Analytical biochemistry最新文献

Acute lymphoblastic leukemia (ALL) is a disease of lymphocyte origin predominantly diagnosed in children. While its 5-year survival rate is high, resistance to chemotherapy drugs is still an obstacle. Our aim is to determine differentially expressed genes (DEGs) related to Asparaginase, Daunorubicin, Prednisolone, and Vincristine resistance and identify potential inhibitors via docking. Three datasets were accessed from the Gene Expression Omnibus database; GSE635, GSE19143, and GSE22529. The microarray data was analyzed using R4.2.0 and Bioconductor packages, and pathway and protein-protein interaction analysis were performed. We identified 1294 upregulated DEGs, with 12 genes consistently upregulated in all four resistant groups. KEGG analysis revealed an association with the PI3K-Akt pathway. Among DEGs, 33 hub genes including MDM2 and USP7 were pinpointed. Within common genes, CLDN9 and HS3ST3A1 were subjected to molecular docking against 3556 molecules. Following ADMET analysis, three drugs emerged as potential inhibitors: Flunarizine, Talniflumate, and Eltrombopag. Molecular dynamics analysis for HS3ST3A1 indicated all candidates had the potential to overcome drug resistance, Eltrombopag displaying particularly promising results. This study promotes a further understanding of drug resistance in ALL, introducing novel genes for consideration in diagnostic screening. It also presents potential inhibitor candidates to tackle drug resistance through repurposing.

Through the utilization of fluorescence spectroscopy, electrochemical, and molecular docking methods, this research investigates the interaction between the antihistamine drug desloratadine and calf thymus double-stranded DNA (ct-dsDNA). Deoxyguanosine (dGuo) and deoxyadenosine (dAdo) oxidation signals were diminished by incubation with varying concentrations of desloratadine, as determined by differential pulse voltammetry (DPV). This change was ascribed to desloratadine's binding mechanism to ct-dsDNA. The binding constant (K_b) between desloratadine and ct-dsDNA was determined to be 2.2 × 10⁵ M⁻¹ throughout electrochemical experiments. In order to further develop our comprehension of the interaction mechanism between desloratadine and ct-dsDNA, a series of spectroscopic experiments and molecular docking simulations were conducted. The K_b value was found to be 8.85 × 10⁴ M⁻¹ at a temperature of 25 °C by the use of fluorescence spectroscopic techniques. In summary, the utilization of electrochemical and spectroscopic techniques, alongside molecular docking investigations, has led to the prediction that desloratadine has the capability to interact with ct-dsDNA by groove binding.

Mutational study is a cornerstone methodology in biochemistry and genetics, and many mutagenesis strategies have been invented to promote the efficiency of gene engineering. In this study, we developed a simple and timesaving approach to integrate simultaneous mutagenesis at discrete sites. By using plasmid as a template and compatible oligonucleotide primers per the QuikChange strategy, our method was able to introduce multiple nucleotide insertions, deletions and replacements in one round of polymerase chain reaction. The longest insertion and deletion were achieved with 28 bp and 16 bp mismatch respectively. For minor nucleotide replacements (mismatch no more than 4 bp), mutations were achieved at up to 4 discrete locations. Usually, a successful clone with all desired mutations was found by screening 5 colonies. Clones with a subset of mutations may be stocked into the library of mutants or used as templates in the next rounds of mutagenic PCR to accomplish the entire construction project. This method can be applied to build up a combinatory library of mutants through saturation mutagenesis at multiple sites. It is promising to facilitate the research of protein biochemistry, forward genetics and synthetic biology.

Data are presented demonstrating that absorbance detection can be used during high-speed sedimentation velocity analytical ultracentrifugation (hs-SV-AUC) experiments to characterize the size distribution of adeno-associated virus (AAV) drug products accurately. Advantages and limitations of being able to use this detector in this specific type of SV-AUC experiment are discussed.

Objective

The objective of this research is to develop two methodologies, Enzymatic recombinase amplification (ERA) and Polymerase Chain Reaction (PCR) coupled with Lateral Flow Dipstick (LFD), for the swift authentication of Gastrodia elata.

Methodology

Primers and nfo probes for the ERA of Gastrodia elata were developed based on the ITS2 genome sequences of Gastrodia elata and its counterfeits. Specific primers for the PCR analysis of Gastrodia elata were generated using the NCBI (National Center for Biotechnology Information) online platform. Through experimental validation, the optimal reaction system and conditions for both methodologies were established, and their efficacy was assessed.

Results

The methodologies developed herein are applicable for the targeted analysis of the medicinal species, Gastrodia elata. The sensitivity of the ERA-LFD detection method matched that of the conventional PCR-LFD approach, recorded at 1 ng μL⁻¹. Consistency was observed in the results across three replicates of visualization test strips for both techniques. Upon evaluation, both the PCR-LFD and ERA-LFD methods demonstrated a total compliance rate of 100 %.

Conclusion

The ERA-LFD and PCR-LFD methods facilitate reduced detection times and offer visual results. These techniques are particularly effective for on-site detection and quality control in the authentication of Gastrodia elata within traditional Chinese medicine markets and at the primary level of healthcare provision.

