be controlled with the spray current as the indicator for the instantaneous flow rate without changing the emitter capillary of different sizes. In regard to the application, the nanoelectrospray with a large micropipette tip is easy to use, free of clogging when dealing with viscous and high-salt buffer solutions, and with reduced surface interaction with the emitter inner surface. An acquisition of very clean mass spectra of proteins from concentrated solutions of nonvolatile salts such as phosphate-buffered saline is demonstrated.

On-Site Biolayer Interferometry-Based Biosensing of Carbamazepine in Whole Blood of Epileptic Patients.

On-site monitoring of carbamazepine (CBZ) that allows rapid, sensitive, automatic, and high-throughput detection directly from whole blood is of urgent demand in current clinical practice for precision medicine. Herein, we developed two types (being indirect vs. direct) of fiber-optic biolayer interferometry (FO-BLI) biosensors for on-site CBZ monitoring. The indirect FO-BLI biosensor preincubated samples with monoclonal antibodies towards CBZ (MA-CBZ), and the mixture competes with immobilized CBZ to bind towards MA-CBZ. The direct FO-BLI biosensor used sample CBZ and CBZ-horseradish peroxidase (CBZ-HRP) conjugate to directly compete for binding with immobilized MA-CBZ, followed by a metal precipitate 3,3′-diaminobenzidine to amplify the signals. Indirect FO-BLI detected CBZ within its therapeutic range and was regenerated up to 12 times with negligible baseline drift, but reported results in 25 min. However, Direct FO-BLI achieved CBZ detection in approximately 7.5 min, down to as low as 10 ng/mL, with good accuracy, specificity and negligible matric interference using a high-salt buffer. Validation of Direct FO-BLI using six paired sera and whole blood from epileptic patients showed excellent agreement with ultra-performance liquid chromatography. Being automated and able to achieve high throughput, Direct FO-BLI proved itself to be more effective for integration into the clinic by delivering CBZ values from whole blood within minutes.

Introducing an SPRi-based titration assay using aptamers for the detection of Legionella pneumophila

Legionella are waterborne bacteria and the causative agents behind a severe respiratory disease known as Legionnaires Disease (LD). Standard ISO-certified methods to detect Legionella (plate count and qPCR) are time-consuming and tedious necessitating the development of novel detection strategies. This study introduces an SPRi-based titration assay that uses L. pneumophila (Lp) aptamers. Multiple parameters including buffer conditions, aptamer concentrations, complementary aptamer probe (cApt) concentrations and incubation times were investigated and evaluated for optimal signal response. For maximum hybridization efficiency on the sensor surface, high salt buffer (SSC) as well 500 nM of immobilized cApt resulted in a maximum signal response. Additionally, it was observed that of the three buffers (PBS, Fraquil, SSC) tested in this assay only SSC facilitated incremental binding of aptamers to Lp such that varying concentrations of Lp could be determined. We were able to detect varying concentrations of Lp down to a limit of 104 cells/ml without any sample processing or signal amplification steps, highlighting the potential of this system for SPRi-based Lp detection. The assay is also specific to Lp and shows negligible detection of Pseudomonas, a common inhabitant of water systems.

Orthogonal pre-use and post-use efficiency testing for single-use anion exchange chromatography

Three efficiency tests for single-use AEX chromatography devices have been developed and applied to six capsule formats of a new, salt tolerant, single-use AEX product. All the tests have been designed to be performed with simple equipment and common reagents. By performing each of the three tests on undamaged capsules and capsules intentionally damaged with small defects, in tandem with Phi-X174 challenges in a high-salt buffer, relationships between test results and viral clearance have been obtained. A pre-use pressure-based installation verification test is simply performed during equilibration of the device and effective at identifying gross bypass defects, for example, due to internal seal breakage. Passing outcomes of a post-use installation validation bubble point test are associated with ≥ 5 log reduction value (LRV) of viral clearance. A new, non-destructive, pre-use AEX capacity test involves challenging the device with chloride ions and is orthogonal to the other two tests in that it can detect chemical defects, as well as mechanical ones. Passing outcomes of this test correspond to > 2 LRV viral clearance and provide in situ assurance of the expected AEX dynamic capacity prior to use. Selection of a pair of pre-use and post-use tests can provide robust risk reduction with respect to viral clearance by single-use AEX devices in biopharmaceutical purifications.