Nasal ions environment plays a crucial role in maintaining nasal physiology and supports olfactory transmission. Addressing the limited research on nasal ion levels and their association with olfactory function, paper-based sensors were developed for determination of sodium, potassium, calcium and chloride in the nasal mucus of healthy volunteers and patients with olfactory dysfunction. Multi-walled carbon nanotubes and carbon quantum dots from beetroot were incorporated into paper substrate where sensors were designed with ion association complexes for sodium, potassium, calcium and chloride enhancing the recognition sensing capabilities. The sensors composition was optimized, including ion-exchange materials and plasticizers, to enhance sensitivity and selectivity. The performance of the sensors is evaluated based on Nernstian slope, dynamic range, detection limit and response time. Selectivity of the sensors was tested and the results demonstrated high selectivity for the target ions. The sensors were successfully determined sodium, potassium, calcium and chloride levels in nasal mucus of healthy volunteers and patients with olfactory dysfunction. The results revealed elevated calcium levels in patients with olfactory dysfunction, highlighting associated diagnostic implications. This suggests that the proposed sensors could serve as a diagnostic tool for olfactory evaluation, particularly in resource-constrained settings where access to advanced diagnostic tools is limited.

With the rise in extreme weather due to global warming, coupled with globalization facilitating the spread of infectious diseases, there's a pressing need for portable testing platforms offering simplicity, low cost, and remote transmission, particularly beneficial in resource-limited and non-urban areas. We have developed a portable device using loop-mediated isothermal amplification (LAMP) with spectrometric detection to identify Salmonella Typhimurium DNA. The device utilizes the LinkIt 7697 microcontroller and a microspectrometer to capture and transmit spectral signals in real-time, allowing for improved monitoring and analysis of the reaction progress. We built a hand-held box containing a microspectrometer, thermoelectric cooler, ultraviolet LED, disposable reaction tube, and homemade thermal module, all powered by rechargeable batteries. Additionally, we conducted thorough experiments to ensure temperature accuracy within 1 °C under thermal control, developed a heating module with a LinkIt 7697 IoT development board to heat the DNA mixture to the reaction temperature within 3 min, and integrated foam insulation and a 3D-printed frame to enhance the device's thermal stability. We successfully demonstrated the amplification of Salmonella Typhimurium DNA with an impressive sensitivity of 2.83 × 10⁻⁴ ng/μL. A remote webpage interface allows for monitoring the temperature and fluorescence during the LAMP process, improving usability. This portable LAMP device with real-time detection offers a cost-effective solution for detecting Salmonella Typhimurium in food products. Its unique design and capabilities make it a promising tool for ensuring food safety.

Chlorogenic acid, a phenolic compound, is prevalent across various plant species and has been known for its pharmacological advantages. Health care experts have identified chlorogenic acid as a potential biomarker for treatment of a wide range of illnesses. Therefore, achieving efficient extraction and analysis of chlorogenic acid from plants and their products has become essential. Molecularly imprinted polymers (MIPs) are highly effective adsorbent for the extraction of chlorogenic acid from complex matrices. Currently, there is a lack of comprehensive review article that consolidate the methods utilized for the purification of chlorogenic acid through molecular imprinting. In this context, we have surveyed the common approaches employed in preparing MIPs specifically designed for the analysis of chlorogenic acid, including both conventional and newly developed. This review discusses the advantages, limitations of polymerization techniques and proposed strategies to produce more efficient MIPs for chlorogenic acid enrichment in complex samples. Additionaly, we present advanced imprinting methods for designing MIPs, which improve the adsorption capacity, sensitivity and selectivity towards chlorogenic acid.

RNA G4, as an integral branch of G4 structure, possesses distinct interactions with ligands compared to the common DNA G4, thus the investigation of RNA G4/ligand interactions might be considered as a fresh breakthrough to improve the biosensing performance of G4/ligand system. In this study, we comparatively explored the structural and functional mechanisms of RNA G4 and DNA G4 in the interaction with ligands, hemin and thioflavin T (ThT), utilizing the classical PS2.M sequence as a model. We found that although the catalytic performance of RNA G4/hemin system was lower than DNA G4/hemin, RNA G4/ThT fluorescence system exhibited a significant improvement (2∼3-fold) compared to DNA G4/ThT, and adenine modification could further enhance the signaling. Further, by exploring the interaction between RNA G4 and ThT, we deemed that RNA G4 and ThT were stacked in a bimolecular mode compared to single-molecule binding of DNA G4/ThT, thus more strongly limiting the structural spin in ThT excited state. Further, RNA G4/ThT displayed higher environmental tolerance and lower ion dependence than DNA G4/ThT. Finally, we employed RNA G4/ThT as a highly sensitive label-free fluorescent signal output system for in situ imaging of isoforms BCR-ABL e13a2 and e14a2. Overall, this study successfully screened a high-performance RNA G4 biosensing system through systematic RNA G4/ligands interaction studies, which was expected to provide a promising reference for subsequent G4/ligand research.

Sepsis is a life-threatening condition characterized by organ dysfunction resulting from a dysregulated host response to infection. Dysregulated tryptophan (TRP) metabolites serve as significant indicators for endogenous immune turnovers and abnormal metabolism in the intestinal microbiota during sepsis. Therefore, a high coverage determination of TRP and its metabolites in sepsis is beneficial for the diagnosis and prognosis of sepsis, as well as for understanding the underlying mechanism of sepsis development. However, similar structures in TRP metabolites make it challenging for separation and metabolite identification. Here, high-performance liquid chromatography coupled with a diode array detector (HPLC-DAD) was developed to determine TRP metabolites in rat serum. The first-order derivative spectrophotometry of targeted metabolites in the serum was investigated and proved to be promising for chromatographic peak annotation across different columns and systems. The established method separating the targeted metabolites was optimized and validated to be sensitive and accurate. Application of the method revealed dysregulated TRP metabolites, associated with immune disorders and NAD + metabolism in both the host and gut flora in septic rats. Our findings indicate that the derivative spectrophotometry-assisted method enhances metabolite identifications for the chromatographic systems based on DAD detectors and holds promise for precision medicine in sepsis.