Effects of Extraction Buffer on the Solubility and Immunoreactivity of the Pacific Oyster Allergens

Despite recent technological advances, novel allergenic protein discovery is limited by their low abundance, often due to specific physical characteristics restricting their recovery during the extraction process from various allergen sources. In this study, eight different extraction buffers were compared for their ability to recover proteins from Pacific oyster (Crassostrea gigas). The protein composition was investigated using high resolution mass spectrometry. The antibody IgE-reactivity of each extract was determined using a pool of serum from five shellfish-allergic patients. Most of the investigated buffers showed good capacity to extract proteins from the Pacific oyster. In general, a higher concentration of proteins was recovered using high salt buffers or high pH buffers, subsequently revealing more IgE-reactive bands on immunoblotting. In contrast, low pH buffers resulted in a poor protein recovery and reduced IgE-reactivity. Discovery of additional IgE-reactive proteins in high salt buffers or high pH buffers was associated with an increase in allergen abundance in the extracts. In conclusion, increasing the ionic strength and pH of the buffer improves the solubility of allergenic proteins during the extraction process for oyster tissue. This strategy could also be applied for other difficult-to-extract allergen sources, thereby yielding an improved allergen panel for increased diagnostic efficiency.

Anti-C1q Autoantibodies: Standard Quantification and Innovative ELISA.

Autoantibodies against complement C1q (anti-C1q) are an excellent marker for active nephritis in SLE patients. Here, we describe a typical protocol for the quantification of anti-C1q using immobilized C1q (important for the presentation of relevant cryptic epitopes) and a high salt buffer for the incubation steps (to prevent immune-complex binding to intact C1q). More recently, a linear epitope on the C1q A chain, that is targeted by anti-C1q, has been described (A08). The assay using this peptide seems to be more specific and more sensitive for the detection of active nephritis in SLE patients than theconventional anti-C1q assay, but further studies are required to establish the role of anti-A08 of C1q in the clinical routine.

Effectiveness of antibody specific for heat-processed milk proteins and incurred calibrants for ELISA-based quantification of milk in dark chocolate matrices

Although undeclared milk is prevalent in chocolate products, processing-induced alterations of milk proteins and matrix composition prevent reliable quantification of this allergen by current enzyme-linked immunosorbent assays (ELISA). High affinity antibodies (Abs) are required to detect milk protein epitopes that may be modified by manufacturing procedures. We therefore developed an Ab specific for heat-processed milk proteins (HPMP), which might allow enhanced milk quantification in processed complex matrices, including chocolate. When characterizing HPMP-Ab by immunoblot analysis, greater signal intensities were observed with heat modified proteins. Using a sandwich (s)-ELISA, HPMP-Ab reacted with high affinity to purified major milk proteins, proteins extracted from milk-derived ingredients and reference materials subjected to several thermal processing procedures. Milk-incurred cookies (0–17.7 ppm) and tempered dark chocolate samples (62% cacao: 0–134 ppm; 100% cacao: 0–75 ppm) were assessed using HPMP-Ab in a revised s-ELISA. To optimize protein extraction, samples were defatted with hexane; cookies were then extracted using a high salt buffer (HSB)/1% Tween (T)-20 while chocolate samples were extracted using HSB/1%T-20/5% polyvinylpyrrolidone (PVP)/1% fish gelatin. Despite reliable detection of milk proteins using incurred cookies and tempered 62% dark chocolate samples, as shown by acceptable dynamic ranges of the HPMP-Ab binding curves, high baseline absorbance/background persisted using 100% dark chocolate samples. The HPMP-Ab ELISA was highly specific; no cross reactivity was observed when testing a broad range of food commodities using incurred cookies as calibrants. The HPMP-Ab demonstrated the capacity to detect declared milk proteins in products containing a variety of milk-derived ingredients and undeclared milk proteins in products with precautionary labeling when used to analyze chocolate market samples (up to 85% cacao). Milk proteins were also detected in cross-contact samples produced on equipment used to manufacture milk chocolate, utilizing tempered 62% dark chocolate samples as calibrants. Our results establish the benefits of using HPMP-Ab and matrix-specific incurred calibrants for milk quantification in chocolate matrices by ELISA.

Directed co-evolution of interacting protein–peptide pairs by compartmentalized two-hybrid replication (C2HR)

Directed evolution methodologies benefit from read-outs quantitatively linking genotype to phenotype. We therefore devised a method that couples protein–peptide interactions to the dynamic read-out provided by an engineered DNA polymerase. Fusion of a processivity clamp protein to a thermostable nucleic acid polymerase enables polymerase activity and DNA amplification in otherwise prohibitive high-salt buffers. Here, we recapitulate this phenotype by indirectly coupling the Sso7d processivity clamp to Taq DNA polymerase via respective fusion to a high affinity and thermostable interacting protein–peptide pair. Escherichia coli cells co-expressing protein–peptide pairs can directly be used in polymerase chain reactions to determine relative interaction strengths by the measurement of amplicon yields. Conditional polymerase activity is further used to link genotype to phenotype of interacting protein–peptide pairs co-expressed in E. coli using the compartmentalized self-replication directed evolution platform. We validate this approach, termed compartmentalized two-hybrid replication, by selecting for high-affinity peptides that bind two model protein partners: SpyCatcher and the large fragment of NanoLuc luciferase. We further demonstrate directed co-evolution by randomizing both protein and peptide components of the SpyCatcher–SpyTag pair and co-selecting for functionally interacting variants.

Transcriptional Profiling of CD8+ CMV-Specific T Cell Functional Subsets Obtained Using a Modified Method for Isolating High-Quality RNA From Fixed and Permeabilized Cells.

Previous studies suggest that the presence of antigen-specific polyfunctional T cells is correlated with improved pathogen clearance, disease control, and clinical outcomes; however, the molecular mechanisms responsible for the generation, function, and survival of polyfunctional T cells remain unknown. The study of polyfunctional T cells has been, in part, limited by the need for intracellular cytokine staining (ICS), necessitating fixation and cell membrane permeabilization that leads to unacceptable degradation of RNA. Adopting elements from prior research efforts, we developed and optimized a modified protocol for the isolation of high-quality RNA (i.e., RIN > 7) from primary human T cells following aldehyde-fixation, detergent-based permeabilization, intracellular cytokines staining, and sorting. Additionally, this method also demonstrated utility preserving RNA when staining for transcription factors. This modified protocol utilizes an optimized combination of an RNase inhibitor and high-salt buffer that is cost-effective while maintaining the ability to identify and resolve cell populations for sorting. Overall, this protocol resulted in minimal loss of RNA integrity, quality, and quantity during cytoplasmic staining of cytokines and subsequent flourescence-activated cell sorting. Using this technique, we obtained the transcriptional profiles of functional subsets (i.e., non-functional, monofunctional, bifunctional, polyfunctional) of CMV-specific CD8+T cells. Our analyses demonstrated that these functional subsets are molecularly distinct, and that polyfunctional T cells are uniquely enriched for transcripts involved in viral response, inflammation, cell survival, proliferation, and metabolism when compared to monofunctional cells. Polyfunctional T cells demonstrate reduced activation-induced cell death and increased proliferation after antigen re-challenge. Further in silico analysis of transcriptional data suggested a critical role for STAT5 transcriptional activity in polyfunctional cell activation. Pharmacologic inhibition of STAT5 was associated with a significant reduction in polyfunctional cell cytokine expression and proliferation, demonstrating the requirement of STAT5 activity not only for proliferation and cell survival, but also cytokine expression. Finally, we confirmed this association between CMV-specific CD8+ polyfunctionality with STAT5 signaling also exists in immunosuppressed transplant recipients using single cell transcriptomics, indicating that results from this study may translate to this vulnerable patient population. Collectively, these results shed light on the mechanisms governing polyfunctional T cell function and survival and may ultimately inform multiple areas of immunology, including but not limited to the development of new vaccines, CAR-T cell therapies, and adoptive T cell transfer.

Lyse-Reseal Erythrocytes for Transfection of Plasmodium falciparum

Simple and efficient transfection methods for genetic manipulation of Plasmodium falciparum are desirable to identify, characterize and validate the genes with therapeutic potential and better understand parasite biology. Among the available transfection techniques for P. falciparum, electroporation-based methods, particularly electroporation of ring-infected RBCs is routinely used. Nonetheless, transfection of P. falciparum remains a resource-intensive procedure. Here, we report a simple and economic transfection method for P. falciparum, which is termed as the lyse-reseal erythrocytes for transfection (LyRET). It involved lysis of erythrocytes with a hypotonic RBC lysis buffer containing the desired plasmid DNA, followed by resealing by adding a high salt buffer. These DNA-encapsulated lyse-reseal erythrocytes were mixed with P. falciparum trophozoite/schizont stages and subjected to selection for the plasmid-encoded drug resistance. In parallel, transfections were also done by the methods utilizing electroporation of DNA into uninfected RBCs and parasite-infected RBCs. The LyRET method successfully transfected 3D7 and D10 strains with different plasmids in 63 of the 65 attempts, with success rate similar to transfection by electroporation of DNA into infected RBCs. The cost effectiveness and comparable efficiency of LyRET method makes it an alternative to the existing transfection methods for P. falciparum, particularly in resource-limited settings.

Truncated TALE-FP as DNA Staining Dye in a High-salt Buffer

Large DNA molecules are a promising platform for in vitro single-molecule biochemical analysis to investigate DNA-protein interactions by fluorescence microscopy. For many studies, intercalating fluorescent dyes have been primary DNA staining reagents, but they often cause photo-induced DNA breakage as well as structural deformation. As a solution, we previously developed several fluorescent-protein DNA-binding peptides or proteins (FP-DBP) for reversibly staining DNA molecules without structural deformation or photo-induced damage. However, they cannot stain DNA in a condition similar to a physiological salt concentration that most biochemical reactions require. Given these concerns, here we developed a salt-tolerant FP-DBP: truncated transcription activator-like effector (tTALE-FP), which can stain DNA up to 100 mM NaCl. Moreover, we found an interesting phenomenon that the tTALE-FP stained DNA evenly in 1 × TE buffer but showed AT-rich specific patterns from 40 mM to 100 mM NaCl. Using an assay based on fluorescence resonance energy transfer, we demonstrated that this binding pattern is caused by a higher DNA binding affinity of tTALE-FP for AT-rich compared to GC-rich regions. Finally, we used tTALE-FP in a single molecule fluorescence assay to monitor real-time restriction enzyme digestion of single DNA molecules. Altogether, our results demonstrate that this protein can provide a useful alternative as a DNA stain over intercalators.

Isolation of Poly(A)+ Messenger RNA Using Magnetic Oligo(dT) Beads.

This is a general protocol for the isolation of mRNA from total RNA using oligo(dT) coupled to magnetic beads. First, total RNA is dissolved in a high-salt buffer and heated briefly to 65°C-70°C, followed by immediate cooling on ice to disrupt secondary structures. The RNA is subsequently annealed to the oligo(dT)-magnetic beads at room temperature; the high-salt binding buffer stabilizes the poly(A)-oligo(dT) complexes. A high-salt washing buffer is then used to wash away unbound RNAs while retaining oligo(dT)-bound poly(A)+ mRNAs. To elute the poly(A)+ mRNAs from the beads, a low-salt buffer (or water) is used to destabilize the poly(A)-oligo(dT) complexes. Alternatively, poly(A)+ mRNAs can be retained on the beads for downstream applications (e.g., solid-phase cDNA synthesis).

Buffer C (High-Salt Nuclear Extraction Buffer)

Buffer C (High-Salt Nuclear Extraction Buffer)

Standardization of DNA extraction protocol and screening of begomovirus in chilli and tomato plants

Extraction of high-quality genomic DNA is an important requisite for a number of molecular- and genome-based studies. Isolation of good quantity and quality of genomic DNA from plant materials is a major concern for molecular biologists as many of them contain large amount of polysaccharides, phenolics and secondary metabolites. The presence of polyphenols and polysaccharides in plants results in a brown–dark brown-coloured, contaminated DNA which is sticky and viscous in nature. In our present study, we performed DNA isolation from two plants (tomato and chilli) using Dellaporta, modified CTAB, phenanthroline-based, CaCl2-based DNA extraction protocols (with and without high-salt Tris-EDTA buffer treatment). For chilli plants, Dellaporta method with high-salt TE buffer treatment was found to be better than other methods, and for tomato plants modified CTAB and phenanthroline-based methods without high-salt TE treatment were better. To further confirm the applicability, total DNA was isolated from 99 chilli samples using Dellaporta method with high-salt TE treatment. The plants were then screened for geminivirus and 49 were found to be positive. Furthermore, one of the PCR products of Deng primer was cloned and analysis of the clones showed the presence of insert, thus confirming the applicability of the DNA extraction method for detection of virus, PCR and cloning.